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Ravi K, Falkowski NR, Huffnagle GB. Genomic and transcriptomic insights into vertebrate host-specific Lactobacillus johnsonii adaptation in the gastrointestinal tract. mSphere 2025:e0005225. [PMID: 40358235 DOI: 10.1128/msphere.00052-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 04/13/2025] [Indexed: 05/15/2025] Open
Abstract
We conducted a comparative genomic analysis of Lactobacillus johnsonii strains isolated from the gastrointestinal tract of diverse vertebrate hosts to explore the genetic basis of host specificity. We then utilized transcriptomics analysis to investigate the expression profile of identified rodent-specific genes in mouse isolate MR1 during in vitro and in vivo growth conditions. There was significant heterogeneity among strains, in both genome sequence and content, with phylogenetic clustering of strains into distinct clades associated with rodent or avian sources. There were not sufficient genomes to identify whether porcine isolates formed their own genetic clade. However, human isolates did not form a distinct clade. Functional enrichment analysis revealed significant enrichment of several genes, including surface proteins and accessory secretory pathway-related genes, as well as tyrosine decarboxylase genes in rodent isolates compared to avian isolates, including in mouse isolate MR1. A total of 40 genes were identified as rodent-associated, and all were transcriptionally active in L. johnsonii MR1. The global transcriptomic analysis of L. johnsonii MR1 was done using cells grown anaerobically, at 37˚C, under both the late-exponential phase and stationary phase, as well as during in vivo growth in the cecum of mono-colonized germ-free mice. Several of these genes were uniquely regulated during late exponential vs stationary phase growth and in vivo colonization in mice, highlighting their potential role in nutrient adaptation and host-microbe interactions.IMPORTANCELactobacillus johnsonii is a well-known probiotic species with health-beneficial properties, including host immunomodulation and pathogen inhibition. Its growing relevance in the medical industry highlights the need to understand its biology, particularly how it adapts to different host environments. In bacteria, niche adaptation is often accompanied by the loss or gain of coding sequences along with changes in the genome size. In this study, we explored the genetic diversity of L. johnsonii strains from the gastrointestinal tracts of various vertebrates such as rodents, birds, swine, and humans. We found associations between genome content and host species of origin and could conceptually demonstrate that these genes are being differentially transcribed under varying conditions. Several functions were associated with specific host groups, suggesting that L. johnsonii strains have adapted to their hosts over time.
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Affiliation(s)
- Keerthikka Ravi
- Department of Molecular, Cellular & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Gary B Huffnagle
- Department of Molecular, Cellular & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Michigan, USA
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Mamun MAA, Rakib A, Mandal M, Singh UP. Impact of a High-Fat Diet on the Gut Microbiome: A Comprehensive Study of Microbial and Metabolite Shifts During Obesity. Cells 2025; 14:463. [PMID: 40136712 PMCID: PMC11940932 DOI: 10.3390/cells14060463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/14/2025] [Accepted: 03/18/2025] [Indexed: 03/27/2025] Open
Abstract
Over the last few decades, the prevalence of metabolic diseases such as obesity, diabetes, non-alcoholic fatty liver disease, hypertension, and hyperuricemia has surged, primarily due to high-fat diet (HFD). The pathologies of these metabolic diseases show disease-specific alterations in the composition and function of their gut microbiome. How HFD alters the microbiome and its metabolite to mediate adipose tissue (AT) inflammation and obesity is not well known. Thus, this study aimed to identify the changes in the gut microbiome and metabolomic signatures induced by an HFD to alter obesity. To explore the changes in the gut microbiota and metabolites, 16S rRNA gene amplicon sequencing and metabolomic analyses were performed after HFD and normal diet (ND) feeding. We noticed that, at taxonomic levels, the number of operational taxonomic units (OTUs), along with the Chao and Shannon indexes, significantly shifted in HFD-fed mice compared to those fed a ND. Similarly, at the phylum level, an increase in Firmicutes and a decrease in Bacteroidetes were noticed in HFD-fed mice. At the genus level, an increase in Lactobacillus and Ruminococcus was observed, while Allobaculum, Clostridium, and Akkermansia were markedly reduced in the HFD group. Many bacteria from the Ruminococcus genus impair bile acid metabolism and restrict weight loss. Firmicutes are efficient in breaking down complex carbohydrates into short-chain fatty acids (SCFAs) and other metabolites, whereas Bacteroidetes are involved in a more balanced or efficient energy extraction. Thus, an increase in Firmicutes over Bacteroidetes enhances the absorption of more calories from food, which may contribute to obesity. Taken together, the altered gut microbiota and metabolites trigger AT inflammation, which contributes to metabolic dysregulation and disease progression. Thus, this study highlights the potential of the gut microbiome in the development of therapeutic strategies for obesity and related metabolic disorders.
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Affiliation(s)
| | | | | | - Udai P. Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA; (M.A.A.M.); (A.R.); (M.M.)
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Alexander LM, Khalid S, Gallego-Lopez GM, Astmann TJ, Oh JH, Heggen M, Huss P, Fisher R, Mukherjee A, Raman S, Choi IY, Smith MN, Rogers CJ, Epperly MW, Knoll LJ, Greenberger JS, van Pijkeren JP. Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential. Appl Environ Microbiol 2024; 90:e0031224. [PMID: 39480094 DOI: 10.1128/aem.00312-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 09/09/2024] [Indexed: 11/02/2024] Open
Abstract
Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.
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Affiliation(s)
- Laura M Alexander
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Saima Khalid
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gina M Gallego-Lopez
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Theresa J Astmann
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark Heggen
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Phil Huss
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Renee Fisher
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Amitava Mukherjee
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - In Young Choi
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Morgan N Smith
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Michael W Epperly
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joel S Greenberger
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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Correa VG, Garcia-Manieri JAA, Dias MI, Pereira C, Mandim F, Barros L, Ferreira ICFR, Peralta RM, Bracht A. Gastrointestinal digestion of yerba mate, rosemary and green tea extracts and their subsequent colonic fermentation by human, pig or rat inocula. Food Res Int 2024; 194:114918. [PMID: 39232538 DOI: 10.1016/j.foodres.2024.114918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 09/06/2024]
Abstract
Polyphenolic compounds are common constituents of human and animal diets and undergo extensive metabolism by the gut microbiota before entering circulation. In order to compare the transformations of polyphenols from yerba mate, rosemary, and green tea extracts in the gastrointestinal tract, simulated gastrointestinal digestion coupled with colonic fermentation were used. For enhancing the comparative character of the investigation, colonic fermentation was performed with human, pig and rat intestinal microbiota. Chemical analysis was performed using a HPLC system coupled to a diode-array detector and mass spectrometer. Gastrointestinal digestion diminished the total amount of phenolics in the rosemary and green tea extracts by 27.5 and 59.2 %, respectively. These reductions occurred mainly at the expense of the major constituents of these extracts, namely rosmarinic acid (-45.7 %) and epigalocatechin gallate (-60.6 %). The yerba mate extract was practically not affected in terms of total phenolics, but several conversions and isomerizations occurred (e.g., 30 % of trans-3-O-caffeoylquinic acid was converted into the cis form). The polyphenolics of the yerba mate extract were also the least decomposed by the microbiota of all three species, especially in the case of the human one (-10.8 %). In contrast, the human microbiota transformed the polyphenolics of the rosemary and green extracts by 95.9 and 88.2 %, respectively. The yerba mate-extract had its contents in cis 3-O-caffeoylquinic acid diminished by 78 % by the human microbiota relative to the gastrointestinal digestion, but the content of 5-O-caffeoylquinic acid (also a chlorogenic acid), was increased by 22.2 %. The latter phenomenon did not occur with the rat and pig microbiota. The pronounced interspecies differences indicate the need for considerable caution when translating the results of experiments on the effects of polyphenolics performed in rats, or even pigs, to humans.
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Affiliation(s)
- Vanesa Gesser Correa
- Departamento de Bioquímica, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | | | - Maria Inês Dias
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Carla Pereira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Filipa Mandim
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Isabel C F R Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | | | - Adelar Bracht
- Departamento de Bioquímica, Universidade Estadual de Maringá, Maringá, PR, Brazil
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. Lab Anim (NY) 2024; 53:43-55. [PMID: 38297075 PMCID: PMC10834367 DOI: 10.1038/s41684-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1-P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung-immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.
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Affiliation(s)
- Lan Zhao
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
| | - Christine M Cunningham
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Adam M Andruska
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Katharina Schimmel
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Md Khadem Ali
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Dongeon Kim
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Shenbiao Gu
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Jason L Chang
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Edda Spiekerkoetter
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Mark R Nicolls
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
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Niu LN, Zhang GN, Xuan DD, Lin C, Lu Z, Cao PP, Chen SW, Zhang Y, Cui XJ, Hu SK. Comparative analysis of the gut microbiota of wild adult rats from nine district areas in Hainan, China. World J Gastroenterol 2023; 29:3469-3481. [PMID: 37389235 PMCID: PMC10303509 DOI: 10.3748/wjg.v29.i22.3469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Wild rats have the potential to hold zoonotic infectious agents that can spread to humans and cause disease.
AIM To better understand the composition of gut bacterial communities in rats is essential for preventing and treating such diseases. As a tropical island located in the south of China, Hainan province has abundant rat species. Here, we examined the gut bacterial composition in wild adult rats from Hainan province.
METHODS Fresh fecal samples were collected from 162 wild adult rats, including three species (Rattus norvegicus, Leopoldamys edwardsi, and Rattus losea), from nine regions of Hainan province between 2017-2018.
RESULTS We analyzed the composition of gut microbiota using the 16S rRNA gene amplicon sequencing. We identified 4903 bacterial operational taxonomic units (30 phyla, 175 families, and 498 genera), which vary between samples of different rat species in various habitats at various times of the year. In general, Firmicutes were the most abundant phyla, followed by Bacteroidetes (15.55%), Proteobacteria (6.13%), and Actinobacteria (4.02%). The genus Lactobacillus (20.08%), unidentified_Clostridiales (5.16%), Romboutsia (4.33%), unidentified_Ruminococcaceae (3.83%), Bacteroides (3.66%), Helicobacter (2.40%) and Streptococcus (2.37%) were dominant.
CONCLUSION The composition and abundance of the gut microbial communities varied between rat species and locations. This work provides fundamental information to identify microbial communities useful for disease control in Hainan province.
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Affiliation(s)
- Li-Na Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Guan-Nan Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Duan-Duan Xuan
- Department of Laboratory, Xinxiang First People's Hospital, Xinxiang 453000, Henan Province, China
| | - Chong Lin
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Zi Lu
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Pei-Pei Cao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Shao-Wen Chen
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Yong Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Xiu-Ji Cui
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Shou-Kui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing 100144, China
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Su S, Chen M, Wu Y, Lin Q, Wang D, Sun J, Hai J. Fecal microbiota transplantation and short-chain fatty acids protected against cognitive dysfunction in a rat model of chronic cerebral hypoperfusion. CNS Neurosci Ther 2023; 29 Suppl 1:98-114. [PMID: 36627762 PMCID: PMC10314111 DOI: 10.1111/cns.14089] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023] Open
Abstract
AIMS Clear roles and mechanisms in explaining gut microbial dysbiosis and microbial metabolites short-chain fatty acids (SCFAs) alterations in chronic cerebral ischemic pathogenesis have yet to be explored. In this study, we investigated chronic cerebral hypoperfusion (CCH)-induced gut microbiota and metabolic profiles of SCFAs as well as the effects and mechanisms of fecal microbiota transplantation (FMT) and SCFAs treatment on CCH-induced hippocampal neuronal injury. METHODS Bilateral common carotid artery occlusion (BCCAo) was used to establish the CCH model. Gut microbiota and SCFAs profiles in feces and hippocampus were evaluated by 16S ribosomal RNA sequencing and gas chromatography-mass spectrometry. RNA sequencing analysis was performed in hippocampal tissues. The potential molecular pathways and differential genes were verified through western blot, immunoprecipitation, immunofluorescence, and ELISA. Cognitive function was assessed via the Morris water maze test. Ultrastructures of mitochondria and synapses were tested through a transmission electron microscope. RESULTS Chronic cerebral hypoperfusion induced decreased fecal acetic and propionic acid and reduced hippocampal acetic acid, which were reversed after FMT and SCFAs administration by changing fecal microbial community structure and compositions. Furthermore, in the hippocampus, FMT and SCFAs replenishment exerted anti-neuroinflammatory effects through inhibiting microglial and astrocytic activation as well as switching microglial phenotype from M1 toward M2. Moreover, FMT and SCFAs treatment alleviated neuronal loss and microglia-mediated synaptic loss and maintained the normal process of synaptic vesicle fusion and release, resulting in the improvement of synaptic plasticity. In addition, FMT and SCFAs supplement prevented oxidative phosphorylation dysfunction via mitochondrial metabolic reprogramming. The above effects of FMT and SCFAs treatment led to the inhibition of CCH-induced cognitive impairment. CONCLUSION Our findings highlight FMT and SCFAs replenishment would be the feasible gut microbiota-based strategy to mitigate chronic cerebral ischemia-induced neuronal injury.
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Affiliation(s)
- Shao‐Hua Su
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Ming Chen
- Department of Neurosurgery, Xinhua hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Yi‐Fang Wu
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qi Lin
- Department of Pharmacy, Institutes of Medical Sciences, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Da‐Peng Wang
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jun Sun
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jian Hai
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
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8
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541527. [PMID: 37293045 PMCID: PMC10245737 DOI: 10.1101/2023.05.19.541527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman's correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB's presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.
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Li ZP, Liu JX, Lu LL, Wang LL, Xu L, Guo ZH, Dong QJ. Overgrowth of Lactobacillus in gastric cancer. World J Gastrointest Oncol 2021; 13:1099-1108. [PMID: 34616515 PMCID: PMC8465450 DOI: 10.4251/wjgo.v13.i9.1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Dysbiosis of the gastric microbiome is involved in the development of gastric cancer (GC). A number of studies have demonstrated an increase in the relative abundance of Lactobacillus in GC. In this review, we present data that support the overgrowth of Lactobacillus in GC from studies on molecular and bacterial culture of the gastric microbiome, discuss the heterogenic effects of Lactobacillus on the health of human stomach, and explore the potential roles of the overgrowth of Lactobacillus in gastric carcinogenesis. Further studies are required to examine the association between Lactobacillus and GC at strain and species levels, which would facilitate to elucidate its role in the carcinogenic process.
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Affiliation(s)
- Zhi-Peng Li
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Ju-Xin Liu
- Clinical Laboratories, Qingdao Municipal Hospital, Qingdao 266071, Shandong Province, China
| | - Lin-Lin Lu
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Li-Li Wang
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Lin Xu
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Zong-Hao Guo
- Department of Clinical Medicine, Jining Medical University, Jining 272000, Shandong Province, China
| | - Quan-Jiang Dong
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
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10
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Čoklo M, Maslov DR, Kraljević Pavelić S. Modulation of gut microbiota in healthy rats after exposure to nutritional supplements. Gut Microbes 2020; 12:1-28. [PMID: 32845788 PMCID: PMC7524141 DOI: 10.1080/19490976.2020.1779002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Rats are experimental animals, frequently used as model organisms in the biomedical studies, and increasingly used to study the gut microbiota. Specifically, the aim of latter studies is either the elucidation of relationship between intestinal dysbiosis and diseases or the determination of nutrients or pharmaceutical agents which can cause the modulation in the presence or abundance of gut microbiota. AIM Herein, the research studies conducted on the gut microbiota of healthy rats are presented in a summarized and concise overview. The focus is on studies aimed to reveal the shifts in microbial composition and functional changes after exposure to various types of nutritional supplements. METHODS We performed the search of PubMed database using the term "rat gut microbiome microbiota" and examined studies aimed to assess the composition of gut microbiota in physiological homeostasis as well as the effect of various nutritional supplements on the gut microbiota of healthy rats.
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Affiliation(s)
- Mirna Čoklo
- Department of Biotechnology, Centre for High-throughput Technologies, University of Rijeka, Rijeka, Croatia
| | - Dina Rešetar Maslov
- Department of Biotechnology, Centre for High-throughput Technologies, University of Rijeka, Rijeka, Croatia
| | - Sandra Kraljević Pavelić
- Department of Biotechnology, Centre for High-throughput Technologies, University of Rijeka, Rijeka, Croatia
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11
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Patil R, Arvindekar A. Glycation of gut proteins initiates microbial dysbiosis and can promote establishment of diabetes in experimental animals. Microb Pathog 2020; 152:104589. [PMID: 33171259 DOI: 10.1016/j.micpath.2020.104589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022]
Abstract
Diabetes and obesity is associated with change in the gut microbiota, however, the reason for such transition is still unknown. The secondary complications in diabetes mainly stem from protein glycation, oxidative stress and inflammatory response. It is intended to study the correlation between gut proteins glycation and microbial dysbiosis and thereby progression to diabetes. The study was carried out through feeding high fructose to male Wistar rats and evaluating their gut microbiota. The rate of gut flora excretion via faecal matter was found to decrease on fructose feed for 7 days. Intestinal flora was drastically reduced and pathogenic succession observed. Intestinal fluorescence studies confirmed that there is heavy glycation of gut proteins. Microbes obtained from fructose fed animals could grow on glycated BSA. There was significant increase in level of TNF-α and IFN-γ providing evidence of inflammation. Though microbial dysbiosis was observed in diabetes, the cause for this remained elusive. In the present study we prove that high fructose feed and glycation of the gut proteins probably prevent adherence/survival of the gut microflora in control animals and promotes transition to a changed microflora which is capable of adhering/utilizing glycated proteins as well as high fructose. The changed microbiota, enhanced protein glycation and inflammation help in establishing insulin resistance.
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Affiliation(s)
- Rahul Patil
- Department of Biochemistry, Shivaji University, Kolhapur, 416 004, M.S, India
| | - Akalpita Arvindekar
- Department of Biochemistry, Shivaji University, Kolhapur, 416 004, M.S, India.
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12
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Singh RP, Halaka DA, Hayouka Z, Tirosh O. High-Fat Diet Induced Alteration of Mice Microbiota and the Functional Ability to Utilize Fructooligosaccharide for Ethanol Production. Front Cell Infect Microbiol 2020; 10:376. [PMID: 32850478 PMCID: PMC7426704 DOI: 10.3389/fcimb.2020.00376] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/18/2020] [Indexed: 01/20/2023] Open
Abstract
High-fat diet (HFD) leads to enhancement in various parameters of mice like weight, fasting glucose levels, adipose tissue, and also the liver weight in male C57 BL/6 J mice. Additionally, high-fat diet causes severe liver damage with significant increase in the level of aspartate amino transferase (AST) and alanine transaminase (ALT). The variations in microbiota induced by different diet were analyzed by Illumina MiSeq platform with sequencing of 16S ribosomal RNA (rRNA) gene, and QIIME pipeline was used. The population of Proteobacteria was found to be higher in HFD cecum sample as compared to other treatments. Microbiota analysis suggests that phylum Proteobacteria and Firmicutes were found to be higher in high-fat diet groups as compared to mice fed with normal diet (ND). At the genus level, Bacteroides showed higher population in HFD diet. Bacterial strains belonging to Enterobacteriaceae like Escherichia, Klebsiella, and Shigella were also dominant in HFD treatments. Furthermore, we explored the effects of ethanol production in vitro with supplementation of dietary fibers following inoculation of ND and HFD microbiotas. HFD microbiota of cecum and feces showed high level (P < 0.05) of ethanol production with 2% fructooligosaccharide (FOS) as compared to 2% galactomannan. Microbial fermentation also generated short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate. High levels (P < 0.05) of propionate were found after fermentation of FOS with HFD cecum and feces microbiota. The present study highlights the HFD-induced population of phylum Proteobacteria and genus Bacteroides for ethanol production using FOS as a dietary supplement, and these findings may imply on the harmful effect of HFD even at the microbiota level.
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13
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Simpson S, Kimbrough A, Boomhower B, McLellan R, Hughes M, Shankar K, de Guglielmo G, George O. Depletion of the Microbiome Alters the Recruitment of Neuronal Ensembles of Oxycodone Intoxication and Withdrawal. eNeuro 2020; 7:ENEURO.0312-19.2020. [PMID: 32341122 PMCID: PMC7242819 DOI: 10.1523/eneuro.0312-19.2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Substance use disorders have a complex etiology. Genetics, the environment, and behavior all play a role in the initiation, escalation, and relapse of drug use. Recently, opioid use disorder has become a national health crisis. One aspect of opioid addiction that has yet to be fully examined is the effects of alterations of the microbiome and gut-brain axis signaling on central nervous system activity during opioid intoxication and withdrawal. The effect of microbiome depletion on the activation of neuronal ensembles was measured by detecting Fos-positive (Fos+) neuron activation during intoxication and withdrawal using a rat model of oxycodone dependence. Daily oxycodone administration (2 mg/kg) increased pain thresholds and increased Fos+ neurons in the basolateral amygdala (BLA) during intoxication, with a decrease in pain thresholds and increase in Fos+ neurons in the periaqueductal gray (PAG), central nucleus of the amygdala (CeA), locus coeruleus (LC), paraventricular nucleus of the thalamus (PVT), agranular insular cortex (AI), bed nucleus of the stria terminalis (BNST), and lateral habenula medial parvocellular region during withdrawal. Microbiome depletion produced widespread but region- and state-specific changes in neuronal ensemble activation. Oxycodone intoxication and withdrawal also increased functional connectivity among brain regions. Microbiome depletion resulted in a decorrelation of this functional network. These data indicate that microbiome depletion by antibiotics produces widespread changes in the recruitment of neuronal ensembles that are activated by oxycodone intoxication and withdrawal, suggesting that the gut microbiome may play a role in opioid use and dependence. Future studies are needed to better understand the molecular, neurobiological, and behavioral effects of microbiome depletion on addiction-like behaviors.
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Affiliation(s)
- Sierra Simpson
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037
| | - Adam Kimbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
| | - Brent Boomhower
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
| | - Rio McLellan
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
| | - Marcella Hughes
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
| | - Kokila Shankar
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Olivier George
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093,
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037
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14
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Alexander LM, Oh JH, Stapleton DS, Schueler KL, Keller MP, Attie AD, van Pijkeren JP. Exploiting Prophage-Mediated Lysis for Biotherapeutic Release by Lactobacillus reuteri. Appl Environ Microbiol 2019; 85:e02335-18. [PMID: 30683744 PMCID: PMC6498169 DOI: 10.1128/aem.02335-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus reuteri has the potential to be developed as a microbial therapeutic delivery platform because of an established safety profile, health-promoting properties, and available genome editing tools. Here, we show that L. reuteri VPL1014 exhibits a low mutation rate compared to other Gram-positive bacteria, which we expect will contribute to the stability of genetically modified strains. VPL1014 encodes two biologically active prophages, which are induced during gastrointestinal transit. We hypothesized that intracellularly accumulated recombinant protein can be released following bacteriophage-mediated lysis. To test this, we engineered VPL1014 to accumulate leptin, our model protein, inside the cell. In vitro prophage induction of recombinant VPL1014 released leptin into the extracellular milieu, which corresponded to bacteriophage production. We also employed a plasmid system that does not require antibiotic in the growth medium for plasmid maintenance. Collectively, these data provide new avenues to exploit native prophages to deliver therapeutic molecules.IMPORTANCE Lactic acid bacteria (LAB) have been explored as potential biotherapeutic vehicles for the past 20 years. To secrete a therapeutic in the extracellular milieu, one typically relies on the bacterial secretion pathway, i.e., the Sec pathway. Overexpression of a secreted protein can overload the secretory pathway and impact the organism's fitness, and optimization of the signal peptide is also required to maximize the efficiency of the release of mature protein. Here, we describe a previously unexplored approach to release therapeutics from the probiotic Lactobacillus reuteri We demonstrate that an intracellularly accumulated recombinant protein is released following prophage activation. Since we recently demonstrated that prophages are activated during gastrointestinal transit, we propose that this method will provide a straightforward and efficient approach to deliver therapeutics in vivo.
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Affiliation(s)
- Laura M Alexander
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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15
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Boudreau MD, Olson GR, Tryndyak VP, Bryant MS, Felton RP, Beland FA. From the Cover: Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestines of F344/N Male Rats. Toxicol Sci 2018; 158:302-318. [PMID: 28525602 DOI: 10.1093/toxsci/kfx105] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In a previous study, the oral administration of an Aloe vera whole leaf extract induced dose-related mucosal and goblet cell hyperplasia in the rat colon after 13 weeks and colon cancer after 2 years. The primary goal of this study was to determine whether or not the administration of aloin, a component of the Aloe vera plant leaf, would replicate the pathophysiological effects that were observed in rats in the previous study with an Aloe vera whole leaf extract. Groups of 10 male F344/N rats were administered aloin at 0, 6.95, 13.9, 27.8, 55.7, 111, 223, and 446 mg/kg drinking water for 13 weeks. At the end of study, rat feces were collected, and the composition of fecal bacteria was investigated by next generation sequencing of the PCR-amplified V3/V4 region of the 16S rRNA gene. At necropsy, blood was collected by cardiac puncture and organs and sections of the large intestine were collected for histopathology. Aloin induced dose-related increased incidences and severities of mucosal and goblet cell hyperplasia that extended from the cecum to the rectum, with increased incidences and severities detected at aloin doses ≥55.7 mg/kg drinking water. Analysis of the 16S rRNA metagenomics sequencing data revealed marked shifts in the structure of the gut microbiota in aloin-treated rats at each taxonomic rank. This study highlights the similarities in effects observed for aloin and the Aloe vera whole leaf extract, and points to a potential mechanism of action to explain the observed pathological changes via modulation of the gut microbiota composition.
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Affiliation(s)
| | - Greg R Olson
- Toxicologic Pathology Associates, Inc., Jefferson Laboratories, Jefferson, Arkansas
| | | | | | - Robert P Felton
- Division of Informatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas
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16
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Zhao L, Zhang Q, Ma W, Tian F, Shen H, Zhou M. A combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota. Food Funct 2018; 8:4644-4656. [PMID: 29152632 DOI: 10.1039/c7fo01383c] [Citation(s) in RCA: 392] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Resveratrol and quercetin, widely found in foods and vegetables, are plant polyphenols reported to have a wide range of biological activities. Despite their limited bioavailabilities, both resveratrol and quercetin are known to exhibit anti-inflammation and anti-obesity effects. We hypothesized that gut microbiota may be a potential target for resveratrol and quercetin to prevent the development of obesity. The aim of this research was to confirm whether a combination of quercetin and resveratrol (CQR) could restore the gut microbiota dysbiosis induced by a high-fat diet (HFD). In this study, Wistar rats were divided into three groups: a normal diet (ND) group, a HFD group and a CQR group. The CQR group was treated with a HFD and administered with a combination of quercetin [30 mg per kg body weight (BW) per day] and resveratrol [15 mg per kg body weight (BW) per day] by oral gavage. At the end of 10 weeks, CQR reduced the body weight gain and visceral (epididymal, perirenal) adipose tissue weight. Moreover, CQR also reduced serum lipids, attenuated serum inflammatory markers [interleukin (IL)-6, tumor necrosis factor (TNF)-α, monocyte chemotactic protein (MCP)-1] and reversed serum biochemical parameters (adiponectin, insulin, leptin, etc.). Importantly, our results demonstrated that CQR could modulate the gut microbiota composition. 16S rRNA gene sequencing revealed that CQR had an impact on gut microbiota, decreasing Firmicutes (P < 0.05) and the proportion of Firmicutes to Bacteroidetes (P = 0.052). CQR also significantly inhibited the relative abundance of Desulfovibrionaceae (P < 0.01), Acidaminococcaceae (P < 0.05), Coriobacteriaceae (P < 0.05), Bilophila (P < 0.05), Lachnospiraceae (P < 0.05) and its genus Lachnoclostridium (P < 0.001), which were reported to be potentially related to diet-induced obesity. Moreover, compared with the HFD group, the relative abundance of Bacteroidales_S24-7_group (P < 0.01), Christensenellaceae (P < 0.001), Akkermansia (P < 0.01), Ruminococcaceae (P < 0.01) and its genera Ruminococcaceae_UCG-014 (P < 0.01), and Ruminococcaceae_UCG-005 (P < 0.01), which were reported to have an effect of relieving HFD-induced obesity, was markedly increased in the CQR group. Overall, these results indicated that administration of CQR may have beneficial effects on ameliorating HFD-induced obesity and reducing HFD-induced gut microbiota dysbiosis.
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Affiliation(s)
- Le Zhao
- Center for Chinese Medical Therapy and Systems Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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17
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Masarwi M, Solnik HI, Phillip M, Yaron S, Shamir R, Pasmanic-Chor M, Gat-Yablonski G. Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats. J Nutr Biochem 2018; 51:27-39. [DOI: 10.1016/j.jnutbio.2017.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 08/20/2017] [Accepted: 08/29/2017] [Indexed: 01/01/2023]
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18
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Masuda N, Mantani Y, Yuasa H, Yoshitomi C, Arai M, Nishida M, Qi WM, Kawano J, Yokoyama T, Hoshi N, Kitagawa H. Immunohistochemical study on the distribution of β-defensin 1 and β-defensin 2 throughout the respiratory tract of healthy rats. J Vet Med Sci 2018; 80:395-404. [PMID: 29311494 PMCID: PMC5880817 DOI: 10.1292/jvms.17-0686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The distributions of β-defensin 1 and 2 in secretory host defense system throughout respiratory tract of healthy rats were immunohistochemically investigated. In the nasal epithelium, a
large number of non-ciliated and non-microvillous cells (NCs) were immunopositive for both β-defensin 1 and 2, whereas a small number of goblet cells (GCs) were immunopositive only for
β-defensin 1. Beta-defensin 2-immunopositive GCs were few. In the nasal glands, a small number of acinar cells and a large number of ductal epithelial cells were immunopositive for both
β-defensins. In the laryngeal and tracheal epithelia, a very few NCs and GCs were immunopositive for both β-defensins. In laryngeal and tracheal glands, a very few acinar cells and a large
number of ductal epithelial cells were immunopositive for both β-defensins. In the extra-pulmonary bronchus, a small number of NCs were immunopositive for both β-defensins. A small number of
GCs were immunopositive for β-defensin 1, whereas few GCs were immunopositive for β-defensin 2. From the intra-pulmonary bronchus to alveoli, a very few or no epithelial cells were
immunopositive for both β-defensins. In the mucus and periciliary layers, β-defensin 1 was detected from the nose to the extra-pulmonary bronchus, whereas β-defensin 2 was weakly detected
only in the nose and the larynx. These findings suggest that the secretory sources of β-defensin 1 and 2 are mainly distributed in the nasal mucosa and gradually decrease toward the caudal
airway in healthy rats.
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Affiliation(s)
- Natsumi Masuda
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hideto Yuasa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Yoshitomi
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Masaya Arai
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Miho Nishida
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Wang-Mei Qi
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Huhhot, Inner Mongolia 010018, P. R. China
| | - Junichi Kawano
- Laboratory of Microbiology and Immunology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Kitagawa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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19
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Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial Ecology along the Gastrointestinal Tract. Microbes Environ 2017; 32:300-313. [PMID: 29129876 PMCID: PMC5745014 DOI: 10.1264/jsme2.me17017] [Citation(s) in RCA: 349] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/19/2017] [Indexed: 02/06/2023] Open
Abstract
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.
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Affiliation(s)
- Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Hang Lu
- Department of Animal Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Tianming Yao
- Department of Food Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Cindy H. Nakatsu
- Department of Agronomy, Purdue UniversityWest Lafayette, Indiana 47907USA
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20
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Masuda N, Mantani Y, Yoshitomi C, Yuasa H, Nishida M, Arai M, Kawano J, Yokoyama T, Hoshi N, Kitagawa H. Immunohistochemical study on the secretory host defense system with lysozyme and secretory phospholipase A2 throughout rat respiratory tract. J Vet Med Sci 2017; 80:323-332. [PMID: 29225322 PMCID: PMC5836772 DOI: 10.1292/jvms.17-0503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The host defense system with lysozyme and secretory phospholipase A2 (sPLA2) was immunohistochemically investigated in rat respiratory tract under healthy conditions. In the nasal epithelium, a large number of non-ciliated and non-microvillous cells (NC) and a small number of goblet cells (GC) were immunopositive for lysozyme and sPLA2. A few acinar cells and almost all epithelial cells of intercalated ducts were immunopositive for both bactericidal substances in the nasal glands. In the laryngeal and tracheal epithelia, few NC and GC were immunopositive for both bactericidal substances. In the laryngeal and tracheal glands, a few acinar cells and most ductal epithelial cells were immunopositive for both bactericidal substances. In extra-pulmonary bronchus, small numbers of NC and GC were immunopositive for lysozyme and sPLA2, whereas few NC and no GC were immunopositive in the intra-pulmonary bronchus. No secretory source of either bactericidal substance was located in the bronchioles. In the alveolus, many glandular epithelial cells and alveolar macrophages were immunopositive for lysozyme but immunonegative for sPLA2. Moreover, lysozyme and sPLA2 were detected in the mucus layer and in the periciliary layer from the nose to the extra-pulmonary bronchus. These findings suggest that secretory sources of lysozyme and sPLA2 are distributed in almost all the respiratory tract. Their secretory products are probably transported to the pharynx and contribute to form the first line of defense against inhaled bacteria throughout the respiratory tract.
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Affiliation(s)
- Natsumi Masuda
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Yoshitomi
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hideto Yuasa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Miho Nishida
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Masaya Arai
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Junichi Kawano
- Laboratory of Microbiology and Immunology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Kitagawa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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Flemer B, Gaci N, Borrel G, Sanderson IR, Chaudhary PP, Tottey W, O'Toole PW, Brugère JF. Fecal microbiota variation across the lifespan of the healthy laboratory rat. Gut Microbes 2017; 8:428-439. [PMID: 28586297 PMCID: PMC5628645 DOI: 10.1080/19490976.2017.1334033] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Laboratory rats are commonly used in life science research as a model for human biology and disease, but the composition and development of their gut microbiota during life is poorly understood. We determined the fecal microbiota composition of healthy Sprague Dawley laboratory rats from 3 weeks to 2 y of age, kept under controlled environmental and dietary conditions. Additionally, we determined fecal short-chain fatty acid profiles, and we compared the rat fecal microbiota with that of mice and humans. Gut microbiota and to a lesser extent SCFAs profiles separated rats into 3 different clusters according to age: before weaning, first year of life (12- to 26-week-old animals) and second year of life (52- to 104-week-old). A core of 46 bacterial species was present in all rats but its members' relative abundance progressively decreased with age. This was accompanied by an increase of microbiota α-diversity, likely due to the acquisition of environmental microorganisms during the lifespan. Contrastingly, the functional profile of the microbiota across animal species became more similar upon aging. Lastly, the microbiota of rats and mice were most similar to each other but at the same time the microbiota profile of rats was more similar to that of humans than was the microbiota profile of mice. These data offer an explanation as to why germ-free rats are more efficient recipients and retainers of human microbiota than mice. Furthermore, experimental design should take into account dynamic changes in the microbiota of model animals considering that their changing gut microbiota interacts with their physiology.
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Affiliation(s)
- Burkhardt Flemer
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland
| | - Nadia Gaci
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Guillaume Borrel
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Ian R. Sanderson
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Prem P. Chaudhary
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - William Tottey
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Paul W. O'Toole
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,Paul W. O'Toole School of Microbiology and APC Microbiome Institute, University College Cork, College Road, Cork, Ireland
| | - Jean-François Brugère
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France,CONTACT Jean-François Brugère 5e CBRV, Facultés de Médecine et de Pharmacie de Clermont-Ferrand, 28 place Henri Dunant, F-63000 Clermont-Ferrand France
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β2-1 Fructan supplementation alters host immune responses in a manner consistent with increased exposure to microbial components: results from a double-blinded, randomised, cross-over study in healthy adults. Br J Nutr 2016; 115:1748-59. [PMID: 26987626 DOI: 10.1017/s0007114516000908] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
β2-1 Fructans are purported to improve health by stimulating growth of colonic bifidobacteria, increasing host resistance to pathogens and stimulating the immune system. However, in healthy adults, the benefits of supplementation remain undefined. Adults (thirteen men, seventeen women) participated in a double-blinded, placebo-controlled, randomised, cross-over study consisting of two 28-d treatments separated by a 14-d washout period. Subjects' regular diets were supplemented with β2-1 fructan or placebo (maltodextrin) at 3×5 g/d. Fasting blood and 1-d faecal collections were obtained at the beginning and at the end of each phase. Blood was analysed for clinical, biochemical and immunological variables. Determinations of well-being and general health, gastrointestinal (GI) symptoms, regularity, faecal SCFA content, residual faecal β2-1 fructans and faecal bifidobacteria content were undertaken. β2-1 Fructan supplementation had no effect on blood lipid or cholesterol concentrations or on circulating lymphocyte and macrophage numbers, but significantly increased serum lipopolysaccharide, faecal SCFA, faecal bifidobacteria and indigestion. With respect to immune function, β2-1 fructan supplementation increased serum IL-4, circulating percentages of CD282+/TLR2+ myeloid dendritic cells and ex vivo responsiveness to a toll-like receptor 2 agonist. β2-1 Fructans also decreased serum IL-10, but did not affect C-reactive protein or serum/faecal Ig concentrations. No differences in host well-being were associated with either treatment, although the self-reported incidence of GI symptoms and headaches increased during the β2-1 fructan phase. Although β2-1 fructan supplementation increased faecal bifidobacteria, this change was not directly related to any of the determined host parameters.
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Spatial Localization and Binding of the Probiotic Lactobacillus farciminis to the Rat Intestinal Mucosa: Influence of Chronic Stress. PLoS One 2015; 10:e0136048. [PMID: 26367538 PMCID: PMC4569280 DOI: 10.1371/journal.pone.0136048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/29/2015] [Indexed: 02/07/2023] Open
Abstract
The present study aimed at detecting the exogenously applied probiotic Lactobacillus farciminis in rats, after exposure to IBS-like chronic stress, based on 4-day Water Avoidance Stress (WAS). The presence of L. farciminis in both ileal and colonic mucosal tissues was demonstrated by FISH and qPCR, with ileum as the preferential niche, as for the SFB population. A different spatial distribution of the probiotic was observed: in the ileum, bacteria were organized in micro-colonies more or less close to the epithelium whereas, in the colon, they were mainly visualized far away from the epithelium. When rats were submitted to WAS, the L. farciminis population substantially decreased in both intestinal regions, due to a stress-induced increase in colonic motility and defecation, rather than a modification of bacterial binding to the intestinal mucin Muc2.
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Lecomte V, Kaakoush NO, Maloney CA, Raipuria M, Huinao KD, Mitchell HM, Morris MJ. Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters. PLoS One 2015; 10:e0126931. [PMID: 25992554 PMCID: PMC4436290 DOI: 10.1371/journal.pone.0126931] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/09/2015] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota is emerging as a new factor in the development of obesity. Many studies have described changes in microbiota composition in response to obesity and high fat diet (HFD) at the phylum level. In this study we used 16s RNA high throughput sequencing on faecal samples from rats chronically fed HFD or control chow (n = 10 per group, 16 weeks) to investigate changes in gut microbiota composition at the species level. 53.17% dissimilarity between groups was observed at the species level. Lactobacillus intestinalis dominated the microbiota in rats under the chow diet. However this species was considerably less abundant in rats fed HFD (P<0.0001), this being compensated by an increase in abundance of propionate/acetate producing species. To further understand the influence of these species on the development of the obese phenotype, we correlated their abundance with metabolic parameters associated with obesity. Of the taxa contributing the most to dissimilarity between groups, 10 presented significant correlations with at least one of the tested parameters, three of them correlated positively with all metabolic parameters: Phascolarctobacterium, Proteus mirabilis and Veillonellaceae, all propionate/acetate producers. Lactobacillus intestinalis was the only species whose abundance was negatively correlated with change in body weight and fat mass. This species decreased drastically in response to HFD, favouring propionate/acetate producing bacterial species whose abundance was strongly correlated with adiposity and deterioration of metabolic factors. Our observations suggest that these species may play a key role in the development of obesity in response to a HFD.
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Affiliation(s)
- Virginie Lecomte
- School of Medical Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Nadeem O. Kaakoush
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | | | - Mukesh Raipuria
- School of Medical Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Karina D. Huinao
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Hazel M. Mitchell
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Margaret J. Morris
- School of Medical Sciences, UNSW Australia, Sydney, New South Wales, Australia
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Kim M, Kim J, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. Investigation of bacterial diversity in the feces of cattle fed different diets. J Anim Sci 2013; 92:683-94. [PMID: 24352967 DOI: 10.2527/jas.2013-6841] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.
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Affiliation(s)
- M Kim
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933
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26
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Use of pigs as a potential model for research into dietary modulation of the human gut microbiota. Nutr Res Rev 2013; 26:191-209. [DOI: 10.1017/s0954422413000152] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The human intestinal microbial ecosystem plays an important role in maintaining health. A multitude of diseases including diarrhoea, gastrointestinal inflammatory disorders, such as necrotising enterocolitis (NEC) of neonates, and obesity are linked to microbial composition and metabolic activity. Therefore, research on possible dietary strategies influencing microbial composition and activity, both preventive and curative, is being accomplished. Interest has focused on pre- and probiotics that stimulate the intestinal production of beneficial bacterial metabolites such as butyrate, and beneficially affect microbial composition. The suitability of an animal model to study dietary linked diseases is of much concern. The physiological similarity between humans and pigs in terms of digestive and associated metabolic processes places the pig in a superior position over other non-primate models. Furthermore, the pig is a human-sized omnivorous animal with comparable nutritional requirements, and shows similarities to the human intestinal microbial ecosystem. Also, the pig has been used as a model to assess microbiota–health interactions, since pigs exhibit similar syndromes to humans, such as NEC and partly weanling diarrhoea. In contrast, when using rodent models to study diet–microbiota–health interactions, differences between rodents and humans have to be considered. For example, studies with mice and human subjects assessing possible relationships between the composition and metabolic activity of the gut microbiota and the development of obesity have shown inconsistencies in results between studies. The present review displays the similarities and differences in intestinal microbial ecology between humans and pigs, scrutinising the pig as a potential animal model, with regard to possible health effects.
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27
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Statement on Allura Red AC and other sulphonated mono azo dyes authorised as food and feed additives. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3234] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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28
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The intestinal microbiota in the rat model: major breakthroughs from new technologies. Anim Health Res Rev 2013; 13:54-63. [PMID: 22853927 DOI: 10.1017/s1466252312000072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mammalian intestine harbors a large and diverse community of micro-organisms, known as the intestinal microbiota. Recent developments in molecular profiling methods, mainly based on microbial 16S ribosomal RNA gene sequencing, have provided unprecedented insights into the make-up and diversity of intestinal microbial communities. Using these culture-independent analyses, gut microbiota of several mammals including laboratory rodents, have been revisited. The laboratory rat is one of the major species bred and kept for scientific research. Although this animal is bred in confined environments and subjected to procedures for satisfying health requirements that hamper natural colonization, some major features of mammalian gut microbiota are conserved. However, the gut microbiota varies according to the breeding conditions of the rats and this could impact reproducibility of the experimental models. Determining the non-pathogenic microbial community might be relevant in standards of quality control of laboratory animals. Molecular profiling techniques could be applied to document this information.
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Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx. PLoS One 2012; 7:e51521. [PMID: 23251564 PMCID: PMC3520844 DOI: 10.1371/journal.pone.0051521] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2012] [Indexed: 11/20/2022] Open
Abstract
Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of ‘presumptive’ aquaporin aqpZ genes and genes encoding ‘active’ lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80–100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed.
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Nordgård L, Brusetti L, Raddadi N, Traavik T, Averhoff B, Nielsen KM. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats. BMC Res Notes 2012; 5:170. [PMID: 22463741 PMCID: PMC3364145 DOI: 10.1186/1756-0500-5-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. RESULTS Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates. CONCLUSIONS The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 10(8) cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.
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Affiliation(s)
- Lise Nordgård
- GenØk, Centre for Biosafety, Science Park, 9294 Tromsø, Norway
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31
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Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis. Mol Biol Rep 2011; 39:5669-76. [DOI: 10.1007/s11033-011-1375-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 12/13/2011] [Indexed: 01/20/2023]
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32
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Diversity and novelty of the gut microbial community of an herbivorous rodent (Neotoma bryanti). Symbiosis 2011. [DOI: 10.1007/s13199-011-0125-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rosenberg E, Zilber-Rosenberg I. Symbiosis and development: the hologenome concept. ACTA ACUST UNITED AC 2011; 93:56-66. [PMID: 21425442 DOI: 10.1002/bdrc.20196] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
All animals and plants establish symbiotic relationships with microorganisms; often the combined genetic information of the diverse microbiota exceeds that of the host. How the genetic wealth of the microbiota affects all aspects of the holobiont's (host plus all of its associated microorganisms) fitness (adaptation, survival, development, growth and reproduction) and evolution is reviewed, using selected coral, insect, squid, plant, and human/mouse published experimental results. The data are discussed within the framework of the hologenome theory of evolution, which demonstrates that changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont in the short term but also can be transmitted to offspring and lead to long lasting cooperations. As acquired characteristics (microbes) are heritable, consideration of the holobiont as a unit of selection in evolution leads to neo-Lamarckian principles within a Darwinian framework. The potential application of these principles can be seen in the growing fields of prebiotics and probiotics.
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Affiliation(s)
- Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Givat Shmuel, Israel.
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34
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Schwab C, Gänzle M. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears. Can J Microbiol 2011; 57:177-85. [PMID: 21358758 DOI: 10.1139/w10-113] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.
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Affiliation(s)
- Clarissa Schwab
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
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35
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Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NCK, Patil PB, Juge N, MacKenzie DA, Pearson BM, Lapidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC, Walter J. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 2011; 7:e1001314. [PMID: 21379339 PMCID: PMC3040671 DOI: 10.1371/journal.pgen.1001314] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 01/18/2011] [Indexed: 02/07/2023] Open
Abstract
Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process. The gastrointestinal microbiota of vertebrates is important for nutrient utilization, resistance against pathogens, and immune maturation of its host, but little is known about the evolutionary relationships between vertebrates and individual bacterial members of these communities. Here we provide robust evidence that the evolution of the gut symbiont Lactobacillus reuteri with vertebrates resulted in the emergence of host specialization. Genomic approaches using a combination of genome sequence comparisons and microarray analysis were used to identify the host-specific genome content in rodent and human strains and the evolutionary events that resulted in host adaptation. The study revealed divergent patterns of genome evolution in rodent and human lineages and a distinct genome inventory in host-restricted sub-populations of L. reuteri that reflected the niche characteristics in the gut of their particular vertebrate hosts. The ecological significance of representative rodent-specific genes was demonstrated in gnotobiotic mice. In conclusion, this work provided evidence that the vertebrate gut symbiont Lactobacillus reuteri, despite the likelihood of horizontal transmission, has remained stably associated with related groups of vertebrate hosts over evolutionary time and has evolved a lifestyle specialized to these host animals.
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Affiliation(s)
- Steven A. Frese
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Andrew K. Benson
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Diane M. Loach
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jaehyoung Kim
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Min Zhang
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Nicholas C. K. Heng
- Sir John Walsh Research Institute (Faculty of Dentistry), University of Otago, Dunedin, New Zealand
| | - Prabhu B. Patil
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
- Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Nathalie Juge
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | | | - Bruce M. Pearson
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Alla Lapidus
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Eileen Dalin
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Hope Tice
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Eugene Goltsman
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Loren Hauser
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
- * E-mail:
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36
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Kerckhoffs APM, Ben-Amor K, Samsom M, van der Rest ME, de Vogel J, Knol J, Akkermans LMA. Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in irritable bowel syndrome. J Med Microbiol 2010; 60:236-245. [PMID: 20947663 DOI: 10.1099/jmm.0.022848-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Intestinal microbiota may play a role in the pathophysiology of irritable bowel syndrome (IBS). In this case-control study, mucosa-associated small intestinal and faecal microbiota of IBS patients and healthy subjects were analysed using molecular-based methods. Duodenal mucosal brush and faecal samples were collected from 37 IBS patients and 20 healthy subjects. The bacterial 16S rRNA gene was amplified and analysed using PCR denaturing gradient gel electrophoresis (DGGE). Pooled average DGGE profiles of all IBS patients and all healthy subjects from both sampling sites were generated and fingerprints of both groups were compared. The DGGE band fragments which were confined to one group were further characterized by sequence analysis. Quantitative real-time PCR (q-PCR) was used to quantify the disease-associated microbiota. Averaged DGGE profiles of both groups were identical for 78.2 % in the small intestinal samples and for 86.25 % in the faecal samples. Cloning and sequencing of the specific bands isolated from small intestinal and faecal DGGE patterns of IBS patients showed that 45.8 % of the clones belonged to the genus Pseudomonas, of which Pseudomonas aeruginosa was the predominant species. q-PCR analysis revealed higher levels (P<0.001) of P. aeruginosa in the small intestine of IBS patients (8.3 %±0.950) than in the small intestine of healthy subjects (0.1 %±0.069). P. aeruginosa was also significantly (P<0.001) more abundant (2.34 %±0.31) in faeces of IBS patients than in faeces of healthy subjects (0.003 %±0.0027). This study shows that P. aeruginosa is detected more frequently and at higher levels in IBS patients than in healthy subjects, suggesting its potential role in the pathophysiology of IBS.
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Affiliation(s)
- Angèle P M Kerckhoffs
- Gastrointestinal Research Unit, Departments of Gastroenterology and Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kaouther Ben-Amor
- Danone Research - Centre for Specialised Nutrition, Wageningen, The Netherlands
| | - Melvin Samsom
- Gastrointestinal Research Unit, Departments of Gastroenterology and Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Jan Knol
- Danone Research - Centre for Specialised Nutrition, Wageningen, The Netherlands
| | - Louis M A Akkermans
- Gastrointestinal Research Unit, Departments of Gastroenterology and Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
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37
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MacKenzie DA, Jeffers F, Parker ML, Vibert-Vallet A, Bongaerts RJ, Roos S, Walter J, Juge N. Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri. MICROBIOLOGY-SGM 2010; 156:3368-3378. [PMID: 20847011 DOI: 10.1099/mic.0.043265-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mucus-binding proteins (MUBs) have been revealed as one of the effector molecules involved in mechanisms of the adherence of lactobacilli to the host; mub, or mub-like, genes are found in all of the six genomes of Lactobacillus reuteri that are available. We recently reported the crystal structure of a Mub repeat from L. reuteri ATCC 53608 (also designated strain 1063), revealing an unexpected recognition of immunoglobulins. In the current study, we explored the diversity of the ATCC 53608 mub gene, and MUB expression levels in a large collection of L. reuteri strains isolated from a range of vertebrate hosts. This analysis revealed that the MUB was only detectable on the cell surface of two highly related isolates when using antibodies that were raised against the protein. There was considerable variation in quantitative mucus adhesion in vitro among L. reuteri strains, and mucus binding showed excellent correlation with the presence of cell-surface ATCC 53608 MUB. ATCC 53608 MUB presence was further highly associated with the autoaggregation of L. reuteri strains in washed cell suspensions, suggesting a novel role of this surface protein in cell aggregation. We also characterized MUB expression in representative L. reuteri strains. This analysis revealed that one derivative of strain 1063 was a spontaneous mutant that expressed a C-terminally truncated version of MUB. This frameshift mutation was caused by the insertion of a duplicated 13 nt sequence at position 4867 nt in the mub gene, producing a truncated MUB also lacking the C-terminal LPxTG region, and thus unable to anchor to the cell wall. This mutant, designated 1063N (mub-4867(i)), displayed low mucus-binding and aggregation capacities, further providing evidence for the contribution of cell-wall-anchored MUB to such phenotypes. In conclusion, this study provided novel information on the functional attributes of MUB in L. reuteri, and further demonstrated that MUB and MUB-like proteins, although present in many L. reuteri isolates, show a high genetic heterogeneity among strains.
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Affiliation(s)
- Donald A MacKenzie
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Faye Jeffers
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Mary L Parker
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | | | - Roy J Bongaerts
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Stefan Roos
- Department of Microbiology, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Nathalie Juge
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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38
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Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A 2010; 108 Suppl 1:4645-52. [PMID: 20615995 DOI: 10.1073/pnas.1000099107] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Vertebrates engage in symbiotic associations with vast and complex microbial communities that colonize their gastrointestinal tracts. Recent advances have provided mechanistic insight into the important contributions of the gut microbiome to vertebrate biology, but questions remain about the evolutionary processes that have shaped symbiotic interactions in the gut and the consequences that arise for both the microbes and the host. Here we discuss the biological principles that underlie microbial symbiosis in the vertebrate gut and the potential of the development of mutualism. We then review phylogenetic and experimental studies on the vertebrate symbiont Lactobacillus reuteri that have provided novel insight into the ecological and evolutionary strategy of a gut microbe and its relationship with the host. We argue that a mechanistic understanding of the microbial symbiosis in the vertebrate gut and its evolution will be important to determine how this relationship can go awry, and it may reveal possibilities by which the gut microbiome can be manipulated to support health.
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39
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Zhang H, Chen L. Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus). Mol Biol Rep 2010; 37:4013-22. [PMID: 20306230 DOI: 10.1007/s11033-010-0060-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/05/2010] [Indexed: 01/01/2023]
Abstract
The aim of this study was to describe the microbial communities in the distal gut of wild wolves (Canis lupus). Fecal samples were collected from three healthy unrelated adult wolves captured at the nearby of Dalai Lake Nature Reserve in Inner Mongolia of China. The diversity of fecal bacteria was investigated by constructing PCR-amplified 16S rRNA gene clone libraries using the universal bacterial primers 27 F and 1493 R. A total of 307 non-chimeric near-full-length 16S rRNA gene sequences were analyzed and 65 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified. Seventeen OTUs (26%) showed less than 98% sequence similarity to 16S rRNA gene sequences were reported previously. Five different bacterial phyla were identified, with the majority of OTUs being classified within the phylum Firmicutes (60%), followed by Bacteroidetes (16.9%), Proteobacteria (9.2%), Fusobacteria (9.2%) and Actinobacteria (4.6%). The majority of clones fell within the order Clostridiales (53.8% of OTUs). It was predominantly affiliated with five families: Lachnospiraceae was the most diverse bacterial family in this order, followed by Ruminococcaceae, Clostridiaceae, Peptococcaceae and Peptostreptococcaceae.
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Affiliation(s)
- Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, 273165, China.
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40
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Glad T, Bernhardsen P, Nielsen KM, Brusetti L, Andersen M, Aars J, Sundset MA. Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard. BMC Microbiol 2010; 10:10. [PMID: 20074323 PMCID: PMC2822771 DOI: 10.1186/1471-2180-10-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 01/14/2010] [Indexed: 11/29/2022] Open
Abstract
Background Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. Results A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 104 to 1.6 × 106 colony forming units (cfu)/ml for the rectum swabs and 4.0 × 103 to 1.0 × 105 cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic β-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. Conclusion The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.
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Affiliation(s)
- Trine Glad
- Department of Pharmacy, University of Tromsø, 9037 Tromsø, Norway.
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41
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Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME JOURNAL 2009; 4:377-87. [PMID: 19924154 DOI: 10.1038/ismej.2009.123] [Citation(s) in RCA: 198] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The vertebrate digestive tract, including that of humans, is the habitat to trillions of bacteria that are of significant importance to host biology and health. Although these communities are often postulated to have coevolved with their hosts, evidence is lacking, yet critical for our understanding of microbial symbiosis in vertebrates. To gain insight into the evolution of a gut symbiont, we have characterized the population genetic structure and phylogeny of Lactobacillus reuteri strains isolated from six different host species (human, mouse, rat, pig, chicken and turkey) using Amplified-Fragment Length Polymorphism (AFLP) and Multi-Locus Sequence Analysis (MLSA). The results revealed considerable genetic heterogeneity within the L. reuteri population and distinct monophyletic clades reflecting host origin but not provenance. The evolutionary patterns detected indicate a long-term association of L. reuteri lineages with particular vertebrate species and host-driven diversification. Results from a competition experiment in a gnotobiotic mouse model revealed that rodent isolates showed elevated ecological performance, indicating that evolution of L. reuteri lineages was adaptive. These findings provide evidence that some vertebrate gut microbes are not promiscuous, but have diversified into host-adapted lineages by a long-term evolutionary process, allowing the development of a highly specialized symbiosis.
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Affiliation(s)
- Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA
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42
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Donovan CJ, Garduño RA, Kalmokoff M, Ku JC, Quilliam MA, Gill TA. Pseudoalteromonas bacteria are capable of degrading paralytic shellfish toxins. Appl Environ Microbiol 2009; 75:6919-23. [PMID: 19717625 PMCID: PMC2772429 DOI: 10.1128/aem.01384-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/21/2009] [Indexed: 11/20/2022] Open
Abstract
Marine bacterial isolates cultured from the digestive tracts of blue mussels (Mytilus edulis) contaminated with paralytic shellfish toxins (PSTs) were screened for the ability to reduce the toxicity of a PST mixture. Seven isolates reduced the overall toxicity of the algal extract by > or = 90% within 3 days. These isolates shared at least 99% 16S rRNA gene sequence similarity with five Pseudoalteromonas spp. Phenotypic tests suggested that all are novel strains of Pseudoalteromonas haloplanktis.
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Affiliation(s)
- Carrie J. Donovan
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Rafael A. Garduño
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Martin Kalmokoff
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
| | - John C. Ku
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Michael A. Quilliam
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Tom A. Gill
- Food Science Program, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Nova Scotia, Canada B3J 2X4, Department of Microbiology and Immunology and Department of Medicine—Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5, Agriculture and Agrifood Canada, Kentville, Nova Scotia, Canada B4N 1J5, National Research Council of Canada—Institute for Marine Biosciences, Halifax, Nova Scotia, Canada B3H 3Z1
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Abnous K, Brooks SPJ, Kwan J, Matias F, Green-Johnson J, Selinger LB, Thomas M, Kalmokoff M. Diets enriched in oat bran or wheat bran temporally and differentially alter the composition of the fecal community of rats. J Nutr 2009; 139:2024-31. [PMID: 19776187 DOI: 10.3945/jn.109.109470] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A clear understanding of how diet alters gastrointestinal communities is important given the suggested link between gut community composition and a wide variety of disease pathologies. To characterize this link for commonly consumed dietary fiber sources, we investigated the change in the fecal community of rats fed diets containing 5% nonnutritive fiber (control), 3% (wt:wt) oat bran plus 2% nonnutritive fiber (OB), or 5% (w/w) wheat bran (WB) over a 28-d feeding trial using both molecular- and cultivation-based methodologies. Pooled fecal samples from 8 rats fed the same diet were analyzed at 4 time points. On d 28, bran-fed rats had approximately twice the total cultivable bacteria than rats fed the control diet. Over the course of feeding, the cultivable community was initially dominated by bacteroides, then by bifidobacteria, lactobacilli, enterococci, and various enterics. In contrast, molecular analysis revealed the appearance of new operational taxonomic units (phylotypes) that were both temporally and inequitably distributed throughout the fecal community. The majority of change occurred in 2 major lineages within the Firmicutes: the Clostridium coccoides group and the Clostridium leptum subgroup. The time course of change depended on the source of bran, with the majority of new phylotypes appearing by d 14 (OB) or d 28 (WB), although adaptation of the fecal community was slow and continued over the entire feeding trial. Bacterial community richness was higher in bran-fed rats than in those fed the control diet. Change within the C. coccoides and C. leptum lineages likely reflect their high abundance within the gut bacterial community and the role of clostridia in fiber digestion. The results illustrate the limitations of relying solely on cultivation to assess bacterial changes and illustrate that community changes are complex in an ecosystem containing high numbers of interdependent and competing species of bacteria.
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Affiliation(s)
- Khalil Abnous
- Bureau of Nutritional Sciences, Health Canada, Ottawa, Ontario, Canada
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44
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Intestinal microflora functions in laboratory mice claimed to harbor a "normal" intestinal microflora. Is the SPF concept running out of date? Anaerobe 2009; 16:311-3. [PMID: 19854284 DOI: 10.1016/j.anaerobe.2009.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 10/08/2009] [Accepted: 10/16/2009] [Indexed: 11/22/2022]
Abstract
For many years, laboratory animal breeders have used a mixture of eight bacterial strains, the so-called Altered Schaedler Flora (ASF) to inoculate Caesarian derived offspring when establishing colonies of Specific Pathogen Free (SPF) rodents fulfilling the criteria worked out by regulatory agencies as AALAS, FELASA, etc. However, recently it was shown in this journal that such SPF animals harbored a fecal flora far different from that of feral mice. Over the years, we have worked with functional aspects of host-microbe interactions(s) and the aim of the present study was to analyze some intestinal microbial biochemical activities in mice harboring an ASF flora. In the five parameter studied, the ASF mice showed a pattern similar to what is found in germfree mice and rats, demonstrating an absence of microorganisms capable of performing these reactions. These findings call for a re-considering of the SPF concept. Presence of important microbiological functions should be taken into consideration when rodents are used in biomedical research.
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45
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Stehr M, Greweling MC, Tischer S, Singh M, Blöcker H, Monner DA, Müller W. Charles River altered Schaedler flora (CRASF®) remained stable for four years in a mouse colony housed in individually ventilated cages. Lab Anim 2009; 43:362-70. [DOI: 10.1258/la.2009.0080075] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
As recommendations for specific pathogen-free housing change, mouse facilities need to re-derive their colonies repeatedly in order to eliminate specified bacteria or viruses. This paper describes the establishment of a new mouse facility using as starting point a small colony of CD-1 mice colonized with the Charles River altered Schaedler flora (CRASF®) housed in individually ventilated cages (IVCs). The import of new strains was performed exclusively via embryo transfer using CD-1 mice as recipients. The integrity of the CRASF® in caecum samples of the original CD-1 colony and of three inbred mouse lines imported into the colony was proven by a quantitative realtime polymerase chain reaction approach. Furthermore, we searched for bacterial contaminants in the gut flora using non-specific 16S rRNA primers. The bacterial sequences found were closely related to but not exclusively sequences of altered Schaedler flora (ASF) members, suggesting that the ASF is heterogeneous rather than restricted to the eight defined bacteria. Moreover, no pathogens were found, neither using the non-specific 16S rRNA primers nor in routine quarterly health monitoring. As one effect of this defined gut flora, interleukin-10 knockout mice are devoid of colitis in our facility. In conclusion, our approach building up a mouse facility using foster mothers and embryo transfer as well as a strict barrier system and IVCs is suitable to maintain a colony free from contaminating bacteria over the long term. CRASF® remained stable for seven mouse generations and was efficiently transferred to the imported mouse strains.
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Affiliation(s)
- Matthias Stehr
- Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- The first two authors contributed equally to this work
| | - Marina C Greweling
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Present address: Division of Thoracic and Cardiovascular Surgery, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
- The first two authors contributed equally to this work
| | - Sabine Tischer
- Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Present address: Institute for Transfusion Medicine, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Mahavir Singh
- Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Helmut Blöcker
- Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - David A Monner
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Werner Müller
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Present address: Bill Ford Chair of Cellular Immunology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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46
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Brooks S, Kheradpir E, McAllister M, Kwan J, Burgher-McLellan K, Kalmokoff M. In-feed administered sub-therapeutic chlortetracycline alters community composition and structure but not the abundance of community resistance determinants in the fecal flora of the rat. Anaerobe 2009; 15:145-54. [DOI: 10.1016/j.anaerobe.2009.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Abell GC, McOrist AL. Assessment of the diversity and stability of faecal bacteria from healthy adults using molecular methods. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.1080/08910600701662248] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Guy C.J. Abell
- Preventative Health Flagship, CSIRO Division of Molecular and Health Technologies, Adelaide, South Australia, Australia
| | - Alexandra L. McOrist
- Preventative Health Flagship, CSIRO Division of Molecular and Health Technologies, Adelaide, South Australia, Australia
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48
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Fahey GC, Barry KA, Swanson KS. Age-Related Changes in Nutrient Utilization by Companion Animals. Annu Rev Nutr 2008; 28:425-45. [DOI: 10.1146/annurev.nutr.28.061807.155325] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- George C. Fahey
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801; , ,
| | - Kathleen A. Barry
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801; , ,
| | - Kelly S. Swanson
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801; , ,
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49
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Suchodolski JS, Camacho J, Steiner JM. Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis. FEMS Microbiol Ecol 2008; 66:567-78. [PMID: 18557939 DOI: 10.1111/j.1574-6941.2008.00521.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The study aim was to describe the diversity of the intraluminal intestinal microbial community in dogs by direct sequence analysis of the 16S rRNA gene. Intestinal content was collected from the duodenum, jejunum, ileum, and colon from six healthy dogs. Bacterial 16S rRNA gene was amplified with universal bacterial primers. Amplicons were ligated into cloning vectors and near-full-length 16S rRNA gene inserts were analyzed. From a total of 864 clones analyzed, 106 nonredundant 16S rRNA gene sequences were identified. Forty-two (40%) sequences showed<98% sequence similarity to 16S rRNA gene sequences reported previously. Operation taxonomic units were classified into four phyla: Firmicutes, Fusobacteria, Bacteroidetes, and Proteobacteria. Clostridiales predominated in the duodenum (40% of clones) and jejunum (39%), and were highly abundant in the ileum (25%) and colon (26%). Sequences affiliated with Clostridium cluster XI and Clostridium cluster XIVa dominated in the proximal small intestine and colon, respectively. Fusobacteriales and Bacteroidales were the most abundant bacterial order in the ileum (33%) and colon (30%). Enterobacteriales were more commonly observed in the small intestine than in the colon. Lactobacillales occurred commonly in all parts of the intestine.
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Affiliation(s)
- Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA.
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Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol 2008; 74:4985-96. [PMID: 18539818 DOI: 10.1128/aem.00753-08] [Citation(s) in RCA: 507] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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