• Metatranscriptomics
• Microbiome function
• Sequence analysis pipeline
• Taxonomic annotation

• Crohn’s disease
• SNP
• microbiota

• #FZSM-2023-0013 The work was supported by the Kazan Federal University Strategic Academic Leadership Program (PRIORITY-2030) and by the subsidy allocated to Kazan Federal University for the state assignment in the sphere of scientific activities.

• ROS
• aging
• collagen
• genetic variants
• microbiota
• single nucleotide polymorphisms
• skin

• Italian Ministry of University and Research (ex 60% 2021) Italian Ministry of University and Research (ex 60% 2021)

• SCFA
• fidarestat
• microbiota
• mitochondria
• ulcerative colitis
• ꞵ-glucan

• Antibiotics
• Dysbiosis
• Fecal microbiota transplantation
• Inflammatory bowel diseases
• Microbiota
• Probiotics

Inflammatory bowel disease (IBD), Crohn’s disease and ulcerative colitis are chronic inflammatory disorders of the intestines. The underlying inflammation activates the coagulation cascade leading to an increased risk of developing arterial and venous thromboembolic events such as deep vein thrombosis and pulmonary embolism. Patients with IBD are at a 2–3-fold increased risk of developing thromboembolism. This risk increases in patients with active IBD disease, flare-ups, surgery, steroid treatment, and hospitalization. These complications are associated with significant morbidity and mortality making them important in clinical practice. Clinicians should consider the increased risk of thromboembolic events in patients with IBD and manage them with appropriate prophylaxis based on the risk. In this review, we discuss the literature associated with the pathophysiology of thromboembolism in patients with IBD, summarize the studies describing the various thromboembolic events, and the management of thromboembolism in patients with IBD.

• disease
• gut microbiota
• intestinal barrier
• intestine
• leaky gut
• microbiome
• nutrition
• permeability

Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (Apodemus draco, Leopoldamys edwardsi, Niviventer confucianus, and Niviventer fulvescens) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of A. draco, N. fulvescens, and N. confucianus was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of L. edwardsi was significantly higher than those of A. draco and N. confucianus, and its beta diversity showed significant difference from A. draco. Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.

• Chinese Academy of Sciences
• National Key Research and Development Program
• National Natural Science Foundation of China

Recent studies have revealed the importance of the gut microbiota in the regulation of metabolic phenotypes of highly prevalent metabolic diseases such as obesity, type II diabetes mellitus (T2DM) and cardiovascular disease. Peroxisome proliferator-activated receptors (PPARs) are a family of ligand-activated nuclear receptors that interact with PPAR-γ co-activator-1α (PPARGC1A) to regulate lipid and glucose metabolism. Genetic polymorphisms in PPARD (rs 2267668; A/G) and PPARGC1A (rs 8192678; G/A) are linked to T2DM. We studied the association between the single-nucleotide polymorphisms (SNPs) rs 2267668 and rs 8192678 and microbiota signatures and their relation to predicted metagenome functions, with the aim of determining possible microbial markers in a healthy population. Body composition, physical exercise and diet were characterized as potential confounders. Microbiota analysis of subjects with PPARGC1A (rs 8192678) and PPARD (rs 2267668) SNPs revealed certain taxa associated with the development of insulin resistance and T2DM. Kyoto encyclopedia of gene and genomes analysis of metabolic pathways predicted from metagenomes highlighted an overrepresentation of ABC sugar transporters for the PPARGC1A (rs 8192678) SNP. Our findings suggest an association between sugar metabolism and the PPARGC1A rs 8192678 (G/A) genotype and support the notion of specific microbiota signatures as factors related to the onset of T2DM.

• Diabetes Mellitus, Type 2/genetics
• Gastrointestinal Microbiome/genetics
• Heat-Shock Proteins/genetics
• Humans
• PPAR delta/genetics
• Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics
• Polymorphism, Single Nucleotide/genetics
• Sugars
• Transcription Factors/genetics

• colonization resistance
• commensals
• enteric infections
• gut microbiota
• microbial interaction
• pathogens

• Animals
• Bacteria
• Bacterial Infections
• Gastrointestinal Microbiome
• Virulence

• Bacteroides
• DDG and DGH
• alginate-degrading consortia
• extracellular alginate lyase (EC 4.2.2.3)
• new Entner−Doudoroff pathway
• two chemostats in series

• Alginates
• Bacteria
• Glucuronic Acid
• Metabolic Networks and Pathways
• Sewage

The main functions of adipose tissue are thought to be storage and mobilization of the body’s energy reserves, active and passive thermoregulation, participation in the spatial organization of internal organs, protection of the body from lipotoxicity, and ectopic lipid deposition. After the discovery of adipokines, the endocrine function was added to the above list, and after the identification of crosstalk between adipocytes and immune cells, an immune function was suggested. Nonetheless, it turned out that the mechanisms underlying mutual regulatory relations of adipocytes, preadipocytes, immune cells, and their microenvironment are complex and redundant at many levels. One possible way to elucidate the picture of adipose-tissue regulation is to determine genetic variants correlating with obesity. In this review, we examine various aspects of adipose-tissue involvement in innate immune responses as well as variants of immune-response genes associated with obesity.

• adipose tissue
• gene knockout
• genetic predisposition
• innate immunity
• microbiome
• obesity
• polymorphism

• 16S rRNA gene
• colorectal cancer
• microbial subtypes
• tumour microbiome

• dysbiosis
• immune system
• microbiota

• Multiple Sclerosis
• dysbiosis
• gut microbiome
• host genetics

• Animals
• Disease Models, Animal
• Encephalomyelitis, Autoimmune, Experimental/immunology
• Gastrointestinal Microbiome
• Genome-Wide Association Study
• Humans
• Mice
• Multiple Sclerosis/genetics
• Multiple Sclerosis/microbiology

Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and the intestinal microbiota that has rarely been described in human infections. Besides its role in halitosis and oral infections, S. moorei is considered to be an opportunistic pathogen causing mainly bloodstream and surgical wound infections. We performed a retrospective study of 27 cases of infections involving S. moorei in two French university hospitals between 2006 and 2021 with the aim of increasing our knowledge of this unrecognized opportunistic pathogen. We also reviewed all the data available in the literature and in genetic and metagenomic sequence databases. In addition to previously reported infections, S. moorei had been isolated from various sites and involved in intra-abdominal, osteoarticular, and cerebral infections more rarely or not previously reported. Although mostly involved in polymicrobial infections, in seven cases, it was the only pathogen recovered. Not included in all mass spectrometry databases, its identification can require 16S rRNA gene sequencing. High susceptibility to antibiotics (apart from rifampicin, moxifloxacin, and clindamycin; 91.3%, 11.8%, and 4.3% of resistant strains, respectively) has been noted. Our global search strategy revealed S. moorei to be human-associated, widely distributed in the human microbiota, including the vaginal and skin microbiota, which may be other sources for infection in addition to the oral and gut microbiota.

• Solobacterium moorei
• antimicrobial susceptibility
• habitat
• human infections
• human microbiota
• identification
• metagenomes
• sequence databases

Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.

We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs.

We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.

The online version contains supplementary material available at 10.1186/s12864-021-07607-0.

• Canine microbiome
• Dog microbiome
• Fecal microbiome
• Gastrointestinal microbiome
• Long-read metagenomics
• Long-reads
• Metagenome-assembled genomes
• Nanopore
• Sutterella

• Crohn’s disease
• biomarkers
• gut microbiome
• inflammatory bowel disease
• ulcerative colitis

• microbiome
• bacterial genes
• ulcerative colitis

• Butyribacter intestine
• Butyric acid-producing
• Lachnospiraceae

Inflammatory bowel disease (IBD) is a complex multifactorial disorder in which external and environmental factors have a large influence on its onset and development, especially in genetically susceptible individuals. Crohn’s disease (CD), one of the two types of IBD, is characterized by transmural inflammation, which is most frequently located in the region of the terminal ileum. Oxidative stress, caused by an overabundance of reactive oxygen species, is present locally and systemically in patients with CD and appears to be associated with the well-described imbalanced immune response and dysbiosis in the disease. Oxidative stress could also underlie some of the environmental risk factors proposed for CD. Although the exact etiopathology of CD remains unknown, the key role of oxidative stress in the pathogenesis of CD is extensively recognized. Epigenetics can provide a link between environmental factors and genetics, and numerous epigenetic changes associated with certain environmental risk factors, microbiota, and inflammation are reported in CD. Further attention needs to be focused on whether these epigenetic changes also have a primary role in the pathogenesis of CD, along with oxidative stress.

• Crohn’s disease
• antioxidants
• dysbiosis
• environmental factors
• epigenetics
• inflammation
• microbiota
• oxidative stress
• pathogenesis

• Crohn's disease
• gut microbiome
• metabolism
• prognosis
• ulcerative colitis

• R01 DK124095 NIDDK NIH HHS
• P30 MH062261 NIMH NIH HHS
• P30 CA036727 NCI NIH HHS
• I01 BX002761 BLRD VA
• P20 GM103427 NIGMS NIH HHS

• Fecal microbiota
• Healthy human
• Inflammatory bowel disease
• Microbiome
• NOD2
• rs2066844
• rs2066845
• rs2066847

• Chinese populations
• Han nationality
• ethnicity
• geography
• gut microbiota

• Chinese populations
• Han nationality
• ethnicity
• geography
• gut microbiota

• Crohn disease
• Inflammatory bowel disease
• antibiotics
• environmental factors
• fecal microbiota transplantation
• genetics
• inflammation
• microbiome
• microbiota
• prebiotics
• probiotics
• ulcerative colitis

• Peptacetobacter hiranonis comb. nov.
• Peptacetobacter hominis gen. nov., sp. nov
• genome analysis
• polyphasic taxonomy

• symbiosis
• microbiome

• Animals
• Animals, Newborn
• Feces/microbiology
• Female
• Gastrointestinal Microbiome
• Gene Dosage
• Horses
• Mouth/microbiology
• RNA, Ribosomal, 16S/genetics
• Vagina/microbiology

• Classification
• Colonic
• Crohn's Disease
• Ileal

• Beta-carotene
• LAR1
• Lichen endophytes
• Lichenibacterium
• Phylogenetic analysis
• Rhizobiales
• Symbiotic bacteria

Ovariectomy is a common procedure in laboratory rodents used to create a post-menopausal state. Complications including post-surgical abscess are rarely reported, but merit consideration for the health and safety of experimental animals.

A female C57/black6 mouse was ovariectomized as part of a cohort study. At Day 14 post-surgery, she developed a visible swelling on the right side, which 7 days later increased in size over 24 h, leading to euthanasia of the animal. Gross pathology was consistent with abscess. A core of necrotic tissue was present in the uterine horn. Abscess fluid and affected tissue were collected for Gram stain and bacteriological culture. The abscess core and fluid yielded three distinct types of bacterial colonies identified by 16S ribosomal RNA sequencing as Streptococcus acidominimus, Pasteurella caecimuris, and a novel species in the genus Gemella.

This is the first report of polymicrobial abscess in a rodent as a complication of ovariectomy, and the first description of a novel Gemella species for which we have proposed the epithet Gemella muriseptica. This presentation represents a potential complication of ovariectomy in laboratory animals.

• Abscess
• Gemella
• Gemella muriseptica
• Mouse
• Ovariectomy
• Pasteurella caecimuris
• Polymicrobial abscess
• Streptococcus acidominimus

• community dynamics
• fitness
• health
• longitudinal
• microbial ecology
• time series

• Animals
• Ecosystem
• Feces/microbiology
• Gastrointestinal Microbiome
• Host Microbial Interactions
• Longitudinal Studies
• Primates/microbiology
• Social Environment

• R01 AG053330 NIA NIH HHS
• R01 AG071684 NIA NIH HHS
• R21 AG055777 NIA NIH HHS

Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.

• bacterial pathogenesis
• bacterial infection
• drug delivery

• Animals
• Anti-Bacterial Agents/chemistry
• Anti-Bacterial Agents/pharmacokinetics
• Anti-Bacterial Agents/pharmacology
• Ciprofloxacin/chemistry
• Ciprofloxacin/pharmacokinetics
• Ciprofloxacin/pharmacology
• Drug Liberation
• Female
• Gastrointestinal Microbiome/drug effects
• Gastrointestinal Microbiome/physiology
• Glucuronates/chemistry
• Glucuronates/metabolism
• Hydrogen Sulfide/chemistry
• Hydrogen Sulfide/pharmacokinetics
• Hydrogen Sulfide/pharmacology
• Mice
• Oligosaccharides/chemistry
• Oligosaccharides/metabolism
• Salmonella/drug effects
• Salmonella/physiology
• Salmonella Infections/drug therapy
• Salmonella Infections/microbiology
• Treatment Outcome

• National Natural Science Foundation of China (National Science Foundation of China)

Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.

• fecal microbiota transplantation (FMT)
• gut microbiota
• inflammatory bowel disease
• pathogenesis
• prebiotics
• probiotics
• synbiotics

Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.

• Adaptation, Physiological
• Alphaproteobacteria/classification
• Alphaproteobacteria/genetics
• Alphaproteobacteria/isolation & purification
• Alphaproteobacteria/physiology
• Base Composition
• China
• Cold Temperature
• DNA, Bacterial
• Genome, Bacterial
• Geologic Sediments/microbiology
• Operon
• Permafrost/microbiology
• Phylogeny
• Whole Genome Sequencing

• Crohn’s disease
• biologic onset
• disease markers
• early diagnosis
• microbiome
• pre-clinical disease
• screening
• ulcerative colitis

• Biomarkers/metabolism
• Colitis, Ulcerative/diagnosis
• Colitis, Ulcerative/metabolism
• Crohn Disease/diagnosis
• Crohn Disease/drug therapy
• Crohn Disease/metabolism
• Humans
• Inflammatory Bowel Diseases/diagnosis
• Inflammatory Bowel Diseases/drug therapy
• Inflammatory Bowel Diseases/metabolism
• Infliximab/therapeutic use
• Microbiota

Ulcerative colitis is a chronic, idiopathic inflammatory disease that destroys the colon structure. Nevertheless, the exact pathogenesis is not clear and needs to be fully elucidated.

Stool and plasma samples were used for 16S ribosomal RNA sequencing and liquid chromatography mass spectrometry, respectively. In addition, we detected the level of trimethylamine N-oxide. Finally, we performed Pearson correlation analysis between the microbiome and the metabolome.

Twenty-three active ulcerative colitis, 25 inactive ulcerative colitis, and 30 control cases were included. Thirty-four significantly different metabolites were found between the active ulcerative colitis and control groups, 38 were found between the inactive ulcerative colitis and control groups, and only 1 was found between the active ulcerative colitis and inactive ulcerative colitis groups. The plasma trimethylamine N-oxide level of the inactive ulcerative colitis and active ulcerative colitis groups was significantly higher than that of the control group. Moreover, we identified significant changes in 24, 18, and 12 bacterial genera for active ulcerative colitis-control, inactive ulcerative colitis-control, and active ulcerative colitis-inactive ulcerative colitis, respectively. Cross-correlation indicated an association between sphingosine 1-phosphate and Roseburia, Klebsiella, and Escherichia-Shigella. Through the pathway analysis, we found sphingolipid metabolism was one of the most significantly increased pathways.

Although levels of trimethylamine N-oxide were higher in ulcerative colitis patients, they did not achieve statistical significance in active ulcerative colitis and inactive ulcerative colitis groups. Sphingosine 1-phosphate was increased in ulcerative colitis patients and there were several microbiota associated with it. Although further study is still needed, sphingosine 1-phosphate will probably become a new target for treatment of ulcerative colitis.