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For: Zhang X, Li L, Butcher J, Stintzi A, Figeys D. Advancing functional and translational microbiome research using meta-omics approaches. Microbiome 2019;7:154. [PMID: 31810497 PMCID: PMC6898977 DOI: 10.1186/s40168-019-0767-6] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/11/2019] [Indexed: 05/05/2023]
Number Cited by Other Article(s)
1
Jeyaraman N, Jeyaraman M, Dhanpal P, Ramasubramanian S, Nallakumarasamy A, Muthu S, Santos GS, da Fonseca LF, Lana JF. Integrative review of the gut microbiome’s role in pain management for orthopaedic conditions. World J Exp Med 2025;15:102969. [DOI: 10.5493/wjem.v15.i2.102969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Revised: 03/03/2025] [Accepted: 04/01/2025] [Indexed: 04/16/2025]  Open
2
Ray D, Bose P, Mukherjee S, Roy S, Kaity S. Recent drug delivery systems targeting the gut-brain-microbiome axis for the management of chronic diseases. Int J Pharm 2025;680:125776. [PMID: 40425058 DOI: 10.1016/j.ijpharm.2025.125776] [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: 02/25/2025] [Revised: 05/14/2025] [Accepted: 05/24/2025] [Indexed: 05/29/2025]
3
Bhattacharya A, Shepherd C, El-Assaad F, Mather KA. Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer's disease? Curr Opin Psychiatry 2025;38:252-257. [PMID: 40013501 PMCID: PMC11957443 DOI: 10.1097/yco.0000000000000989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2025]
4
Mosquera FEC, de la Rosa Caldas M, Naranjo Rojas A, Perlaza CL, Liscano Y. Probiotic, Prebiotic, and Synbiotic Supplementation for the Prevention and Treatment of Acute Otitis Media: A Systematic Review and Meta-Analysis. CHILDREN (BASEL, SWITZERLAND) 2025;12:591. [PMID: 40426770 DOI: 10.3390/children12050591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/23/2025] [Accepted: 04/29/2025] [Indexed: 05/29/2025]
5
Iwasaki S, Také A, Uojima H, Horio K, Sakaguchi Y, Gotoh K, Satoh T, Hidaka H, Tanaka Y, Hayashi S, Kusano C. Quantification of Streptococcus salivarius using the digital polymerase chain reaction as a liver fibrosis marker. World J Hepatol 2025;17:102027. [PMID: 40308822 PMCID: PMC12038421 DOI: 10.4254/wjh.v17.i4.102027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 02/21/2025] [Accepted: 04/09/2025] [Indexed: 04/25/2025]  Open
6
Corbin KD, Igudesman D, Smith SR, Zengler K, Krajmalnik-Brown R. Targeting the Gut Microbiota's Role in Host Energy Absorption With Precision Nutrition Interventions for the Prevention and Treatment of Obesity. Nutr Rev 2025:nuaf046. [PMID: 40233201 DOI: 10.1093/nutrit/nuaf046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]  Open
7
Gebrehiwot NT, Liu Y, Li J, Liu HM. Molecular Alterations in Gastric Intestinal Metaplasia Shed Light on Alteration of Methionine Metabolism: Insight into New Diagnostic and Treatment Approaches. Biomedicines 2025;13:964. [PMID: 40299656 PMCID: PMC12025106 DOI: 10.3390/biomedicines13040964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2025] [Revised: 04/03/2025] [Accepted: 04/08/2025] [Indexed: 05/01/2025]  Open
8
Pei X, Liu L, Han Y. Advances in human microbiome and prostate cancer research. Front Immunol 2025;16:1576679. [PMID: 40297591 PMCID: PMC12034659 DOI: 10.3389/fimmu.2025.1576679] [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: 02/14/2025] [Accepted: 03/26/2025] [Indexed: 04/30/2025]  Open
9
Yang SY, Han SM, Lee JY, Kim KS, Lee JE, Lee DW. Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives. J Microbiol Biotechnol 2025;35:e2412001. [PMID: 40223273 PMCID: PMC12010094 DOI: 10.4014/jmb.2412.12001] [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: 12/02/2024] [Revised: 02/14/2025] [Accepted: 02/24/2025] [Indexed: 04/15/2025]
10
Fang X, Wang Y, Wei H, Huang Y. Precision Microbiome: A New Era of Targeted Therapy with Core Probiotics. RESEARCH (WASHINGTON, D.C.) 2025;8:0658. [PMID: 40143943 PMCID: PMC11938712 DOI: 10.34133/research.0658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Accepted: 03/11/2025] [Indexed: 03/28/2025]
11
Ma W, Han Z, Liu X, Cui W, Zhen D, Zhou X, Song Y, Jiang S. Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine. Microorganisms 2025;13:731. [PMID: 40284568 PMCID: PMC12029867 DOI: 10.3390/microorganisms13040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Accepted: 03/18/2025] [Indexed: 04/29/2025]  Open
12
Kelliher JM, Rodriguez FE, Johnson LYD, Roux S, Smith M, Clum A, Lynch W, Bias CH, Finks SS, Keenum I, Kiledal EA, Lin HA, Longley R, McDonald R, Pitot TM, Rodríguez-Ramos J, Shen J, Sprockett DD, Swift J, Yadav A, Eloe-Fadrosh EA. Quantifying the impact of workshops promoting microbiome data standards and data stewardship. Sci Rep 2025;15:9887. [PMID: 40121238 PMCID: PMC11929805 DOI: 10.1038/s41598-025-89991-1] [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: 11/20/2024] [Accepted: 02/10/2025] [Indexed: 03/25/2025]  Open
13
France MT, Chaudry I, Rutt L, Quain M, Shirtliff B, McComb E, Maros A, Alizadeh M, Hussain FA, Elovitz MA, Relman DA, Rahman A, Brotman RM, Price J, Kassaro M, Holm JB, Ma B, Ravel J. VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.04.641479. [PMID: 40093185 PMCID: PMC11908257 DOI: 10.1101/2025.03.04.641479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
14
Vande Moortele T, Verschaffelt P, Huang Q, Doncheva NT, Holstein T, Jachmann C, Dawyndt P, Martens L, Mesuere B, Van Den Bossche T. PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways. Mol Cell Proteomics 2025;24:100918. [PMID: 39880083 PMCID: PMC11903815 DOI: 10.1016/j.mcpro.2025.100918] [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: 09/06/2024] [Revised: 12/17/2024] [Accepted: 01/23/2025] [Indexed: 01/31/2025]  Open
15
Huang YJ. The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations. Immunol Rev 2025;330:e70015. [PMID: 40072031 PMCID: PMC11899502 DOI: 10.1111/imr.70015] [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: 09/11/2024] [Revised: 02/13/2025] [Accepted: 02/28/2025] [Indexed: 03/15/2025]
16
Cui Z, Wu Y, Zhang QH, Wang SG, Guo ZH. NPENN: A Noise Perturbation Ensemble Neural Network for Microbiome Disease Phenotype Prediction. IEEE J Biomed Health Inform 2025;29:2210-2221. [PMID: 40030297 DOI: 10.1109/jbhi.2024.3507789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2025]
17
Park H, Yeo S, Lee T, Han Y, Ryu CB, Huh CS. Culture-based characterization of gut microbiota in inflammatory bowel disease. Front Microbiol 2025;16:1538620. [PMID: 40051478 PMCID: PMC11884817 DOI: 10.3389/fmicb.2025.1538620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 02/03/2025] [Indexed: 03/09/2025]  Open
18
Lin T. Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using 'meta-omics' techniques. Front Cell Infect Microbiol 2025;15:1541881. [PMID: 39991711 PMCID: PMC11843044 DOI: 10.3389/fcimb.2025.1541881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 01/02/2025] [Indexed: 02/25/2025]  Open
19
Lista S, Munafò A, Caraci F, Imbimbo C, Emanuele E, Minoretti P, Pinto-Fraga J, Merino-País M, Crespo-Escobar P, López-Ortiz S, Monteleone G, Imbimbo BP, Santos-Lozano A. Gut microbiota in Alzheimer's disease: Understanding molecular pathways and potential therapeutic perspectives. Ageing Res Rev 2025;104:102659. [PMID: 39800223 DOI: 10.1016/j.arr.2025.102659] [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: 07/19/2024] [Revised: 11/29/2024] [Accepted: 01/09/2025] [Indexed: 01/15/2025]
20
Bai D, Ma C, Xun J, Luo H, Yang H, Lyu H, Zhu Z, Gai A, Yousuf S, Peng K, Xu S, Gao Y, Wang Y, Liu Y. MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics. IMETA 2025;4:e70002. [PMID: 40027478 PMCID: PMC11865346 DOI: 10.1002/imt2.70002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 01/21/2025] [Accepted: 01/23/2025] [Indexed: 03/05/2025]
21
Kennedy EC, Ross FC, O'Shea CA, Lavelle A, Ross P, Dempsey E, Stanton C, Hawkes CP. Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort. BMJ Open 2025;15:e089206. [PMID: 39890137 PMCID: PMC11784173 DOI: 10.1136/bmjopen-2024-089206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 12/06/2024] [Indexed: 02/03/2025]  Open
22
Al-Adham ISI, Agha ASAA, Al-Akayleh F, Al-Remawi M, Jaber N, Al Manasur M, Collier PJ. Prebiotics Beyond the Gut: Omics Insights, Artificial Intelligence, and Clinical Trials in Organ-Specific Applications. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10465-x. [PMID: 39878922 DOI: 10.1007/s12602-025-10465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2025] [Indexed: 01/31/2025]
23
Misu IJ, Kayess MO, Siddiqui MN, Gupta DR, Islam MN, Islam T. Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience. Microorganisms 2025;13:233. [PMID: 40005600 PMCID: PMC11857137 DOI: 10.3390/microorganisms13020233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/11/2025] [Accepted: 01/14/2025] [Indexed: 02/27/2025]  Open
24
Reuben RC, Torres C. Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications. World J Microbiol Biotechnol 2025;41:41. [PMID: 39826029 PMCID: PMC11742929 DOI: 10.1007/s11274-024-04242-1] [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: 10/13/2024] [Accepted: 12/26/2024] [Indexed: 01/20/2025]
25
Zeng J, Cheong LYT, Lo CH. Therapeutic targeting of obesity-induced neuroinflammation and neurodegeneration. Front Endocrinol (Lausanne) 2025;15:1456948. [PMID: 39897964 PMCID: PMC11781992 DOI: 10.3389/fendo.2024.1456948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 12/30/2024] [Indexed: 02/04/2025]  Open
26
Wawryk MMH, Ley P, Vasquez-Cardenas D, Tabor RF, Cook PLM. Multidisciplinary methodologies used in the study of cable bacteria. FEMS Microbiol Rev 2025;49:fuae030. [PMID: 39673715 PMCID: PMC11774119 DOI: 10.1093/femsre/fuae030] [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: 05/09/2024] [Revised: 10/21/2024] [Accepted: 12/11/2024] [Indexed: 12/16/2024]  Open
27
Fan S, Qin P, Lu J, Wang S, Zhang J, Wang Y, Cheng A, Cao Y, Ding W, Zhang W. Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides. IMETA 2024;3:e244. [PMID: 39742298 PMCID: PMC11683478 DOI: 10.1002/imt2.244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/25/2024] [Accepted: 09/27/2024] [Indexed: 01/03/2025]
28
Chen S, Jiao Y, Han C, Li Y, Zou W, Liu J. Drug-Resistant Epilepsy and Gut-Brain Axis: an Overview of a New Strategy for Treatment. Mol Neurobiol 2024;61:10023-10040. [PMID: 38087164 DOI: 10.1007/s12035-023-03757-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2024]
29
Ouwehand J, Peijnenburg WJGM, Vijver MG. Microbial function matters: Microbiome-aware nano-ecotoxicology needs functional endpoints besides compositional data. CHEMOSPHERE 2024;369:143905. [PMID: 39643017 DOI: 10.1016/j.chemosphere.2024.143905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/03/2024] [Accepted: 12/03/2024] [Indexed: 12/09/2024]
30
Aggeletopoulou I, Triantos C. Microbiome Shifts and Their Impact on Gut Physiology in Irritable Bowel Syndrome. Int J Mol Sci 2024;25:12395. [PMID: 39596460 PMCID: PMC11594715 DOI: 10.3390/ijms252212395] [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: 11/01/2024] [Revised: 11/17/2024] [Accepted: 11/18/2024] [Indexed: 11/28/2024]  Open
31
Pérez-Prieto I, Plaza-Florido A, Ubago-Guisado E, Ortega FB, Altmäe S. Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis. J Sci Med Sport 2024;27:793-804. [PMID: 39048485 DOI: 10.1016/j.jsams.2024.07.003] [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: 05/16/2023] [Revised: 05/18/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
32
Duong VA, Enkhbayar A, Bhasin N, Senavirathna L, Preisner EC, Hoffman KL, Shukla R, Jenq RR, Cheng K, Bronner MP, Figeys D, Britton RA, Pan S, Chen R. A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies. Proteomics 2024;24:e2400078. [PMID: 38824665 PMCID: PMC11576236 DOI: 10.1002/pmic.202400078] [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: 03/08/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
33
Mancini A, Vitucci D, Lasorsa VA, Lupo C, Brustio PR, Capasso M, Orrù S, Rainoldi A, Schena F, Buono P. Six months of different exercise type in sedentary primary schoolchildren: impact on physical fitness and saliva microbiota composition. Front Nutr 2024;11:1465707. [PMID: 39512522 PMCID: PMC11542257 DOI: 10.3389/fnut.2024.1465707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 10/15/2024] [Indexed: 11/15/2024]  Open
34
Brennan C, Belda-Ferre P, Zuffa S, Charron-Lamoureux V, Mohanty I, Ackermann G, Allaband C, Ambre M, Boyer T, Bryant M, Cantrell K, Gonzalez A, McDonald D, Salido RA, Song SJ, Wright G, Dorrestein PC, Knight R. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems 2024;9:e0098524. [PMID: 39283083 PMCID: PMC11494942 DOI: 10.1128/msystems.00985-24] [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: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 10/23/2024]  Open
35
Jiang S, Pei L, Chen L, Sun J, Song Y. Mechanisms of Electroacupuncture in Alleviating Visceral Hypersensitivity in Post-Infectious Irritable Bowel Syndrome Mice: The Role of GDNF Signaling Pathway and Gut Microbiota. Microb Physiol 2024;34:255-263. [PMID: 39396501 DOI: 10.1159/000541888] [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: 11/09/2023] [Accepted: 10/07/2024] [Indexed: 10/15/2024]
36
Hiremath G, Choksi Y, Correa H, Jacobse J, Das SR, Ma S, Goettel JA, Rajagopala SV. Children with eosinophilic esophagitis non-responsive to combination therapy have distinct esophageal transcriptomic and microbiome profile. Allergy 2024;79:2798-2811. [PMID: 38993131 PMCID: PMC11528550 DOI: 10.1111/all.16208] [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: 01/05/2024] [Revised: 04/22/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024]
37
DeFord L, Yoon JY. Soil microbiome characterization and its future directions with biosensing. J Biol Eng 2024;18:50. [PMID: 39256848 PMCID: PMC11389470 DOI: 10.1186/s13036-024-00444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024]  Open
38
Reddy N, Chiwhane A, Acharya S, Kumar S, Parepalli A, Nelakuditi M. Harnessing the Power of the Gut Microbiome: A Review of Supplementation Therapies for Metabolic Syndrome. Cureus 2024;16:e69682. [PMID: 39429422 PMCID: PMC11489520 DOI: 10.7759/cureus.69682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 09/18/2024] [Indexed: 10/22/2024]  Open
39
Sola F, Ayala D, Pulido M, Ayala R, López-Cerero L, Hernández I, Ruiz D. ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases. BIOINFORMATICS ADVANCES 2024;4:vbae129. [PMID: 39262905 PMCID: PMC11387618 DOI: 10.1093/bioadv/vbae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
40
Herrera-Quintana L, Vázquez-Lorente H, Hinojosa-Nogueira D, Plaza-Diaz J. Relationship between Infant Feeding and the Microbiome: Implications for Allergies and Food Intolerances. CHILDREN (BASEL, SWITZERLAND) 2024;11:1030. [PMID: 39201963 PMCID: PMC11353207 DOI: 10.3390/children11081030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024]
41
Sajid S, Mashkoor M, Jørgensen MG, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation. Mol Cell Biochem 2024;479:1957-1968. [PMID: 37610616 DOI: 10.1007/s11010-023-04827-8] [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: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
42
Meier TA, Refahi MS, Hearne G, Restifo DS, Munoz-Acuna R, Rosen GL, Woloszynek S. The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain. Curr Pain Headache Rep 2024;28:769-784. [PMID: 38822995 DOI: 10.1007/s11916-024-01264-0] [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] [Accepted: 04/28/2024] [Indexed: 06/03/2024]
43
Kruk ME, Mehta S, Murray K, Higgins L, Do K, Johnson JE, Wagner R, Wendt CH, O’Connor JB, Harris JK, Laguna TA, Jagtap PD, Griffin TJ. An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems 2024;9:e0092923. [PMID: 38934598 PMCID: PMC11264604 DOI: 10.1128/msystems.00929-23] [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: 09/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024]  Open
44
Wang A, Fekete EEF, Creskey M, Cheng K, Ning Z, Pfeifle A, Li X, Figeys D, Zhang X. Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry. MICROBIOME RESEARCH REPORTS 2024;3:39. [PMID: 39421247 PMCID: PMC11480776 DOI: 10.20517/mrr.2024.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 10/19/2024]
45
Do K, Mehta S, Wagner R, Bhuming D, Rajczewski AT, Skubitz APN, Johnson JE, Griffin TJ, Jagtap PD. A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. mSphere 2024;9:e0079323. [PMID: 38780289 PMCID: PMC11332332 DOI: 10.1128/msphere.00793-23] [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: 12/18/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]  Open
46
Hu L, Sun L, Yang C, Zhang DW, Wei YY, Yang MM, Wu HM, Fei GH. Gut microbiota-derived acetate attenuates lung injury induced by influenza infection via protecting airway tight junctions. J Transl Med 2024;22:570. [PMID: 38879538 PMCID: PMC11179378 DOI: 10.1186/s12967-024-05376-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/06/2024] [Indexed: 06/19/2024]  Open
47
Xu MQ, Pan F, Peng LH, Yang YS. Advances in the isolation, cultivation, and identification of gut microbes. Mil Med Res 2024;11:34. [PMID: 38831462 PMCID: PMC11145792 DOI: 10.1186/s40779-024-00534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024]  Open
48
Shinde DB, Mahore JG, Giram PS, Singh SL, Sharda A, Choyan D, Musale S. Microbiota of Saliva: A Non-invasive Diagnostic Tool. Indian J Microbiol 2024;64:328-342. [PMID: 39010986 PMCID: PMC11246313 DOI: 10.1007/s12088-024-01219-4] [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: 06/23/2023] [Accepted: 01/30/2024] [Indexed: 07/17/2024]  Open
49
Porcari S, Fusco W, Spivak I, Fiorani M, Gasbarrini A, Elinav E, Cammarota G, Ianiro G. Fine-tuning the gut ecosystem: the current landscape and outlook of artificial microbiome therapeutics. Lancet Gastroenterol Hepatol 2024;9:460-475. [PMID: 38604200 DOI: 10.1016/s2468-1253(23)00357-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 04/13/2024]
50
Liu D, Xie LS, Lian S, Li K, Yang Y, Wang WZ, Hu S, Liu SJ, Liu C, He Z. Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. mSphere 2024;9:e0081623. [PMID: 38470044 PMCID: PMC11036815 DOI: 10.1128/msphere.00816-23] [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: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024]  Open
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