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Page 1
Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium. Human Microbiome Project Consortium. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. Nature. 2012. PMID: 22699609 Free PMC article.
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. ...The project encountered an estimated 81-99% of the genera, enzyme families and community configurations o …
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats su …
Next-generation sequencing: insights to advance clinical investigations of the microbiome.
Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Wensel CR, et al. J Clin Invest. 2022 Apr 1;132(7):e154944. doi: 10.1172/JCI154944. J Clin Invest. 2022. PMID: 35362479 Free PMC article. Review.
We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disea …
We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata …
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.
Mills RH, Dulai PS, Vázquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ. Mills RH, et al. Nat Microbiol. 2022 Feb;7(2):262-276. doi: 10.1038/s41564-021-01050-3. Epub 2022 Jan 27. Nat Microbiol. 2022. PMID: 35087228 Free PMC article.
Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. ...These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations …
Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host infl …
The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain.
Salliss ME, Farland LV, Mahnert ND, Herbst-Kralovetz MM. Salliss ME, et al. Hum Reprod Update. 2021 Dec 21;28(1):92-131. doi: 10.1093/humupd/dmab035. Hum Reprod Update. 2021. PMID: 34718567 Review.
SEARCH METHODS: PubMed databases were searched using the following keywords: endometriosis AND microbiome, infertility AND microbiome, pelvic pain AND microbiome, IVF (in-vitro fertilization) AND microbiome, endometriosis AND infertility. ...Animal stu …
SEARCH METHODS: PubMed databases were searched using the following keywords: endometriosis AND microbiome, infertility AND microbi …
Population-level Metagenomics Uncovers Distinct Effects of Multiple Medications on the Human Gut Microbiome.
Nagata N, Nishijima S, Miyoshi-Akiyama T, Kojima Y, Kimura M, Aoki R, Ohsugi M, Ueki K, Miki K, Iwata E, Hayakawa K, Ohmagari N, Oka S, Mizokami M, Itoi T, Kawai T, Uemura N, Hattori M. Nagata N, et al. Gastroenterology. 2022 Oct;163(4):1038-1052. doi: 10.1053/j.gastro.2022.06.070. Epub 2022 Jul 2. Gastroenterology. 2022. PMID: 35788347 Free article.
BACKGROUND & AIMS: Medication is a major determinant of human gut microbiome structure, and its overuse increases the risks of morbidity and mortality. However, effects of certain commonly prescribed drugs and multiple medications on the gut microbiome are still …
BACKGROUND & AIMS: Medication is a major determinant of human gut microbiome structure, and its overuse increases the risks of mo …
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. Vangay P, et al. mSystems. 2021 Feb 23;6(1):e01194-20. doi: 10.1128/mSystems.01194-20. mSystems. 2021. PMID: 33622857 Free PMC article.
Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contribution …
Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable …
Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs.
Gauglitz JM, Morton JT, Tripathi A, Hansen S, Gaffney M, Carpenter C, Weldon KC, Shah R, Parampil A, Fidgett AL, Swafford AD, Knight R, Dorrestein PC. Gauglitz JM, et al. mSystems. 2020 Mar 10;5(2):e00635-19. doi: 10.1128/mSystems.00635-19. mSystems. 2020. PMID: 32156796 Free PMC article.
Even high-quality collection and reporting of study metadata in microbiome studies can lead to various forms of inadvertently missing or mischaracterized information that can alter the interpretation or outcome of the studies, especially with nonmodel organisms. ... …
Even high-quality collection and reporting of study metadata in microbiome studies can lead to various forms of inadvertently …
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.
Dai D, Zhu J, Sun C, Li M, Liu J, Wu S, Ning K, He LJ, Zhao XM, Chen WH. Dai D, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D777-D784. doi: 10.1093/nar/gkab1019. Nucleic Acids Res. 2022. PMID: 34788838 Free PMC article.
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. ...
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpo …
Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome.
Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R, Payami H. Hill-Burns EM, et al. Mov Disord. 2017 May;32(5):739-749. doi: 10.1002/mds.26942. Epub 2017 Feb 14. Mov Disord. 2017. PMID: 28195358 Free PMC article.
BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE: The objective of this study was to determine if PD involves dysbiosis of gut microbiome …
BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota cou …
Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours.
Mishra S, Tejesvi MV, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen OS, Peñate Medina T, Peñate Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari PP, Lahti L, Karihtala P, Ruuska TS, Reunanen J. Mishra S, et al. J Adv Res. 2025 Feb;68:375-386. doi: 10.1016/j.jare.2024.03.003. Epub 2024 Mar 7. J Adv Res. 2025. PMID: 38458256 Free PMC article.
However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. ...OBJECTIVES: Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique asp …
However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbi …
421 results