Cited by 811Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

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Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

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Maurice, Corinne Ferrier, Haiser, Henry Joseph, Turnbaugh, Peter James·2013·Cell

DOI 10.1016/j.cell.2012.10.052PMC PMC3552296

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Abstract

The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider interindividual variations in the active human gut microbiome.

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Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Self-citation
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,996
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815

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Haugland, R.P. (2005). The Handbook: A Guide to Fluorescent Probes and Labeling Technologies, Tenth Edition (Carlsbad, CA: Invitrogen Corp).

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Authors: Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J.
Affiliations: Harvard University (US)
Corresponding author: Turnbaugh, Peter James
ORCID: Maurice, Corinne Ferrier
Turnbaugh, Peter James
Venue: Cell
Publisher: Elsevier BV
Published: 2013-01
Volume: 152
Issue: 1-2
Pages: 39-50
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2012.10.052
PMC: PMC3552296
OpenAlex: W2063856799
Cited by: 811
References: 68
Citations by year: 2026: 22 · 2025: 37 · 2024: 48 · 2023: 42 · 2022: 51 · 2021: 75 · 2020: 79 · 2019: 69 · 2018: 100 · 2017: 62 · 2016: 66 · 2015: 60 · 2014: 58 · 2013: 42
FWCI: 33.55
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 381 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: Canadian Institutes of Health Research (112991_1)
National Institute of General Medical Sciences (P50GM068763)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords: gut microbiota, xenobiotics, Firmicutes, antibiotic resistance, drug metabolism, stress response, microbial gene expression, metatranscriptomics, 16S rRNA gene sequencing, flow cytometry, personalized medicine, interindividual variability
MeSH terms: Anti-Bacterial Agents, Feces, Gram-Positive Bacteria, Humans, Xenobiotics, Gene Expression Profiling, Gastrointestinal Tract, Metagenome, Metagenomics

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Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

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