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Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome
Open accessAbstract
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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“The impact of short-term exposure of human feces to various non-antibiotic drugs including cardiac glycosides, a gastric-acid suppressant (nizatidine), an anthelmintic (levamisole), an analgesic (phenacetin), and sulfasalazine, significantly changed the expression of microbial genes linked to drug import and metabolism (Maurice et al., 2013).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Maurice et al., 2013
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“Exposure in incubation experiments to a panel of hosttargeted drugs, including digoxin and sulfasalazine, induces subtle changes in community structure, but more marked changes in the genes expressed by the gut microbiome, including those genes involved in xenobiotic metabolism (Maurice et al., 2013).”
From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Maurice et al., 2013
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“One of the major functions of the gut microbiota is metabolism of dietary components leading to the generation of active metabolites that directly regulate human physiology including gut barrier function.21”
From Regulation of Intestinal Barrier Function by Microbial Metabolites (2021) · cites this paper as [21]
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QIIME allows analysis of high-throughput community sequencing data
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-citationSearch 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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Research works printed but not linked: 1
- Haugland, R.P. (2005). The Handbook: A Guide to Fluorescent Probes and Labeling Technologies, Tenth Edition (Carlsbad, CA: Invitrogen Corp).
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David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
Self-citationBokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M. R., Bolyen, E. K., Knight, R. D., Huttley, G. A., & Caporaso, J. G. (2018) · Microbiome · doi:10.1186/s40168-018-0470-z · Cited by 6,037
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Introduction to the human gut microbiota
Thursby, E., & Juge, N. (2017) · Biochemical Journal · doi:10.1042/bcj20160510 · Cited by 3,600
The Human Intestinal Microbiome in Health and Disease
Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637
Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Human gut microbiome: Hopes, threats and promises
Cani, P. D. (2018) · Gut · doi:10.1136/gutjnl-2018-316723 · Cited by 1,386
How informative is the mouse for human gut microbiota research?
Nguyen, T. L. A., Vieira-Silva, S., Liston, A., & Raes, J. (2015) · Disease Models & Mechanisms · doi:10.1242/dmm.017400 · Cited by 1,334
“It is also possible that, in such a semiclosed system, stochastic effects will influence the available microbiota pool over time (McCafferty et al., 2013).”
BackgroundImmunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease
Palm, N. W., de Zoete, M. R., Cullen, T. W., Barry, N. A., Stefanowski, J., Hao, L., Degnan, P. H., Hu, J., Peter, I., Zhang, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.006 · Cited by 1,286
The microbiome in early life: Implications for health outcomes
Tamburini, S., Shen, N., Wu, H. C., & Clemente, J. C. (2016) · Nature Medicine · doi:10.1038/nm.4142 · Cited by 1,213
Diet dominates host genotype in shaping the murine gut microbiota
Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103
Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children
Kang, D.-W., Park, J. G., Ilhan, Z. E., Wallstrom, G., LaBaer, J., Adams, J. B., & Krajmalnik-Brown, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068322 · Cited by 976
Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances
Francino, M. P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01543 · Cited by 990
The gut microbiome: Relationships with disease and opportunities for therapy
Durack, J., & Lynch, S. V. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20180448 · Cited by 979
Langdon, A. E., Crook, N., & Dantas, G. A. (2016) · Genome Medicine · doi:10.1186/s13073-016-0294-z · Cited by 967
Microbiota: a key orchestrator of cancer therapy
Roy, S., & Trinchieri, G. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.13 · Cited by 883
Regulation of Intestinal Barrier Function by Microbial Metabolites
Ghosh, S., Whitley, C. S., Haribabu, B., & Jala, V. R. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2021.02.007 · Cited by 835
Host genetic variation impacts microbiome composition across human body sites
Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., Spector, T. D., Keinan, A., Ley, R. E., Gevers, D., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0759-1 · Cited by 745
Commensal clostridia: Leading players in the maintenance of gut homeostasis
Lopetuso, L. R., Scaldaferri, F., Petito, V., & Gasbarrini, A. (2013) · Gut Pathogens · doi:10.1186/1757-4749-5-23 · Cited by 753
Human Gut Microbiome: Function Matters
Heintz‐Buschart, A., & Wilmes, P. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.11.002 · Cited by 779
The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism
Spanogiannopoulos, P., Bess, E. N., Carmody, R. N., & Turnbaugh, P. J. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.17 · Cited by 717
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling
Franzosa, E. A., Hsu, T. Y., Sirota‐Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3451 · Cited by 761
Microbiome-wide association studies link dynamic microbial consortia to disease
Gilbert, J. A., Quinn, R. A., Debelius, J. W., Xu, Z. Z., Morton, J. T., Garg, N., Jansson, J. K., Dorrestein, P. C., & Knight, R. D. (2016) · Nature · doi:10.1038/nature18850 · Cited by 730
Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta
Haiser, H. J., Gootenberg, D. B., Chatman, K., Sirasani, G., Balskus, E. P., & Turnbaugh, P. J. (2013) · Science · doi:10.1126/science.1235872 · Cited by 704
Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R., & Ley, R. E. (2014) · Cell · doi:10.1016/j.cell.2014.06.037 · Cited by 714
Relating the metatranscriptome and metagenome of the human gut
Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J. A., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319284111 · Cited by 731
Gut mucosal microbiome across stages of colorectal carcinogenesis
Nakatsu, G., Li, X., Zhou, H., Sheng, J., Wong, S. H., Wu, W. K. K., Ng, S. C., Tsoi, H., Dong, Y., Zhang, N., et al. (2015) · Nature Communications · doi:10.1038/ncomms9727 · Cited by 701
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Docter, D., Westmeier, D., Markiewicz, M., Stolte, S., Knauer, S. K., & Stauber, R. H. (2015) · Chemical Society Reviews · doi:10.1039/c5cs00217f · Cited by 719
Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance
Moya, A., & Ferrer, M. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.02.002 · Cited by 690
The gut microbiota: a major player in the toxicity of environmental pollutants?
Claus, S. P., Guillou, H., & Ellero-Simatos, S. (2016) · npj Biofilms and Microbiomes · doi:10.1038/npjbiofilms.2016.3 · Cited by 678
Wang, J., Thingholm, L. B., Skiecevičienė, J., Rausch, P., Kummen, M., Hov, J. R., Degenhardt, F., Heinsen, F.-A., Rühlemann, M. C., Szymczak, S., et al. (2016) · Nature Genetics · doi:10.1038/ng.3695 · Cited by 625
Gut microbiome interactions with drug metabolism, efficacy, and toxicity
Wilson, I. D., & Nicholson, J. K. (2017) · Translational Research · doi:10.1016/j.trsl.2016.08.002 · Cited by 656
Wolfe, B. E., Button, J. E., Santarelli, M., & Dutton, R. J. (2014) · Cell · doi:10.1016/j.cell.2014.05.041 · Cited by 648
Microbial endocrinology: the interplay between the microbiota and the endocrine system
Neuman, H., Debelius, J. W., Knight, R. D., & Koren, O. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuu010 · Cited by 624
Rosser, E. C., Piper, C. J. M., Matei, D. E., Blair, P. A., Rendeiro, A. F., Orford, M., Alber, D. G., Krausgruber, T., Catalan, D., Klein, N., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.03.003 · Cited by 579
Microbial regulation of organismal energy homeostasis
Cani, P. D., Van Hul, M., Lefort, C., Depommier, C., Rastelli, M., & Everard, A. (2019) · Nature Metabolism · doi:10.1038/s42255-018-0017-4 · Cited by 569
(2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.08.014 · Cited by 536
Probiotics, Prebiotics and Immunomodulation of Gut Mucosal Defences: Homeostasis and Immunopathology
Hardy, H., Harris, J., Lyon, E., Beal, J., & Foey, A. (2013) · Nutrients · doi:10.3390/nu5061869 · Cited by 564
Durable coexistence of donor and recipient strains after fecal microbiota transplantation
Li, S. S., Zhu, A., Beneš, V., Costea, P. I., Hercog, R., Hildebrand, F., Huerta‐Cepas, J., Nieuwdorp, M., Salojärvi, J., Voigt, A. Y., et al. (2016) · Science · doi:10.1126/science.aad8852 · Cited by 553
Specialized metabolites from the microbiome in health and disease
Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.016 · Cited by 544
Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness
Pickard, J. M., Maurice, C. F., Kinnebrew, M. A., Abt, M. C., Schenten, D., Golovkina, T. V., Bogatyrev, S. R., Ismagilov, R. F., Pamer, E. G., Turnbaugh, P. J., et al. (2014) · Nature · doi:10.1038/nature13823 · Cited by 550
Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota
Karl, J. P., Hatch‐McChesney, A., Arcidiacono, S. M., Pearce, S., Pantoja-Feliciano, I. G., Doherty, L. A., & Soares, J. W. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02013 · Cited by 563
Lü, K., Abo, R., Schlieper, K. A., Graffam, M. E., Levine, S. S., Wishnok, J. S., Swenberg, J. A., Tannenbaum, S. R., & Fox, J. G. (2014) · Environmental Health Perspectives · doi:10.1289/ehp.1307429 · Cited by 527
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Aguiar‐Pulido, V., Huang, W., Suárez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s36436 · Cited by 547
Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further
Rodríguez-Daza, M.-C., Pulido-Mateos, E. C., Lupien‐Meilleur, J., Guyonnet, D., Desjardins, Y., & Roy, D. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.689456 · Cited by 511
Gut microbiota: A player in aging and a target for anti-aging intervention
Vaiserman, A. M., Koliada, A. K., & Marotta, F. (2017) · Ageing Research Reviews · doi:10.1016/j.arr.2017.01.001 · Cited by 465
Gut Bacteria and Neurotransmitters
Dicks, L. M. T. (2022) · Microorganisms · doi:10.3390/microorganisms10091838 · Cited by 482
Use of Metatranscriptomics in Microbiome Research
Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s34610 · Cited by 496
Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells
Berry, D., Mader, E., Lee, T. K., Woebken, D., Wang, Y., Zhu, D., Palatinszky, M., Schintlmeister, A., Schmid, M. C., Hanson, B. T., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420406112 · Cited by 465
Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., et al. (2017) · mSystems · doi:10.1128/msystems.00164-16 · Cited by 445
Temporal variability is a personalized feature of the human microbiome
Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala, D., Chase, J., Leff, J. W., Vázquez-Baeza, Y., Gonzalez, A., Knight, R., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0531-y · Cited by 446
A biosynthetic pathway for a prominent class of microbiota-derived bile acids
Devlin, A. S., & Fischbach, M. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1864 · Cited by 448
The role of the intestinal microbiota in type 1 diabetes mellitus
Knip, M., & Siljander, H. (2016) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2015.218 · Cited by 444
Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction
Bouter, K. E. C., van Raalte, D. H., Groen, A. K., & Nieuwdorp, M. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.12.048 · Cited by 443
Metronidazole: an update on metabolism, structure–cytotoxicity and resistance mechanisms
Dingsdag, S. A., & Hunter, N. (2017) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkx351 · Cited by 433
Ménage à trois in the human gut: interactions between host, bacteria and phages
Mirzaei, M. K., & Maurice, C. F. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.30 · Cited by 412
Marked seasonal variation in the wild mouse gut microbiota
Maurice, C. F., Knowles, S. C. L., Ladau, J., Pollard, K. S., Fenton, A., Pedersen, A. B., & Turnbaugh, P. J. (2015) · The ISME Journal · doi:10.1038/ismej.2015.53 · Cited by 404
The links between gut microbiota and obesity and obesity related diseases
Geng, J., Ni, Q., Sun, W., Li, L., & Feng, X. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.112678 · Cited by 422
Flandroy, L., Poutahidis, T., Berg, G., Clarke, G. A., Dao, M. C., Decaestecker, E., Furman, E., Haahtela, T., Massart, S., Plovier, H., et al. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.01.288 · Cited by 416
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Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022438 · Cited by 373
Metatranscriptomics of the Human Oral Microbiome during Health and Disease
Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., & Whiteley, M. (2014) · mBio · doi:10.1128/mbio.01012-14 · Cited by 386
A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism
Russell, A. B., Wexler, A. G., Harding, B. N., Whitney, J. C. C., Bohn, A., Goo, Y. A., Tran, B. Q., Barry, N. A., Zheng, H., Peterson, S. B., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.07.007 · Cited by 379
Kau, A. L., Planer, J. D., Liu, J., Rao, S. M., Yatsunenko, T., Trehan, I., MANARY, M. J., Liu, T., Stappenbeck, T. S., Maleta, K. M., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa4877 · Cited by 376
Interactions between Intestinal Microbiota and Host Immune Response in Inflammatory Bowel Disease
Zhang, M., Sun, K., Wu, Y., Yang, Y., Tso, P., & Wu, Z. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00942 · Cited by 347
The initial state of the human gut microbiome determines its reshaping by antibiotics
Raymond, F., Ouameur, A. A., Déraspe, M., Iqbal, N., Gingras, H., Dridi, B., Leprohon, P., Plante, P.-L., Giroux, R., Bérubé, È., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.148 · Cited by 368
Gut microbes of mammalian herbivores facilitate intake of plant toxins
Kohl, K. D., Weiss, R. B., Cox, J. E., Dale, C., & Dearing, M. D. (2014) · Ecology Letters · doi:10.1111/ele.12329 · Cited by 356
The Intestinal Metabolome: An Intersection Between Microbiota and Host
Ursell, L. K., Haiser, H. J., Treuren, W. V., Garg, N., Reddivari, L., Vanamala, J., Dorrestein, P. C., Turnbaugh, P. J., & Knight, R. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.03.001 · Cited by 365
Jing, T., Qi, F., & Wang, Z.-Y. (2020) · Microbiome · doi:10.1186/s40168-020-00823-y · Cited by 356
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Zhang, X., Li, L., Butcher, J., Stintzi, A., & Figeys, D. (2019) · Microbiome · doi:10.1186/s40168-019-0767-6 · Cited by 351
Nakajima, A., Vogelzang, A., Maruya, M., Miyajima, M., Murata, M., Son, A., Kuwahara, T., Tsuruyama, T., Yamada, S., Matsuura, M., et al. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20180427 · Cited by 351
Irritable bowel syndrome: A microbiome-gut-brain axis disorder?
Kennedy, P. J. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i39.14105 · Cited by 347
The gut microbiome: an orchestrator of xenobiotic metabolism
Collins, S. L., & Patterson, A. D. (2020) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2019.12.001 · Cited by 348
High throughput sequencing methods and analysis for microbiome research
Bella, J. M. D., Bao, Y., Gloor, G. B., Burton, J. P., & Reid, G. (2013) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2013.08.011 · Cited by 341
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Clarke, G., Sandhu, K. V., Griffin, B. T., Dinan, T. G., Cryan, J. F., & Hyland, N. P. (2019) · Pharmacological Reviews · doi:10.1124/pr.118.015768 · Cited by 319
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Mimee, M., Citorik, R. J., & Lu, T. K. (2016) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2016.04.032 · Cited by 324
Maternal IgG and IgA Antibodies Dampen Mucosal T Helper Cell Responses in Early Life
Koch, M. A., Reiner, G. L., Lugo, K. A., Kreuk, L. S. M., Stanbery, A. G., Ansaldo, E., Seher, T. D., Ludington, W. B., & Barton, G. M. (2016) · Cell · doi:10.1016/j.cell.2016.04.055 · Cited by 315
Medical Uses of Silver: History, Myths, and Scientific Evidence
Medici, S., Peana, M., Nurchi, V. M., & Zoroddu, M. A. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01439 · Cited by 312
Specific Gut Microbiome Signature Predicts the Early-Stage Lung Cancer
Zheng, Y., Fang, Z., Xue, Y., Zhang, J., Zhu, J., Gao, R., Yao, S., Ye, Y., Wang, S., Lin, C., et al. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1737487 · Cited by 301
Zhang, L., Nichols, R. G., Correll, J. B., Murray, I. A., Tanaka, N., Smith, P. B. W., Hubbard, T. D., Sebastian, A., Albert, I. U., Hatzakis, E., et al. (2015) · Environmental Health Perspectives · doi:10.1289/ehp.1409055 · Cited by 307
Antibiotic use and microbiome function
Ferrer, M., Méndez–García, C., Rojo, D., Barbas, C., & Moyá, A. (2016) · Biochemical Pharmacology · doi:10.1016/j.bcp.2016.09.007 · Cited by 315
Dzutsev, A., Badger, J. H., Perez-Chanona, E., Roy, S., Salcedo, R., Smith, C. K., & Trinchieri, G. (2017) · Annual Review of Immunology · doi:10.1146/annurev-immunol-051116-052133 · Cited by 302
Allali, I., Arnold, J. W., Roach, J., Cadenas, M. B., Butz, N., Hassan, H. M., Koci, M., Ballou, A., Mendoza, M., Ali, R., et al. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1101-8 · Cited by 298
An atlas of β-glucuronidases in the human intestinal microbiome
Pollet, R. M., D'Agostino, E. H., Walton, W. G., Xu, Y., Little, M. S., Biernat, K. A., Pellock, S. J., Patterson, L. M., Creekmore, B. C., Isenberg, H. N., et al. (2017) · Structure · doi:10.1016/j.str.2017.05.003 · Cited by 289
Toward Accurate and Quantitative Comparative Metagenomics
Nayfach, S., & Pollard, K. S. (2016) · Cell · doi:10.1016/j.cell.2016.08.007 · Cited by 304
An integrative view of microbiome-host interactions in inflammatory bowel diseases
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Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14451 · Cited by 263
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Napolitano, A., Miller, S. L., Nicholls, A. W., Baker, D., Horn, S. V., Thomas, E., Rajpal, D. K., Spivak, A., Brown, J. R., & Nunez, D. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100778 · Cited by 293
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Mehta, R. S., Abu-Ali, G. S., Drew, D. A., Lloyd-Price, J., Subramanian, A., Lochhead, P., Joshi, A. D., Ivey, K. L., Khalili, H., Brown, G. T., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0096-0 · Cited by 273
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Meijnikman, A. S., Gerdes, V. E. A., Nieuwdorp, M., & Herrema, H. (2017) · Endocrine Reviews · doi:10.1210/er.2017-00192 · Cited by 283
Huang, Y. J., & Boushey, H. A. (2015) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2014.11.011 · Cited by 280
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Motta, J., Wallace, J. L., Buret, A. G., Deraison, C., & Vergnolle, N. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00397-y · Cited by 286
Watson, E. V., MacNeil, L. T., Ritter, A. D., Yilmaz, L. S., Rosebrock, A. P., Caudy, A. A., & Walhout, A. J. M. (2014) · Cell · doi:10.1016/j.cell.2014.01.047 · Cited by 269
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Bucci, V., Tzen, B., Li, N., Simmons, M., Tanoue, T., Bogart, E., Deng, L., Yeliseyev, V., Delaney, M. L., Liu, Q., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0980-6 · Cited by 264
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Evariste, L., Barret, M., Mottier, A., Mouchet, F., Gauthier, L., & Pinelli, É. (2019) · Environmental Pollution · doi:10.1016/j.envpol.2019.02.101 · Cited by 269
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Yao, Y., Cai, X. T., Ye, Y., Wang, F., Chen, F., & Zheng, C. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.708472 · Cited by 271
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Tian, Y., Gui, W., Koo, I., Smith, P. B. W., Allman, E. L., Nichols, R. G., Rimal, B., Cai, J., Liu, Q., & Patterson, A. D. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1732268 · Cited by 255
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O’Hara, E., Neves, A. L. A., Song, Y., & Guan, L. L. (2020) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-021419-083952 · Cited by 254
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Caballero, S., & Pamer, E. G. (2015) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032713-120238 · Cited by 238
Dai, X., Tian, Y., Li, J., Su, X., Wang, X., Zhao, S., Liu, L., Luo, Y., Liu, D., Zheng, H., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03682-14 · Cited by 236
Metadata
- Authors
- Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J.
- Affiliations
- Harvard University (US)
- Corresponding author
- Turnbaugh, Peter James
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-01
- Volume
- 152
- Issue
- 1-2
- Pages
- 39-50
- ISSN
- 0092-8674 (ISSN-L)
- 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
- 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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