The Human Gut Microbiome: From Association to Modulation

Schmidt, Thomas S.B.; Raes, Jeroen; Bork, Peer

doi:10.1016/j.cell.2018.02.044

Cited by 853Gut microbiota and healthOral microbiology and periodontitis researchGastrointestinal motility and disorders

The Human Gut Microbiome: From Association to Modulation

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Schmidt, Thomas S.B., Raes, Jeroen, Bork, Peer·2018·Cell

DOI 10.1016/j.cell.2018.02.044

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Abstract

Our understanding of the human gut microbiome continues to evolve at a rapid pace, but practical application of thisknowledge is still in its infancy. This review discusses the type of studies that will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host.

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The microbiome co-regulates many physiological functions involving the immune, neuroendocrine and metabolic systems via complex reciprocal feedback mechanisms that operate between the microbial ecosystem and the host.
“The microbiome is known to co-regulate many physiological functions involving the immune, neuroendocrine and metabolic systems via complex reciprocal feedback mechanisms that operate between the microbial ecosystem and the host [116,117].”
From Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment (2022) · cites this paper as [117]
The “Intrinsic host factors such as genetics” section describes reciprocal links between the microbiome and the immune system, and increasing evidence for a reciprocal brain–gut–microbiota axis. Box 3 discusses microbial effects on drug metabolism and dietary responses. These passages support host–microbiome interactions, but do not establish the claim’s broader account of co-regulation across immune, neuroendocrine, and metabolic systems through reciprocal feedback mechanisms. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Existing pharmacological treatments for PD could be improved through an appreciation of the gut microbiome.
“Existing pharmacological treatments for PD could be improved through an appreciation of the gut microbiome [151, 152].”
From The gut–brain axis in early Parkinson’s disease: from prodrome to prevention (2025) · cites this paper as [152]
Box 3 (page unavailable) reports that gut-microbiome features can affect responses to some drugs, supporting the general possibility of improving treatment through microbiome knowledge. It does not address pharmacological treatments for Parkinson’s disease specifically; its mention of anti-PD1 concerns cancer immunotherapy, not PD treatment. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Microbiome-targeted interventions may impact psychological health in a manner strongly shaped by individual lifestyle patterns.
“Consequently, it has been proposed that microbiome-targeted interventions may impact psychological health in a manner that is strongly shaped by individual lifestyle patterns (Schmidt et al., 2018; Morales-Torres et al., 2023).”
From Psychobiotics in mental health: insights from human clinical trials via the gut-brain axis (2026) · cites this paper as Schmidt et al., 2018
The “Prebiotics and dietary intervention” section (page not provided) describes microbiome-mediated therapy options and says responses to dietary intervention may be individual. Box 3 (page not provided) reports that models incorporating lifestyle factors predicted dietary responses. The paper does not establish psychological-health effects or say that such effects are strongly shaped by individual lifestyle patterns. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Inter-individual differences in enterotype composition are increasingly thought to explain the variation in response to a dietary intervention or perturbation.
“Inter-individual differences in enterotype composition are increasingly thought to explain the variation in response to a dietary intervention or perturbation [86].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [86]
The microbiota composition is deeply influenced by environmental factors, including diet, lifestyle, and medication use.
“The microbiota composition is in fact deeply influenced by environmental factors, including diet, lifestyle, and medication use [43,44].”
From Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia (2019) · cites this paper as [43]

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Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
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 · see citing works
Self-citation
Diet rapidly and reproducibly alters the human gut microbiome
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 · see citing works
Untitled work
Hill (2014) · doi:10.1038/nrgastro.2014.66 · Cited by 9,592 · see citing works
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works
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 · see citing works
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 · see citing works
Enterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548 · see citing works
Self-citation
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors
Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671 · see citing works
Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics
Gibson, G. R., Hutkins, R., Sanders, M. E., Prescott, S. L., Reimer, R. A., Salminen, S. J., Scott, K., Stanton, C., Swanson, K. S., Cani, P. D., et al. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.75 · Cited by 5,634 · see citing works
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597 · see citing works
Pathogenic Escherichia coli
Kaper, J. B., Nataro, J. P., & Mobley, H. L. T. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro818 · Cited by 5,583 · cited 1× · see citing works
“Indeed, some strains of Escherichia coli are highly beneficial probiotics (Wassenaar, 2016), whereas others are potent pathogens (Kaper et al., 2004).”
Role of the microbiota in immunity and inflammation.
Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385 · see citing works
Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients
Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., Prieto, P. A., Vicente, D., Hoffman, K., Wei, S. C., et al. (2018) · Science · doi:10.1126/science.aan4236 · Cited by 4,812 · see citing works
Richness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works
Self-citation
Interactions Between the Microbiota and the Immune System
Hooper, L. V., Littman, D. R., & Macpherson, A. J. (2012) · Science · doi:10.1126/science.1223490 · Cited by 4,173 · see citing works
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,138 · see citing works
Self-citation
Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy
Sivan, A., Corrales, L., Hubert, N., Williams, J. B., Aquino-Michaels, K., Earley, Z. M., Benyamin, F. W., Man Lei, Y., Jabri, B., Alegre, M.-L., et al. (2015) · Science · doi:10.1126/science.aac4255 · Cited by 3,888 · see citing works
Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile
van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708 · see citing works
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 · see citing works
Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota
Vétizou, M., Pitt, J. M., Daillère, R., Lepage, P., Waldschmitt, N., Flament, C., Rusakiewicz, S., Routy, B., Roberti, M. P., Duong, C. P. M., et al. (2015) · Science · doi:10.1126/science.aad1329 · Cited by 3,488 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Human Genetics Shape the Gut Microbiome
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · see citing works
The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients
Matson, V., Fessler, J., Bao, R., Chongsuwat, T., Zha, Y., Alegre, M.-L., Luke, J. J., & Gajewski, T. F. (2018) · Science · doi:10.1126/science.aao3290 · Cited by 3,107 · see citing works
Personalized nutrition by prediction of glycemic responses
Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.001 · Cited by 2,929 · see citing works
Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome
Vrieze, A., Van Nood, E., Holleman, F., Salojärvi, J., Kootte, R. S., Bartelsman, J. F. W. M., Dallinga–Thie, G. M., Ackermans, M. T., Serlie, M. J., Oozeer, R., et al. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.06.031 · Cited by 2,913 · see citing works
Environment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works
Inferring Correlation Networks from Genomic Survey Data
Friedman, J., & Alm, E. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002687 · Cited by 2,688 · see citing works
The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems.
(2015) · PubMed Central · Cited by 2,540 · see citing works
Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540 · see citing works
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421 · see citing works
Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400 · see citing works
Self-citation
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277 · see citing works
Diet–microbiota interactions as moderators of human metabolism
Sonnenburg, J. L., & Bäckhed, F. (2016) · Nature · doi:10.1038/nature18846 · Cited by 2,257 · see citing works
The role of the gut microbiota in nutrition and health
Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.156 · Cited by 2,203 · see citing works
An integrated catalog of reference genes in the human gut microbiome
MetaHIT Consortium, Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2942 · Cited by 2,164 · see citing works
Normalization and microbial differential abundance strategies depend upon data characteristics
Weiss, S. J., Xu, Z. Z., Peddada, S. D., Amir, A., Bittinger, K. L., González, A., Lozupone, C., Zaneveld, J., Vázquez‐Baeza, Y., Birmingham, A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0237-y · Cited by 2,123 · see citing works
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116 · see citing works
Self-citation
Human gut microbes impact host serum metabolome and insulin sensitivity
Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., et al. (2016) · Nature · doi:10.1038/nature18646 · Cited by 2,116 · see citing works
Self-citation
The Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058 · see citing works
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047 · see citing works
The microbiome and innate immunity
Thaiss, C. A., Zmora, N., Levy, M., & Elinav, E. (2016) · Nature · doi:10.1038/nature18847 · Cited by 2,012 · see citing works
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988 · see citing works
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., et al. (2016) · Science · doi:10.1126/science.aad3369 · Cited by 1,914 · see citing works
Self-citation
Extensive impact of non-antibiotic drugs on human gut bacteria
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E. E., Brochado, A. R., Fernandez, K. C., Dose, H., Mori, H., et al. (2018) · Nature · doi:10.1038/nature25979 · Cited by 1,905 · see citing works
The healthy human microbiome
Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891 · see citing works
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872 · see citing works
Dietary intervention impact on gut microbial gene richness
Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., et al. (2013) · Nature · doi:10.1038/nature12480 · Cited by 1,832 · see citing works
Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow
Kim, H. J., Huh, D., Hamilton, G., & Ingber, D. E. (2012) · Lab on a Chip · doi:10.1039/c2lc40074j · Cited by 1,734 · see citing works
Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella
Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., Hallen, A., Martens, E., Björck, I., & Bäckhed, F. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.10.001 · Cited by 1,731 · see citing works
Fundamentals of Microbial Community Resistance and Resilience
Shade, A. L., Peter, H., Allison, S., Baho, D. L., Berga, M., Bürgmann, H., Huber, D. H., Langenheder, S., Lennon, J. T., Martiny, J. B. H., et al. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00417 · Cited by 1,728 · see citing works
Self-citation
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment
Zhang, X., Zhang, D., Jia, H., Feng, Q., Wang, D., Liang, D., Wu, X., Li, J., Tang, L., Li, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3914 · Cited by 1,690 · see citing works
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug
Wu, H., Esteve, E., Tremaroli, V., Khan, M. T., Caesar, R., Mannerås-Holm, L., Ståhlman, M., Olsson, L. M., Serino, M., Planas-Fèlix, M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4345 · Cited by 1,632 · see citing works
Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study
Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J.-Z., Abe, F., & Osawa, R. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0708-5 · Cited by 1,521 · see citing works
Exercise and associated dietary extremes impact on gut microbial diversity
Clarke, S. F., Murphy, E. F., O'Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., Hayes, P., O'Reilly, M., Jeffery, I. B., Wood-Martin, R., et al. (2014) · Gut · doi:10.1136/gutjnl-2013-306541 · Cited by 1,439 · see citing works
A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites
Dodd, D., Spitzer, M. H., Van Treuren, W., Merrill, B. D., Hryckowian, A. J., Higginbottom, S. K., Le, A., Cowan, T. M., Nolan, G. P., Fischbach, M. A., et al. (2017) · Nature · doi:10.1038/nature24661 · Cited by 1,425 · see citing works
Potential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375 · see citing works
Proton pump inhibitors affect the gut microbiome
Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., Tigchelaar, E. F., Jankipersadsing, S. A., Cenit, M. C., Harmsen, H. J. M., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-310376 · Cited by 1,371 · cited 2× · see citing works
“Similarly, proton pump 177 inhibitors (Freedberg et al., 2015; Imhann et al., 2016; Jackson et al., 2016), atypical 178 antipsychotics (Bahr et al., 2015; Flowers et al., 2017; Mäkivuokko et al., 2010) and non-179 steroidal anti-inflammatory drugs (Rogers and Aronoff, 2016), among others, have been…”
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 · cited 2× · see citing works
“In consequence, many perturbation studies have been conducted in mouse models which allow control of host effects to some extent, in spite of other limitations (Nguyen et al., 2015).”
BackgroundSelf-citation
Fungal microbiota dysbiosis in IBD
Sokol, H., Leducq, V., Aschard, H., Pham, H., Jégou, S., Landman, C., Cohen, D., Liguori, G., Bourrier, A., Nion–Larmurier, I., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-310746 · Cited by 1,313 · see citing works
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease
Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., Timmis, K. N., & Schreiber, S. (2004) · Gut · doi:10.1136/gut.2003.025403 · Cited by 1,311 · see citing works
Salt-responsive gut commensal modulates TH17 axis and disease
Wilck, N., Matus, M. G., Kearney, S. M., Olesen, S. W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., et al. (2017) · Nature · doi:10.1038/nature24628 · Cited by 1,310 · see citing works
Strains, functions and dynamics in the expanded Human Microbiome Project
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works
Perturbation Experiments in Community Ecology: Theory and Practice
Bender, E. A., Case, T. J., & Gilpin, M. E. (1984) · Ecology · doi:10.2307/1939452 · Cited by 1,245 · see citing works
Quantitative microbiome profiling links gut community variation to microbial load
Vandeputte, D., Kathagen, G., D’hoe, K., Vieira-Silva, S., Valles-Colomer, M., Sabino, J., Wang, J., Tito, R. Y., De Commer, L., Darzi, Y., et al. (2017) · Nature · doi:10.1038/nature24460 · Cited by 1,218 · see citing works
Self-citation
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 · see citing works
Gut microbiota and aging
O’Toole, P. W., & Jeffery, I. B. (2015) · Science · doi:10.1126/science.aac8469 · Cited by 1,202 · see citing works
Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation
Fujimura, K. E., Sitarik, A. R., Havstad, S. L., Lin, D. L., Levan, S., Fadrosh, D. W., Panzer, A. R., LaMere, B. J., Rackaityte, E., Lukacs, N. W., et al. (2016) · Nature Medicine · doi:10.1038/nm.4176 · Cited by 1,168 · see citing works
Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works
Enterotypes in the landscape of gut microbial community composition
Costea, P. I., Hildebrand, F., Arumugam, M., Bäckhed, F., Blaser, M. J., Bushman, F. D., de Vos, W. M., Ehrlich, S. D., Fraser, C. M., Hattori, M., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0072-8 · Cited by 1,138 · see citing works
Self-citation
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134 · see citing works
Cohabiting family members share microbiota with one another and with their dogs
Song, S. J., Lauber, C. L., Costello, E. K., Lozupone, C., Humphrey, G., Berg-Lyons, D., Caporaso, J. G., Knights, D., Clemente, J. C., Nakielny, S., et al. (2013) · eLife · doi:10.7554/elife.00458 · Cited by 1,075 · see citing works
Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery
Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063 · see citing works
The resilience of the intestinal microbiota influences health and disease
Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.58 · Cited by 1,058 · see citing works
Self-citation
Genetic determinants of the gut microbiome in UK twins
Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.017 · Cited by 1,048 · see citing works
Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition
Kootte, R. S., Levin, E., Salojärvi, J., Smits, L. P., Hartstra, A. V., Udayappan, S. D., Hermes, G., Bouter, K. E., Koopen, A. M., Holst, J. J., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.09.008 · Cited by 1,039 · see citing works
Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates
Vandeputte, D., Falony, G., Vieira-Silva, S., Tito, R. Y., Joossens, M., & Raes, J. (2016) · Gut · doi:10.1136/gutjnl-2015-309618 · Cited by 1,028 · see citing works
Self-citation
Meta-analysis of gut microbiome studies identifies disease-specific and shared responses
(2017) · doi:10.1038/s41467-017-01973-8 · Cited by 986 · see citing works
Stress and stability: applying the Anna Karenina principle to animal microbiomes
Zaneveld, J. R., McMinds, R., & Vega Thurber, R. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.121 · Cited by 977 · see citing works
Longitudinal analysis of microbial interaction between humans and the indoor environment
Lax, S. M., Smith, D. P., Hampton‐Marcell, J., Owens, S. M., Handley, K. M., Scott, N. M., Gibbons, S. M., Larsen, P. E., Shogan, B. D., Weiss, S. J., et al. (2014) · Science · doi:10.1126/science.1254529 · Cited by 920 · see citing works
The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation
Langdon, A. E., Crook, N., & Dantas, G. A. (2016) · Genome Medicine · doi:10.1186/s13073-016-0294-z · Cited by 917 · see citing works
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907 · see citing works
Antibiotic-Induced Changes in the Intestinal Microbiota and Disease
Becattini, S., Taur, Y., & Pamer, E. G. (2016) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2016.04.003 · Cited by 901 · see citing works
Towards standards for human fecal sample processing in metagenomic studies
Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.-E., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3960 · Cited by 893 · see citing works
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885 · see citing works
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
Weiss, S. J., Treuren, W. V., Lozupone, C., Faust, K., Friedman, J., Deng, Y., Xia, L. C., Xu, Z. Z., Ursell, L. K., Alm, E. J., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.235 · Cited by 868 · see citing works
Self-citation
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
Meta‐analyses of human gut microbes associated with obesity and IBD
Walters, W. A., Xu, Z., & Knight, R. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.09.039 · Cited by 836 · see citing works
The effect of host genetics on the gut microbiome
Bonder, M. J., Kurilshikov, A., Tigchelaar, E. F., Mujagic, Z., Imhann, F., Vila, A. V., Deelen, P., Vatanen, T., Schirmer, M., Smeekens, S. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3663 · Cited by 819 · see citing works
Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation
Tremaroli, V., Karlsson, F., Werling, M., Ståhlman, M., Kovatcheva-Datchary, P., Olbers, T., Fändriks, L., le Roux, C. W., Nielsen, J., & Bäckhed, F. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.009 · Cited by 757 · see citing works
Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis
Ford, A. C., Quigley, E. M. M., Lacy, B. E., Lembo, A. J., Saito, Y. A., Schiller, L. R., Soffer, E. E., Spiegel, B. M. R., & Moayyedi, P. (2014) · American Journal of Gastroenterology · doi:10.1038/ajg.2014.202 · Cited by 747 · cited 3× · see citing works
“, 2014), have been shown to be clinically efficient treatment options in some indications (Ford et al., 2014).”
Influential
Human Gut Microbiome: Function Matters
Heintz‐Buschart, A., & Wilmes, P. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.11.002 · Cited by 747 · see citing works
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 727 · see citing works
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 714 · see citing works
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 · see citing works
A Catalog of Reference Genomes from the Human Microbiome
The Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K. E., Weinstock, G. M., Highlander, S. K., Worley, K. C., Creasy, H. H., Wortman, J. R., Rusch, D. B., Mitreva, M., Sodergren, E., et al. (2010) · Science · doi:10.1126/science.1183605 · Cited by 702 · see citing works
A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
Shah, P., Fritz, J. V., Glaab, E., Desai, M. S., Greenhalgh, K., Frachet, A., Niegowska, M., Estes, M., Jäger, C., Seguin-Devaux, C., et al. (2016) · Nature Communications · doi:10.1038/ncomms11535 · Cited by 660 · see citing works
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
Pasolli, E., Truong, D. T., Malik, F., Waldron, L., & Segata, N. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004977 · Cited by 659 · see citing works
The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level
Barton, W., Penney, N. C., Cronin, O., Garcia-Perez, I., Molloy, M. G., Holmes, E., Shanahan, F., Cotter, P. D., & O'Sullivan, O. (2018) · Gut · doi:10.1136/gutjnl-2016-313627 · Cited by 647 · cited 2× · see citing works
“, 2017), and physical exercise (Barton et al., 2017; Clarke et al., 2014; Petersen et al., 2017) have been linked to microbiome composition but were not among the top-ranking covariates in recent population studies.”
Our gut microbiome: The evolving inner self
Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017) · Cell · doi:10.1016/j.cell.2017.11.024 · Cited by 633 · see citing works
Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota
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 · see citing works
Maturation of the gut microbiome and risk of asthma in childhood
Stokholm, J., Blaser, M. J., Thorsen, J., Rasmussen, M. A., Waage, J., Vinding, R. K., Schoos, A.-M. M., Kunøe, A., Fink, N. R., Chawes, B. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02573-2 · Cited by 614 · see citing works
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
Stein, R. R., Bucci, V., Toussaint, N. C., Buffie, C. G., Rätsch, G., Pamer, E. G., Sander, C., & Xavier, J. B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003388 · Cited by 604 · see citing works
Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome
Sze, M. A., & Schloss, P. D. (2016) · mBio · doi:10.1128/mbio.01018-16 · Cited by 600 · see citing works
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
The Microbiome Quality Control Project Consortium, Sinha, R., Abu-Ali, G., Vogtmann, E., Fodor, A. A., Ren, B., Amir, A., Schwager, E., Crabtree, J., Ma, S., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3981 · Cited by 587 · see citing works
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587 · see citing works
Mouse models for human intestinal microbiota research: a critical evaluation
Hugenholtz, F., & de Vos, W. M. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2693-8 · Cited by 585 · see citing works
Patterned progression of bacterial populations in the premature infant gut
Rosa, P. S. L., Warner, B. B., Zhou, Y., Weinstock, G. M., Sodergren, E. J., Hall-Moore, C. M., Stevens, H. J., Bennett, W. E., Shaikh, N., Linneman, L. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409497111 · Cited by 573 · see citing works
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
Schirmer, M., Franzosa, E. A., Lloyd‐Price, J., McIver, L. J., Schwager, R., Poon, T. W., Ananthakrishnan, A. N., Andrews, E., Barron, G., Lake, K., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0089-z · Cited by 570 · see citing works
Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials
Kristensen, N. B., Bryrup, T., Allin, K. H., Nielsen, T., Hansen, T. H., & Pedersen, O. (2016) · Genome Medicine · doi:10.1186/s13073-016-0300-5 · Cited by 561 · see citing works
Prebiotic inulin-type fructans induce specific changes in the human gut microbiota
Vandeputte, D., Falony, G., Vieira-Silva, S., Wang, J., Sailer, M., Theis, S., Verbeke, K., & Raes, J. (2017) · Gut · doi:10.1136/gutjnl-2016-313271 · Cited by 554 · see citing works
Self-citation
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 544 · see citing works
Precision editing of the gut microbiota ameliorates colitis
Zhu, W., Winter, M. G., Byndloss, M. X., Spiga, L., Duerkop, B. A., Hughes, E. R., Büttner, L., Romão, E. D. L., Behrendt, C. L., Lopez, C. A., et al. (2018) · Nature · doi:10.1038/nature25172 · Cited by 544 · see citing works
Human genetic variation and the gut microbiome in disease
Hall, A. B., Tolonen, A. C., & Xavier, R. J. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.63 · Cited by 517 · see citing works
Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2693 · Cited by 503 · see citing works
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
Song, S. J., Amir, A., Metcalf, J. L., Amato, K. R., Xu, Z. Z., Humphrey, G. C., & Knight, R. D. (2016) · mSystems · doi:10.1128/msystems.00021-16 · Cited by 484 · see citing works
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works
Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
Dubinkina, V. B., Tyakht, A., Odintsova, V. Y., Yarygin, K. S., Kovarsky, B. A., Pavlenko, A. V., Ischenko, D. S., Popenko, A., Alexeev, D. G., Taraskina, A. Y., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0359-2 · Cited by 464 · see citing works
Association of host genome with intestinal microbial composition in a large healthy cohort
GEM Project Research Consortium, Turpin, W., Espin-Garcia, O., Xu, W., Silverberg, M. S., Kevans, D., Smith, M. I., Guttman, D. S., Griffiths, A., Panaccione, R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3693 · Cited by 460 · see citing works
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut
Roager, H. M., Hansen, L. B. S., Bahl, M. I., Frandsen, H. L., Carvalho, V., Gøbel, R. J., Dalgaard, M. D., Plichta, D. R., Sparholt, M. H., Vestergaard, H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.93 · Cited by 449 · see citing works
Gut Microbiota Linked to Sexual Preference and HIV Infection
Noguera-Julián, M., Rocafort, M., Guillén, Y., Rivera, J., Casadellà, M., Nowak, P., Hildebrand, F., Zeller, G., Parera, M., Bellido, R., et al. (2016) · EBioMedicine · doi:10.1016/j.ebiom.2016.01.032 · Cited by 448 · see citing works
Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling
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 · see citing works
Metagenome-wide association studies: fine-mining the microbiome
Wang, J., & Jia, H. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.83 · Cited by 429 · see citing works
Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula
Xu, J. Y., Lian, F., Zhao, L., Zhao, Y., Chen, X., Zhang, X., Guo, Y., Zhang, C., Zhou, Q., Xue, Z., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.177 · Cited by 423 · see citing works
Archaea and the Human Gut: New Beginning of an Old Story
Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W., & Brugère, J.-F. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i43.16062 · Cited by 422 · see citing works
Composition and temporal stability of the gut microbiota in older persons
Jeffery, I. B., Lynch, D. B., & O’Toole, P. W. (2016) · The ISME Journal · doi:10.1038/ismej.2015.88 · Cited by 421 · see citing works
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie, S., Ghaffari, P., Kovatcheva‐Datchary, P., Mardinoğlu, A., Sen, P., Pujos‐Guillot, E., de Wouters, T., Juste, C., Rizkalla, S. W., Chilloux, J., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.001 · Cited by 417 · see citing works
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children
Zhang, C., Yin, A., Li, H., Wang, R., Wu, G. G., Shen, J., Zhang, M. H., Wang, L., Hou, Y., OuYang, H., et al. (2015) · EBioMedicine · doi:10.1016/j.ebiom.2015.07.007 · Cited by 416 · see citing works
Self-citation
Smoking Cessation Induces Profound Changes in the Composition of the Intestinal Microbiota in Humans
Biedermann, L., Zeitz, J., Mwinyi, J., Sutter-Minder, E., Rehman, A., Ott, S. J., Steurer-Stey, C. A., Frei, A. L., Frei, P., Scharl, M. M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059260 · Cited by 411 · see citing works
Systematic Review: Adverse Events of Fecal Microbiota Transplantation
Wang, S., Xu, M., Wang, W., Cao, X., Piao, M., Khan, S., Yan, F., Cao, H., & Wang, B. (2016) · PLoS ONE · doi:10.1371/journal.pone.0161174 · Cited by 410 · see citing works
Metagenomics meets time series analysis: unraveling microbial community dynamics
Faust, K., Lahti, L., Gonze, D., de Vos, W. M., & Raes, J. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.04.004 · Cited by 407 · see citing works
Self-citation
Molecular eco-systems biology: towards an understanding of community function
Raes, J., & Bork, P. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1935 · Cited by 396 · see citing works
Self-citation
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Erickson, A. R., Cantarel, B. L., Lamendella, R., Darzi, Y., Mongodin, E. F., Pan, C., Shah, M., Halfvarson, J., Tysk, C., Henrissat, B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049138 · Cited by 395 · see citing works
Self-citation
Absolute quantification of microbial taxon abundances
Props, R., Kerckhof, F., Rubbens, P., Vrieze, J. D., Hernandez‐Sanabria, E., Waegeman, W., Monsieurs, P., Hammes, F., & Boon, N. (2016) · The ISME Journal · doi:10.1038/ismej.2016.117 · Cited by 384 · see citing works
Community characteristics of the gut microbiomes of competitive cyclists
Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., Sodergren, E., & Weinstock, G. M. (2017) · Microbiome · doi:10.1186/s40168-017-0320-4 · Cited by 377 · see citing works
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 374 · see citing works
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 359 · see citing works
Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis
Hughes, E. R., Winter, M. G., Duerkop, B. A., Spiga, L., Furtado de Carvalho, T., Zhu, W., Gillis, C. C., Büttner, L., Smoot, M. P., Behrendt, C. L., et al. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.01.005 · Cited by 353 · see citing works
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome
Rogers, M. A. M., & Aronoff, D. M. (2016) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2015.10.003 · Cited by 346 · see citing works
Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome
Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341 · see citing works
Recovery of the Gut Microbiome following Fecal Microbiota Transplantation
Seekatz, A. M., Aas, J., Gessert, C. E., Rubin, T. A., Saman, D. M., Bakken, J., & Young, V. B. (2014) · mBio · doi:10.1128/mbio.00893-14 · Cited by 331 · see citing works
Selective maternal seeding and environment shape the human gut microbiomePreprint
Korpela, K., Costea, P. I., Coelho, L. P., Kandels-Lewis, S. E., Willemsen, G. A. H. M., Boomsma, D. I., Segata, N., & Bork, P. (2018) · Genome Research · doi:10.1101/gr.233940.117 · Cited by 325 · see citing works
Adapting to an invasive species: Toxic cane toads induce morphological change in Australian snakes
Phillips, B. L., & Shine, R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406440101 · Cited by 323 · see citing works
Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial
Freedberg, D. E., Toussaint, N. C., Chen, S. P., Ratner, A. J., Whittier, S., Wang, T. C., Wang, H. H., & Abrams, J. A. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.06.043 · Cited by 322 · see citing works
Fecal microbiota transplantation in metabolic syndrome: History, present and future
de Groot, P. F., Frissen, M. N., de Clercq, N. C., & Nieuwdorp, M. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1293224 · Cited by 322 · see citing works
A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Finucane, M. M., Sharpton, T. J., Laurent, T. J., & Pollard, K. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084689 · Cited by 321 · see citing works
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
Heintz-Buschart, A., May, P., Laczny, C. C., Lebrun, L. A., Bellora, C., Krishna, A., Wampach, L., Schneider, J. G., Hogan, A., de Beaufort, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.180 · Cited by 316 · see citing works
Donor species richness determines faecal microbiota transplantation success in inflammatory bowel disease
Vermeire, S., Joossens, M., Verbeke, K., Wang, J., Machiels, K., Sabino, J., Ferrante, M., Van Assche, G., Rutgeerts, P., & Raes, J. (2016) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjv203 · Cited by 311 · see citing works
Self-citation
Host Genetics and Gut Microbiome: Challenges and Perspectives
Kurilshikov, A., Wijmenga, C., Fu, J., & Zhernakova, A. (2017) · Trends in Immunology · doi:10.1016/j.it.2017.06.003 · Cited by 309 · see citing works
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Tramontano, M., Andrejev, S., Pruteanu, M., Klünemann, M., Kuhn, M., Galardini, M., Jouhten, P., Zelezniak, A., Zeller, G., Bork, P., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0123-9 · Cited by 295 · see citing works
The microbiome beyond the horizon of ecological and evolutionary theory
Koskella, B. L., Hall, L. J., & Metcalf, C. J. E. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0340-2 · Cited by 292 · see citing works
An integrative view of microbiome-host interactions in inflammatory bowel diseases
Wlodarska, M., Kostic, A. D., & Xavier, R. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.008 · Cited by 287 · see citing works
Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis
Tito, R. Y., Cypers, H., Joossens, M., Varkas, G., Praet, L. V., Glorieus, E., den Bosch, F. E. V., Vos, M. D., Raes, J., & Elewaut, D. S. (2016) · Arthritis & Rheumatology · doi:10.1002/art.39802 · Cited by 277 · see citing works
Self-citation
Beneficial modulation of the gut microbiota
Walsh, C. J., Guinane, C. M., O'Toole, P. W., & Cotter, P. D. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.03.035 · Cited by 274 · see citing works
Adjusting microbiome profiles for differences in microbial load by spike-in bacteria
Stämmler, F., Gläsner, J., Hiergeist, A., Holler, E., Weber, D., Oefner, P. J., Gessner, A., & Spang, R. (2016) · Microbiome · doi:10.1186/s40168-016-0175-0 · Cited by 271 · see citing works
Implausible results in human nutrition research
Ioannidis, J. P. A. (2013) · BMJ · doi:10.1136/bmj.f6698 · Cited by 270 · see citing works
Effects of bowel cleansing on the intestinal microbiota
Jalanka, J., Salonen, A., Salojärvi, J., Ritari, J., Immonen, O., Marciani, L., Gowland, P. A., Hoad, C. L., Garsed, K. C., Lam, C., et al. (2014) · Gut · doi:10.1136/gutjnl-2014-307240 · Cited by 270 · see citing works
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
Yutin, N., Makarova, K., Gussow, A. B., Krupovic, M., Segall, A., Edwards, R., & Koonin, E. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0053-y · Cited by 270 · see citing works
Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications
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 · see citing works
Host-microbe co-metabolism dictates cancer drug efficacy in C. elegans
Scott, T. A., Quintaneiro, L. M., Norvaisas, P., Lui, P. P., Wilson, M. P., Leung, K.-Y., Herrera-Dominguez, L., Sudiwala, S., Pessia, A., Clayton, P. T., et al. (2017) · Cell · doi:10.1016/j.cell.2017.03.040 · Cited by 254 · see citing works
Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease
Zmora, N., Zeevi, D., Korem, T., Segal, E., & Elinav, E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2015.12.016 · Cited by 252 · see citing works
Moving beyond microbiome-wide associations to causal microbe identification
Surana, N. K., & Kasper, D. L. (2017) · Nature · doi:10.1038/nature25019 · Cited by 249 · see citing works
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe‐Fadrosh, E. A., Meier‐Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Páez-Espino, D., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3886 · Cited by 246 · see citing works
Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions
Parfrey, L. W., Walters, W. A., & Knight, R. D. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00153 · Cited by 243 · see citing works
The effect of age and non-steroidal anti-inflammatory drugs on human intestinal microbiota composition
Mäkivuokko, H., Tiihonen, K., Tynkkynen, S., Paulin, L. G., & Rautonen, N. (2009) · British Journal Of Nutrition · doi:10.1017/s0007114509991553 · Cited by 243 · see citing works
Bacterial metabolism affects the C. elegans response to cancer chemotherapeutics
García-González, A. P., Ritter, A. D., Shrestha, S., Andersen, E. C., Yilmaz, L. S., & Walhout, A. J. M. (2017) · Cell · doi:10.1016/j.cell.2017.03.046 · Cited by 243 · see citing works
Practical considerations for large-scale gut microbiome studies
Vandeputte, D., Tito, R. Y., Vanleeuwen, R., Falony, G., & Raes, J. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux027 · Cited by 237 · see citing works
Self-citation
Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort
Flowers, S. A., Evans, S. J., Ward, K. M., McInnis, M. G., & Ellingrod, V. L. (2017) · Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy · doi:10.1002/phar.1890 · Cited by 235 · cited 2× · see citing works
“, 2016), atypical antipsychotics (Bahr et al., 2015; Flowers et al., 2017; Mäkivuokko et al., 2010), and nonsteroidal anti-inflammatory drugs (Rogers and Aronoff, 2016), among others, have been reported to impact the gut microbiome.”
Metatranscriptome of human faecal microbial communities in a cohort of adult men
Abu-Ali, G., Mehta, R. S., Lloyd‐Price, J., Mallick, H., Branck, T. A., Ivey, K. L., Drew, D. A., DuLong, C. R., Rimm, E. B., Izard, J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0084-4 · Cited by 230 · see citing works
Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation
Fuentes, S., Rossen, N., van der Spek, M. J., Hartman, J., Huuskonen, L., Korpela, K., Salojärvi, J., Aalvink, S., de Vos, W. M., D’Haens, G., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.44 · Cited by 220 · see citing works
Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients
Ticinesi, A., Milani, C., Lauretani, F., Nouvenne, A., Mancabelli, L., Lugli, G. A., Turroni, F., Duranti, S., Mangifesta, M., Viappiani, A., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10734-y · Cited by 211 · see citing works
Geographical variation of human gut microbial composition
Suzuki, T. A., & Worobey, M. (2014) · Biology Letters · doi:10.1098/rsbl.2013.1037 · Cited by 210 · see citing works
The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro
Marzorati, M., Vanhoecke, B. W. A., Ryck, T. D., Sadabad, M. S., Pinheiro, I., Possemiers, S., den Abbeele, P. V., Derycke, L., Bracke, M., Pieters, J., et al. (2014) · BMC Microbiology · doi:10.1186/1471-2180-14-133 · Cited by 208 · see citing works
The human gut virome: a multifaceted majority
Ogilvie, L. A., & Jones, B. V. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00918 · Cited by 206 · see citing works
Systematic Review and Meta-analysis
Narula, N., Kassam, Z., Yuan, Y., Colombel, J., Ponsioen, C. Y., Reinisch, W., & Moayyedi, P. (2017) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000001228 · Cited by 206 · see citing works
Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children
Bahr, S. M., Tyler, B. C., Wooldridge, N., Butcher, B. D., Burns, T. L., Teesch, L. M., Oltman, C. L., Azcarate-Peril, M. A., Kirby, J. R., & Calarge, C. A. (2015) · Translational Psychiatry · doi:10.1038/tp.2015.135 · Cited by 197 · see citing works
Microbial Enterotypes, Inferred by the Prevotella-to-Bacteroides Ratio, Remained Stable during a 6-Month Randomized Controlled Diet Intervention with the New Nordic Diet
Roager, H. M., Licht, T. R., Poulsen, S. K., Larsen, T. M., & Bahl, M. I. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03549-13 · Cited by 194 · see citing works
Experimental design and quantitative analysis of microbial community multiomics
Mallick, H., Ma, S., Franzosa, E. A., Vatanen, T., Morgan, X. C., & Huttenhower, C. (2017) · Genome Biology · doi:10.1186/s13059-017-1359-z · Cited by 192 · see citing works
Studying complex biological systems using multifactorial perturbation
Jansen, R. C. (2003) · Nature Reviews Genetics · doi:10.1038/nrg996 · Cited by 187 · see citing works
A systematic review and meta-analysis of the prebiotics and synbiotics effects on glycaemia, insulin concentrations and lipid parameters in adult patients with overweight or obesity
Beserra, B. T. S., Fernandes, R., do Rosario, V. A., Mocellin, M. C., Kuntz, M. G. F., & Trindade, E. B. S. D. M. (2014) · Clinical Nutrition · doi:10.1016/j.clnu.2014.10.004 · Cited by 181 · see citing works
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
Rodrigues, J. F. M., Schmidt, T., Tackmann, J., & von Mering, C. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx517 · Cited by 181 · see citing works
Self-citation
Temporal and technical variability of human gut metagenomes
Voigt, A. Y., Costea, P. I., Kultima, J. R., Li, S. S., Zeller, G., Sunagawa, S., & Bork, P. (2015) · Genome biology · doi:10.1186/s13059-015-0639-8 · Cited by 177 · see citing works
DESMAN: a new tool for de novo extraction of strains from metagenomes
Quince, C., Delmont, T., Raguideau, S., Alneberg, J., Darling, A., Collins, G., & Eren, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1309-9 · Cited by 175 · see citing works
Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection
Fuentes, S., van Nood, E., Tims, S., Jong, I. H., ter Braak, C. J. F., Keller, J. J., Zoetendal, E. G., & de Vos, W. M. (2014) · The ISME Journal · doi:10.1038/ismej.2014.13 · Cited by 174 · see citing works
Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria
Rettedal, E. A., Gumpert, H., & Sommer, M. O. A. (2014) · Nature Communications · doi:10.1038/ncomms5714 · Cited by 168 · see citing works
The impact of nutrition on intestinal bacterial communities
Flint, H. J., Duncan, S. H., & Louis, P. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.005 · Cited by 149 · see citing works
Insights from 100 years of research with probiotic E. coli
Wassenaar, T. M. (2016) · European Journal of Microbiology and Immunology · doi:10.1556/1886.2016.00029 · Cited by 147 · see citing works
Subspecies in the global human gut microbiome
Costea, P. I., Coelho, L. P., Sunagawa, S., Munch, R., Huerta‐Cepas, J., Forslund, S. K., Hildebrand, F., Kushugulova, A. R., Zeller, G., & Bork, P. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177589 · Cited by 141 · see citing works
The path towards microbiome-based metabolite treatment
Suez, J., & Elinav, E. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.75 · Cited by 133 · see citing works
Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis
Satinsky, B. M., Gifford, S., Crump, B. C., & Moran, M. A. (2013) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-407863-5.00012-5 · Cited by 131 · see citing works
Gut microbiota composition associated with stool consistency
Tigchelaar, E. F., Bonder, M. J., Jankipersadsing, S. A., Fu, J., Wijmenga, C., & Zhernakova, A. (2015) · Gut · doi:10.1136/gutjnl-2015-310328 · Cited by 114 · see citing works
Towards Predictive Models of the Human Gut Microbiome
Bucci, V., & Xavier, J. B. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.03.017 · Cited by 113 · see citing works
Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems
Kolmeder, C. A., & de Vos, W. M. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.05.018 · Cited by 106 · see citing works
metaSNV: A tool for metagenomic strain level analysis
Costea, P. I., Munch, R., Coelho, L. P., Paoli, L., Sunagawa, S., & Bork, P. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182392 · Cited by 103 · see citing works
Commensal Koch's postulates: establishing causation in human microbiota research
Neville, B. A., Forster, S. C., & Lawley, T. D. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.001 · Cited by 102 · see citing works
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
Lee, S. T. M., Kahn, S. A., Delmont, T. O., Shaiber, A., Esen, Ö. C., Hubert, N. A., Morrison, H. G., Antonopoulos, D. A., Rubin, D. T., & Eren, A. M. (2017) · Microbiome · doi:10.1186/s40168-017-0270-x · Cited by 97 · see citing works
The microbiome of the built environment and mental health
Hoisington, A. J., Brenner, L. A., Kinney, K. A., Postolache, T. T., & Lowry, C. A. (2015) · Microbiome · doi:10.1186/s40168-015-0127-0 · Cited by 91 · see citing works

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Facing up to the global challenges of ageing
Partridge, L., Deelen, J., & Slagboom, P. E. (2018) · Nature · doi:10.1038/s41586-018-0457-8 · Cited by 1,475 · see citing works
Gut microbial metabolites in obesity, NAFLD and T2DM
Canfora, E. E., Meex, R. C. R., Venema, K., & Blaak, E. E. (2019) · Nature Reviews Endocrinology · doi:10.1038/s41574-019-0156-z · Cited by 1,493 · see citing works
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0406-6 · Cited by 1,373 · see citing works
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030 · see citing works
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration
Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I. (2019) · Nutrients · doi:10.3390/nu11122862 · Cited by 817 · see citing works
Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health
Fassarella, M., Blaak, E. E., Penders, J., Nauta, A., Smidt, H., & Zoetendal, E. G. (2020) · Gut · doi:10.1136/gutjnl-2020-321747 · Cited by 784 · see citing works
Metabolites and the Tumour Microenvironment: From Cellular Mechanisms to Systemic Metabolism
Elia, I., & Haigis, M. C. (2021) · Nature Metabolism · doi:10.1038/s42255-020-00317-z · Cited by 651 · see citing works
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Gregory, A., Zablocki, O., Zayed, A. A., Howell, A., Bolduc, B., & Sullivan, M. B. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.003 · Cited by 635 · see citing works
Extensive transmission of microbes along the gastrointestinal tract
Schmidt, T. S., Hayward, M. R., Coelho, L. P., Li, S. S., Costea, P. I., Voigt, A. Y., Wirbel, J., Maistrenko, O. M., Alves, R. J., Bergsten, E., et al. (2019) · eLife · doi:10.7554/elife.42693 · Cited by 596 · see citing works
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Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents
Walter, J., Armet, A. M., Finlay, B. B., & Shanahan, F. (2020) · Cell · doi:10.1016/j.cell.2019.12.025 · Cited by 596 · see citing works
Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model
Hsu, B. B., Gibson, T. E., Yeliseyev, V., Liu, Q., Lyon, L., Bry, L., Silver, P. A., & Gerber, G. K. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.001 · Cited by 573 · see citing works
Gut Microbiota and Cancer: From Pathogenesis to Therapy
Vivarelli, S., Salemi, R., Candido, S., Falzone, L., Santagati, M., Stefani, S., Torino, F., Banna, G. L., Tonini, G., & Libra, M. (2019) · Cancers · doi:10.3390/cancers11010038 · Cited by 586 · see citing works
Gut microbiota and dysbiosis in Alzheimer's disease: Implications for pathogenesis and treatment
Liu, S., Gao, J., Zhu, M., Liu, K., & Zhang, H.-L. (2020) · Molecular Neurobiology · doi:10.1007/s12035-020-02073-3 · Cited by 516 · see citing works
The evolving metabolic landscape of chromatin biology and epigenetics
Dai, Z., Ramesh, V., & Locasale, J. W. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0270-8 · Cited by 494 · see citing works
Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review
Yang, Q., Liang, Q., Balakrishnan, B., Belobrajdic, D. P., Feng, Q.-J., & Zhang, W. Y. (2020) · Nutrients · doi:10.3390/nu12020381 · Cited by 475 · see citing works
Diversity within Species: Interpreting Strains in Microbiomes
Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0368-1 · Cited by 441 · see citing works
Metagenome-wide association of gut microbiome features for schizophrenia
Zhu, F., Ju, Y., Wang, W., Wang, Q., Guo, R., Ma, Q., Sun, Q., Fan, Y., Xie, Y., Yang, Z., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15457-9 · Cited by 409 · see citing works
Akkermansia muciniphila phospholipid induces homeostatic immune responses
Bae, M., Cassilly, C. D., Liu, X., Park, S.-M., Tusi, B. K., Chen, X., Kwon, J., Filipčík, P., Bolze, A. S., Liu, Z., et al. (2022) · Nature · doi:10.1038/s41586-022-04985-7 · Cited by 413 · see citing works
Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia
Ticinesi, A., Nouvenne, A., Cerundolo, N., Catania, P., Prati, B., Tana, C., & Meschi, T. (2019) · Nutrients · doi:10.3390/nu11071633 · Cited by 418 · see citing works
Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential
Guo, R., Chen, L., Xing, C., & Liu, T. (2019) · British Journal of Anaesthesia · doi:10.1016/j.bja.2019.07.026 · Cited by 416 · see citing works
The microbiome–gut–brain axis in Parkinson disease — from basic research to the clinic
Tan, A. H., Lim, S. Y., & Lang, A. E. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00681-2 · Cited by 392 · see citing works
Unravelling the collateral damage of antibiotics on gut bacteria
Maier, L., Goemans, C., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., García‐Santamarina, S., Cacace, E., Zhang, B., et al. (2021) · Nature · doi:10.1038/s41586-021-03986-2 · Cited by 389 · see citing works
Gut–organ axis: a microbial outreach and networking
Ahlawat, S., Asha, A., & Sharma, K. K. (2020) · Letters in Applied Microbiology · doi:10.1111/lam.13333 · Cited by 363 · see citing works
Human-origin probiotic cocktail increases short-chain fatty acid production via modulation of mice and human gut microbiome
Nagpal, R., Wang, S., Ahmadi, S., Hayes, J., Gagliano, J., Subashchandrabose, S., Kitzman, D. W., Becton, T., Read, R., & Yadav, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-30114-4 · Cited by 355 · see citing works
Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential
Saus, E., Iraola‐Guzmán, S., Willis, J. R., Brunet‐Vega, A., & Gabaldón, T. (2019) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2019.05.001 · Cited by 348 · see citing works
Yogurt, cultured fermented milk, and health: A systematic review
Savaiano, D. A., & Hutkins, R. W. (2021) · Nutrition Reviews · doi:10.1093/nutrit/nuaa013 · Cited by 339 · see citing works
Live biotherapeutic products: The importance of a defined regulatory framework
Cordaillat-Simmons, M., Rouanet, A., & Pot, B. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0437-6 · Cited by 328 · see citing works
The Microbiota–Gut–Brain Axis and Alzheimer’s Disease: Neuroinflammation Is to Blame?
Megur, A., Baltriukienė, D., Bukelskienė, V., & Burokas, A. (2020) · Nutrients · doi:10.3390/nu13010037 · Cited by 323 · see citing works
The lung–gut axis during viral respiratory infections: the impact of gut dysbiosis on secondary disease outcomes
Sencio, V., Machado, M. G., & Trottein, F. (2021) · Mucosal Immunology · doi:10.1038/s41385-020-00361-8 · Cited by 315 · see citing works
A faecal microbiota signature with high specificity for pancreatic cancer
Kartal, E., Schmidt, T. S. B., Molina-Montes, E., Rodríguez-Perales, S., Wirbel, J., Maistrenko, O. M., Akanni, W. A., Alashkar Alhamwe, B., Alves, R. J., Carrato, A., et al. (2022) · Gut · doi:10.1136/gutjnl-2021-324755 · Cited by 290 · see citing works
Self-citation
The unmapped chemical complexity of our diet
Barabási, A.-Ĺ., Menichetti, G., & Loscalzo, J. (2019) · Nature Food · doi:10.1038/s43016-019-0005-1 · Cited by 295 · see citing works
Generation of systemic antitumour immunity via the in situ modulation of the gut microbiome by an orally administered inulin gel
Han, K., Nam, J., Xu, J., Sun, X., Huang, X., Animasahun, O., Achreja, A., Jeon, J. H., Pursley, B., Kamada, N., et al. (2021) · Nature Biomedical Engineering · doi:10.1038/s41551-021-00749-2 · Cited by 287 · see citing works
Evolutionary and Ecological Consequences of Gut Microbial Communities
Moran, N. A., Ochman, H., & Hammer, T. J. (2019) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062453 · Cited by 271 · see citing works
The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain
Salliss, M. E., Farland, L. V., Mahnert, N. D., & Herbst‐Kralovetz, M. M. (2021) · Human Reproduction Update · doi:10.1093/humupd/dmab035 · Cited by 287 · see citing works
Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy
Pryor, R., Norvaisas, P., Marinos, G., Best, L., Thingholm, L. B., Quintaneiro, L. M., De Haes, W., Esser, D., Waschina, S., Lujan, C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.003 · Cited by 274 · see citing works
A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation
Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works
Obesity in Type 1 Diabetes: Pathophysiology, Clinical Impact, and Mechanisms
Corbin, K. D., Driscoll, K. A., Pratley, R. E., Smith, S. R., Maahs, D. M., Mayer-Davis, E. J., & Advancing Care for Type 1 Diabetes and Obesity Network (ACT1ON) (2018) · Endocrine Reviews · doi:10.1210/er.2017-00191 · Cited by 262 · see citing works
Problems with the concept of gut microbiota dysbiosis
Brüssow, H. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13479 · Cited by 250 · see citing works
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., Sunagawa, S., & Zeller, G. (2021) · Genome Biology · doi:10.1186/s13059-021-02306-1 · Cited by 269 · see citing works
Horizons in the evolution of aging
Flatt, T., & Partridge, L. (2018) · BMC Biology · doi:10.1186/s12915-018-0562-z · Cited by 255 · see citing works
Characterizing Dysbiosis of Gut Microbiome in PD: Evidence for Overabundance of Opportunistic Pathogens
Wallen, Z. D., Appah, M., Dean, M. N., Sesler, C. L., Factor, S. A., Molho, E., Zabetian, C. P., Standaert, D. G., & Payami, H. (2020) · npj Parkinson s Disease · doi:10.1038/s41531-020-0112-6 · Cited by 252 · see citing works
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Schmidt, T. S. B., Li, S. S., Maistrenko, O. M., Akanni, W., Coelho, L. P., Dolai, S., Fullam, A., Glazek, A. M., Hercog, R., Herrema, H., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01913-0 · Cited by 233 · see citing works
Self-citation
Gut Microbiota and Their Neuroinflammatory Implications in Alzheimer’s Disease
Giau, V. V., Wu, S., Jamerlan, A., An, S. S. A., Kim, S., & Hulme, J. (2018) · Nutrients · doi:10.3390/nu10111765 · Cited by 235 · see citing works
Microbiota and Thyroid Interaction in Health and Disease
Fröhlich, E., & Wahl, R. (2019) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2019.05.008 · Cited by 233 · see citing works
Combinatorial, additive and dose-dependent drug–microbiome associations
Forslund, S. K., Chakaroun, R., Zimmermann‐Kogadeeva, M., Markó, L., Aron‐Wisnewsky, J., Nielsen, T., Moitinho‐Silva, L., Schmidt, T., Falony, G., Vieira‐Silva, S., et al. (2021) · Nature · doi:10.1038/s41586-021-04177-9 · Cited by 221 · see citing works
Self-citation
Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins
Dunne, M., Rupf, B., Tala, M., Qabrati, X., Ernst, P. J., Shen, Y., Sumrall, E. T., Heeb, L., Plückthun, A., Loessner, M. J., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.062 · Cited by 227 · see citing works
Portal hypertension in cirrhosis: Pathophysiological mechanisms and therapy
Iwakiri, Y., & Trebicka, J. (2021) · JHEP Reports · doi:10.1016/j.jhepr.2021.100316 · Cited by 237 · see citing works
Gut microbiota, cognitive frailty and dementia in older individuals: A systematic review
Ticinesi, A., Tana, C., Nouvenne, A., Prati, B., Lauretani, F., & Meschi, T. (2018) · Clinical Interventions in Aging · doi:10.2147/cia.s139163 · Cited by 215 · see citing works
Update of probiotics in human world: A nonstop source of benefactions till the end of time
Zommiti, M., Feuilloley, M. G. J., & Connil, N. (2020) · Microorganisms · doi:10.3390/microorganisms8121907 · Cited by 225 · see citing works
Correlation and association analyses in microbiome study integrating multiomics in health and disease
Xia, Y. (2020) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2020.04.003 · Cited by 217 · see citing works
High fat diet, gut microbiome and gastrointestinal cancer
Tong, Y., Gao, H., Qi, Q., Liu, X., Li, J., Gao, J., Li, P., Wang, Y., Du, L., & Wang, C. (2021) · Theranostics · doi:10.7150/thno.56157 · Cited by 205 · see citing works
Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure
Trebicka, J., Bork, P., Krag, A. A., & Arumugam, M. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00376-3 · Cited by 203 · see citing works
Symposium review: The uterine microbiome associated with the development of uterine disease in dairy cows
Galvão, K. N., Bicalho, R. C., & Jeon, S. J. (2019) · Journal of Dairy Science · doi:10.3168/jds.2019-17106 · Cited by 200 · see citing works
Oral Administration of miR-30d from Feces of MS Patients Suppresses MS-like Symptoms in Mice by Expanding Akkermansia muciniphila
Liu, S., Rezende, R. M., Moreira, T. G., Tankou, S. K., Cox, L. M., Wu, M., Song, A., Dhang, F. H., Wei, Z., Costamagna, G., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.10.008 · Cited by 196 · see citing works
Synthetic ecology of the human gut microbiota
Vrancken, G., Gregory, A., Huys, G. R. B., Faust, K., & Raes, J. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0264-8 · Cited by 192 · see citing works
Self-citation
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden
Olsson, L. M., Boulund, F., Nilsson, S., Khan, M. T., Gummesson, A., Fagerberg, L., Engstrand, L. G., Perkins, R., Uhlén, M., Bergström, G. M. L., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.002 · Cited by 189 · see citing works
Host-microbiome interactions: Gut-Liver axis and its connection with other organs
Anand, S., & Mande, S. S. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00352-6 · Cited by 196 · see citing works
ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs
Yang, H., Wu, J., Huang, X., Zhou, Y., Zhang, Y., Liu, M., Liu, Q., Ke, S., He, M., Fu, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04769-z · Cited by 195 · see citing works
Understanding the gut–kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers
Ticinesi, A., Milani, C., Guerra, A., Allegri, F., Lauretani, F., Nouvenne, A., Mancabelli, L., Lugli, G. A., Turroni, F., Duranti, S., et al. (2018) · Gut · doi:10.1136/gutjnl-2017-315734 · Cited by 186 · see citing works
Health-Promoting of Polysaccharides Extracted from Ganoderma lucidum
Seweryn, E., Ziała, A., & Gamian, A. (2021) · Nutrients · doi:10.3390/nu13082725 · Cited by 183 · see citing works
Ensuring the future of functional foods
Birch, C., & Bonwick, G. (2018) · International Journal of Food Science & Technology · doi:10.1111/ijfs.14060 · Cited by 198 · see citing works
Probiotic‐Inspired Nanomedicine Restores Intestinal Homeostasis in Colitis by Regulating Redox Balance, Immune Responses, and the Gut Microbiome
Xu, J., Xu, J., Shi, T., Zhang, Y., Chen, F., Yang, C., Guo, X., Liu, G., Shao, D., Leong, K. W., et al. (2022) · Advanced Materials · doi:10.1002/adma.202207890 · Cited by 180 · see citing works
The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review
Aslam, H., Marx, W., Rocks, T., Loughman, A., Chandrasekaran, V., Ruusunen, A., Dawson, S. L., West, M., Mullarkey, E., Pasco, J. A., et al. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1799533 · Cited by 170 · see citing works
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals
The Milieu Intérieur Consortium, Scepanovic, P., Hodel, F., Mondot, S., Partula, V., Byrd, A., Hammer, C., Alanio, C., Bergstedt, J., Patin, E., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0747-x · Cited by 171 · see citing works
Microbiota-Immune Interaction in the Pathogenesis of Gut-Derived Infection
Wang, C., Li, Q., & Ren, J. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01873 · Cited by 167 · see citing works
Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer’s Disease
Chen, Y., Fang, L., Chen, S., Zhou, H., Fan, Y., Li, L., Li, J., Xu, J., Chen, Y., Ma, Y., et al. (2020) · BioMed Research International · doi:10.1155/2020/8456596 · Cited by 150 · see citing works
The Relationship between the Gut Microbiome and Metformin as a Key for Treating Type 2 Diabetes Mellitus
Lee, C. B., Chae, S. U., Jo, S. J., Jerng, U. M., & Bae, S. K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073566 · Cited by 149 · see citing works
Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications
Nagata, N., Takeuchi, T., Masuoka, H., Aoki, R., Ishikane, M., Iwamoto, N., Sugiyama, M., Suda, W., Nakanishi, Y., Terada-Hirashima, J., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.09.024 · Cited by 148 · see citing works
Paving the Way to Precision Nutrition Through Metabolomics
Tebani, A., & Bekri, S. (2019) · Frontiers in Nutrition · doi:10.3389/fnut.2019.00041 · Cited by 143 · see citing works
Association Between Sex Hormone Levels and Gut Microbiota Composition and Diversity—A Systematic Review
d’Afflitto, M., Upadhyaya, A., Green, A., & Peiris, M. (2022) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0000000000001676 · Cited by 142 · see citing works
Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2020) · eLife · doi:10.7554/elife.56998 · Cited by 146 · see citing works
Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works
Aryl hydrocarbon receptor activation by Lactobacillus reuteri tryptophan metabolism alleviates Escherichia coli-induced mastitis in mice
Zhao, C., Hu, X., Bao, L., Wu, K., Feng, L., Qiu, M., Hao, H., Fu, Y., & Zhang, N. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009774 · Cited by 143 · see citing works
The Use of Rifaximin in Patients With Cirrhosis
Caraceni, P., Vargas, V., Solà, E., Alessandria, C., de Wit, K., Trebicka, J., Angeli, P., Mookerjee, R. P., Durand, F., Pose, E., et al. (2021) · Hepatology · doi:10.1002/hep.31708 · Cited by 142 · see citing works
Integrated gut virome and bacteriome dynamics in COVID-19 patients
Cao, J., Wang, C., Zhang, Y., Lei, G., Xu, K., Zhao, N., Lu, J., Meng, F., Yu, L., Yan, J., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1887722 · Cited by 138 · see citing works
Role of gut microbiome in cancer immunotherapy: from predictive biomarker to therapeutic target
Zhang, M., Liu, J., & Xia, Q. (2023) · Experimental Hematology and Oncology · doi:10.1186/s40164-023-00442-x · Cited by 149 · see citing works
Metagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health
Jia, B., Park, D., Hahn, Y., & Jeon, C. O. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1748261 · Cited by 135 · see citing works
Metagenomic reconstructions of gut microbial metabolism in weanling pigs
Wang, W., Hu, H., Zijlstra, R. T., Zheng, J., & Gänzle, M. G. (2019) · Microbiome · doi:10.1186/s40168-019-0662-1 · Cited by 134 · see citing works
Gut microbiome in Parkinson's disease: New insights from meta-analysis
Toh, T. S., Chong, C. W., Lim, S., Bowman, J. S., Cirstea, M. S., Lin, C., Chen, C., Appel‐Cresswell, S., Finlay, B. B., & Tan, A. H. (2021) · Parkinsonism & Related Disorders · doi:10.1016/j.parkreldis.2021.11.017 · Cited by 133 · see citing works
Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions
Tsiaoussis, J., Antoniou, M. N., Koliarakis, I., Mesnage, R., Vardavas, C. I., Izotov, B. N., Psaroulaki, A., & Tsatsakis, A. M. (2019) · Toxicology Letters · doi:10.1016/j.toxlet.2019.04.014 · Cited by 134 · see citing works
Triangulating nutrigenomics, metabolomics and microbiomics toward personalized nutrition and healthy living
Lagoumintzis, G., & Patrinos, G. P. (2023) · Human Genomics · doi:10.1186/s40246-023-00561-w · Cited by 132 · see citing works
Gut Microbiome Toxicity: Connecting the Environment and Gut Microbiome-Associated Diseases
Tu, P., Chi, L., Bodnar, W. M., Zhang, Z., Gao, B., Bian, X., Stewart, J. R., Fry, R. C., & Lü, K. (2020) · Toxics · doi:10.3390/toxics8010019 · Cited by 130 · see citing works
Gut microbiota controlling radiation-induced enteritis and intestinal regeneration
Moraitis, I., Guiu, J., & Rubert, J. (2023) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2023.05.006 · Cited by 128 · see citing works
Prenatal and postnatal contributions of the maternal microbiome on offspring programming
Jašarević, E., & Bale, T. L. (2019) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2019.100797 · Cited by 127 · see citing works
Gut microbes in neurocognitive and mental health disorders
Halverson, T., & Alagiakrishnan, K. (2020) · Annals of Medicine · doi:10.1080/07853890.2020.1808239 · Cited by 125 · see citing works
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
Nishijima, S., Stankevič, E., Aasmets, O., Schmidt, T., Nagata, N., Keller, M. I., Ferretti, P., Juel, H. B., Fullam, A., Robbani, S. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.022 · Cited by 127 · see citing works
Self-citation
Prevotella histicola Protects From Arthritis by Expansion of Allobaculum and Augmenting Butyrate Production in Humanized Mice
Balakrishnan, B., Luckey, D. H., Bodkhe, R., Chen, J., Marietta, E. V., Jeraldo, P., Murray, J. A., & Taneja, V. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.609644 · Cited by 125 · see citing works
Mutual Interactions among Exercise, Sport Supplements and Microbiota
Zeppa, S. D., Agostini, D., Gervasi, M., Annibalini, G., Amatori, S., Ferrini, F., Sisti, D., Piccoli, G., Barbieri, E., Sestili, P., et al. (2019) · Nutrients · doi:10.3390/nu12010017 · Cited by 122 · see citing works
Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis
Chen, P. B., Black, A. S., Sobel, A. L., Zhao, Y., Mukherjee, P., Molparia, B., Moore, N. E., Muench, G. R. A., Wu, J., Chen, W., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0549-5 · Cited by 119 · see citing works
Revisiting the Hallmarks of Aging to Identify Markers of Biological Age
Guerville, F., Barreto, P. D. S., Ader, I., Andrieu, S., Casteilla, L., Dray, C., Fazilleau, N., Guyonnet, S., Langin, D., Liblau, R., et al. (2020) · The Journal of Prevention of Alzheimer s Disease · doi:10.14283/jpad.2019.50 · Cited by 120 · see citing works
Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements
Tourlousse, D. M., Narita, K., Miura, T., Sakamoto, M., Ohashi, A., Shiina, K., Matsuda, M., Miura, D., Shimamura, M., Ohyama, Y., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01048-3 · Cited by 118 · see citing works
Irritable bowel syndrome and gut microbiota
Canakis, A., Haroon, M., & Weber, H. C. (2019) · Current Opinion in Endocrinology Diabetes and Obesity · doi:10.1097/med.0000000000000523 · Cited by 120 · see citing works
Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome
Williams, M. R., Cau, L., Wang, Y., Kaul, D., Sanford, J. A., Zaramela, L. S., Khalil, S., Butcher, A. M., Zengler, K., Horswill, A. R., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.02.021 · Cited by 113 · see citing works
How can we define “optimal microbiota?”: a comparative review of structure and functions of microbiota of animals, fish, and plants in agriculture
Ikeda-Ohtsubo, W., Brugman, S., Warden, C. H., Rebel, J. M. J., Folkerts, G., & Pieterse, C. M. J. (2018) · Frontiers in Nutrition · doi:10.3389/fnut.2018.00090 · Cited by 115 · see citing works
Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
Moreno‐Indias, I., Lahti, L., Nedyalkova, M., Elbere, I., Roshchupkin, G. V., Adilović, M., Aydemir, Ö., Bakır-Güngör, B., Pau, E. C. D. S., D’Elia, D., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.635781 · Cited by 112 · see citing works
Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment
parker, J., O'Brien, C., Hawrelak, J., & Gersh, F. (2021) · doi:10.20944/preprints202112.0088.v1 · Cited by 113 · see citing works
No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population
Hugerth, L. W., Andreasson, A., Talley, N. J., Forsberg, A. M., Kjellström, L., Schmidt, P. T., Agreus, L., & Engstrand, L. (2020) · Gut · doi:10.1136/gutjnl-2019-318717 · Cited by 102 · see citing works
Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment
Parker, J., O’Brien, C., Hawrelak, J., & Gersh, F. L. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19031336 · Cited by 114 · see citing works
“The microbiome is known to co-regulate many physiological functions involving the immune, neuroendocrine and metabolic systems via complex reciprocal feedback mechanisms that operate between the microbial ecosystem and the host (116,117).”
Background
Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Bahram, M., Netherway, T., Frioux, C., Ferretti, P., Coelho, L. P., Geisen, S., Bork, P., & Hildebrand, F. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15314 · Cited by 106 · see citing works
Metabolic independence drives gut microbial colonization and resilience in health and disease
Watson, A. R., Füssel, J., Veseli, I., DeLongchamp, J. Z., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J. M., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02924-x · Cited by 92 · see citing works

Human Gut Microbiome: Function Matters
Heintz‐Buschart, A., & Wilmes, P. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.11.002 · Cited by 747 · see citing works
The human gut microbiome: current knowledge, challenges, and future directions
Dave, M., Higgins, P., Middha, S., & Rioux, K. P. (2012) · Translational research · doi:10.1016/j.trsl.2012.05.003 · Cited by 338 · see citing works
An Integrated Multi-Disciplinary Perspective for Addressing Challenges of the Human Gut Microbiome
Shah, R., McKenzie, E. J., Rosin, M., Jadhav, S. R., Gondalia, S. V., Rosendale, D., & Beale, D. J. (2020) · Metabolites · doi:10.3390/metabo10030094 · Cited by 24 · see citing works
Understanding the human gut microbiome: from composition to disease association
Alali, M. A., & Shori, A. B. (2026) · Frontiers in Microbiomes · doi:10.3389/frmbi.2026.1717288 · Cited by 8 · see citing works
Stratification and variation of the human gut microbiota
Costea, P. I. (2016) · Online Publication Service of Würzburg University (Würzburg University)

Authors: Schmidt, T. S. B., Raes, J., & Bork, P.
Affiliations: European Molecular Biology Laboratory (DE)
VIB-KU Leuven Center for Microbiology (BE)
Corresponding author: Raes, Jeroen
ORCID: Schmidt, Thomas S.B.
Raes, Jeroen
Venue: Cell
Publisher: Elsevier BV
Published: 2018-03
Volume: 172
Issue: 6
Pages: 1198-1215
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2018.02.044
OpenAlex: W2790856964
Cited by: 845
References: 213
Citations by year: 2026: 61 · 2025: 89 · 2024: 122 · 2023: 116 · 2022: 99 · 2021: 126 · 2020: 111 · 2019: 90 · 2018: 30
FWCI: 8.86
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, 372 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
Lirias (KU Leuven) (submittedVersion)
Funders: EMBL
European Research Council MicrobioS (ERC-AdG-669830)
Luxembourg National Research Fund (FNR) CORE microCancer
KU Leuven/Rega
VIB
FWO EOS programme (G0G4118N)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
Keywords: human gut microbiome, microbiota composition, microbiota modulation, longitudinal cohort, perturbation experiments, absolute quantification, taxonomic resolution, in vitro and in vivo models
MeSH terms: Gastrointestinal Microbiome, Host Microbial Interactions, Disease, Health Status, Humans, Research, Gastrointestinal Tract, Metabolomics

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The Human Gut Microbiome: From Association to Modulation

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