Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · see citing works

Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · 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

Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics

Gibson, G. R., & Roberfroid, M. B. (1995) · Journal of Nutrition · doi:10.1093/jn/125.6.1401 · Cited by 7,659 · see citing works

The gut microbiota as an environmental factor that regulates fat storage

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works

Host-Bacterial Mutualism in the Human Intestine

Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · see citing works

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,933 · see citing works

Metagenomic Analysis of the Human Distal Gut Microbiome

Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works

Environmental genome shotgun sequencing of the sargasso sea

Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376 · see citing works

Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis

Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251 · see citing works

An efficient algorithm for large-scale detection of protein families

Enright, A. J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1575 · Cited by 3,536 · see citing works

Gut flora in health and disease

Guarner, F., & Malagelada, J. (2003) · The Lancet · doi:10.1016/s0140-6736(03)12489-0 · Cited by 3,395 · see citing works

Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine

Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358 · see citing works

Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis

Yachi, S., & Loreau, M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1463 · Cited by 3,211 · see citing works

Open source clustering software

de Hoon, M., Imoto, S., Nolan, J., & Miyano, S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth078 · Cited by 3,043 · see citing works

Commensal Host-Bacterial Relationships in the Gut

Hooper, L. V., & Gordon, J. I. (2001) · Science · doi:10.1126/science.1058709 · Cited by 2,362 · see citing works

Pfam: clans, web tools and services

FINN, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj149 · Cited by 2,307 · 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

Comparative Metagenomics of Microbial Communities

Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., et al. (2005) · Science · doi:10.1126/science.1107851 · Cited by 1,694 · see citing works

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior

DeLong, E. F., Preston, C. M., Mincer, T. J., Rich, V. I., Hallam, S., Frigaard, N., Martinez, A., Sullivan, M. B., Edwards, R. A., Brito, B. R., et al. (2006) · Science · doi:10.1126/science.1120250 · Cited by 1,319 · see citing works

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences

Noguchi, H., Park, J., & Takagi, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl723 · Cited by 1,163 · see citing works

The co-evolution of host cationic antimicrobial peptides and microbial resistance

Peschel, A., & Sahl, H. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1441 · Cited by 1,052 · see citing works

Immunity, Inflammation, and Allergy in the Gut

MacDonald, T. T., & Monteleone, G. (2005) · Science · doi:10.1126/science.1106442 · Cited by 1,035 · see citing works

Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis

Paulsen, I. T., Banerjei, L., Myers, G. S. A., Nelson, W. C., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., et al. (2003) · Science · doi:10.1126/science.1080613 · Cited by 930 · see citing works

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

Sebaihia, M., Wren, B. W., Mullany, P. P., Fairweather, N. F., Minton, N. P., Stabler, R. A., Thomson, N. R., Roberts, A. P., Cerdeño-Tárraga, A. M., Wang, H., et al. (2006) · Nature Genetics · doi:10.1038/ng1830 · Cited by 877 · see citing works

Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

Favier, C. F., Vaughan, E. E., de Vos, W. M., & Akkermans, A. D. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.1.219-226.2002 · Cited by 859 · see citing works

Intestinal microflora in early infancy: composition and development

Fanaro, S., Chierici, R., Guerrini, P., & Vigi, V. (2003) · Acta Paediatrica · doi:10.1111/j.1651-2227.2003.tb00646.x · Cited by 738 · see citing works

A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism

Samuel, B. S., & Gordon, J. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602187103 · Cited by 674 · see citing works

Metagenomics: DNA sequencing of environmental samples

Green, S., & Rubin, E. M. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1709 · Cited by 634 · see citing works

Normal Indigenous Intestinal Flora

Finegold, S. M., Sutter, V. L., & Mathisen, G. E. (1983) · Elsevier eBooks · doi:10.1016/b978-0-12-341280-5.50007-0 · Cited by 618 · see citing works

A Model of Host-Microbial Interactions in an Open Mammalian Ecosystem

Bry, L., Falk, P. G., Midtvedt, T., & Gordon, J. I. (1996) · Science · doi:10.1126/science.273.5280.1380 · Cited by 607 · see citing works

Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles

Hopkins, M. J., Sharp, R., & Macfarlane, G. T. (2001) · Gut · doi:10.1136/gut.48.2.198 · Cited by 577 · see citing works

Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of "conjugal" transfer in the absence of a conjugative plasmid

Franke, A. E., & Clewell, D. B. (1981) · Journal of Bacteriology · doi:10.1128/jb.145.1.494-502.1981 · Cited by 552 · see citing works

Food-derived mutagens and carcinogens.

Wakabayashi, K., Nagao, M., Esumi, H., et al. (1992) · PubMed · Cited by 450 · see citing works

PCAP: A Whole-Genome Assembly ProgramPreprint

Huang, X., Wang, J., Aluru, S., Yang, S., & Hillier, L. (2003) · Genome Research · doi:10.1101/gr.1390403 · Cited by 289 · see citing works

Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature.

McGarr, S. E., Ridlon, J. M., & Hylemon, P. B. (2005) · PubMed · Cited by 259 · see citing works

Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus

Beres, S. B., Richter, E. W., Nagiec, M. J., Sumby, P., Porcella, S. F., DeLeo, F. R., & Musser, J. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510279103 · Cited by 214 · see citing works

Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children

Stewart, J. A., CHADWICK, V. S., & Murray, A. (2005) · Journal of Medical Microbiology · doi:10.1099/jmm.0.46189-0 · Cited by 205 · see citing works

Comparison of fecal microflora of elderly persons in rural and urban areas of Japan

Benno, Y., Endo, K., Mizutani, T., Namba, Y., Komori, T., & MITSUOKA, T. (1989) · Applied and Environmental Microbiology · doi:10.1128/aem.55.5.1100-1105.1989 · Cited by 195 · see citing works

SHOT: a web server for the construction of genome phylogenies

Korbel, J. O., Snel, ‎., Huynen, M. A., & Peer Bork, B. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(01)02597-5 · Cited by 178 · see citing works

Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp. The GenBank accession number for the 33803 bp sequence of Tn1549 is AJ192329.

Garnier, F., Taourit, S., Glaser, P., Courvalin, P. M., & Galimand, M. (2000) · Microbiology · doi:10.1099/00221287-146-6-1481 · Cited by 170 · see citing works

Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease

Seksik, P., Sokol, H., Lepage, P., Vasquez, N., Manichanh, C., Mangin, I., Pochart, P., Dore, J. M., & Marteau, P. R. (2006) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2006.03053.x · Cited by 166 · see citing works

Role of human microflora in health and disease

Tancrède, C. (1992) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/bf01967791 · Cited by 143 · see citing works

Transfer of Vancomycin Resistance Transposon Tn 1549 from Clostridium symbiosum to Enterococcus spp. in the Gut of Gnotobiotic Mice

Launay, A., Ballard, S. A., Johnson, P. D. R., Grayson, M. L., & Lambert, T. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.50.3.1054-1062.2006 · Cited by 113 · see citing works

Microbial biota of the human intestine: a tribute to some pioneering scientists.

Savage, D. C. (2001) · PubMed · Cited by 79 · see citing works

A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus

Hattori, M., Tsukahara, F., Furuhata, Y., et al. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.9.1802 · Cited by 70 · see citing works

Measuring genome conservation across taxa: divided strains and united kingdoms

Kunin, V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki181 · Cited by 64 · see citing works

The Butyrivibrio fibrisolvens tet (W) Gene Is Carried on the Novel Conjugative Transposon Tn B1230 , Which Contains Duplicated Nitroreductase Coding Sequences

Melville, C. M., Brunel, R., Flint, H. J., & Scott, K. P. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.11.3656-3659.2004 · Cited by 44 · see citing works

Characterization of a Tn5382-like transposon containing the vanB2 gene cluster in a Clostridium strain isolated from human faeces

Domingo, M.-C., Huletsky, A., Bernal, A., Giroux, R., Boudreau, D. K., Picard, F. J., & Bergeron, M. G. (2005) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dki029 · Cited by 43 · see citing works

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 · 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

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

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

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

Gut microbiota in health and disease

Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182 · 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

Influence of diet on the gut microbiome and implications for human health

Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., et al. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-017-1175-y · Cited by 2,599 · 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

The Placenta Harbors a Unique Microbiome

Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008599 · Cited by 2,494 · see citing works

Bifidobacteria can protect from enteropathogenic infection through production of acetate

Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., et al. (2011) · Nature · doi:10.1038/nature09646 · Cited by 2,387 · see citing works

Microbial degradation of complex carbohydrates in the gut

Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012) · Gut Microbes · doi:10.4161/gmic.19897 · Cited by 2,331 · 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

The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon

Donohoe, D. R., Garge, N., Zhang, X., Sun, W., O'Connell, T. M., Bunger, M. K., & Bultman, S. J. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.02.018 · Cited by 2,003 · see citing works

Gut feelings: the emerging biology of gut-brain communication

Mayer, E. A. (2011) · Nature Reviews Neuroscience · doi:10.1038/nrn3071 · Cited by 1,726 · see citing works

How glycan metabolism shapes the human gut microbiota

Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works

The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information

Chen, T., Yu, W.-H., Izard, J., Baranova, O. V., Lakshmanan, A., & Dewhirst, F. E. (2010) · Database · doi:10.1093/database/baq013 · Cited by 1,162 · see citing works

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117 · see citing works

Chemical transformation of xenobiotics by the human gut microbiota

Koppel, N., Maini Rekdal, V., & Balskus, E. P. (2017) · Science · doi:10.1126/science.aag2770 · Cited by 1,080 · see citing works

Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation

Hemarajata, P., & Versalovic, J. (2013) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x12459294 · Cited by 1,083 · see citing works

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

Jones, B. V., Begley, M., Hill, C., Gahan, C. G. M., & Marchesi, J. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804437105 · Cited by 1,098 · see citing works

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076 · see citing works

Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity

Leclercq, S., Matamoros, S., Cani, P. D., Neyrinck, A. M., Jamar, F., Stärkel, P., Windey, K., Tremaroli, V., Bäckhed, F., Verbeke, K., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1415174111 · Cited by 972 · see citing works

Brain-gut-microbe communication in health and disease

Grenham, S., Clarke, G., Cryan, J. F., & Dinan, T. G. (2011) · Frontiers in Physiology · doi:10.3389/fphys.2011.00094 · Cited by 952 · see citing works

Intestinal microbiota in functional bowel disorders: a Rome foundation report

Simrén, M., Barbara, G., Flint, H. J., Spiegel, B. M. R., Spiller, R. C., Vanner, S., Verdu, E. F., Whorwell, P. J., & Zoetendal, E. G. (2013) · Gut · doi:10.1136/gutjnl-2012-302167 · Cited by 939 · see citing works

Towards the human intestinal microbiota phylogenetic core

Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927 · see citing works

Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System

Postler, T. S., & Ghosh, S. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.05.008 · Cited by 876 · see citing works

<i>Escherichia coli</i> induces DNA damage in vivo and triggers genomic instability in mammalian cells

Cuevas-Ramos, G., Petit, C. R., Marcq, I., Boury, M., Oswald, E., & Nougayrède, J.-P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001261107 · Cited by 855 · see citing works

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

Greenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821 · see citing works

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

Kim, S., Covington, A., & Pamer, E. G. (2017) · Immunological Reviews · doi:10.1111/imr.12563 · Cited by 741 · see citing works

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C. C. G. M., Troost, F. J., Bork, P., Wels, M., de Vos, W. M., & Kleerebezem, M. (2012) · The ISME Journal · doi:10.1038/ismej.2011.212 · Cited by 722 · see citing works

Intestinal microbiota in human health and disease: the impact of probiotics

Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011) · Genes &amp; Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724 · see citing works

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

Zivkovic, A. M., German, J. B., Lebrilla, C. B., & Mills, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000083107 · Cited by 679 · see citing works

Interactions of gut microbiota with functional food components and nutraceuticals

Laparra, J. M., & Sanz, Y. (2010) · Pharmacological Research · doi:10.1016/j.phrs.2009.11.001 · Cited by 684 · see citing works

Antibiotics and the Gut Microbiota

Modi, S. R., Collins, J. J., & Relman, D. A. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72333 · Cited by 667 · see citing works

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

Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans

Fernandes, J., Su, W., Rahat-Rozenbloom, S., Wolever, T. M. S., & Comelli, E. M. (2014) · Nutrition &amp; Diabetes · doi:10.1038/nutd.2014.23 · Cited by 628 · see citing works

Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: a review

Duda-Chodak, A., Tarko, T., Satora, P., & Sroka, P. (2015) · European Journal of Nutrition · doi:10.1007/s00394-015-0852-y · Cited by 599 · see citing works

Regulation of the stress response by the gut microbiota: implications for psychoneuroendocrinology

Dinan, T. G., & Cryan, J. F. (2012) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2012.03.007 · Cited by 577 · see citing works

Metabolic fate of polyphenols in the human superorganism

van Duynhoven, J., Vaughan, E. E., Jacobs, D. M., A. Kemperman, R., van Velzen, E. J. J., Gross, G., Roger, L. C., Possemiers, S., Smilde, A. K., Doré, J., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000098107 · Cited by 540 · see citing works

Modulation of intestinal barrier by intestinal microbiota: Pathological and therapeutic implications

Natividad, J. M. M., & Verdu, E. F. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.10.007 · Cited by 525 · see citing works

Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria

Fu, X., Liu, Z., Zhu, C., Mou, H., & Kong, Q. (2019) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2018.1542587 · Cited by 497 · see citing works

The microbiome: a key regulator of stress and neuroinflammation

Rea, K., Dinan, T. G., & Cryan, J. F. (2016) · Neurobiology of Stress · doi:10.1016/j.ynstr.2016.03.001 · Cited by 508 · see citing works

Feeding the microbiota–gut–brain axis: Diet, microbiome, and neuropsychiatry

Sandhu, K. V., Sherwin, E., Schellekens, H., Stanton, C., Dinan, T. G., & Cryan, J. F. (2017) · Translational Research · doi:10.1016/j.trsl.2016.10.002 · Cited by 491 · see citing works

Chapter 12: Human Microbiome Analysis

Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496 · see citing works

Microbiota-gut-brain axis: Modulator of host metabolism and appetite

van de Wouw, M., Schellekens, H., Dinan, T. G., & Cryan, J. F. (2017) · The Journal of Nutrition · doi:10.3945/jn.116.240481 · Cited by 461 · see citing works

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

Rajilić‐Stojanović, M., Heilig, H. G. H. J., Molenaar, D., Kajander, K., Surakka, A., Smidt, H., & De Vos, W. M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01900.x · Cited by 484 · see citing works

Intestinal microbiota, diet and health

Power, S. E., O'Toole, P. W., Stanton, C., Ross, R. P., & Fitzgerald, G. F. (2014) · British Journal Of Nutrition · doi:10.1017/s0007114513002560 · Cited by 476 · see citing works

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides

Sela, D. A., & Mills, D. A. (2010) · Trends in Microbiology · doi:10.1016/j.tim.2010.03.008 · Cited by 468 · see citing works

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms

Alcock, J., Maley, C. C., & Aktipis, C. A. (2014) · BioEssays · doi:10.1002/bies.201400071 · Cited by 454 · see citing works

Microbial shifts in the aging mouse gut

Langille, M. G., Meehan, C. J., Koenig, J. E., Dhanani, A. S., Rose, R. A., Howlett, S. E., & Beiko, R. G. (2014) · Microbiome · doi:10.1186/s40168-014-0050-9 · Cited by 437 · 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

Mood and gut feelings

Forsythe, P., Sudo, N., Dinan, T., Taylor, V. H., & Bienenstock, J. (2010) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2009.05.058 · Cited by 429 · see citing works

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults

Tap, J., Furet, J., Bensaada, M., Philippe, C., Roth, H., Rabot, S., Lakhdari, O., Lombard, V., Henrissat, B., Corthier, G., et al. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13006 · Cited by 397 · see citing works

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., Patel, S., Cutting, M., Madden, T., Hamilton, H., et al. (2013) · The FASEB Journal · doi:10.1096/fj.12-220806 · Cited by 383 · see citing works

Functional metagenomic profiling of intestinal microbiome in extreme ageing

Rampelli, S., Candela, M., Turroni, S., Biagi, E., Collino, S., Franceschi, C., O'Toole, P. W., & Brigidi, P. (2013) · Aging · doi:10.18632/aging.100623 · Cited by 359 · see citing works

Impact of intestinal microbiota on intestinal luminal metabolome

Matsumoto, M., Kibe, R., Ooga, T., Aiba, Y., Kurihara, S., Sawaki, E., Koga, Y., & Benno, Y. (2012) · Scientific Reports · doi:10.1038/srep00233 · Cited by 334 · see citing works

The neuroendocrinology of the microbiota-gut-brain axis: a behavioural perspective

Cussotto, S., Sandhu, K. V., Dinan, T. G., & Cryan, J. F. (2018) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2018.04.002 · Cited by 326 · see citing works

High temporal and inter‐individual variation detected in the human ileal microbiota

Booijink, C. C. G. M., El‐Aidy, S., Rajilić‐Stojanović, M., Heilig, H. G. H. J., Troost, F. J., Smidt, H., Kleerebezem, M., De Vos, W. M., & Zoetendal, E. G. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02294.x · Cited by 324 · see citing works

Decreased abundance of <i> <scp>F</scp> aecalibacterium prausnitzii </i> in the gut microbiota of <scp>C</scp> rohn's disease

Fujimoto, T., Imaeda, H., Takahashi, K., Kasumi, E., Bamba, S., Fujiyama, Y., & Andoh, A. (2013) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.12073 · Cited by 304 · see citing works

Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life

Roger, L. C., Costabile, A., Holland, D. T., Hoyles, L., & McCartney, A. L. (2010) · Microbiology · doi:10.1099/mic.0.043224-0 · Cited by 291 · see citing works

Commensal microbiota modulate murine behaviors in a strictly contamination-free environment confirmed by culture-based methods

Nishino, R., Mikami, K., Takahashi, H., Tomonaga, S., Furuse, M., Hiramoto, T., Aiba, Y., Koga, Y., & Sudo, N. (2013) · Neurogastroenterology &amp; Motility · doi:10.1111/nmo.12110 · Cited by 266 · see citing works

Broad Conservation of Milk Utilization Genes in<i>Bifidobacterium longum</i>subsp.<i>infantis</i>as Revealed by Comparative Genomic Hybridization

LoCascio, R. G., Desai, P., Sela, D. A., Weimer, B., & Mills, D. A. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00675-10 · Cited by 229 · see citing works

Intestinal Microbiota in Healthy U.S. Young Children and Adults—A High Throughput Microarray Analysis

Ringel-Kulka, T., Cheng, J., Ringel, Y., Salojärvi, J., Carroll, I., Palva, A., de Vos, W. M., & Satokari, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064315 · Cited by 230 · see citing works

The human gut microbiome in health: Establishment and resilience of microbiota over a lifetime

Greenhalgh, K., Meyer, K. M., Aagaard, K. M., & Wilmes, P. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13318 · Cited by 218 · see citing works

Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease

Codagnone, M. G., Spichak, S., O’Mahony, S. M., O’Leary, O. F., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2019) · Biological Psychiatry · doi:10.1016/j.biopsych.2018.06.014 · Cited by 198 · see citing works

Dietary Factors: Major Regulators of the Gut's Microbiota

Moschen, A. R., Wieser, V., & Tilg, H. (2012) · Gut and Liver · doi:10.5009/gnl.2012.6.4.411 · Cited by 173 · see citing works

Comparison of the Complete Genome Sequences of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> DSM 10140 and Bl-04

Barrangou, R., Briczinski, E. P., Traeger, L. L., Loquasto, J. R., Richards, M., Horvath, P., Coûté-Monvoisin, A.-C., Leyer, G., Rendulic, S., Steele, J. L., et al. (2009) · Journal of Bacteriology · doi:10.1128/jb.00155-09 · Cited by 150 · see citing works

Microbiomic analysis of the bifidobacterial population in the human distal gut

Turroni, F., Marchesi, J. R., Foroni, E., Gueimonde, M., Shanahan, F., Margolles, A., van Sinderen, D., & Ventura, M. (2009) · The ISME Journal · doi:10.1038/ismej.2009.19 · Cited by 137 · see citing works

The human microbiome: A hot spot of microbial horizontal gene transfer

Liu, L., Chen, X., Skogerbø, G., Zhang, P., Chen, R., He, S., & Huang, D.-W. (2012) · Genomics · doi:10.1016/j.ygeno.2012.07.012 · Cited by 131 · see citing works

Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates

Ling, Z., Liu, X., Luo, Y., Yuan, L., Nelson, K. E., Wang, Y., Xiang, C., & Li, L. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-390 · Cited by 127 · see citing works

The connection between microbiome and schizophrenia

Golofast, B., & Vales, K. (2020) · Neuroscience &amp; Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.12.011 · Cited by 92 · see citing works

Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides

Ziemer, C. J. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03016-13 · Cited by 82 · see citing works

Gut–Brain Axis in Regulation of Blood Pressure

Yang, T., & Zubcevic, J. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00845 · Cited by 74 · see citing works

The abundance of antibiotic resistance genes in human guts has correlation to the consumption of antibiotics in animal

Hu, Y., Yang, X., Lu, N., & Zhu, B. (2014) · Gut Microbes · doi:10.4161/gmic.27916 · Cited by 70 · see citing works

Bacterial biofilms associated with food particles in the human large bowel

Van Wey, A. S., Cookson, A. L., Roy, N. C., McNabb, W. C., Soboleva, T. K., & Shorten, P. R. (2011) · Molecular Nutrition &amp; Food Research · doi:10.1002/mnfr.201000589 · Cited by 31 · see citing works

Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Golob, M., Zdovc, I., & Bogovič Matijašić, B. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2127438 · Cited by 21 · see citing works

Dietary Protein and Colonic Microbiota

Boudry, G., Le Huërou-Luron, I., & Michel, C. (2016) · The Molecular Nutrition of Amino Acids and Proteins · doi:10.1016/b978-0-12-802167-5.00015-3 · Cited by 5 · see citing works

The Gastrointestinal Tract and Its Microflora

Aimutis, W. R., & Polzin, K. (2010) · Nondigestible Carbohydrates and Digestive Health · doi:10.1002/9780470958186.ch2 · Cited by 1 · see citing works

Vitamins for the Gut Microbiome

Steinert, R. E., Lee, Y. K., & Sybesma, W. (2019) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2019.11.005 · Cited by 115 · see citing works

Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

Colin, P.-Y., Kintses, B., Gielen, F., Miton, C. M., Fischer, G. W., Mohamed, M. F., Hyvönen, M., Morgavi, D., Janssen, D. B., & Hollfelder, F. (2015) · Nature Communications · doi:10.1038/ncomms10008 · Cited by 276 · see citing works

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes

Hernández, M., Neufeld, J. D., & Dumont, M. G. (2017) · Springer eBooks · doi:10.1007/978-3-319-61510-3_8 · Cited by 6 · see citing works

Microbiome-based stratification to guide dietary interventions to improve human health

Liu, Z., de Vries, B., Gerritsen, J., Smidt, H., & Zoetendal, E. G. (2020) · Nutrition Research · doi:10.1016/j.nutres.2020.07.004 · Cited by 42 · see citing works

A Microbiome Restoration Strategy Modulates the Gut Microbiome and Metabolic Markers in Healthy Adults

Li, F. (2021) · doi:10.52843/cassyni.wk4b29