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

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

Molecular cloning: A laboratory manual

Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works

Measurement of Diversity

Simpson, E. (1949) · Nature · doi:10.1038/163688a0 · Cited by 14,328 · see citing works

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.695-700.1993 · Cited by 11,379 · 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

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

ARB: a software environment for sequence data

Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,649 · 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

Multivariate Analysis of Ecological Data using CANOCO

Lepš, J., & Šmilauer, P. (2003) · Cambridge University Press eBooks · doi:10.1017/cbo9780511615146 · Cited by 4,546 · see citing works

MICROBIAL STRESS-RESPONSE PHYSIOLOGY AND ITS IMPLICATIONS FOR ECOSYSTEM FUNCTION

Schimel, J. P., Balser, T. C., & Wallenstein, M. D. (2007) · Ecology · doi:10.1890/06-0219 · Cited by 3,055 · see citing works

Review and re-analysis of domain-specific 16S primers

Baker, G. C., Smith, J. J., & Cowan, D. A. (2003) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2003.08.009 · Cited by 1,867 · see citing works

Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria

Zoetendal, E. G., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3854-3859.1998 · Cited by 1,360 · see citing works

Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis

Nübel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R., Ludwig, W., & Backhaus, H. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.19.5636-5643.1996 · Cited by 1,356 · see citing works

Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays

Suzuki, M. T., Taylor, L. T., & DeLong, E. F. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.11.4605-4614.2000 · Cited by 1,194 · see citing works

Rapid silver staining and recovery of PCR products separated on polyacrylamide gels.

Cj, S., Neto, E. D., & Aj, S. (1994) · PubMed · Cited by 1,179 · see citing works

A Simplified Monte Carlo Significance Test Procedure

Hope, A. C. A. (1968) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.2517-6161.1968.tb00759.x · Cited by 1,092 · 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

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

Claesson, M. J., O’Sullivan, Ó., Wang, Q., Nikkilä, J., Marchesi, J. R., Smidt, H., de Vos, W. M., Ross, R. P., & O’Toole, P. W. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006669 · Cited by 899 · see citing works

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869 · see citing works

Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA

Heilig, H. G. H. J., Zoetendal, E. G., Vaughan, E. E., Marteau, P. R., Akkermans, A. D. L., & de Vos, W. M. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.1.114-123.2002 · Cited by 673 · see citing works

High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota

Zoetendal, E. G., Rajilić-Stojanović, M. D., & de Vos, W. M. (2008) · Gut · doi:10.1136/gut.2007.133603 · Cited by 672 · see citing works

Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Human Feces

Matsuki, T., Watanabe, K., Fujimoto, J., Takada, T., & Tanaka, R. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.12.7220-7228.2004 · Cited by 656 · see citing works

Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum

Baumgart, M., Dogan, B., Rishniw, M., Weitzman, G., Bosworth, B. P., Yantiss, R. K., Orsi, R. H., Wiedmann, M., McDonough, P. L., Kim, S. G., et al. (2007) · The ISME Journal · doi:10.1038/ismej.2007.52 · Cited by 630 · see citing works

Diversity of the human gastrointestinal tract microbiota revisited

Rajilić‐Stojanović, M., Smidt, H., & De Vos, W. M. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01369.x · Cited by 559 · see citing works

The Host Genotype Affects the Bacterial Community in the Human Gastronintestinal Tract

Zoetendal, A. D. L. A. E. G. (2001) · Microbial Ecology in Health and Disease · doi:10.1080/089106001750462669 · Cited by 558 · see citing works

Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Fromin, N., Hamelin, J., Tarnawski, S., Roesti, D., Jourdain-Miserez, K., Forestier, N., Teyssier-Cuvelle, S., Gillet, F., Aragno, M., & Rossi, P. (2002) · Environmental Microbiology · doi:10.1046/j.1462-2920.2002.00358.x · Cited by 551 · see citing works

Assembly of the human intestinal microbiota

Dethlefsen, L., Eckburg, P. B., Bik, E. M., & Relman, D. A. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.06.013 · Cited by 509 · 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

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

Dicksved, J., Halfvarson, J., Rosenquist, M., Järnerot, G., Tysk, C., Apajalahti, J., Engstrand, L. G., & Jansson, J. K. (2008) · The ISME Journal · doi:10.1038/ismej.2008.37 · Cited by 459 · see citing works

Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohnʼs disease

Willing, B., Halfvarson, J., Dicksved, J., Rosenquist, M., Järnerot, G., Engstrand, L., Tysk, C., & Jansson, J. K. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20783 · Cited by 455 · see citing works

Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir

Šimek, K., Horňák, K., Jezbera, J., Nedoma, J., Vrba, J., Straškrabová, V., Macek, M., Dolan, J. R., & Hahn, M. W. (2006) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01053.x · Cited by 439 · see citing works

Quantitative Analysis of Diverse Lactobacillus Species Present in Advanced Dental Caries

Byun, R., Nadkarni, M. A., Chhour, K.-L., Martin, F. E., Jacques, N. A., & Hunter, N. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.7.3128-3136.2004 · Cited by 382 · see citing works

Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes

Wang, M., Ahrné, S., Jeppsson, B. W., & Molin, G. (2005) · FEMS Microbiology Ecology · doi:10.1016/j.femsec.2005.03.012 · Cited by 373 · see citing works

Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism

Hayashi, H., Takahashi, R., Nishi, T., Sakamoto, M., & Benno, Y. (2005) · Journal of Medical Microbiology · doi:10.1099/jmm.0.45935-0 · Cited by 360 · see citing works

Human gut microbiome adopts an alternative state following small bowel transplantation

Hartman, A., Lough, D., Barupal, D. K., Fiehn, O., Fishbein, T., ZASLOFF, M. A., & Eisen, J. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904847106 · Cited by 348 · see citing works

Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences

Kane, M. D., Poulsen, L. K., & Stahl, D. A. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.682-686.1993 · Cited by 323 · see citing works

Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease

Neut, C., Bulois, P., Desreumaux, P., Membré, J., Lederman, E., Gambiez, L. P., Cortot, A., Quandalle, P. A., Kruiningen, H. J. V., & Colombel, J. (2002) · The American Journal of Gastroenterology · doi:10.1111/j.1572-0241.2002.05613.x · Cited by 274 · see citing works

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

Wang, X., Heazlewood, S. P., Krause, D. O., & Florin, T. H. (2003) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.2003.02005.x · Cited by 235 · see citing works

Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples

Ahmed, S., Macfarlane, G. T., Fite, A., McBain, A. J., Gilbert, P., & Macfarlane, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01143-07 · Cited by 227 · see citing works

Isolation of DNA from bacterial samples of the human gastrointestinal tract

Zoetendal, E. G., Heilig, H. G. H. J., Klaassens, E. S., Booijink, C. C., Kleerebezem, M., Smidt, H., & de Vos, W. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.142 · Cited by 224 · see citing works

Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers

Vanhoutte, T., Huys, G. R. B., Brandt, E. D., & Swings, J. (2004) · FEMS Microbiology Ecology · doi:10.1016/j.femsec.2004.03.001 · Cited by 215 · see citing works

Molecular Analysis of Fecal Microbiota in Elderly Individuals Using 16S rDNA Library and T‐RFLP

Hayashi, H., Sakamoto, M., Kitahara, M., & Benno, Y. (2003) · Microbiology and Immunology · doi:10.1111/j.1348-0421.2003.tb03418.x · Cited by 189 · see citing works

The Pearson product‐moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms

Häne, B. G., Jäger, K., & Drexler, H. G. (1993) · Electrophoresis · doi:10.1002/elps.11501401154 · Cited by 189 · see citing works

Studies of Intestinal Microflora

Gorbach, S. L., Nahas, L., Weinstein, L., Levitan, R., & Patterson, J. F. (1967) · Gastroenterology · doi:10.1016/s0016-5085(19)34124-1 · Cited by 130 · see citing works

Intra-individual diversity and similarity of salivary and faecal microbiota

Maukonen, J., Mättö, J., Suihko, M., & Saarela, M. (2008) · Journal of Medical Microbiology · doi:10.1099/jmm.0.47352-0 · Cited by 110 · see citing works

The microflora of the human ileum and intrabdominal colon: results of direct needle aspiration at surgery and evaluation of the technique.

Bentley, D. W., Nichols, R. L., Condon, R. E., & Gorbach, S. L. (1972) · PubMed · Cited by 61 · see citing works

Studies on the Anaerobic Micrococci

Foubert, E. L., & Douglas, H. C. (1948) · Journal of Bacteriology · doi:10.1128/jb.56.1.35-36.1948 · Cited by 57 · see citing works

Diversity of the human gastrointestinal microbiota : novel perspectives from high throughput analyses

Rajilić-Stojanović, M. D. (2007) · doi:10.18174/2282 · Cited by 47 · see citing works

Streptococcus henryi sp. nov. and Streptococcus caballi sp. nov., isolated from the hindgut of horses with oligofructose-induced laminitis

Milinovich, G. J., Burrell, P. C., Pollitt, C. C., Bouvet, A., & Trott, D. J. (2008) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.65063-0 · Cited by 37 · see citing works

The ileostomy model for the study of carbohydrate digestion and carbohydrate effects on sterol excretion in man.

Andersson, H. (1992) · PubMed · Cited by 26 · see citing works

Changes in bacterial composition and enzymatic activity in ileostomy and ileal reservoir during intermittent occlusion: a study using dogs

Embden, J. G. H. R.-V., Schouten, W. R., Lieshout, L. M. C. V., & Auwerda, H. (1992) · Applied and Environmental Microbiology · doi:10.1128/aem.58.1.111-118.1992 · Cited by 18 · see citing works

Food, GI-tract Functionality and Human Health Cluster: PROEUHEALTH

Mattila, T., Blaut, M., Daly, C., Vuyst, L. D., Dore, J. M., Gibson, G. R., Goossens, H., Knorr, D., Lucas, J., Lähteenmäki, L., et al. (2002) · Microbial Ecology in Health and Disease · doi:10.1080/08910600260081702 · Cited by 16 · see citing works

Gut microbiome and health: mechanistic insights

de Vos, W. M., Tilg, H., Van Hul, M., & Cani, P. D. (2022) · Gut · doi:10.1136/gutjnl-2021-326789 · Cited by 2,388 · 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

The composition of the gut microbiota throughout life, with an emphasis on early life

Rodríguez, J. M., Murphy, K., Stanton, C., Ross, R. P., Kober, O. I., Juge, N., Avershina, E., Rudi, K., Narbad, A., Jenmalm, M. C., et al. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26050 · Cited by 1,411 · see citing works

The first 1000 cultured species of the human gastrointestinal microbiota

Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182 · see citing works

Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome

Rajilić–Stojanović, M., Biagi, E., Heilig, H. G. H. J., Kajander, K., Kekkonen, R. A., Tims, S., & de Vos, W. M. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.043 · Cited by 1,041 · 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

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

The human gut microbiome: ecology and recent evolutionary changes

Walter, J., & Ley, R. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102830 · Cited by 720 · 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 & Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724 · see citing works

Microbes inside—from diversity to function: the case of Akkermansia

Belzer, C., & de Vos, W. M. (2012) · The ISME Journal · doi:10.1038/ismej.2012.6 · Cited by 728 · see citing works

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

Bron, P. A., van Baarlen, P., & Kleerebezem, M. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2690 · Cited by 690 · see citing works

The Gut Microbiome and the Brain

Galland, L. (2014) · Journal of Medicinal Food · doi:10.1089/jmf.2014.7000 · Cited by 648 · see citing works

Fate, activity, and impact of ingested bacteria within the human gut microbiota

Derrien, M., & van Hylckama Vlieg, J. E. T. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.03.002 · Cited by 605 · see citing works

Normalization of host intestinal mucus layers requires long-term microbial colonization

Johansson, M. E. V., Jakobsson, H. E., Holmén-Larsson, J., Schütte, A., Ermund, A., Rodríguez-Piñeiro, A. M., Arike, L., Wising, C., Svensson, F., Bäckhed, F., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.007 · Cited by 549 · see citing works

Relevance and challenges in modeling human gastric and small intestinal digestion

Guerra, A., Etienne‐Mesmin, L., Livrelli, V., Denis, S., Blanquet‐Diot, S., & Alric, M. (2012) · Trends in biotechnology · doi:10.1016/j.tibtech.2012.08.001 · Cited by 569 · see citing works

Advances in Oral Drug Delivery for Regional Targeting in the Gastrointestinal Tract - Influence of Physiological, Pathophysiological and Pharmaceutical Factors

Hua, S. (2020) · Frontiers in Pharmacology · doi:10.3389/fphar.2020.00524 · Cited by 565 · see citing works

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh

Sarker, S. A., Sultana, S., Reuteler, G., Moine, D., Descombes, P., Charton, F., Bourdin, G., McCallin, S. E., Ngom‐Bru, C., Neville, T., et al. (2016) · EBioMedicine · doi:10.1016/j.ebiom.2015.12.023 · Cited by 543 · see citing works

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

Aggarwal, N., Kitano, S., Puah, G. R. Y., Kittelmann, S., Hwang, I. Y., & Chang, M. W. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00431 · Cited by 569 · see citing works

Profiling the human intestinal environment under physiological conditions

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature · doi:10.1038/s41586-023-05989-7 · Cited by 484 · see citing works

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Hildebrand, F., Nguyen, T. L. A., Brinkman, B. M. N., Yunta, R. G., Cauwe, B., Vandenabeele, P., Liston, A., & Raes, J. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r4 · Cited by 465 · see citing works

Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices

Tang, Q., Jin, G., Wang, G., Liu, T., Liu, X., Wang, B., & Cao, H. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00151 · Cited by 461 · see citing works

Bacterial Community Mapping of the Mouse Gastrointestinal Tract

Gu, S., Chen, D., Zhang, J., Lv, X., Wang, K., Duan, L.-P., Nie, Y., & Wu, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074957 · Cited by 439 · see citing works

The role of the intestinal microbiota in type 1 diabetes mellitus

Knip, M., & Siljander, H. (2016) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2015.218 · Cited by 434 · see citing works

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Looft, T. P., Allen, H. K., Cantarel, B. L., Levine, U. Y., Bayles, D. O., Alt, D. P., Henrissat, B., & Stanton, T. B. (2014) · The ISME Journal · doi:10.1038/ismej.2014.12 · Cited by 374 · see citing works

Microbial nutrient niches in the gut

Pereira, F. C., & Berry, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13659 · Cited by 365 · see citing works

The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions

Kastl, A., Terry, N. A., Wu, G. D., & Albenberg, L. G. (2019) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2019.07.006 · Cited by 359 · see citing works

The therapeutic potential of manipulating gut microbiota in obesity and type 2 diabetes mellitus

Kootte, R. S., Vrieze, A., Holleman, F., Dallinga‐Thie, G. M., Zoetendal, E. G., de Vos, W. M., Groen, A. K., Hoekstra, J. B. L., Stroes, E. S. G., & Nieuwdorp, M. (2011) · Diabetes Obesity and Metabolism · doi:10.1111/j.1463-1326.2011.01483.x · Cited by 348 · see citing works

The impact of the Fungus-Host-Microbiota interplay uponCandida albicansinfections: current knowledge and new perspectives

d’Enfert, C., Kaune, A.-K., Alaban, L. R., Chakraborty, S., Cole, N. L., Delavy, M., Kosmala, D., Marsaux, B., Fróis-Martins, R., Morelli, M., et al. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa060 · Cited by 367 · see citing works

Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective

Turroni, F., Ventura, M., Buttó, L. F., Duranti, S., O’Toole, P. W., Motherway, M. O., & van Sinderen, D. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1318-0 · Cited by 336 · see citing works

Defining Dysbiosis for a Cluster of Chronic Diseases

Wilkins, L. J., Monga, M., & Miller, A. W. (2019) · Scientific Reports · doi:10.1038/s41598-019-49452-y · Cited by 328 · see citing works

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

Saffouri, G. B., Shields‐Cutler, R. R., Chen, J., Yang, Y., Lekatz, H. R., Hale, V. L., Cho, J. M., Battaglioli, E. J., Bhattarai, Y., Thompson, K. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09964-7 · Cited by 308 · see citing works

Current in vitro digestion systems for understanding food digestion in human upper gastrointestinal tract

Li, C., Yu, W.-W., Wu, P., & Chen, X.-D. (2020) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2019.12.015 · Cited by 264 · see citing works

Effects of Antibiotics on Human Microbiota and Subsequent Disease

Keeney, K. M., Yurist‐Doutsch, S., Arrieta, M., & Finlay, B. B. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091313-103456 · Cited by 296 · see citing works

Long‐term monitoring of the human intestinal microbiota composition

Rajilić-Stojanović, M. D., Heilig, H. G. H. J., Tims, S., Zoetendal, E. G., & de Vos, W. M. (2012) · Environmental Microbiology · doi:10.1111/1462-2920.12023 · Cited by 286 · see citing works

Experimental models of the gut microbiome

Venema, K., & den Abbeele, P. V. (2013) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2013.03.002 · Cited by 248 · see citing works

The small intestine microbiota, nutritional modulation and relevance for health

El Aidy, S., van den Bogert, B., & Kleerebezem, M. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.09.005 · Cited by 244 · see citing works

Interactions in the microbiome: communities of organisms and communities of genes

Boon, E., Meehan, C. J., Whidden, C., Wong, D. H.-J., Langille, M. G. I., & Beiko, R. G. (2013) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12035 · Cited by 227 · see citing works

Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome

Rigsbee, L., Agans, R., Shankar, V., Kenche, H., Khamis, H. J., Michail, S., & Paliy, O. (2012) · American Journal of Gastroenterology · doi:10.1038/ajg.2012.287 · Cited by 207 · see citing works

Functional genomics of lactic acid bacteria: from food to health

Douillard, F. P., & de Vos, W. M. (2014) · Microbial Cell Factories · doi:10.1186/1475-2859-13-s1-s8 · Cited by 209 · see citing works

Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance

Willems, R. J. L., Hanage, W. P., Bessen, D. E., & Feil, E. J. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00284.x · Cited by 203 · see citing works

Altered Duodenal Microbiota Composition in Celiac Disease Patients Suffering From Persistent Symptoms on a Long-Term Gluten-Free Diet

Wacklin, P., Laurikka, P., Lindfors, K., Collin, P., Salmi, T. T., Lähdeaho, M., Saavalainen, P., Mäki, M., Mättö, J., Kurppa, K., et al. (2014) · The American Journal of Gastroenterology · doi:10.1038/ajg.2014.355 · Cited by 202 · see citing works

Gut metabotypes govern health effects of dietary polyphenols

Bolca, S., de Wiele, T. V., & Possemiers, S. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.09.009 · Cited by 201 · see citing works

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

Kolmeder, C. A., de Been, M., Nikkilä, J., Ritamo, I., Mättö, J., Valmu, L., Salojärvi, J., Palva, A., Salonen, A., & de Vos, W. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029913 · Cited by 200 · see citing works

Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective

George, F., Daniel, C., Thomas, M., Singer, E., Guilbaud, A., Tessier, F. J., Revol-Junelles, A.-M., Borges, F., & Foligné, B. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02899 · Cited by 198 · see citing works

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

Li, D., Chen, H., Mao, B., Yang, Q., Zhao, J., Gu, Z., Zhang, H., Chen, Y. Q., & Chen, W. (2017) · Scientific Reports · doi:10.1038/srep45840 · Cited by 184 · see citing works

Systematic review: gastric microbiota in health and disease

Rajilić-Stojanović, M. D., Figueiredo, C., Smet, A., Hansen, R., Kupčinskas, J., Rokkas, T., Andersen, L. P., Machado, J. C., Ianiro, G., Gasbarrini, A., et al. (2020) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.15650 · Cited by 176 · see citing works

Diversity of human small intestinal Streptococcus and Veillonella populations

van den Bogert, B., Erkuş, O., Boekhorst, J., de Goffau, M. C., Smid, E. J., Zoetendal, E. G., & Kleerebezem, M. (2013) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12127 · Cited by 172 · see citing works

Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples

van den Bogert, B., de Vos, W. M., Zoetendal, E. G., & Kleerebezem, M. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02477-10 · Cited by 174 · see citing works

Identification of a Core Bacterial Community within the Large Intestine of the Horse

Dougal, K., de la Fuente, G., Harris, P. A., Girdwood, S. E., Pinloche, E., & Newbold, C. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077660 · Cited by 165 · see citing works

Characterization of the Ileal Microbiota in Rejecting and Nonrejecting Recipients of Small Bowel Transplants

Oh, P. L., Martínez, I., Sun, Y., Walter, J., Peterson, D. A., & Mercer, D. F. F. (2011) · American Journal of Transplantation · doi:10.1111/j.1600-6143.2011.03860.x · Cited by 164 · see citing works

Cross-Domain and Viral Interactions in the Microbiome

Rowan-Nash, A. D., Korry, B. J., Mylonakis, E. E., & Belenky, P. A. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-18 · Cited by 172 · see citing works

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota

van den Bogert, B., Meijerink, M., Zoetendal, E. G., Wells, J. M., & Kleerebezem, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114277 · Cited by 159 · see citing works

The itinerary of Streptococcus gallolyticus infection in patients with colonic malignant disease

Boleij, A., & Tjalsma, H. (2013) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(13)70107-5 · Cited by 158 · see citing works

Impact of the gut microbiota, prebiotics, and probiotics on human health and disease

Lai, H.-C., Young, J., Lin, C.-S., Chang, C.-J., Lu, C.-C., Martel, J., Ojcius, D., & Ko, Y.-F. (2014) · Biomedical Journal · doi:10.4103/2319-4170.138314 · Cited by 153 · see citing works

The Gut Microbiota and Ageing

Maynard, C., & Weinkove, D. (2018) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-981-13-2835-0_12 · Cited by 149 · see citing works

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

Leimena, M. M., Ramiro‐Garcia, J., Davids, M., van den Bogert, B., Smidt, H., Smid, E. J., Boekhorst, J., Zoetendal, E. G., Schaap, P. J., & Kleerebezem, M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-530 · Cited by 143 · see citing works

Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing.

Dougal, K., de la Fuente, G., Harris, P. A., Girdwood, S. E., Pinloche, E., Geor, R. J., Nielsen, B. D., Schott, H. C., Elzinga, S., & Newbold, C. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087424 · Cited by 165 · see citing works

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

Leite, G. G. S., Weitsman, S. R., Parodi, G., Celly, S., Sedighi, R., Sanchez, M., Morales, W., Villanueva-Millán, M. J., Barlow, G. M., Mathur, R., et al. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06173-x · Cited by 138 · see citing works

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use

Korpela, K., Zijlmans, M. A. C., Kuitunen, M., Kukkonen, A. K., Savilahti, E., Salonen, A., de Weerth, C., & de Vos, W. M. (2017) · Microbiome · doi:10.1186/s40168-017-0245-y · Cited by 143 · see citing works

Primary Cell-Derived Intestinal Models: Recapitulating Physiology

Dutton, J. S., Hinman, S. S., Kim, R., Wang, Y., & Allbritton, N. L. (2018) · Trends in biotechnology · doi:10.1016/j.tibtech.2018.12.001 · Cited by 131 · see citing works

The Skin and Intestinal Microbiota and Their Specific Innate Immune Systems

Coates, M., Lee, M. J., Norton, D., & MacLeod, A. S. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02950 · Cited by 134 · see citing works

Discrimination of in vitro and in vivo digestion products of meat proteins from pork, beef, chicken, and fish

Wen, S., Zhou, G., Song, S., Xu, X., Voglmeir, J., Liu, L., Zhao, F., Li, M., Li, L., Yu, X., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500179 · Cited by 128 · 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

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis / Streptococcus equinus complex (SBSEC)

Jans, C., Meile, L., Lacroix, C., & Stevens, M. J. A. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.09.017 · Cited by 123 · see citing works

The Gut Microbiota of Wild Mice

Weldon, L., Abolins, S., Lenzi, L., Bourne, C., Riley, E. M., & Viney, M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134643 · Cited by 120 · see citing works

Current Advances in Chitosan Nanoparticles Based Oral Drug Delivery for Colorectal Cancer Treatment

Choukaife, H., Seyam, S., Alallam, B., Doolaanea, A. A., & Alfatama, M. (2022) · International Journal of Nanomedicine · doi:10.2147/ijn.s375229 · Cited by 122 · see citing works

Gut Microbiota as a Prospective Therapeutic Target for Curcumin: A Review of Mutual Influence

Zam, W. (2018) · Journal of Nutrition and Metabolism · doi:10.1155/2018/1367984 · Cited by 117 · see citing works

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

Shankar, V., Hamilton, M. J., Khoruts, A., Kilburn, A., Unno, T., Paliy, O., & Sadowsky, M. J. (2014) · Microbiome · doi:10.1186/2049-2618-2-13 · Cited by 106 · see citing works

Use of Sourdough in Low FODMAP Baking

Loponen, J., & Gänzle, M. G. (2018) · Foods · doi:10.3390/foods7070096 · Cited by 111 · see citing works

In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls

Isenring, J., Bircher, L., Geirnaert, A., & Lacroix, C. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2022.15 · Cited by 100 · see citing works

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans

Seekatz, A. M., Schnizlein, M. K., Koenigsknecht, M. J., Baker, J. R., Hasler, W. L., Bleske, B. E., Young, V. B., & Sun, D. (2019) · mSphere · doi:10.1128/msphere.00126-19 · Cited by 98 · see citing works

Genomics of Streptococcus salivarius , a major human commensal

Delorme, C., Abraham, A., Renault, P., & Guédon, É. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.10.001 · Cited by 97 · see citing works

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Maga, E. A., Desai, P., Weimer, B. C., Dao, N., Kültz, D., & Murray, J. D. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.00956-12 · Cited by 97 · see citing works

The microbiome: Composition and locations

Kennedy, M. S., & Chang, E. B. (2020) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2020.08.013 · Cited by 100 · see citing works

Characterization of the Gastrointestinal Microbiota in Health and Inflammatory Bowel Disease

Cruz, P. P. D., Prideaux, L., Wagner, J., Ng, S. C., McSweeney, C. S., Kirkwood, C. D., Morrison, M., & Kamm, M. A. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21751 · Cited by 95 · see citing works

Small intestinal bacterial overgrowth

Quigley, E. M. M. (2014) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000040 · Cited by 96 · see citing works

The emerging role of the small intestinal microbiota in human health and disease

Ruigrok, R. A. A. A., Weersma, R. K., & Vila, A. V. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2201155 · Cited by 96 · see citing works

Control of Competence for DNA Transformation in Streptococcus suis by Genetically Transferable Pherotypes

Zaccaria, E., van Baarlen, P., de Greeff, A., Morrison, D. A., Smith, H. E., & Wells, J. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099394 · Cited by 92 · see citing works

Patterns and Processes in Parasite Co-Infection

Viney, M., & Graham, A. L. (2013) · Advances in Parasitology/Advances in parasitology · doi:10.1016/b978-0-12-407706-5.00005-8 · Cited by 91 · see citing works

Species Level Description of the Human Ileal Bacterial Microbiota

Villmones, H. C., Haug, E. S., Ulvestad, E., Grude, N., Stenstad, T., Halland, A., & Kommedal, Ø. (2018) · Scientific Reports · doi:10.1038/s41598-018-23198-5 · Cited by 91 · see citing works

Heterogeneity across the murine small and large intestine

Bowcutt, R. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i41.15216 · Cited by 89 · see citing works

Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora

Cui, Z., Huntley, R. B., Zeng, Q., & Steven, B. T. (2020) · The ISME Journal · doi:10.1038/s41396-020-00784-y · Cited by 84 · see citing works

Jejunum: The understudied meeting place of dietary lipids and the microbiota

Lema, I., Araújo, J. R., Rolhion, N., & Demignot, S. (2020) · Biochimie · doi:10.1016/j.biochi.2020.09.007 · Cited by 86 · see citing works

The human gut microbiome: are we our enterotypes?

Siezen, R. J., & Kleerebezem, M. (2011) · Microbial Biotechnology · doi:10.1111/j.1751-7915.2011.00290.x · Cited by 85 · see citing works

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls

Dlugosz, A., Winckler, B., Lundin, E., Zakikhany, K., Sandström, G., Ye, W., Engstrand, L. G., & Lindberg, G. (2015) · Scientific Reports · doi:10.1038/srep08508 · Cited by 82 · see citing works

Bifidobacterium breve UCC2003 surface exopolysaccharide production is a beneficial trait mediating commensal-host interaction through immune modulation and pathogen protection

Fanning, S., Hall, L. J., & van Sinderen, D. (2012) · Gut Microbes · doi:10.4161/gmic.20630 · Cited by 81 · see citing works

Prevention of loperamide induced constipation in mice by KGM and the mechanisms of different gastrointestinal tract microbiota regulation

Zhang, Q., Zhong, D., Sun, R., Zhang, Y., Pegg, R. B., & Zhong, G. (2020) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2020.117418 · Cited by 83 · see citing works

Cell surface-associated compounds of probiotic lactobacilli sustain the strain-specificity dogma

Bron, P. A., Tomita, S., Mercenier, A., & Kleerebezem, M. (2013) · Current Opinion in Microbiology · doi:10.1016/j.mib.2013.06.001 · Cited by 80 · see citing works

Biological factors controlling starch digestibility in human digestive system

Li, C., Hu, Y., Li, S., Yi, X., Shao, S., Yu, W., & Li, E. (2022) · Food Science and Human Wellness · doi:10.1016/j.fshw.2022.07.037 · Cited by 79 · see citing works

Comparison of the Distal Gut Microbiota from People and Animals in Africa

Ellis, R. J., Bruce, K. D., Jenkins, C., Stothard, J. R., Ajarova, L., Mugisha, L., & Viney, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054783 · Cited by 76 · see citing works

Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface

dos Santos, V. A. P. M., Müller, M. M., & de Vos, W. M. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.08.003 · Cited by 79 · see citing works

Unraveling the Role of the Human Gut Microbiome in Health and Diseases

Khalil, M., Ciaula, A. D., Mahdi, L., Jaber, N., Palo, D. M. D., Graziani, A., Baffy, G., & Portincasa, P. (2024) · Microorganisms · doi:10.3390/microorganisms12112333 · Cited by 98 · see citing works

Therapeutic strategies for functional dyspepsia and irritable bowel syndrome based on pathophysiology

Talley, N. J., Holtmann, G., & Walker, M. M. (2015) · Journal of Gastroenterology · doi:10.1007/s00535-015-1076-x · Cited by 74 · see citing works

Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

van den Bogert, B., Boekhorst, J., Herrmann, R., Smid, E. J., Zoetendal, E. G., & Kleerebezem, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083418 · Cited by 74 · see citing works

Impact of protein on the composition and metabolism of the human gut microbiota and health

Duncan, S. H., Iyer, A. B., & Russell, W. R. (2020) · Proceedings of The Nutrition Society · doi:10.1017/s0029665120008022 · Cited by 69 · see citing works

Probiotics and gut health: linking gut homeostasis and poultry productivity

Shini, S., & Bryden, W. L. (2021) · Animal Production Science · doi:10.1071/an20701 · Cited by 68 · see citing works

The small intestine: dining table of host–microbiota meetings

Delbaere, K., Roegiers, I. H., Bron, A., Durif, C., de Wiele, T. V., Blanquet‐Diot, S., & Marinelli, L. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad022 · Cited by 69 · see citing works

Determination of protein and amino acid digestibility in foods including implications of gut microbial amino acid synthesis

Fuller, M. F. (2012) · British Journal Of Nutrition · doi:10.1017/s0007114512002279 · Cited by 68 · see citing works

Early life establishment of site-specific microbial communities in the gut

Romano-Keeler, J., Moore, D. J., Wang, C., Brucker, R. M., Fonnesbeck, C., Slaughter, J. C., Li, H., Curran, D. P., Meng, S., Correa, H., et al. (2014) · Gut Microbes · doi:10.4161/gmic.28442 · Cited by 66 · see citing works

Molecular Mechanisms of Lacticaseibacillus rhamnosus, LGG® Probiotic Function

Leser, T. D., & Baker, A. (2024) · Microorganisms · doi:10.3390/microorganisms12040794 · Cited by 65 · see citing works

Analysis of diversity and function of the human small intestinal microbiota

Booijink, C. C. (2009) · doi:10.18174/4065 · Cited by 17 · see citing works

Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

Stolaki, M., Minekus, M., Venema, K., Lahti, L., Smid, E. J., Kleerebezem, M., & Zoetendal, E. G. (2019) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiz096 · Cited by 35 · see citing works

Plasticity of the adult human small intestinal stoma microbiota

Yılmaz, B., Fuhrer, T., Morgenthaler, D., Krupka, N., Wang, D., Spari, D., Candinas, D., Misselwitz, B., Beldi, G., Sauer, U., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.10.002 · Cited by 54 · see citing works

Microbiota diversity and stability of the preterm neonatal ileum and colon of two infants

Barrett, E., Guinane, C. M., Ryan, C. A., Dempsey, E. M., Murphy, B. P., O’Toole, P. W., Fitzgerald, G. F., Cotter, P. D., Ross, R. P., & Stanton, C. (2013) · MicrobiologyOpen · doi:10.1002/mbo3.64 · Cited by 41 · see citing works

Species Level Description of the Human Ileal Bacterial Microbiota

Villmones, H. C., Haug, E. S., Ulvestad, E., Grude, N., Stenstad, T., Halland, A., & Kommedal, Ø. (2018) · Scientific Reports · doi:10.1038/s41598-018-23198-5 · Cited by 91 · see citing works