Bifidobacteria can protect from enteropathogenic infection through production of acetate

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,120 · see citing works

Summaries of Affymetrix GeneChip probe level data

Irizarry, R. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng015 · Cited by 4,906 · see citing works

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

Maslowski, K. M., Vieira, A. T., Ng, A., Kranich, J., Sierro, F., Yu, D., Schilter, H. C., Rolph, M. S., Mackay, F., Artis, D., et al. (2009) · Nature · doi:10.1038/nature08530 · Cited by 3,241 · see citing works

Improved microbial gene identification with GLIMMER

Delcher, A. L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.23.4636 · Cited by 2,493 · see citing works

Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome

Tarr, P. I., Gordon, C. A., & Chandler, W. L. (2005) · The Lancet · doi:10.1016/s0140-6736(05)71144-2 · Cited by 1,776 · see citing works

Activation of human aortic smooth-muscle cells is inhibited by PPARα but not by PPARγ activators

Staels, B., Köenig, W., Habib, A., Merval, R., Lebret, M., Pineda‐Torra, I., Delerive, P., Fadel, A., Chinetti, G., Fruchart, J., et al. (1998) · Nature · doi:10.1038/31701 · Cited by 1,134 · see citing works

Liver X receptors as integrators of metabolic and inflammatory signaling

Zelcer, N. (2006) · Journal of Clinical Investigation · doi:10.1172/jci27883 · Cited by 978 · see citing works

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

Schell, M. A., Karmirantzou, M., Snel, ‎., Vilanova, D., Berger, B. W., Pessi, G., Zwahlen, M.-C., Desiere, F., Peer Bork, B., Delley, M., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212527599 · Cited by 942 · see citing works

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

Sela, D. A., Chapman, J., Adeuya, A., Kim, J., Chen, F., Whitehead, T. R., Lapidus, A. L., Rokhsar, D. S., Lebrilla, C. B., German, J. B., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809584105 · Cited by 884 · 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

Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: A study with relevance to inflammatory bowel disease

Tedelind, S., Westberg, F., Kjerrulf, M., & Vidal, A. (2007) · World Journal of Gastroenterology · doi:10.3748/wjg.v13.i20.2826 · Cited by 856 · see citing works

LXRs control lipid-inducible expression of the apolipoprotein E gene in macrophages and adipocytes

Laffitte, B. A., Repa, J. J., Joseph, S. B., Wilpitz, D. C., Kast, H. R., Mangelsdorf, D. J., & Tontonoz, P. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.2.507 · Cited by 683 · see citing works

Review article: bifidobacteria as probiotic agents – physiological effects and clinical benefits

PICARD, C., FIORAMONTI, J., FRANCOIS, A., ROBINSON, T., NEANT, F., & MATUCHANSKY, C. (2005) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2005.02615.x · Cited by 618 · see citing works

Genome-scale analyses of health-promoting bacteria: probiogenomics

Ventura, M., O'Flaherty, S., Claesson, M. J., Turroni, F., Klaenhammer, T. R., van Sinderen, D., & O'Toole, P. W. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2047 · Cited by 471 · see citing works

Gut microbiota: a potential new territory for drug targeting

Jia, W. P., Li, H., Zhao, L., & Nicholson, J. K. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2505 · Cited by 471 · see citing works

Induction of IκBα Expression as a Mechanism Contributing to the Anti-inflammatory Activities of Peroxisome Proliferator-activated Receptor-α Activators

Gervois, P. P., Fruchart, J., Delerive, P., & Staels, B. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004045200 · Cited by 457 · see citing works

Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host

Sonnenburg, J. L., Chen, C. T. L., & Gordon, J. I. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040413 · Cited by 423 · see citing works

Enteropathogenic and EnterohemorrhagicEscherichia coliInfections: Translocation, Translocation, Translocation

Garmendia, J., Frankel, G. M., & Crepin, V. F. (2005) · Infection and Immunity · doi:10.1128/iai.73.5.2573-2585.2005 · Cited by 408 · see citing works

Automated Finishing with AutofinishPreprint

Gordon, D., Desmarais, C., & Green, P. (2001) · Genome Research · doi:10.1101/gr.171401 · Cited by 376 · see citing works

The love–hate relationship between bacterial polysaccharides and the host immune system

Mazmanian, S. K., & Kasper, D. L. (2006) · Nature reviews. Immunology · doi:10.1038/nri1956 · Cited by 357 · see citing works

Probiotic Bifidobacteria Protect Mice from Lethal Infection with Shiga Toxin-Producing Escherichia coli O157:H7

Asahara, T., Shimizu, K., Nomoto, K., Hamabata, T., Ozawa, A., & Takeda, Y. (2004) · Infection and Immunity · doi:10.1128/iai.72.4.2240-2247.2004 · Cited by 277 · see citing works

Mechanisms of probiosis and prebiosis: considerations for enhanced functional foods

Saulnier, D. M. A., Spinler, J. K., Gibson, G. R., & Versalovic, J. A. (2009) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2009.01.002 · Cited by 231 · see citing works

PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics

Akiyama, K., Chikayama, E., Yuasa, H., Shimada, Y., Tohge, T., Shinozaki, K., Hirai, M. Y., Sakurai, T., Kikuchi, J., & Saito, K. (2008) · In Silico Biology · doi:10.3233/isb-00362 · Cited by 206 · see citing works

Acetylated, Propionylated or Butyrylated Starches Raise Large Bowel Short-Chain Fatty Acids Preferentially When Fed to Rats

Annison, G., Illman, R. J., & Topping, D. L. (2003) · Journal of Nutrition · doi:10.1093/jn/133.11.3523 · Cited by 171 · see citing works

Oxidized omega-3 fatty acids in fish oil inhibit leukocyte-endothelial interactions through activation of PPARα

Sethi, S. M., Ziouzenkova, O., Ni, H., Wagner, D. D., Plutzky, J., & Mayadas, T. N. (2002) · Blood · doi:10.1182/blood-2002-01-0316 · Cited by 166 · see citing works

Complete Genome Sequence of Bifidobacterium longum subsp. longum KACC 91563

Ham, J.-S., Lee, T., Byun, M.-J., Lee, K., Kim, M., Han, G.-S., Jeong, S.-G., Oh, M., Kim, D., & Kim, H. (2011) · Journal of Bacteriology · doi:10.1128/jb.05620-11 · Cited by 143 · see citing works

Stable Isotope Labeling of Arabidopsis thaliana for an NMR-Based Metabolomics Approach

Kikuchi, J., Shinozaki, K., & Hirayama, T. (2004) · Plant and Cell Physiology · doi:10.1093/pcp/pch117 · Cited by 140 · see citing works

Statistical Indices for Simultaneous Large-Scale Metabolite Detections for a Single NMR Spectrum

Chikayama, E., Sekiyama, Y., Okamoto, M., Nakanishi, Y., Tsuboi, Y., Akiyama, K., Saito, K., Shinozaki, K., & Kikuchi, J. (2010) · Analytical Chemistry · doi:10.1021/ac9022023 · Cited by 133 · see citing works

Improvement of bacterial transformation efficiency using plasmid artificial modification

Yasui, K., Kano, Y., Tanaka, K. Y., Watanabe, K., Shimizu-Kadota, M., Yoshikawa, H., & Suzuki, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn884 · Cited by 129 · see citing works

Short-Chain Fatty Acids Impact on Intestinal Adaptation, Inflammation, Carcinoma, and Failure

Kles, K. A., & Chang, E. B. (2006) · Gastroenterology · doi:10.1053/j.gastro.2005.11.048 · Cited by 123 · see citing works

Interaction of Shiga toxin from Escherichia coli with human intestinal epithelial cell lines and explants: Stx2 induces epithelial damage in organ culture

Schüller, S., Frankel, G. M., & Phillips, A. D. (2004) · Cellular Microbiology · doi:10.1046/j.1462-5822.2004.00370.x · Cited by 120 · see citing works

Sugar Transport Systems of Bifidobacterium longum NCC2705

Parche, S., Amon, J., Janković, I., Rezzonico, E., Beleut, M., Barutçu, H., Schendel, I., Eddy, M. P., Burkovski, A., Arigoni, F., et al. (2006) · Microbial Physiology · doi:10.1159/000096455 · Cited by 103 · see citing works

A Proteome Reference Map and Proteomic Analysis of Bifidobacterium longum NCC2705

Yuan, J., Zhu, L., Liu, X., et al. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500410-mcp200 · Cited by 99 · see citing works

Regulation of Complement C3 Expression by the Bile Acid Receptor FXR

Li, J., Pircher, P. C., Schulman, I. G., & Westin, S. K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m411473200 · Cited by 93 · see citing works

Cloned Cytosine Deaminase Gene Expression ofBifidobacterium longumand Application to Enzyme/Pro-drug Therapy of Hypoxic Solid Tumors

Nakamura, T., Sasaki, T., FUJIMORI, M., Yazawa, K., Kano, Y., Amano, J., & Taniguchi, S. (2002) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.66.2362 · Cited by 91 · see citing works

Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells

Hijikata, A., Kitamura, H., Kimura, Y., Yokoyama, R., Aiba, Y., Bao, Y.-Y., Fujita, S., Hase, K., Hori, S., Ishii, Y., et al. (2007) · Bioinform. · doi:10.1093/bioinformatics/btm430 · Cited by 88 · see citing works

Pathogenesis of Renal Disease Due to Enterohemorrhagic Escherichia coli in Germ-Free Mice

Eaton, K., Friedman, D., Francis, G. J., et al. (2008) · Infection and Immunity · doi:10.1128/iai.01626-07 · Cited by 88 · see citing works

Distinct Gene Expression Profiles Characterize Cellular Phenotypes of Follicle-Associated Epithelium and M Cells

Hase, K. (2005) · DNA Research · doi:10.1093/dnares/12.2.127 · Cited by 86 · see citing works

Profiling Polar and Semipolar Plant Metabolites throughout Extraction Processes Using a Combined Solution-State and High-Resolution Magic Angle Spinning NMR Approach

Sekiyama, Y., Chikayama, E., & Kikuchi, J. (2010) · Analytical Chemistry · doi:10.1021/ac9019076 · Cited by 76 · see citing works

Activation-Induced Cytidine Deaminase Deficiency Causes Organ-Specific Autoimmune Disease

Hase, K., Takahashi, D., Ebisawa, M., Kawano, S., Itoh, K., & Ohno, H. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003033 · Cited by 63 · see citing works

Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping

Fukuda, S., Nakanishi, Y., Chikayama, E., Ohno, H., Hino, T., & Kikuchi, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004893 · Cited by 62 · see citing works

Top-down Phenomics of Arabidopsis thaliana

Tian, C., Chikayama, E., Tsuboi, Y., Kuromori, T., Shinozaki, K., Kikuchi, J., & Hirayama, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700549200 · Cited by 60 · see citing works

Effect of Bifidobacterium thermacidophilum probiotic feeding on enterohemorrhagic Escherichia coli O157:H7 infection in BALB/c mice

Gagnon, M., Kheadr, E., Dabour, N., Richard, D., & Fliss, I. (2006) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2006.04.041 · Cited by 52 · see citing works

Prevention of Escherichia coli O157:H7 infection in gnotobiotic mice associated with Bifidobacterium strains

Yoshimura, K., MATSUI, T., & Itoh, K. (2009) · Antonie van Leeuwenhoek · doi:10.1007/s10482-009-9391-y · Cited by 38 · see citing works

Ingestion of resistant starch protects endotoxin influx from the intestinal tract and reduces D‐galactosamine‐induced liver injury in rats

Morita, T., TANABE, H., Takahashi, K., & SUGIYAMA, K. (2004) · Journal of Gastroenterology and Hepatology · doi:10.1111/j.1440-1746.2003.03208.x · Cited by 37 · see citing works

Oxysterol and 9-cis-retinoic acid stimulate the group IIA secretory phospholipase A2 gene in rat smooth-muscle cells

Antonio, V., Janvier, B., Brouillet, A., Andréani, M., & Raymondjean, M. (2003) · Biochemical Journal · doi:10.1042/bj20030098 · Cited by 32 · see citing works

Enzyme-linked immunosorbent assay to detect Shiga toxin of Shigella dysenteriae and related toxins

Kongmuang, U., Honda, T., & Miwatani, T. (1987) · Journal of Clinical Microbiology · doi:10.1128/jcm.25.1.115-118.1987 · Cited by 29 · see citing works

Daily bowel movements and Escherichia coli O157 infection

Kitajima, H. (2002) · Archives of Disease in Childhood · doi:10.1136/adc.87.4.335 · Cited by 6 · see citing works

Diversity, stability and resilience of the human gut microbiota

Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

Furusawa, Y., Obata, Y., Fukuda, S., Endo, T. A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., et al. (2013) · Nature · doi:10.1038/nature12721 · Cited by 5,549 · see citing works

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T _reg Cell Homeostasis

Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413 · see citing works

Gut microbiota, metabolites and host immunity

Rooks, M. G., & Garrett, W. S. (2016) · Nature reviews. Immunology · doi:10.1038/nri.2016.42 · Cited by 3,409 · see citing works

Human nutrition, the gut microbiome and the immune system

Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588 · see citing works

The role of short chain fatty acids in health and disease

Tan, J., McKenzie, C., Potamitis, M., Thorburn, A. N., Mackay, C. R., & Macia, L. (2014) · Advances in immunology · doi:10.1016/b978-0-12-800100-4.00003-9 · Cited by 2,425 · see citing works

Role of the gut microbiota in immunity and inflammatory disease

Kamada, N., Seo, S.-U., Chen, G. Y., & Núñez, G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3430 · Cited by 2,256 · see citing works

How colonization by microbiota in early life shapes the immune system

Gensollen, T., Iyer, S. S., Kasper, D. L., & Blumberg, R. S. (2016) · Science · doi:10.1126/science.aad9378 · Cited by 2,044 · see citing works

The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota

Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950 · see citing works

You are what you eat: Diet, health and the gut microbiota

Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792 · see citing works

Microbiota-mediated colonization resistance against intestinal pathogens

Buffie, C. G., & Pamer, E. G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3535 · Cited by 1,564 · see citing works

Control of pathogens and pathobionts by the gut microbiota

Kamada, N., Chen, G. Y., Inohara, N., & Núñez, G. (2013) · Nature Immunology · doi:10.1038/ni.2608 · Cited by 1,625 · see citing works

Reciprocal interactions of the intestinal microbiota and immune system

Maynard, C. L., Elson, C. O., Hatton, R. D., & Weaver, C. T. (2012) · Nature · doi:10.1038/nature11551 · Cited by 1,598 · see citing works

The impact of diet and lifestyle on gut microbiota and human health

Conlon, M., & Bird, A. (2014) · Nutrients · doi:10.3390/nu7010017 · Cited by 1,567 · see citing works

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437 · see citing works

Short-chain fatty acids: Linking diet, the microbiome and immunity

Mann, E. R., Lam, Y. K., & Uhlig, H. H. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01014-8 · Cited by 1,595 · 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

Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome

Macia, L., Tan, J., Vieira, A. T., Leach, K., Stanley, D., Luong, S., Maruya, M., Ian McKenzie, C., Hijikata, A., Wong, C., et al. (2015) · Nature Communications · doi:10.1038/ncomms7734 · Cited by 1,439 · see citing works

Interactions between the microbiota and pathogenic bacteria in the gut

Bäumler, A. J., & Sperandio, V. (2016) · Nature · doi:10.1038/nature18849 · Cited by 1,420 · see citing works

The pros, cons, and many unknowns of probiotics

Suez, J., Zmora, N., Segal, E., & Elinav, E. (2019) · Nature Medicine · doi:10.1038/s41591-019-0439-x · Cited by 1,398 · see citing works

Mechanisms of action of probiotics

Plaza-Diaz, J., Ruiz-Ojeda, F. J., Gil-Campos, M., & Gil, A. (2019) · Advances in Nutrition · doi:10.1093/advances/nmy063 · Cited by 1,423 · see citing works

Microbes, Metabolites, and the Gut-Lung Axis

Dang, A. T., & Marsland, B. J. (2019) · Mucosal Immunology · doi:10.1038/s41385-019-0160-6 · Cited by 1,028 · see citing works

Ectopic colonization of oral bacteria in the intestine drives T _H 1 cell induction and inflammation

Atarashi, K., Suda, W., Luo, C., Kawaguchi, T., Motoo, I., Narushima, S., Kiguchi, Y., Yasuma, K., Watanabe, E., Tanoue, T., et al. (2017) · Science · doi:10.1126/science.aan4526 · Cited by 957 · 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

Intestinal barrier function in health and gastrointestinal disease

Camilleri, M., Madsen, K., Spiller, R., Van Meerveld, B. G., & Verne, G. N. (2012) · Neurogastroenterology & Motility · doi:10.1111/j.1365-2982.2012.01921.x · Cited by 908 · see citing works

Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation

Kasubuchi, M., Hasegawa, S., Hiramatsu, T., Ichimura, A., & Kimura, I. (2015) · Nutrients · doi:10.3390/nu7042839 · Cited by 904 · see citing works

Diet, metabolites, and “western-lifestyle” inflammatory diseases

Thorburn, A. N., Macia, L., & Mackay, C. R. (2014) · Immunity · doi:10.1016/j.immuni.2014.05.014 · Cited by 879 · 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

Diet-microbiota interactions and personalized nutrition

Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879 · see citing works

An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota

Jeffery, I. B., O'Toole, P. W., Öhman, L., Claesson, M. J., Deane, J., Quigley, E. M. M., & Simrén, M. (2012) · Gut · doi:10.1136/gutjnl-2011-301501 · Cited by 835 · see citing works

The microbiome in infectious disease and inflammation

Honda, K., & Littman, D. R. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-074937 · Cited by 791 · see citing works

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

Schroeder, B. O., Birchenough, G. M. H., Ståhlman, M., Arike, L., Johansson, M. E. V., Hansson, G. C., & Bäckhed, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.004 · Cited by 713 · see citing works

Metformin Is Associated With Higher Relative Abundance of Mucin-Degrading <i>Akkermansia muciniphila</i> and Several Short-Chain Fatty Acid–Producing Microbiota in the Gut

de la Cuesta-Zuluaga, J., Mueller, N. T., Corrales-Agudelo, V., Velásquez-Mejía, E. P., Carmona, J. A., Abad, J. M., & Escobar, J. S. (2017) · Diabetes Care · doi:10.2337/dc16-1324 · Cited by 704 · see citing works

Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier

Martens, E. C., Neumann, M., & Desai, M. S. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0036-x · Cited by 711 · see citing works

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes

Mariño, E., Richards, J. L., McLeod, K. H., Stanley, D., Yap, Y. A., Knight, J., McKenzie, C., Kranich, J., Oliveira, A. C., Rossello, F. J., et al. (2017) · Nature Immunology · doi:10.1038/ni.3713 · Cited by 686 · 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

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

Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling

Zheng, H., Powell, J. E., Steele, M. I., Dietrich, C., & Moran, N. A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1701819114 · Cited by 664 · see citing works

Structural Changes of Gut Microbiota during Berberine-Mediated Prevention of Obesity and Insulin Resistance in High-Fat Diet-Fed Rats

Zhang, X., Zhao, Y., Zhang, M., Pang, X., Xu, J., Kang, C., Li, M., Zhang, C., Zhang, Z., Zhang, Y., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042529 · Cited by 615 · see citing works

The influence of the microbiome on respiratory health

Wypych, T. P., Wickramasinghe, L. C., & Marsland, B. J. (2019) · Nature Immunology · doi:10.1038/s41590-019-0451-9 · Cited by 611 · see citing works

Effects of antibiotics on gut microbiota

Lange, K., Buerger, M., Stallmach, A., & Bruns, T. (2016) · Digestive Diseases · doi:10.1159/000443360 · Cited by 607 · see citing works

Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606 · see citing works

Exopolysaccharides from Probiotic Bacteria and Their Health Potential

Angelin, J., & Kavitha, M. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.06.190 · Cited by 617 · see citing works

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition

Charbonneau, M. R., O’Donnell, D., Blanton, L. V., Totten, S. M., Davis, J. C. C., Barratt, M. J., Cheng, J., Guruge, J., Talcott, M., Bain, J. R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.01.024 · Cited by 606 · see citing works

Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection

Ducarmon, Q. R., Zwittink, R. D., Hornung, B. V. H., van Schaik, W., Young, V. B., & Kuijper, E. J. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00007-19 · Cited by 566 · see citing works

Specialized metabolites from the microbiome in health and disease

Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.016 · Cited by 544 · see citing works

Hypertension-Linked Pathophysiological Alterations in the Gut

Santisteban, M. M., Qi, Y., Zubcevic, J., Kim, S., Yang, T., Shenoy, V., Cole-Jeffrey, C. T., Lobaton, G. O., Stewart, D. C., Rubiano, A., et al. (2017) · Circulation Research · doi:10.1161/circresaha.116.309006 · Cited by 525 · see citing works

Analysis of Gut Microbiota in Patients with Parkinson’s Disease

Petrov, V. A., Saltykova, I. V., Zhukova, I. A., Alifirova, V. M., Zhukova, N. G., Dorofeeva, Y. B., Tyakht, A. V., Kovarsky, B. A., Alekseev, D. G., Kostryukova, E. S., et al. (2017) · Bulletin of Experimental Biology and Medicine · doi:10.1007/s10517-017-3700-7 · Cited by 487 · see citing works

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Maldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517 · see citing works

Bifidobacteria and Their Health-Promoting Effects

Hidalgo-Cantabrana, C., Delgado, S., Ruiz, L., Ruas-Madiedo, P., Sánchez, B., & Margolles, A. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.bad-0010-2016 · Cited by 490 · see citing works

The role of inflammation and the gut microbiome in depression and anxiety

Peirce, J. M., & Alviña, K. (2019) · Journal of Neuroscience Research · doi:10.1002/jnr.24476 · Cited by 466 · see citing works

Dietary effects on human gut microbiome diversity

Xu, Z., & Knight, R. (2015) · British Journal Of Nutrition · doi:10.1017/s0007114514004127 · Cited by 456 · see citing works

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children

Gehrig, J. L., Venkatesh, S., Chang, H.-W., Hibberd, M. C., Kung, V. L., Cheng, J., Chen, R. Y., Subramanian, S., Cowardin, C. A., Meier, M. F., et al. (2019) · Science · doi:10.1126/science.aau4732 · Cited by 431 · see citing works

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

Vernocchi, P., Del Chierico, F., & Putignani, L. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01144 · Cited by 426 · see citing works

Elevated fecal short chain fatty acid and ammonia concentrations in children with autism spectrum disorder

Wang, L., Christophersen, C. T., Sorich, M. J., Gerber, J. P., Angley, M. T., & Conlon, M. A. (2012) · Digestive Diseases and Sciences · doi:10.1007/s10620-012-2167-7 · Cited by 412 · see citing works

Breast milk oligosaccharides: structure-function relationships in the neonate

Smilowitz, J. T., Lebrilla, C. B., Mills, D. A., German, J. B., & Freeman, S. L. (2014) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-071813-105721 · Cited by 410 · see citing works

Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon

Shimada, Y., Kinoshita, M., Harada, K., Mizutani, M., Masahata, K., Kayama, H., & Takeda, K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080604 · Cited by 404 · see citing works

Functional genome analysis of <i>Bifidobacterium breve</i> UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor

O'Connell Motherway, M., Zomer, A., Leahy, S. C., Reunanen, J., Bottacini, F., Claesson, M. J., O'Brien, F., Flynn, K., Casey, P. G., Moreno Munoz, J. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105380108 · Cited by 376 · see citing works

A systematic review of the safety of probiotics

Didari, T., Solki, S., Mozaffari, S., Nikfar, S., & Abdollahi, M. (2014) · Expert Opinion on Drug Safety · doi:10.1517/14740338.2014.872627 · Cited by 367 · see citing works

Microbiome-modulated metabolites at the interface of host immunity

Blacher, E., Levy, M., Tatirovsky, E., & Elinav, E. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1601247 · Cited by 354 · see citing works

The first thousand days - intestinal microbiology of early life: Establishing a symbiosis

Wopereis, H., Oozeer, R., Knipping, K., Belzer, C., & Knol, J. (2014) · Pediatric Allergy and Immunology · doi:10.1111/pai.12232 · Cited by 352 · see citing works

The gut microbiome’s role in the development, maintenance, and outcomes of sepsis

Adelman, M. W., Woodworth, M. H., Langelier, C., Busch, L. M., Kempker, J. A., Kraft, C. S., & Martin, G. S. (2020) · Critical Care · doi:10.1186/s13054-020-02989-1 · Cited by 342 · see citing works

Mining the microbiota for microbial and metabolite-based immunotherapies

Skelly, A. N., Sato, Y., Kearney, S., & Honda, K. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-019-0144-5 · Cited by 306 · see citing works

Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?

Pais, P., Almeida, V., Yılmaz, M., & Teixeira, M. C. (2020) · Journal of Fungi · doi:10.3390/jof6020078 · Cited by 327 · see citing works

Gut microbiota role in irritable bowel syndrome: New therapeutic strategies

Distrutti, E., Monaldi, L., Ricci, P., & Fiorucci, S. (2016) · World Journal of Gastroenterology · doi:10.3748/wjg.v22.i7.2219 · Cited by 320 · see citing works

The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

Lindefeldt, M., Eng, A., Darban, H., Bjerkner, A., Zetterström, C. K., Allander, T., Andersson, B., Borenstein, E., Dahlin, M., & Prast-Nielsen, S. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-018-0073-2 · Cited by 310 · see citing works

Longevity in Mice Is Promoted by Probiotic-Induced Suppression of Colonic Senescence Dependent on Upregulation of Gut Bacterial Polyamine Production

Matsumoto, M., Kurihara, S., Kibe, R., Ashida, H., & Benno, Y. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023652 · Cited by 290 · see citing works

Faecal short chain fatty acids profile is changed in Polish depressive women

Skonieczna-Żydecka, K., Grochans, E., Maciejewska, D., Szkup, M., Schneider-Matyka, D., Jurczak, A., Łoniewski, I., Kaczmarczyk, M., Marlicz, W., Czerwińska-Rogowska, M., et al. (2018) · Nutrients · doi:10.3390/nu10121939 · Cited by 284 · see citing works

Nutritional iron turned inside out: intestinal stress from a gut microbial perspective

Kortman, G. A. M., Raffatellu, M., Swinkels, D. W., & Tjalsma, H. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12086 · Cited by 291 · see citing works

Food, immunity, and the microbiome

Tilg, H., & Moschen, A. R. (2015) · Gastroenterology · doi:10.1053/j.gastro.2014.12.036 · Cited by 292 · see citing works

The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract

Malmuthuge, N., Griebel, P. J., & Guan, L. L. (2015) · Frontiers in Veterinary Science · doi:10.3389/fvets.2015.00036 · Cited by 281 · see citing works

The effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review

Paganini, D., & Zimmermann, M. B. (2017) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.117.156067 · Cited by 262 · see citing works

Dietary metabolites and the gut microbiota: an alternative approach to control inflammatory and autoimmune diseases

Richards, J. L., Yap, Y. A., McLeod, K. H., Mackay, C. R., & Mariño, E. (2016) · Clinical &amp; Translational Immunology · doi:10.1038/cti.2016.29 · Cited by 250 · see citing works

Microbiota-mediated inflammation and antimicrobial defense in the intestine

Caballero, S., & Pamer, E. G. (2015) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032713-120238 · Cited by 238 · see citing works

Fatty acid diets: regulation of gut microbiota composition and obesity and its related metabolic dysbiosis

Machate, D. J., Figueiredo, P. S., Marcelino, G., Guimarães, R. D. C. A., Hiane, P. A., Bogo, D., Pinheiro, V. A. Z., Oliveira, L. C. S. D., & Pott, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21114093 · Cited by 243 · see citing works

Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics

Blanton, L. V., Barratt, M. J., Charbonneau, M. R., Ahmed, T., & Gordon, J. I. (2016) · Science · doi:10.1126/science.aad9359 · Cited by 234 · see citing works

<i>Bifidobacterium</i> can mitigate intestinal immunopathology in the context of CTLA-4 blockade

Wang, F., Yin, Q., Chen, L., & Davis, M. M. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712901115 · Cited by 223 · see citing works

Persistence of Supplemented Bifidobacterium longum subsp. <i>infantis</i> EVC001 in Breastfed Infants

Frese, S. A., Hutton, A. A., Contreras, L. N., Shaw, C. A., Palumbo, M. C., Casaburi, G., Xu, G., Davis, J. C. C., Lebrilla, C. B., Henrick, B. M., et al. (2017) · mSphere · doi:10.1128/msphere.00501-17 · Cited by 231 · see citing works

Consumption of human milk glycoconjugates by infant-associated bifidobacteria: mechanisms and implications

Garrido, D., Dallas, D. C., & Mills, D. A. (2013) · Microbiology · doi:10.1099/mic.0.064113-0 · Cited by 228 · see citing works

The immune system bridges the gut microbiota with systemic energy homeostasis: focus on TLRs, mucosal barrier, and SCFAs

Spiljar, M., Merkler, D., & Trajkovski, M. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01353 · Cited by 219 · see citing works

Intestinal microbiota in early life and its implications on childhood health

Zhuang, L., Chen, H., Zhang, S., Zhuang, J., Li, Q., & Feng, Z. (2019) · Genomics, Proteomics &amp; Bioinformatics · doi:10.1016/j.gpb.2018.10.002 · Cited by 219 · see citing works

Indoles from commensal bacteria extend healthspan

Sonowal, R., Swimm, A., Sahoo, A., Luo, L., Matsunaga, Y., Wu, Z., Bhingarde, J. A., Ejzak, E. A., Ranawade, A., Qadota, H., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706464114 · Cited by 197 · see citing works

Immunomodulating activity and therapeutic effects of short chain fatty acids and tryptophan post-biotics in inflammatory bowel disease

Russo, E., Giudici, F., Fiorindi, C., Ficari, F., Scaringi, S., & Amedei, A. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02754 · Cited by 204 · see citing works

Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants

Samara, J., Moossavi, S., Alshaikh, B., Ortega, V. A., Pettersen, V. K., Ferdous, T., Hoops, S. L., Soraisham, A., Vayalumkal, J., Dersch-Mills, D., et al. (2022) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2022.04.005 · Cited by 191 · see citing works

Exopolysaccharides Produced by Lactic Acid Bacteria and Bifidobacteria as Fermentable Substrates by the Intestinal Microbiota

Salazar, N., Gueimonde, M., de los Reyes-Gavilán, C. G., & Ruas-Madiedo, P. (2016) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2013.770728 · Cited by 188 · see citing works

Prebiotic Galacto-Oligosaccharides Mitigate the Adverse Effects of Iron Fortification on the Gut Microbiome: A Randomised Controlled Study in Kenyan Infants

Paganini, D., Uyoga, M. A., Kortman, G. A. M., Cercamondi, C. I., Moretti, D., Barth-Jaeggi, T., Schwab, C., Boekhorst, J., Timmerman, H. M., Lacroix, C., et al. (2017) · Gut · doi:10.1136/gutjnl-2017-314418 · Cited by 172 · see citing works

Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community

Sugahara, H., Odamaki, T., Fukuda, S., Kato, T., Xiao, J.-Z., Abe, F., Kikuchi, J., & Ohno, H. (2015) · Scientific Reports · doi:10.1038/srep13548 · Cited by 169 · see citing works

Human-Derived Bifidobacterium dentium Modulates the Mammalian Serotonergic System and Gut–Brain Axis

Engevik, M. A., Luck, B., Visuthranukul, C., Ihekweazu, F. D., Engevik, A. C., Shi, Z., Danhof, H. A., Chang-Graham, A. L., Hall, A., Endres, B. T., et al. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2020.08.002 · Cited by 164 · see citing works

Celiac Disease and the Microbiome

Valitutti, F., Cucchiara, S., & Fasano, A. (2019) · Nutrients · doi:10.3390/nu11102403 · Cited by 157 · see citing works

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT

Biagi, E., Zama, D., Nastasi, C., Consolandi, C., Fiori, J., Rampelli, S., Turroni, S., Centanni, M., Severgnini, M., Peano, C., et al. (2015) · Bone Marrow Transplantation · doi:10.1038/bmt.2015.16 · Cited by 158 · see citing works

Validating bifidobacterial species and subspecies identity in commercial probiotic products

Lewis, Z. T., Shani, G., Masarweh, C. F., Popovic, M., Frese, S. A., Sela, D. A., Underwood, M. A., & Mills, D. A. (2016) · Pediatric Research · doi:10.1038/pr.2015.244 · Cited by 154 · see citing works

Impact of Probiotics on Colonizing Microbiota of the Gut

Sanders, M. E. (2011) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0b013e318227414a · Cited by 153 · see citing works

Oral Microbiota and Alzheimer’s Disease: Do All Roads Lead to Rome?

Sureda, A., Daglia, M., Argüelles Castilla, S., Sanadgol, N., Fazel Nabavi, S., Khan, H., Belwal, T., Jeandet, P., Marchese, A., Pistollato, F., et al. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2019.104582 · Cited by 143 · see citing works

A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract

Garrido, D., Barile, D., & Mills, D. A. (2012) · Advances in Nutrition · doi:10.3945/an.111.001586 · Cited by 149 · see citing works

Digestibility of sulfated polysaccharide from the brown seaweed Ascophyllum nodosum and its effect on the human gut microbiota in vitro

Chen, L., Xu, W., Chen, D., Chen, G., Liu, J., Zeng, X., Shao, R., & Zhu, H. (2018) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2018.01.183 · Cited by 140 · see citing works

Low iron availability in continuous<i>in vitro</i>colonic fermentations induces strong dysbiosis of the child gut microbial consortium and a decrease in main metabolites

Dostal, A., Fehlbaum, S., Chassard, C., Zimmermann, M. B., & Lacroix, C. (2013) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2012.01461.x · Cited by 129 · see citing works

Consecutive oral administration of <i>Bifidobacterium longum</i> MM‐2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model

Kawahara, T., Takahashi, T., Oishi, K., Tanaka, H., Masuda, M., Takahashi, S., Takano, M., Kawakami, T., Fukushima, K., Kanazawa, H., et al. (2015) · Microbiology and Immunology · doi:10.1111/1348-0421.12210 · Cited by 125 · see citing works

Intestinal microbiota and immune function in the pathogenesis of irritable bowel syndrome

Ringel, Y., & Maharshak, N. (2013) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00207.2012 · Cited by 115 · see citing works

Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning

Song, Y., Malmuthuge, N., Steele, M. A., & Guan, L. L. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix179 · Cited by 115 · see citing works

A Review of the Brain-Gut-Microbiome Axis and the Potential Role of Microbiota in Alzheimer’s Disease

Sun, M., Ma, K., Wen, J., Wang, G., Zhang, C., Li, Q., Bao, X., & Wang, H. (2020) · Journal of Alzheimer’s Disease · doi:10.3233/jad-190872 · Cited by 113 · see citing works

Bacteriostatic Experiment of Twelve Species of Chinese Medicines and Its Compounds Against Escherichia Coli

You-wen, S. (2004)

Damaging effect of pressurized CO_2 on cell membrane of Escherichia coli

Chun, Y. (2013) · Microbiology, China

A study on β-lactamase activity of biofilm Escherichia coli

Sheng-qi, L. (2001) · Zhonghua jiehe he huxi zazhi

Recombinant Protein Expression in Escherichia coli (E.coli): What We Need to Know

Hayat, S. M. G., Farahani, N., Golichenari, B., et al. (2018) · Current Pharmaceutical Design · doi:10.2174/1381612824666180131121940 · Cited by 115 · see citing works

Effect of Mitomycin C on the Expression of Shiga Toxin from Escherichia coli O157

Ya-xian, Y. (2008) · Zhongguo nongye Kexue