Microbiome therapeutics — Advances and challenges

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

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

Enzymatic assembly of DNA molecules up to several hundred kilobases

Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,996

Changes of Intestinal Functions in Liver Cirrhosis

Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,808

Obesity alters gut microbial ecology

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597

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

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

Role of the microbiota in immunity and inflammation.

Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385

The gut microbiota shapes intestinal immune responses during health and disease

Round, J. L., & Mazmanian, S. K. (2009) · Nature Reviews Immunology · doi:10.1038/nri2515 · Cited by 5,029

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., et al. (2013) · Nature · doi:10.1038/nature12726 · Cited by 4,838

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413

Construction of a genetic toggle switch in Escherichia coli

Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000) · Nature · doi:10.1038/35002131 · Cited by 4,268

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708

Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis

Yano, J. M., Yu, K., Donaldson, G. P., Shastri, G. G., Ann, P., Ma, L., Nagler, C. R., Ismagilov, R. F., Mazmanian, S. K., & Hsiao, E. Y. (2015) · Cell · doi:10.1016/j.cell.2015.02.047 · Cited by 3,614

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.024 · Cited by 3,283

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220

Human Genetics Shape the Gut Microbiome

Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · cited 1×

Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice

Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X., Kubo, C., & Koga, Y. (2004) · The Journal of Physiology · doi:10.1113/jphysiol.2004.063388 · Cited by 2,735

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., Reyes, J. A., Shah, S. A., LeLeiko, N., Snapper, S. B., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-r79 · Cited by 2,713

Gut biogeography of the bacterial microbiota

Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro3552 · Cited by 2,535

The Orphan G Protein-coupled Receptors GPR41 and GPR43 Are Activated by Propionate and Other Short Chain Carboxylic Acids

Brown, A. J., Goldsworthy, S. M., Barnes, A. A., Eilert, M. M., Tcheang, L., Daniels, D., Muir, A. I., Wigglesworth, M. J., Kinghorn, I., Fraser, N. J., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211609200 · Cited by 2,409

Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2

Tolhurst, G., Heffron, H., Lam, Y. S., Parker, H. E., Habib, A. M., Diakogiannaki, E., Cameron, J., Grosse, J., Reimann, F., & Gribble, F. M. (2012) · Diabetes · doi:10.2337/db11-1019 · Cited by 2,404

A microbial symbiosis factor prevents intestinal inflammatory disease

Mazmanian, S. K., Round, J. L., & Kasper, D. L. (2008) · Nature · doi:10.1038/nature07008 · Cited by 2,340

The gut microbiota and host health: a new clinical frontier

Marchesi, J. R., Adams, D. H., Fava, F., Hermes, G. D. A., Hirschfield, G. M., Hold, G., Quraishi, M. N., Kinross, J., Smidt, H., Tuohy, K. M., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-309990 · Cited by 2,302

Short-chain fatty acids in control of body weight and insulin sensitivity

Canfora, E. E., Jocken, J. W., & Blaak, E. E. (2015) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2015.128 · Cited by 2,298

Inducible Foxp3 + regulatory T-cell development by a commensal bacterium of the intestinal microbiota

Round, J. L., & Mazmanian, S. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909122107 · Cited by 2,233

Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits

De Vadder, F., Kovatcheva-Datchary, P., Goncalves, D., Vinera, J., Zitoun, C., Duchampt, A., Bäckhed, F., & Mithieux, G. (2014) · Cell · doi:10.1016/j.cell.2013.12.016 · Cited by 2,200

The Long-Term Stability of the Human Gut Microbiota

Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058

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

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872

Early infancy microbial and metabolic alterations affect risk of childhood asthma

Arrieta, M.-C., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist-Doutsch, S., Kuzeljevic, B., Gold, M. J., Britton, H. M., Lefebvre, D. L., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aab2271 · Cited by 1,786

Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes

Cappelletti, M., Presentato, A., Milazzo, G., Turner, R. J., Fedi, S., Frascari, D., & Zannoni, D. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00393 · Cited by 1,776

Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function

Kelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., Wilson, K. E., Glover, L. E., Kominsky, D. J., Magnuson, A., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.005 · Cited by 1,716

Antibiotics in early life alter the murine colonic microbiome and adiposity

Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613

Bacteriophage Therapy

Sulakvelidze, A., Alavidze, Z., & Morris, J. G. (2001) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.45.3.649-659.2001 · Cited by 1,566

Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41

Samuel, B. S., Shaito, A., Motoike, T., Rey, F. E., Backhed, F., Manchester, J. K., Hammer, R. E., Williams, S. C., Crowley, J., Yanagisawa, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808567105 · Cited by 1,564

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

Inhibition of Histone Deacetylase Activity by Butyrate

Davie, J. R. (2003) · The Journal of Nutrition · doi:10.1093/jn/133.7.2485s · Cited by 1,515

Treatment of Murine Colitis by Lactococcus lactis Secreting Interleukin-10

Steidler, L., Hans, W., Schotte, L., Neirynck, S., Obermeier, F., Falk, W., Fiers, W., & Remaut, E. (2000) · Science · doi:10.1126/science.289.5483.1352 · Cited by 1,513

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

Moayyedi, P., Surette, M. G., Kim, P. T., Libertucci, J., Wolfe, M., Onischi, C., Armstrong, D., Marshall, J. K., Kassam, Z., Reinisch, W., et al. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.04.001 · Cited by 1,499

Clostridium difficile infection: new developments in epidemiology and pathogenesis

Rupnik, M., Wilcox, M. H., & Gerding, D. N. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2164 · Cited by 1,380 · cited 1×

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis

Wang, Z., Roberts, A. B., Buffa, J. A., Levison, B. S., Zhu, W., Org, E., Gu, X., Huang, Y., Zamanian-Daryoush, M., Culley, M. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.055 · Cited by 1,317

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.002 · Cited by 1,285

Viruses in the faecal microbiota of monozygotic twins and their mothers

Reyes, A., Haynes, M., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F., & Gordon, J. I. (2010) · Nature · doi:10.1038/nature09199 · Cited by 1,194

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173

Diet dominates host genotype in shaping the murine gut microbiota

Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103

Control of brain development, function, and behavior by the microbiome

Sampson, T. R., & Mazmanian, S. K. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.011 · Cited by 1,093

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

Wallace, B. D., Wang, H., Lane, K. T., Scott, J. E., Orans, J., Koo, J. S., Venkatesh, M., Jobin, C., Yeh, L.-A., Mani, S., et al. (2010) · Science · doi:10.1126/science.1191175 · Cited by 1,080

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., Fischetti, V. A., & Marraffini, L. A. (2014) · Nature Biotechnology · doi:10.1038/nbt.3043 · Cited by 986

Ecology drives a global network of gene exchange connecting the human microbiome

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011) · Nature · doi:10.1038/nature10571 · Cited by 962

Bacteriophage adhering to mucus provide a non–host-derived immunity

Barr, J. J., Auro, R., Furlan, M., Whiteson, K. L., Erb, M. L., Pogliano, J., Stotland, A., Wolkowicz, R., Cutting, A. S., Doran, K. S., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305923110 · Cited by 944

The human gut virome: inter-individual variation and dynamic response to diet

Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

Kim, H. J., Li, H., Collins, J. J., & Ingber, D. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1522193112 · Cited by 922

Oxygenic photosynthesis as a protection mechanism for cyanobacteria against iron-encrustation in environments with high Fe2+ concentrations

Ionescu, D., Buchmann, B., Heim, C., Häusler, S., de Beer, D., & Polerecky, L. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00459 · Cited by 920

Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis

Kassam, Z., Lee, C. H., Yuan, Y., & Hunt, R. H. (2013) · American Journal of Gastroenterology · doi:10.1038/ajg.2013.59 · Cited by 904

AN INVESTIGATION ON THE NATURE OF ULTRA-MICROSCOPIC VIRUSES.

Twort, F. W. (1915) · The Lancet · doi:10.1016/s0140-6736(01)20383-3 · Cited by 901

Dispersing biofilms with engineered enzymatic bacteriophage

Lu, T. K., & Collins, J. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704624104 · Cited by 895

Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118

Corr, S. C., Li, Y., Riedel, C. U., O'Toole, P. W., Hill, C., & Gahan, C. G. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700440104 · Cited by 853

Xenobiotics shape the physiology and gene expression of the active human gut microbiome

Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013) · Cell · doi:10.1016/j.cell.2012.10.052 · Cited by 811

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

Citorik, R. J., Mimee, M., & Lu, T. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.3011 · Cited by 808

Commensal bacteria protect against food allergen sensitization

Stefka, A. T., Feehley, T., Tripathi, P., Qiu, J., McCoy, K., Mazmanian, S. K., Tjota, M. Y., Seo, G.-Y., Cao, S., Theriault, B. R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412008111 · Cited by 795

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

Garrett, W. S., Gallini, C. A., Yatsunenko, T., Michaud, M., DuBois, A., Delaney, M. L., Punit, S., Karlsson, M., Bry, L., Glickman, J. N., et al. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.08.004 · Cited by 788

A Phase I Trial With Transgenic Bacteria Expressing Interleukin-10 in Crohn’s Disease

Braat, H., Rottiers, P., Hommes, D. W., Huyghebaert, N., Remaut, E., Remon, J., van Deventer, S. J. H., Neirynck, S., Peppelenbosch, M. P., & Steidler, L. (2006) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2006.03.028 · Cited by 786

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

Sonnenburg, E. D., Zheng, H., Joglekar, P., Higginbottom, S. K., Firbank, S. J., Bolam, D. N., & Sonnenburg, J. L. (2010) · Cell · doi:10.1016/j.cell.2010.05.005 · Cited by 748

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

Vujkovic-Cvijin, I., Dunham, R. M., Iwai, S., Maher, M. C., Albright, R. G., Broadhurst, M. J., Hernandez, R. D., Lederman, M. M., Huang, Y., Somsouk, M., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006438 · Cited by 738

Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine

Williams, B. B., Van Benschoten, A. H., Cimermancic, P., Donia, M. S., Zimmermann, M., Taketani, M., Ishihara, A., Kashyap, P. C., Fraser, J. S., & Fischbach, M. A. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.09.001 · Cited by 732

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

Petrof, E. O., Gloor, G. B., Vanner, S. J., Weese, S. J., Carter, D., Daigneault, M. C., Brown, E. M., Schroeter, K., & Allen-Vercoe, E. (2013) · Microbiome · doi:10.1186/2049-2618-1-3 · Cited by 731

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

Goodman, A. L., McNulty, N. P., Zhao, Y., Leip, D., Mitra, R. D., Lozupone, C. A., Knight, R., & Gordon, J. I. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.08.003 · Cited by 731

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

Haiser, H. J., Gootenberg, D. B., Chatman, K., Sirasani, G., Balskus, E. P., & Turnbaugh, P. J. (2013) · Science · doi:10.1126/science.1235872 · Cited by 704 · cited 2×

A system for the continuous directed evolution of biomolecules

Esvelt, K. M., Carlson, J. C., & Liu, D. R. (2011) · Nature · doi:10.1038/nature09929 · Cited by 699

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

Van den Abbeele, P., Belzer, C., Goossens, M., Kleerebezem, M., De Vos, W. M., Thas, O., De Weirdt, R., Kerckhof, F.-M., & Van de Wiele, T. (2013) · The ISME Journal · doi:10.1038/ismej.2012.158 · Cited by 638

Bacterial colonization factors control specificity and stability of the gut microbiota

Lee, S. M., Donaldson, G. P., Mikulski, Z., Boyajian, S., Ley, K., & Mazmanian, S. K. (2013) · Nature · doi:10.1038/nature12447 · Cited by 626

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

Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron

Deriu, E., Liu, J. Z., Pezeshki, M., Edwards, R. A., Ochoa, R. J., Contreras, H., Libby, S. J., Fang, F. C., & Raffatellu, M. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.06.007 · Cited by 550

γ-Butyrobetaine Is a Proatherogenic Intermediate in Gut Microbial Metabolism of L-Carnitine to TMAO

Koeth, R. A., Levison, B. S., Culley, M. K., Buffa, J. A., Wang, Z., Gregory, J. C., Org, E., Wu, Y., Li, L., Smith, J. D., et al. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.006 · Cited by 546

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

Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10

Steidler, L., Neirynck, S., Huyghebaert, N., Snoeck, V., Vermeire, A., Goddeeris, B., Cox, E., Remon, J. P., & Remaut, E. (2003) · Nature Biotechnology · doi:10.1038/nbt840 · Cited by 542

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013) · Nature · doi:10.1038/nature12212 · Cited by 542

Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants

Bergström, A., Skov, T. H., Bahl, M. I., Roager, H. M., Christensen, L. B., Ejlerskov, K. T., Mølgaard, C., Michaelsen, K. F., & Licht, T. R. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00342-14 · Cited by 532

Synthetic circuits integrating logic and memory in living cells

Siuti, P., Yazbek, J., & Lu, T. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2510 · Cited by 531

Short-Chain Fatty Acids Regulate the Enteric Neurons and Control Gastrointestinal Motility in Rats

Soret, R., Chevalier, J., De Coppet, P., Poupeau, G., Derkinderen, P., Segain, J. P., & Neunlist, M. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.01.053 · Cited by 530

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

Lu, T. K., & Collins, J. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800442106 · Cited by 529

Focused specificity of intestinal TH17 cells towards commensal bacterial antigens

Yang, Y., Torchinsky, M. B., Gobert, M., Xiong, H., Xu, M., Linehan, J. L., Alonzo, F., Ng, C., Chen, A., Lin, X., et al. (2014) · Nature · doi:10.1038/nature13279 · Cited by 520

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

Haberman, Y., Tickle, T. L., Dexheimer, P. J., Kim, M.-O., Tang, D., Karns, R., Baldassano, R. N., Noe, J. D., Rosh, J., Markowitz, J., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci75436 · Cited by 519

The outer mucus layer hosts a distinct intestinal microbial niche

Li, H., Limenitakis, J. P., Fuhrer, T., Geuking, M. B., Lawson, M. A., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J. A., Rupp, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9292 · Cited by 511

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

Fischbach, M. A., & Sonnenburg, J. L. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.002 · Cited by 507

Amplifying Genetic Logic Gates

Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P., & Endy, D. (2013) · Science · doi:10.1126/science.1232758 · Cited by 505

Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations

Zhang, C., Zhang, M., Pang, X., Zhao, Y., Wang, L., & Zhao, L. (2012) · The ISME Journal · doi:10.1038/ismej.2012.27 · Cited by 499

Diet and the development of the human intestinal microbiome

Voreades, N., Kozil, A., & Weir, T. L. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00494 · Cited by 498

Identifying personal microbiomes using metagenomic codes

Franzosa, E. A., Huang, K., Meadow, J. F., Gevers, D., Lemon, K. P., Bohannan, B. J. M., & Huttenhower, C. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1423854112 · Cited by 497

Vitamin B 12 as a Modulator of Gut Microbial Ecology

Degnan, P. H., Taga, M. E., & Goodman, A. L. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.002 · Cited by 488

Transmission of Atherosclerosis Susceptibility with Gut Microbial Transplantation

Gregory, J. C., Buffa, J. A., Org, E., Wang, Z., Levison, B. S., Zhu, W., Wagner, M. A., Bennett, B. J., Li, L., DiDonato, J. A., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.618249 · Cited by 486

Quantifying cellular capacity identifies gene expression designs with reduced burden

Ceroni, F., Algar, R., Stan, G.-B., & Ellis, T. (2015) · Nature Methods · doi:10.1038/nmeth.3339 · Cited by 484

A Meta-Analysis of Probiotic Efficacy for Gastrointestinal Diseases

Ritchie, M. L., & Romanuk, T. N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034938 · Cited by 474

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids

Lukovac, S., Belzer, C., Pellis, L., Keijser, B. J., de Vos, W. M., Montijn, R. C., & Roeselers, G. (2014) · mBio · doi:10.1128/mbio.01438-14 · Cited by 474

Programmable probiotics for detection of cancer in urine

Danino, T., Prindle, A., Kwong, G. A., Skalak, M., Li, H., Allen, K., Hasty, J., & Bhatia, S. N. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa3519 · Cited by 467

Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract

Kommineni, S., Bretl, D. J., Lam, V., Chakraborty, R., Hayward, M., Simpson, P., Cao, Y., Bousounis, P., Kristich, C. J., & Salzman, N. H. (2015) · Nature · doi:10.1038/nature15524 · Cited by 458

Quantitative imaging of gut microbiota spatial organization

Earle, K. A., Billings, G., Sigal, M., Lichtman, J. S., Hansson, G. C., Elias, J. E., Amieva, M. R., Huang, K. C., & Sonnenburg, J. L. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.002 · Cited by 433

Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

Ando, H., Lemire, S., Pires, D. P., & Lu, T. K. (2015) · Cell Systems · doi:10.1016/j.cels.2015.08.013 · Cited by 426

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

Levy, R., & Borenstein, E. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300926110 · Cited by 405

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

Chan, C. T. Y., Lee, J. W., Cameron, D. E., Bashor, C. J., & Collins, J. J. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.1979 · Cited by 399

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

Cullen, T. W., Schofield, W. B., Barry, N. A., Putnam, E. E., Rundell, E. A., Trent, M. S., Degnan, P. H., Booth, C. J., Yu, H., & Goodman, A. L. (2015) · Science · doi:10.1126/science.1260580 · Cited by 395

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

Mimee, M., Tucker, A. C., Voigt, C. A., & Lu, T. K. (2015) · Cell Systems · doi:10.1016/j.cels.2015.06.001 · Cited by 387

Probiotics for the prevention of allergy: A systematic review and meta-analysis of randomized controlled trials

Cuello-Garcia, C. A., Brożek, J. L., Fiocchi, A., Pawankar, R., Yepes-Nuñez, J. J., Terracciano, L., Gandhi, S., Agarwal, A., Zhang, Y., & Schünemann, H. J. (2015) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2015.04.031 · Cited by 383

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance

Ferreyra, J. A., Wu, K. J., Hryckowian, A. J., Bouley, D. M., Weimer, B. C., & Sonnenburg, J. L. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.003 · Cited by 378

A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism

Russell, A. B., Wexler, A. G., Harding, B. N., Whitney, J. C., Bohn, A. J., Goo, Y. A., Tran, B. Q., Barry, N. A., Zheng, H., Peterson, S. B., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.07.007 · Cited by 372

Programmable bacteria detect and record an environmental signal in the mammalian gut

Kotula, J. W., Kerns, S. J., Shaket, L. A., Siraj, L., Collins, J. J., Way, J. C., & Silver, P. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1321321111 · Cited by 361

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

Seedorf, H., Griffin, N. W., Ridaura, V. K., Reyes, A., Cheng, J., Rey, F. E., Smith, M. I., Simon, G. M., Scheffrahn, R. H., Woebken, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.008 · Cited by 360

Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & Gordon, J. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319470110 · Cited by 355

Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut

Shulzhenko, N., Morgun, A., Hsiao, W., Battle, M., Yao, M., Gavrilova, O., Orandle, M., Mayer, L., Macpherson, A. J., McCoy, K. D., et al. (2011) · Nature Medicine · doi:10.1038/nm.2505 · Cited by 349

No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens

Sassone-Corsi, M., & Raffatellu, M. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1403169 · Cited by 328

Modulation of immune development and function by intestinal microbiota

Kabat, A. M., Srinivasan, N., & Maloy, K. J. (2014) · Trends in Immunology · doi:10.1016/j.it.2014.07.010 · Cited by 314

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

Farzadfard, F., & Lu, T. K. (2014) · Science · doi:10.1126/science.1256272 · Cited by 298

Orally administered L. lactis secreting an anti-TNF Nanobody demonstrate efficacy in chronic colitis

Vandenbroucke, K., de Haard, H., Beirnaert, E., Dreier, T., Lauwereys, M., Huyck, L., Van Huysse, J., Demetter, P., Steidler, L., Remaut, E., et al. (2010) · Mucosal Immunology · doi:10.1038/mi.2009.116 · Cited by 289

Sur un microbe invisible antagoniste des bacilles dysenteriques

D'Herelle, M. F. (1961) · Americanae (AECID Library) · Cited by 288

An integrative view of microbiome-host interactions in inflammatory bowel diseases

Wlodarska, M., Kostic, A. D., & Xavier, R. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.008 · Cited by 287

Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity

Chen, Z., Guo, L., Zhang, Y., L. Walzem, R., Pendergast, J. S., Printz, R. L., Morris, L. C., Matafonova, E., Stien, X., Kang, L., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72517 · Cited by 277

Probiotics for prevention of atopic diseases in infants: systematic review and meta-analysis

Zuccotti, G., Meneghin, F., Aceti, A., Barone, G., Callegari, M. L., Di Mauro, A., Fantini, M. P., Gori, D., Indrio, F., Maggio, L., et al. (2015) · Allergy · doi:10.1111/all.12700 · Cited by 273

Spatial organization of intestinal microbiota in the mouse ascending colon

Nava, G. M., Friedrichsen, H. J., & Stappenbeck, T. S. (2011) · The ISME Journal · doi:10.1038/ismej.2010.161 · Cited by 270

Engineered commensal bacteria reprogram intestinal cells into glucose-responsive insulin-secreting cells for the treatment of diabetes

Duan, F. F., Liu, J. H., & March, J. C. (2015) · Diabetes · doi:10.2337/db14-0635 · Cited by 263

Movers and shakers: Influence of bacteriophages in shaping the mammalian gut microbiota

Mills, S., Shanahan, F., Stanton, C., Hill, C., Coffey, A., & Ross, R. P. (2013) · Gut Microbes · doi:10.4161/gmic.22371 · Cited by 261

Digoxin-Inactivating Bacteria: Identification in Human Gut Flora

Dobkin, J. F., Saha, J. R., Butler, V. P., Neu, H. C., & Lindenbaum, J. (1983) · Science · doi:10.1126/science.6836275 · Cited by 259

Food-Grade Bacteria Expressing Elafin Protect Against Inflammation and Restore Colon Homeostasis

Motta, J.-P., Bermúdez-Humarán, L. G., Deraison, C., Martin, L., Rolland, C., Rousset, P., Boue, J., Dietrich, G., Chapman, K., Kharrat, P., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004212 · Cited by 257

Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model

Duan, F., & March, J. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001294107 · Cited by 247

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

Wu, M., McNulty, N. P., Rodionov, D. A., Khoroshkin, M. S., Griffin, N. W., Cheng, J., Latreille, P., Kerstetter, R. A., Terrapon, N., Henrissat, B., et al. (2015) · Science · doi:10.1126/science.aac5992 · Cited by 245

Phage therapy gets revitalized

Reardon, S. (2014) · Nature · doi:10.1038/510015a · Cited by 241

Prebiotics, probiotics, synbiotics, and the immune system: experimental data and clinical evidence

Frei, R., Akdis, M., & O’Mahony, L. (2015) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000151 · Cited by 240

Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease

(2014) · Advances in Experimental Medicine and Biology · doi:10.1007/978-1-4939-0897-4 · Cited by 232

Reversing Bacterial Resistance to Antibiotics by Phage-Mediated Delivery of Dominant Sensitive Genes

Edgar, R., Friedman, N., Molshanski-Mor, S., & Qimron, U. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.05741-11 · Cited by 217

Use of Genetically Engineered Phage To Deliver Antimicrobial Agents to Bacteria: an Alternative Therapy for Treatment of Bacterial Infections

Westwater, C., Kasman, L. M., Schofield, D. A., Werner, P. A., Dolan, J. W., Schmidt, M. G., & Norris, J. S. (2003) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.47.4.1301-1307.2003 · Cited by 214

Pathways and functions of gut microbiota metabolism impacting host physiology

Krishnan, S., Alden, N., & Lee, K. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.08.015 · Cited by 212

Further Investigations on the Nature of Ultra-Microscopic Viruses and their Cultivation

Twort, F. W. (1936) · Journal of Hygiene · doi:10.1017/s0022172400043606 · Cited by 210

Reversal of autoimmune diabetes by restoration of antigen-specific tolerance using genetically modified Lactococcus lactis in mice

Takiishi, T., Korf, H., Van Belle, T. L., Robert, S., Grieco, F. A., Caluwaerts, S., Galleri, L., Spagnuolo, I., Steidler, L., Van Huynegem, K., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci60530 · Cited by 201

Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel

Dey, N., Wagner, V. E., Blanton, L. V., Cheng, J., Fontana, L., Haque, R., Ahmed, T., & Gordon, J. I. (2015) · Cell · doi:10.1016/j.cell.2015.08.059 · Cited by 195

Therapy of Experimental Pseudomonas Infections with a Nonreplicating Genetically Modified Phage

Hagens, S., Habel, A., von Ahsen, U., von Gabain, A., & Bläsi, U. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.10.3817-3822.2004 · Cited by 187

Programming adaptive control to evolve increased metabolite production

Chou, H. H., & Keasling, J. D. (2013) · Nature Communications · doi:10.1038/ncomms3595 · Cited by 184

Engineering the gut microbiota to treat hyperammonemia

Shen, T.-C. D., Albenberg, L., Bittinger, K., Chehoud, C., Chen, Y.-Y., Judge, C. A., Chau, L., Ni, J., Sheng, M., Lin, A., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci79214 · Cited by 180

Prevention of vaginal SHIV transmission in macaques by a live recombinant Lactobacillus

Lagenaur, L. A., Sanders-Beer, B. E., Brichacek, B., Pal, R., Liu, X., Liu, Y., Yu, R., Venzon, D., Lee, P. P., & Hamer, D. H. (2011) · Mucosal Immunology · doi:10.1038/mi.2011.30 · Cited by 175

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

McDonald, J. A. K., Schroeter, K., Fuentes, S., Heikamp-deJong, I., Khursigara, C. M., de Vos, W. M., & Allen-Vercoe, E. (2013) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2013.08.008 · Cited by 175

Targeted DNA degradation using a CRISPR device stably carried in the host genome

Caliando, B. J., & Voigt, C. A. (2015) · Nature Communications · doi:10.1038/ncomms7989 · Cited by 173

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

Auchtung, J. M., Robinson, C. D., & Britton, R. A. (2015) · Microbiome · doi:10.1186/s40168-015-0106-5 · Cited by 168

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

Ellefson, J. W., Meyer, A. J., Hughes, R. A., Cannon, J. R., Brodbelt, J. S., & Ellington, A. D. (2014) · Nature Biotechnology · doi:10.1038/nbt.2714 · Cited by 162

Probiotic-based strategies for therapeutic and prophylactic use against multiple gastrointestinal diseases

Varankovich, N. V., Nickerson, M. T., & Korber, D. R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00685 · Cited by 161

Oral Delivery of Glutamic Acid Decarboxylase (GAD)-65 and IL10 by Lactococcus lactis Reverses Diabetes in Recent-Onset NOD Mice

Robert, S., Gysemans, C., Takiishi, T., Korf, H., Spagnuolo, I., Sebastiani, G., Van Huynegem, K., Steidler, L., Caluwaerts, S., Demetter, P., et al. (2014) · Diabetes · doi:10.2337/db13-1236 · Cited by 160

Capacity of Human Nisin- and Pediocin-Producing Lactic Acid Bacteria To Reduce Intestinal Colonization by Vancomycin-Resistant Enterococci

Millette, M., Cornut, G., Dupont, C., Shareck, F., Archambault, D., & Lacroix, M. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02150-07 · Cited by 158

Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system

Kiro, R., Shitrit, D., & Qimron, U. (2014) · RNA Biology · doi:10.4161/rna.27766 · Cited by 158

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

Walsh, C. J., Guinane, C. M., Hill, C., Ross, R. P., O’Toole, P. W., & Cotter, P. D. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0515-4 · Cited by 150

Diversity and dynamics of bacteriocins from human microbiome

Zheng, J., Gänzle, M. G., Lin, X. B., Ruan, L., & Sun, M. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12662 · Cited by 142

Policy: how to regulate faecal transplants

Smith, M. B., Kelly, C., & Alm, E. J. (2014) · Nature · doi:10.1038/506290a · Cited by 140

Butyrate elicits a metabolic switch in human colon cancer cells by targeting the pyruvate dehydrogenase complex

Blouin, J., Penot, G., Collinet, M., Nacfer, M., Forest, C. D., Laurent‐Puig, P., Coumoul, X., Barouki, R., Benelli, C., & Bortoli, S. (2010) · International Journal of Cancer · doi:10.1002/ijc.25599 · Cited by 137

GeneGuard: A Modular Plasmid System Designed for Biosafety

Wright, O., Delmans, M., Stan, G.-B. V., & Ellis, T. (2014) · ACS Synthetic Biology · doi:10.1021/sb500234s · Cited by 137

Phase 1b, multicenter, single blinded, placebo‐controlled, sequential dose escalation study to assess the safety and tolerability of topically applied AG013 in subjects with locally advanced head and neck cancer receiving induction chemotherapy

Limaye, S. A., Haddad, R. I., Cilli, F., Sonis, S. T., Colevas, A. D., Brennan, M. T., Hu, K. S., & Murphy, B. A. (2013) · Cancer · doi:10.1002/cncr.28365 · Cited by 131

Xylan-regulated delivery of human keratinocyte growth factor-2 to the inflamed colon by the human anaerobic commensal bacterium Bacteroides ovatus

Hamady, Z. Z. R., Scott, N., Farrar, M. D., Lodge, J. P. A., Holland, K. T., Whitehead, T., & Carding, S. R. (2010) · Gut · doi:10.1136/gut.2008.176131 · Cited by 131

AG013, a mouth rinse formulation of Lactococcus lactis secreting human Trefoil Factor 1, provides a safe and efficacious therapeutic tool for treating oral mucositis

Caluwaerts, S., Vandenbroucke, K., Steidler, L., Neirynck, S., Vanhoenacker, P., Corveleyn, S., Watkins, B. A., Sonis, S. T., Coulie, B. J., & Rottiers, P. (2010) · Oral Oncology · doi:10.1016/j.oraloncology.2010.04.008 · Cited by 129

3-D Intestinal Scaffolds for Evaluating the Therapeutic Potential of Probiotics

Costello, C. M., Sorna, R. M., Goh, Y.-L., Cengic, I., Jain, N. K., & March, J. C. (2014) · Molecular Pharmaceutics · doi:10.1021/mp5001422 · Cited by 115

In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli

Weiss, M., Denou, E., Bruttin, A., Serra-Moreno, R., Dillmann, M.-L., & Brüssow, H. (2009) · Virology · doi:10.1016/j.virol.2009.07.020 · Cited by 113

Treatment of colitis with a commensal gut bacterium engineered to secrete human tgf-β1 under the control of dietary xylan

Hamady, Z. Z. R., Scott, N. A., Farrar, M. D., Wadhwa, M., Dilger, P., Whitehead, T. R., Thorpe, R., Holland, K. T., Lodge, P. J. A., & Carding, S. R. (2010) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21565 · Cited by 110

Engineered Phagemids for Nonlytic, Targeted Antibacterial Therapies

Krom, R. J., Bhargava, P., Lobritz, M. A., & Collins, J. J. (2015) · Nano Letters · doi:10.1021/acs.nanolett.5b01943 · Cited by 108

Effect of probiotic administration on the intestinal microbiota, current knowledge and potential applications

de LeBlanc, A. D. M., & LeBlanc, J. G. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i44.16518 · Cited by 104

Fecal Microbiota Transplantation in Inflammatory Bowel Disease: Beyond the Excitement

Ianiro, G., Bibbò, S., Scaldaferri, F., Gasbarrini, A., & Cammarota, G. (2014) · Medicine · doi:10.1097/md.0000000000000097 · Cited by 101

Intestinal colonization by enteroaggregative Escherichia coli supports long‐term bacteriophage replication in mice

Maura, D., Morello, E., du Merle, L., Bomme, P., Bouguénec, C. L., & Debarbieux, L. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02644.x · Cited by 99

Modular, Multi-Input Transcriptional Logic Gating with Orthogonal LacI/GalR Family Chimeras

Shis, D. L., Hussain, F., Meinhardt, S., Swint‐Kruse, L., & Bennett, M. R. (2014) · ACS Synthetic Biology · doi:10.1021/sb500262f · Cited by 93

Probiotic treatments for induction and maintenance of remission in inflammatory bowel diseases: a meta-analysis of randomized controlled trials

Fujiya, M., Ueno, N., & Kohgo, Y. (2013) · Clinical Journal of Gastroenterology · doi:10.1007/s12328-013-0440-8 · Cited by 91

Bacteriophage therapies re-enter clinical trials

Kingwell, K. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4695 · Cited by 79

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

Greenblum, S. I., Chiu, H.-C., Levy, R., Carr, R., & Borenstein, E. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.04.001 · Cited by 66

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota.

Mimee, M., Tucker, A. C., Voigt, C. A., & Lu, T. (2016) · Cell Systems · doi:10.1016/j.cels.2016.03.007 · Cited by 62

Erratum: The gut microbiota shapes intestinal immune responses during health and disease

Round, J. L., & Mazmanian, S. K. (2009) · Nature reviews. Immunology · doi:10.1038/nri2614 · Cited by 61

Fecal Microbiota Transplantation in Inflammatory Bowel Disease

Reinisch, W. (2017) · Digestive Diseases · doi:10.1159/000449092 · Cited by 56

Survival of the probiotic Escherichia coli Nissle 1917 (EcN) in the gastrointestinal tract given in combination with oral mesalamine to healthy volunteers

Joeres-Nguyen-Xuan, T. H., Böhm, S., Joeres, L., Schulze, J., & Kruis, W. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21042 · Cited by 52

Evolutionary Stability of a Refactored Phage Genome

Springman, R., Molineux, I. J., Duong, C., Bull, R. J., & Bull, J. J. (2012) · ACS Synthetic Biology · doi:10.1021/sb300040v · Cited by 31

Microbial cocktails join fecal transplants in IBD treatment trials

Ratner, M. (2015) · Nature Biotechnology · doi:10.1038/nbt0815-787 · Cited by 28

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

Tanoue, T., Morita, S., Plichta, D. R., Skelly, A. N., Suda, W., Sugiura, Y., Narushima, S., Vlamakis, H., Motoo, I., Sugita, K., et al. (2019) · Nature · doi:10.1038/s41586-019-0878-z · Cited by 1,145

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., Gerber, G. K., Way, J. C., & Silver, P. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3879 · Cited by 426

Microbiota and metabolic diseases

Pascale, A., Marchesi, N., Marelli, C., Coppola, A., Luzi, L., Govoni, S., Giustina, A., & Gazzaruso, C. (2018) · Endocrine · doi:10.1007/s12020-018-1605-5 · Cited by 423

Synthetic biology 2020–2030: six commercially-available products that are changing our world

Voigt, C. A. (2020) · Nature Communications · doi:10.1038/s41467-020-20122-2 · Cited by 294

The effect of microbiome modulation on the intestinal health of poultry

Kogut, M. H. (2019) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2018.10.008 · Cited by 283