Cultured microbes represent a substantial fraction of the human and mouse gut microbiota
Open accessAbstract
During the last 15 years, molecular techniques have been preferred over culture-based approaches for the study of mammalian gut microbiota, i.e. the communities of microorganisms dwelling in the intestine of mammals. The main reason is the belief that the majority of gut bacteria, especially strict anaerobes, escape cultivation. Despite numerous such statements in publications, the literature does not provide a clear overview on the subject. In the present manuscript, we highlight recent work on the cultivation of bacteria from the intestine of mammals, review the literature and provide novel data pertaining to cultured fractions of mammalian gut microbiota. These data show that, despite marked inter-sample variations, 35 to 65% of molecular species detected by sequencing have representative strains in culture.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
A reasonably large proportion of the bacterial and archaeal component of the human microbiota has already been cultured, while viruses and fungi remain underrepresented.
“In fact, a reasonably large proportion of the bacterial and archaeal component of our microbiota has already been cultured 41 (viruses and fungi remain underrepresented)”
From Human microbiome myths and misconceptions (2023) · cites this paper as [41]
The Conclusion (page unavailable) says that roughly 50% of human gut prokaryotes being cultured is a reasonable, though very rough, estimate. Figure 1 also identifies the analysis as covering gut bacteria and archaea. The citing sentence extends this gut-specific finding to the human microbiota generally; the parenthetical about viruses and fungi follows the citation and is not established by these passages. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
1 retracted
Lagier, J.-C., Khelaifia, S., Alou, M. T., Ndongo, S., Dione, N., Hugon, P., Caputo, A., Cadoret, F., Traore, S. I., Seck, E. H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.203 · Cited by 951 · see citing works
RetractedBasic 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
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
AFRC, R. F. (1989) · Journal of Applied Bacteriology · doi:10.1111/j.1365-2672.1989.tb05105.x · Cited by 4,831 · see citing works
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
Yilmaz, P., Parfrey, L., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., & Glöckner, F. (2013) · Nucleic Acids Res. · doi:10.1093/nar/gkt1209 · Cited by 3,547 · see citing works
Formation of propionate and butyrate by the human colonic microbiota
Louis, P., & Flint, H. J. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13589 · Cited by 3,028 · see citing works
Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., SCHLEIFER, K. H., Whitman, W. B., Euzéby, J. P., Amann, R., & Rossello-Mora, R. A. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3330 · Cited by 2,563 · see citing works
Human gut microbes impact host serum metabolome and insulin sensitivity
Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., et al. (2016) · Nature · doi:10.1038/nature18646 · Cited by 2,116 · see citing works
Chun, J., Lee, J., Jung, Y., Kim, M., Kim, S., Kim, B. K., & Lim, Y. (2007) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64915-0 · Cited by 2,096 · see citing works
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijs.0.02873-0 · Cited by 2,094 · see citing works
Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans
Sender, R., Fuchs, S., & Milo, R. (2016) · Cell · doi:10.1016/j.cell.2016.01.013 · Cited by 2,050 · see citing works
A new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039 · see citing works
Staley, J. T., & Konopka, A. E. (1985) · Annual Review of Microbiology · doi:10.1146/annurev.mi.39.100185.001541 · Cited by 1,512 · see citing works
Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.11.4799-4807.1999 · Cited by 1,490 · see citing works
Lamas, B., Richard, M. L., Leducq, V., Pham, H.-P., Michel, M.-L., Da Costa, G., Bridonneau, C., Jegou, S., Hoffmann, T. W., Natividad, J. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4102 · Cited by 1,482 · see citing works
Marine microorganisms and global nutrient cycles
Arrigo, K. R. (2004) · Nature · doi:10.1038/nature04159 · Cited by 1,445 · see citing works
Functional overlap of the Arabidopsis leaf and root microbiota
Bai, Y., Müller, D. B., Srinivas, G., Garrido‐Oter, R., Potthoff, E., Rott, M., Dombrowski, N., Münch, P. C., Spaepen, S., Remus‐Emsermann, M. N. P., et al. (2015) · Nature · doi:10.1038/nature16192 · Cited by 1,322 · see citing works
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
Browne, H. P., Forster, S. C., Anonye, B. O., Kumar, N., Neville, B. A., Stares, M. D., Goulding, D., & Lawley, T. D. (2016) · Nature · doi:10.1038/nature17645 · Cited by 1,299 · see citing works
Probiotics in man and animals.
Fuller, R. (1989) · PubMed · Cited by 1,292 · see citing works
Gut immune maturation depends on colonization with a host-specific microbiota
Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241 · see citing works
Faecalibacterium prausnitzii and human intestinal health
Miquel, S., Martín, R., Rossi, O., Bermúdez‐Humarán, L. G., Chatel, J., Sokol, H., Thomas, M., Wells, J. M., & Langella, P. (2013) · Current Opinion in Microbiology · doi:10.1016/j.mib.2013.06.003 · Cited by 1,239 · see citing works
Scaling laws predict global microbial diversity
Locey, K. J., & Lennon, J. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521291113 · Cited by 1,184 · 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
Estimating prokaryotic diversity and its limits
Curtis, T., Sloan, W., & Scannell, J. (2002) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.142680199 · Cited by 1,175 · see citing works
Human Fecal Flora: The Normal Flora of 20 Japanese-Hawaiians
Moore, W. E. C., & Holdeman, L. V. (1974) · Applied Microbiology · doi:10.1128/am.27.5.961-979.1974 · Cited by 1,144 · see citing works
Akkermansia muciniphila and its role in regulating host functions
Derrien, M., Belzer, C., & de Vos, W. M. (2017) · Microbial Pathogenesis · doi:10.1016/j.micpath.2016.02.005 · Cited by 1,044 · cited 1× · see citing works
“Its role in the development of metabolic disorders has been studied in detail and beneficial attributes have been associated with this species.(37) Other bacteria of particular interest are butyrate producers, as this shortchain fatty acid is an important product of bacterial fermentation in the intestine, usually det…”
BackgroundLangendijk-Genevaux, P. S., Schut, F., Jansen, G. J., Raangs, G. C., Kamphuis, G. R., Wilkinson, M. H. F., & Welling, G. W. (1995) · Applied and Environmental Microbiology · doi:10.1128/aem.61.8.3069-3075.1995 · Cited by 974 · see citing works
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907 · see citing works
(1938) · Tubercle · doi:10.1016/s0041-3879(38)80086-6 · Cited by 906 · see citing works
Review: Diversity of Microorganisms in Global Fermented Foods and Beverages
Tamang, J. P., Watanabe, K., & Holzapfel, W. H. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00377 · Cited by 824 · see citing works
Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 779 · see citing works
Database resources of the National Center for Biotechnology Information
Sayers, E. W., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M. N., Edgar, R., Federhen, S., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn741 · Cited by 767 · see citing works
Duncan, S. H., Hold, G. L., Harmsen, H. J. M., Stewart, C. S., & Flint, H. J. (2002) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-52-6-2141 · Cited by 735 · 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
High-fat diet alters gut microbiota physiology in mice
Daniel, H., Gholami, A. M., Berry, D., Desmarchelier, C., Hahne, H., Loh, G., Mondot, S., Lepage, P., Rothballer, M., Walker, A., et al. (2013) · The ISME Journal · doi:10.1038/ismej.2013.155 · Cited by 680 · see citing works
Self-citationOrmerod, K. L., Wood, D., Lachner, N., Gellatly, S. L., Daly, J. N., Parsons, J. D., Dal’Molin, C. G. D. O., Palfreyman, R. W., Nielsen, L. K., Cooper, M. A., et al. (2016) · Microbiome · doi:10.1186/s40168-016-0181-2 · Cited by 675 · see citing works
Tannock, G. W., Munro, K., Harmsen, H. J. M., Welling, G. W., Smart, J., & Gopal, P. K. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2578-2588.2000 · Cited by 671 · see citing works
Medium Without Rumen Fluid for Nonselective Enumeration and Isolation of Rumen Bacteria
Caldwell, D. R., & Bryant, M. P. (1966) · Applied Microbiology · doi:10.1128/am.14.5.794-801.1966 · Cited by 623 · see citing works
Human colonic biota studied by ribosomal DNA sequence analysis
Wilson, K. H., & Blitchington, R. B. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.7.2273-2278.1996 · Cited by 526 · see citing works
Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B. U., Meier‐Kolthoff, J. P., Kumar, N., Bresciani, A., Martínez, I., Just, S., Ziegler, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.131 · Cited by 508 · see citing works
Self-citationHoldeman, L. V., Good, I. J., & Moore, W. E. (1976) · Applied and Environmental Microbiology · doi:10.1128/aem.31.3.359-375.1976 · Cited by 498 · see citing works
Lagkouvardos, I., Joseph, D., Kapfhammer, M., Giritli, S., Horn, M., Haller, D., & Clavel, T. (2016) · Scientific Reports · doi:10.1038/srep33721 · Cited by 498 · see citing works
Self-citationBrugiroux, S., Beutler, M., Pfann, C., Garzetti, D., Ruscheweyh, H., Ring, D., Diehl, M., Herp, S., Loetscher, Y., Hussain, S., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.215 · Cited by 463 · see citing works
Self-citationHayashi, H., Sakamoto, M., & Benno, Y. (2002) · Microbiology and Immunology · doi:10.1111/j.1348-0421.2002.tb02731.x · Cited by 458 · see citing works
A metagenomic insight into our gut's microbiome
Lepage, P., Leclerc, M., Joossens, M., Mondot, S., Blottière, H. M., Raes, J., Ehrlich, S. D., & Dore, J. M. (2012) · Gut · doi:10.1136/gutjnl-2011-301805 · Cited by 371 · see citing works
Cell factories for insulin production
Baeshen, N. A., Baeshen, M. N., Sheikh, A., Bora, R. S., Ahmed, M. M. M., Ramadan, H. A. I., Saini, K. S., & Redwan, E. M. M. M. (2014) · Microbial Cell Factories · doi:10.1186/s12934-014-0141-0 · Cited by 362 · see citing works
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 361 · see citing works
The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri
Frese, S. A., Benson, A. K., Tannock, G. W., Loach, D. M., Kim, J., Zhang, M., Oh, P. L., Heng, N. C. K., Patil, P. B., Juge, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001314 · Cited by 309 · see citing works
Medium Without Rumen Fluid for Nonselective Enumeration and Isolation of Rumen Bacteria
Caldwell, D. R., & Bryant, M. P. (1966) · Applied Microbiology · doi:10.1128/aem.14.5.794-801.1966 · Cited by 302 · see citing works
Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal
Bui, T. P. N., Ritari, J., Boeren, S. A., de Waard, P., Plugge, C. M., & de Vos, W. M. (2015) · Nature Communications · doi:10.1038/ncomms10062 · Cited by 272 · see citing works
ASSOCIATION OF GERMFREE MICE WITH BACTERIA ISOLATED FROM NORMAL MICE
Schaedler, R. W., Dubos, R. J., & Costello, R. L. (1965) · The Journal of Experimental Medicine · doi:10.1084/jem.122.1.77 · Cited by 258 · see citing works
Phylogeny, culturing, and metagenomics of the human gut microbiota
Walker, A. W., Duncan, S. H., Louis, P., & Flint, H. J. (2014) · Trends in Microbiology · doi:10.1016/j.tim.2014.03.001 · Cited by 239 · see citing works
Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
Pope, P. B., Smith, W. J. M., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C., & Morrison, M. (2011) · Science · doi:10.1126/science.1205760 · Cited by 225 · see citing works
Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling
Lau, J. Y. F., Whelan, F., Herath, I., Lee, C., Collins, S. M., Berčík, P., & Surette, M. G. (2016) · Genome Medicine · doi:10.1186/s13073-016-0327-7 · Cited by 219 · see citing works
Genome-based design of a cell-free culture medium for Tropheryma whipplei
Renesto, P., Crapoulet, N., Ogata, H., Scola, B. L., Vestris, G., Claverie, J., & Raoult, D. (2003) · The Lancet · doi:10.1016/s0140-6736(03)14071-8 · Cited by 203 · see citing works
Growth and host interaction of mouse segmented filamentous bacteria in vitro
Schnupf, P., Gaboriau‐Routhiau, V., Gros, M., Friedman, R. C., Moya‐Nilges, M., Nigro, G., Cerf–Bensussan, N., & Sansonetti, P. J. (2015) · Nature · doi:10.1038/nature14027 · Cited by 175 · see citing works
Determining the culturability of the rumen bacterial microbiome
Creevey, C. J., Kelly, W. J., Henderson, G., & Leahy, S. C. (2014) · Microbial Biotechnology · doi:10.1111/1751-7915.12141 · Cited by 173 · see citing works
Insights into the bovine rumen plasmidome
Kav, A. B., Sasson, G., Jami, E., Doron‐Faigenboim, A., Benhar, I., & Mizrahi, I. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116410109 · Cited by 150 · see citing works
THE FECAL FLORA OF VARIOUS STRAINS OF MICE. ITS BEARING ON THEIR SUSCEPTIBILITY TO ENDOTOXIN
Schaedler, R. W., & Dubos, R. J. (1962) · The Journal of Experimental Medicine · doi:10.1084/jem.115.6.1149 · Cited by 143 · see citing works
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
Rozov, R., Kav, A. B., Bogumil, D. D., Shterzer, N., Halperin, E., Mizrahi, I., & Ron Shamir, A. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw651 · Cited by 142 · see citing works
Fecal bacteriology of colonic polyp patients and control patients.
Finegold, S. M., Flora, D. J., Attebery, H. R., & Sutter, V. L. (1975) · PubMed · Cited by 137 · see citing works
Bui, T. P. N., Shetty, S. A., Lagkouvardos, I., Ritari, J., Chamlagain, B., Douillard, F. P., Paulin, L. G., Piironen, V. I., Clavel, T., Plugge, C. M., et al. (2016) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12483 · Cited by 131 · see citing works
Self-citationEffect of a partially chemically defined diet on normal human fecal flora
Attebery, H. R., Sutter, V. L., & Finegold, S. M. (1972) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/25.12.1391 · Cited by 130 · see citing works
Kläring, K., Hanske, L., Bui, T. P. N., Charrier, C., Blaut, M., Haller, D., Plugge, C. M., & Clavel, T. (2013) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.051441-0 · Cited by 125 · see citing works
Self-citationWlodarczyk, V., Pinabiaux, C., & Goumi, A. (2026) · HAL (Le Centre pour la Communication Scientifique Directe) · doi:10.1146/annurev · Cited by 125 · see citing works
Hydrogen-oxidizing Methane Bacteria I. Cultivation and Methanogenesis
Bryant, M. P., McBride, B. C., & WOLFE, R. S. (1968) · Journal of Bacteriology · doi:10.1128/jb.95.3.1118-1123.1968 · Cited by 99 · see citing works
Élie Metchnikoff (1845–1916): celebrating 100 years of cellular immunology and beyond
Underhill, D. M., Gordon, S., Imhof, B. A., Núñez, G., & Bousso, P. (2016) · Nature reviews. Immunology · doi:10.1038/nri.2016.89 · Cited by 97 · see citing works
Types and Distribution of Anaerobic Bacteria in the Large Intestine of Pigs
Russell, E. G. (1979) · Applied and Environmental Microbiology · doi:10.1128/aem.37.2.187-193.1979 · Cited by 95 · see citing works
Ziemer, C. J. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03016-13 · Cited by 82 · see citing works
Principles of Enrichment, Isolation, Cultivation, and Preservation of Prokaryotes
Overmann, J. (2013) · Springer eBooks · doi:10.1007/978-3-642-30194-0_7 · Cited by 79 · see citing works
Self-citationStudies of the cultivable flora of normal human feces
van Houte, J., & Gibbons, R. J. (1966) · Antonie van Leeuwenhoek · doi:10.1007/bf02097463 · Cited by 69 · see citing works
Anaerobic bacteria from the large intestine of mice
Harris, M. A., Reddy, C. A., & Carter, G. R. (1976) · Applied and Environmental Microbiology · doi:10.1128/aem.31.6.907-912.1976 · Cited by 62 · see citing works
BacDive – The Bacterial Diversity Metadatabase in 2016
Söhngen, C., Podstawka, A., Bunk, B., Gleim, D., Vetcininova, A., Reimer, L. C., Ebeling, C., Pendarovski, C., & Overmann, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv983 · Cited by 61 · see citing works
Self-citationSuitability of Butyl Rubber Stoppers for Closing Anaerobic Roll Culture Tubes
Hungate, R. E., Smith, W. W., & Clarke, R. T. J. (1966) · Journal of Bacteriology · doi:10.1128/jb.91.2.908-909.1966 · Cited by 55 · see citing works
Microbiome sequencing: challenges and opportunities for molecular medicine
Clavel, T., Lagkouvardos, I., & Hiergeist, A. (2016) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2016.1184574 · Cited by 42 · see citing works
Self-citationPrinciples of Enrichment, Isolation, Cultivation and Preservation of Prokaryotes
Overmann, J. (2006) · Springer eBooks · doi:10.1007/0-387-30741-9_5 · Cited by 33 · see citing works
Self-citationWalker, A. W. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-31248-4_2 · Cited by 31 · see citing works
Changes in the microflora of man during long-term confinement.
Vm, S., Nn, L., Borisova, O. K., & Vy, P. (1971) · PubMed · Cited by 20 · see citing works
Noel, S. J. (2013) · Massey Research Online (Massey University) · Cited by 8 · see citing works
Ducluzeau, R., & Raibaud, P. (1969) · PubMed · Cited by 1 · see citing works
(2018) · Digital Commons@Becker (Washington University School of Medicine) · doi:10.1371/journal
Flagged first, then by citations
Research works printed but not linked: 2
- [33]33. Noel S. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD thesis 2013. Available at: http://mro.massey.ac.nz/handle/10179/4972
- [48]48. Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Diehl M, et al. Design of a defined mouse microbiota community to investigate colonization resistance mecha- nisms using a bottom-up approach. 2016; https://www. ncbi.nlm.nih.gov/pubmed/27869789
Cited by
Sorted by citations
Microbiome definition re-visited: old concepts and new challenges
Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00875-0 · Cited by 2,275 · see citing works
GABA-modulating bacteria of the human gut microbiota
Strandwitz, P., Kim, K. H., Terekhova, D., Liu, J. K., Sharma, A., Levering, J., McDonald, D., Dietrich, D., Ramadhar, T. R., Lekbua, A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0307-3 · Cited by 1,170 · see citing works
Lagkouvardos, I., Lesker, T. R., Hitch, T. C. A., Gálvez, E. J. C., Smit, N., Neuhaus, K., Wang, J., Baines, J. F., Abt, B., Stecher, B., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0637-2 · Cited by 777 · see citing works
Self-citationChicken Gut Microbiota: Importance and Detection Technology
Shang, Y., Kumar, S., Oakley, B. B., & Kim, W. K. (2018) · Frontiers in Veterinary Science · doi:10.3389/fvets.2018.00254 · Cited by 502 · see citing works
Lung microbiome: new insights into the pathogenesis of respiratory diseases
Li, R., Li, J., & Zhou, X. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01722-y · Cited by 466 · see citing works
Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome
Borda-Molina, D., Seifert, J., & Camarinha‐Silva, A. (2018) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2018.03.002 · Cited by 285 · see citing works
Moon, C., Young, W., Maclean, P., Cookson, A., & Bermingham, E. (2018) · MicrobiologyOpen · doi:10.1002/mbo3.677 · Cited by 223 · see citing works
Campanaro, S., Treu, L., Rodriguez‐R, L. M., Kovalovszki, A., Ziels, R. M., Maus, I., Zhu, X., Kougias, P., Basile, A., Luo, G., et al. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01679-y · Cited by 255 · see citing works
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity
Wylensek, D., Hitch, T. C. A., Riedel, T., Afrizal, A., Kumar, N., Wortmann, E., Liu, T., Devendran, S., Lesker, T. R., Hernández, S. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19929-w · Cited by 232 · see citing works
Self-citationHuman microbiome myths and misconceptions
Walker, A. W., & Hoyles, L. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01426-7 · Cited by 163 · see citing works
Smith, B. J., Miller, R. A., & Schmidt, T. M. (2021) · mSphere · doi:10.1128/msphere.00851-21 · Cited by 151 · see citing works
Accessing Bioactive Natural Products from the Human Microbiome
Milshteyn, A., Colosimo, D. A., & Brady, S. F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.05.013 · Cited by 147 · see citing works
Human Gut Microbiota: Toward an Ecology of Disease
Selber‐Hnatiw, S., Rukundo, B., Ahmadi, M., Akoubi, H., Al-Bizri, H., Aliu, A. F., Ambeaghen, T. U., Avetisyan, L., Bahar, I., Baird, A., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01265 · Cited by 145 · see citing works
Qin, P., Zou, Y., Dai, Y., Luo, G., Zhang, X., & Xiao, L. (2019) · Microorganisms · doi:10.3390/microorganisms7030078 · Cited by 131 · see citing works
Clavel, T., Neto, J. C. G., Lagkouvardos, I., & Ramer‐Tait, A. E. (2017) · Immunological Reviews · doi:10.1111/imr.12578 · Cited by 125 · see citing works
Self-citationThumann, T. A., Pferschy‐Wenzig, E., Moissl‐Eichinger, C., & Bauer, R. (2019) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2019.112153 · Cited by 101 · see citing works
Functions of the Microbiota for the Physiology of Animal Metaorganisms
Esser, D., Lange, J., Μαρίνος, Γ., Sieber, M., Best, L., Prasse, D., Bathia, J., Rühlemann, M. C., Boersch, K., Jaspers, C., et al. (2018) · Journal of Innate Immunity · doi:10.1159/000495115 · Cited by 90 · see citing works
Barlow, J. T., Leite, G., Romano, A. E., Sedighi, R., Chang, C. Y.-Y., Celly, S., Rezaie, A. R., Mathur, R., Pimentel, M., & Ismagilov, R. F. (2021) · Microbiome · doi:10.1186/s40168-021-01162-2 · Cited by 88 · see citing works
Hydrolytic Profile of the Culturable Gut Bacterial Community Associated With Hermetia illucens
Callegari, M., Jucker, C., Fusi, M., Leonardi, M. G., Daffonchio, D. G., Borin, S., Savoldelli, S., & Crotti, E. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01965 · Cited by 83 · see citing works
Alshehri, D., Saadah, O. I., Mosli, M. H., Edris, S., Al-Hindi, R. R., & Bahieldin, A. (2020) · Biomolecules and Biomedicine · doi:10.17305/bjbms.2020.5016 · Cited by 76 · see citing works
A Comprehensive Review of Thyroid Hormone Metabolism in the Gut and Its Clinical Implications
Fenneman, A. C., Bruinstroop, E., Nieuwdorp, M., van der Spek, A. H., & Boelen, A. (2022) · Thyroid · doi:10.1089/thy.2022.0491 · Cited by 76 · see citing works
Gnotobiotics: Past, present and future
Basic, M., & Bleich, A. (2019) · Laboratory Animals · doi:10.1177/0023677219836715 · Cited by 73 · see citing works
Gut microbiome: An intermediary to neurotoxicity
Dempsey, J. L., Little, M., & Cui, J. Y. (2019) · NeuroToxicology · doi:10.1016/j.neuro.2019.08.005 · Cited by 62 · see citing works
Anaerobic single‐cell dispensing facilitates the cultivation of human gut bacteria
Afrizal, A., Hitch, T. C. A., Viehof, A., Treichel, N. S., Riedel, T., Abt, B., Buhl, E. M., Kohlheyer, D., Overmann, J., & Clavel, T. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.15935 · Cited by 59 · see citing works
Self-citationInsights Into Culturomics of the Rumen Microbiome
Zehavi, T., Probst, M., & Mizrahi, I. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01999 · Cited by 58 · see citing works
Shine, E. E., & Crawford, J. M. (2021) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-080320-115307 · Cited by 55 · see citing works
Liu, C., Vervoort, J. J. M., Beekmann, K., Baccaro, M., Kamelia, L., Wesseling, S., & Rietjens, I. M. C. M. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c05890 · Cited by 51 · see citing works
Liu, C., Gan, R., Chen, D., Zheng, L., Ng, S. B., & Rietjens, I. M. C. M. (2023) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2023.2180478 · Cited by 50 · see citing works
Probiotics: Comprehensive Exploration of the Growth Promotion Mechanisms in Shrimps
Goh, J. X. H., Tan, L. T., Law, J. W., Khaw, K. Y., Zengin, G., Chan, K., Letchumanan, V., Lee, L., & Goh, B. H. (2023) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000324 · Cited by 50 · see citing works
Recent advances in culture-based gut microbiome research
Hitch, T. C. A., Afrizal, A., Riedel, T., Kioukis, A., Haller, D., Lagkouvardos, I., Overmann, J., & Clavel, T. (2021) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2021.151485 · Cited by 45 · see citing works
Self-citationLeyva, L. L., Brereton, N. J. B., & Koski, K. G. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.057 · Cited by 45 · see citing works
Kurt, F., Leventhal, G. E., Spalinger, M. R., Anthamatten, L., von Bieberstein, P. R., Menzi, C., Reichlin, M., Meola, M., Rosenthal, F., Rogler, G., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2177486 · Cited by 40 · see citing works
Noecker, C. A., Sánchez, J. M., Bisanz, J. E., Escalante, V., Alexander, M., Trepka, K. R., Heinken, A., Liu, Y., Dodd, D., Thiele, I., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002125 · Cited by 40 · see citing works
Trait biases in microbial reference genomes
Albright, S., & Louca, S. (2023) · Scientific Data · doi:10.1038/s41597-023-01994-7 · Cited by 40 · see citing works
Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health
Duncan, S. H., Conti, E., Ricci, L., & Walker, A. W. (2023) · Biomedicines · doi:10.3390/biomedicines11051338 · Cited by 38 · see citing works
Muribaculum gordoncarteri sp. nov., an anaerobic bacterium from the faeces of C57BL/6J mice
Miyake, S., Ding, Y., Soh, M., Low, A., & Seedorf, H. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004338 · Cited by 36 · see citing works
From complex gut communities to minimal microbiomes via cultivation
Clavel, T., Lagkouvardos, I., & Stecher, B. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.05.013 · Cited by 33 · see citing works
Self-citationMiyake, S., Ding, Y., Soh, M., Low, A., & Seedorf, H. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004137 · Cited by 31 · see citing works
The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis
Rehner, J., Schmartz, G. P., Kramer, T., Keller, V., Keller, A., & Becker, S. L. (2023) · Nutrients · doi:10.3390/nu15081924 · Cited by 30 · see citing works
Wang, Q., Spenkelink, B., Boonpawa, R., Rietjens, I. M. C. M., & Beekmann, K. (2020) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201900912 · Cited by 29 · see citing works
Candida albicans culture from a rectal swab can be associated with newly diagnosed colorectal cancer
Starý, L., Mezerová, K., Vyslouzil, K., Zbořil, P., Skalický, P., Stašek, M., & Raclavský, V. (2020) · Folia Microbiologica · doi:10.1007/s12223-020-00807-3 · Cited by 27 · see citing works
Louca, S., & Pennell, M. W. (2019) · Systematic Biology · doi:10.1093/sysbio/syz055 · Cited by 26 · see citing works
Verstraeten, S., Sencio, V., Raise, A., Huillet, E., Layec, S., Deruyter, L., Heumel, S., Auger, S., Robert, V., Langella, P., et al. (2022) · Nutrients · doi:10.3390/nu14071478 · Cited by 26 · see citing works
Bolsega, S., Bleich, A., & Basic, M. (2021) · Nutrients · doi:10.3390/nu13114173 · Cited by 26 · see citing works
Regulation of microbial gene expression: the key to understanding our gut microbiome
Sinha, A. K., Laursen, M. F., & Licht, T. R. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.07.005 · Cited by 24 · see citing works
The impact of the human gut microbiome on the treatment of autoimmune disease
Nayak, R. R., & Orellana, D. A. (2024) · Immunological Reviews · doi:10.1111/imr.13358 · Cited by 23 · see citing works
The Microbiome and Its Potential for Pharmacology
Chavira, A., Belda‐Ferre, P., Kościółek, T., Ali, F., Dorrestein, P. C., & Knight, R. D. (2019) · Handbook of experimental pharmacology · doi:10.1007/164_2019_317 · Cited by 21 · see citing works
The new microbiology: cultivating the future of microbiome-directed medicine
Ha, C. W. Y., & Devkota, S. (2020) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00093.2020 · Cited by 21 · see citing works
Liu, C., Vervoort, J. J. M., van den Elzen, J., Beekmann, K., Baccaro, M., de Haan, L., & Rietjens, I. M. C. M. (2020) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202000934 · Cited by 20 · see citing works
Gut microbial interactions based on network construction and bacterial pairwise cultivation
Jiang, M.-Z., Liu, C., Xu, C., Jiang, H., Wang, Y., & Liu, S. (2024) · Science China Life Sciences · doi:10.1007/s11427-023-2537-0 · Cited by 19 · see citing works
Kioukis, A., Pourjam, M., Neuhaus, K., & Lagkouvardos, I. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.864597 · Cited by 18 · see citing works
Self-citationCultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi
Weiland‐Bräuer, N., Prasse, D., Bräuer, A., Jaspers, C., Reusch, T. B. H., & Schmitz, R. A. (2020) · MicrobiologyOpen · doi:10.1002/mbo3.1094 · Cited by 18 · see citing works
Oral antibiotics reduce voluntary exercise behavior in athletic mice
McNamara, M. P., Cadney, M. D., Castro, A. A., Hillis, D. A., Kallini, K. M., Macbeth, J. C., Schmill, M. P., Schwartz, N. E., Hsiao, A., & Garland, T. (2022) · Behavioural Processes · doi:10.1016/j.beproc.2022.104650 · Cited by 15 · see citing works
Grégory, D., Chaudet, H., Lagier, J., & Raoult, D. (2018) · Expert Review of Proteomics · doi:10.1080/14789450.2018.1429271 · Cited by 15 · see citing works
The gut microbiota: cause and cure of gut diseases
White, L. S., van den Bogaerde, J., & Kamm, M. A. (2018) · The Medical Journal of Australia · doi:10.5694/mja17.01067 · Cited by 14 · see citing works
Jo, H. H., Lee, M. Y., Ha, S. E., Yeom, D. H., & Kim, Y. S. (2024) · Clinical Endoscopy · doi:10.5946/ce.2024.147 · Cited by 12 · see citing works
Complete Genome Sequence of Duncaniella muris Strain B8, Isolated from the Feces of C57/BL6 Mice
Miyake, S., Ding, Y., Soh, M., & Seedorf, H. (2019) · Microbiology Resource Announcements · doi:10.1128/mra.00566-19 · Cited by 11 · see citing works
Chen, Y., Lei, Z., Gu, D., Huiling, Z., Yu, R., He, Q., Xu, M., & Du, H. (2025) · Fitoterapia · doi:10.1016/j.fitote.2025.106570 · Cited by 12 · see citing works
Tronel, A., Roger‐Margueritat, M., Plazy, C., Biennier, S., Craspay, A., Mohanty, I., Cools-Portier, S., Laiola, M., Roeselers, G., Mathieu, N., et al. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf224 · Cited by 9 · see citing works
Bacterial Insights: Unraveling the Ocular Microbiome in Glaucoma Pathogenesis
Gagliano, C., Salvetat, M. L., Musa, M., D’Esposito, F., Rusciano, D., Maniaci, A., Pellegrini, F., Scibilia, G., & Zeppieri, M. (2024) · Frontiers in Bioscience-Landmark · doi:10.31083/j.fbl2908310 · Cited by 7 · see citing works
Microbiome and Diseases: Metabolic Disorders
Clavel, T., & Ecker, J. (2018) · Springer eBooks · doi:10.1007/978-3-319-90545-7_16 · Cited by 7 · see citing works
Self-citationAre we any closer to screening for colorectal cancer using microbial markers?A critical review
Starý, L., Mezerová, K., Skalický, P., Zbořil, P., & Raclavský, V. (2017) · Biomedical Papers · doi:10.5507/bp.2017.051 · Cited by 7 · see citing works
Piscotta, F. J., Whitfield, S. T., Nakashige, T. G., Estrela, A. B., Ali, T. A., & Brady, S. F. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109746 · Cited by 7 · see citing works
Rettenmaier, R., Duerr, C., Neuhaus, K., Liebl, W., & Zverlov, V. V. (2019) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2019.05.002 · Cited by 7 · see citing works
Human gut microbiota and endocrinology: paradigm shift from genome to its regulation
Lamaudière, M. T. F., Turner, M. C., Arasaradnam, R. P., & Morozov, I. Y. (2023) · Journal of Endocrinology · doi:10.1530/joe-23-0348 · Cited by 7 · see citing works
Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
Pfister, C. A., Light, S. H., Bohannan, B. J. M., Schmidt, T. M., Martiny, A. C., Hynson, N. A., Devkota, S., David, L. A., & Whiteson, K. (2022) · mSystems · doi:10.1128/msystems.01374-21 · Cited by 6 · see citing works
Wang, J., Zhang, W., Wang, M., Wei, J., Yang, L. J., & Wu, G. S. (2021) · Life Sciences · doi:10.1016/j.lfs.2021.119468 · Cited by 5 · see citing works
Prasse, D., Weiland‐Bräuer, N., Jaspers, C., Reusch, T. B. H., & Schmitz, R. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/602268 · Cited by 5 · see citing works
Bacterial nitrite production oxidizes Fe(II) bioremediating acidic abandoned coal mine drainage
Vietmeier, A., Valkanas, M. M., Lamagna, N., Flett, S., Gulliver, D. M., & Trun, N. J. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.00405-25 · Cited by 4 · see citing works
la Vega-Camarillo, E. D., Quattrone, A. C., Okumoto, S., Rajan, N., Hernández‐Rodríguez, C., Bernal, J. S., & Antony‐Babu, S. (2026) · MicrobiologyOpen · doi:10.1002/mbo3.70268 · Cited by 4 · see citing works
Strategizing the human microbiome for small molecules: Approaches and perspectives
Hussain, A., Patwekar, U., Mongad, D., & Shouche, Y. S. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.103459 · Cited by 5 · see citing works
Paradigms for microbiome analysis in infectious and non-communicable diseases
Autenrieth, I. B., Bury, L., Rooney, A. M., Willmann, M., Vehreschild, M. J. G. T., & Egli, A. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.11.016 · Cited by 3 · see citing works
Harlow, C., Mohamad, M., Bajaj, J. S., Nibali, L., Banerjee, A., & Patel, V. H. (2026) · Journal of Hepatology · doi:10.1016/j.jhep.2026.04.023 · Cited by 3 · see citing works
Gut Check: In Vitro Diagnostics for Gut Microbiome Analysis
Hernandez, D. R. (2019) · Clinical Microbiology Newsletter · doi:10.1016/j.clinmicnews.2019.03.005 · Cited by 3 · see citing works
Systems biology illuminates alternative metabolic niches in the human gut microbiomePreprint
Noecker, C. A., Sánchez, J. M., Bisanz, J. E., Escalante, V., Alexander, M., Trepka, K. R., Heinken, A., Liu, Y., Dodd, D., Thiele, I., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.19.508335 · Cited by 3 · see citing works
Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea
Prabhaharan, D., Go, Y. W., Kim, H., Kang, S., & Sang, B. (2025) · Scientific Data · doi:10.1038/s41597-024-04315-8 · Cited by 3 · see citing works
Yang, Y., He, F.-J., Xie, S.-Y., Luo, X.-W., & Wang, X. (2025) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2025.118119 · Cited by 2 · see citing works
Konkol, D., Kuźmińska-Bajor, M., Madej, J. P., Popiela, E., Lis, M., Kuczkowski, M., Szczypka, M., Sierżant, K., Ashgar, M. U., Leicht, K., et al. (2025) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2025.116529 · Cited by 2 · see citing works
Teo, Y., Lavrinienko, A., Torres, D. A., Asare, P. T., Ruder, A., Dominguez-Bello, M. G., Egli, A., Bokulich, N. A., & Vonaesch, P. (2025) · Gut Microbes Reports · doi:10.1080/29933935.2025.2594958 · Cited by 2 · see citing works
An Update on the Ocular Surface Bacterial Microbiota in Small Animals
Leis, M. L. (2023) · Veterinary Clinics of North America Small Animal Practice · doi:10.1016/j.cvsm.2022.10.004 · Cited by 2 · see citing works
Gut Microbiology – A Relatively Unexplored Domain
O’Donovan, C. M., O’Sullivan, Ó., & Cotter, P. D. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.09233-5 · Cited by 2 · see citing works
Camarinha‐Silva, A., & Fricke, W. F. (2018) · Springer eBooks · doi:10.1007/978-3-319-90545-7_4 · Cited by 2 · see citing works
Proteomics and the human microbiome: where we are today and where we would like to be
Kolmeder, C. A. (2017) · Emerging Topics in Life Sciences · doi:10.1042/etls20170051 · Cited by 2 · see citing works
High levels of dietary digestible protein transiently promote beneficial bacteria in adult dog feces
Carpintero, K. C., Olvera, C. G., Marquez-Mota, C. C., Ortega-Cerrilla, M. E., Sánchez-González, M. G., & Gutiérrez, L. (2022) · Veterinaria México OA · doi:10.22201/fmvz.24486760e.2022.985 · Cited by 1 · see citing works
Alshehri, D., Mosli, M. H., & Bahieldin, A. (2020) · Applied Ecology and Environmental Research · doi:10.15666/aeer/1806_82518265 · Cited by 1 · see citing works
Li, S., Zhang, S., Li, B., Sha, S., Kang, J., Li, P., Zhang, A., Ji, Q., Lv, Q., Zhang, X., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.29.926196 · Cited by 1 · see citing works
Profiling the human luminal small intestinal microbiome using a novel ingestible medical devicePreprint
Tronel, A., Roger‐Margueritat, M., Plazy, C., Biennier, S., Craspay, A., Mohanty, I., Cools-Portier, S., Laiola, M., Roeselers, G., Mathieu, N., et al. (2025) · medRxiv · doi:10.1101/2025.04.18.25326056 · Cited by 1 · see citing works
Darmmikrobiom des Menschen: Status quo und Perspektiven
Clavel, T., & Hörmannsperger, G. (2017) · Pädiatrie up2date · doi:10.1055/s-0043-115278
Self-citationSterrett, J. D., Clark, W. A., & Chandley, M. (2020) · Digital Commons - East Tennessee State University (East Tennessee State University)
Faculty Opinions recommendation of GABA-modulating bacteria of the human gut microbiota.
Pieper, D. H. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734611208.793557840
Lawson, P. A. (2018) · Bergey's Manual of Systematics of Archaea and Bacteria · doi:10.1002/9781118960608.gbm01449
Entwicklungen in der Methodik zum Nachweis von Bakterien: Von der Kultur zur Sequenzierung
Neuhaus, K. (2024) · Springer eBooks · doi:10.1007/978-3-662-68455-9_3
Taxonomy of Bacteria and Archaea
Lawson, P. A. (2023) · ClinMicroNow · doi:10.1002/9781683670438.mcm0018
Barlow, J. T., Leite, G., Romano, A. E., Sedighi, R., Chang, C., Celly, S., Rezaie, A. R., Mathur, R., Pimentel, M., & Ismagilov, R. F. (2021) · Figshare · doi:10.6084/m9.figshare.16916674
Sprason, C., Donkersley, P., Chin, J. P., & Benedetto, A. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuag031
- Authors
- Lagkouvardos, I., Overmann, J., & Clavel, T.
- Affiliations
- Technical University of Munich (DE)
- German Center for Infection Research (DE)
- Universitätsklinikum Aachen (DE)
- Corresponding author
- Clavel, Thomas
- Venue
- Gut Microbes
- Publisher
- Informa UK Limited
- Published
- 2017-04-18
- Volume
- 8
- Issue
- 5
- Pages
- 493-503
- ISSN
- 1949-0976 (ISSN-L)
- 1949-0984
- PMC
- PMC5628658
- OpenAlex
- W2606877093
- Cited by
- 104
- References
- 80
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 7 · 2023: 11 · 2022: 10 · 2021: 9 · 2020: 19 · 2019: 12 · 2018: 14 · 2017: 6
- FWCI
- 1.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Gut Microbes (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- RWTH Publications (RWTH Aachen) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (SPP-1656)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, bacterial culture, human gut microbiome, mouse gut microbiome, obligate anaerobes, representative strain
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteria, Humans, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
