The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
Open accessAbstract
Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability.
Overview
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
Verification
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?
The cited source says what the claim attributes to it.
In the citing paper
“Many more species continue to be cultured as laboratory-based efforts have become more high-throughput 43,44 .”
From Human microbiome myths and misconceptions (2023) · cites this paper as [44]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
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
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01043-13 · Cited by 7,246
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,714
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
Kraken: ultrafast metagenomic sequence classification using exact alignments
Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521
Flagged first, then by citations
Cited by
Sorted by citations
Items 101–200 of 1,000
Early life colonization of the human gut: microbes matter everywhere
Korpela, K., & de Vos, W. M. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.06.003 · Cited by 211
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Liu, C., Du, M., Abuduaini, R., Yu, H., Li, D., Wang, Y., Zhou, N., Jiang, M.-Z., Niu, P.-X., Han, S.-S., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01064-3 · Cited by 210
The lung microbiome in health and disease
Moffatt, M. F., & Cookson, W. (2017) · Clinical Medicine · doi:10.7861/clinmedicine.17-6-525 · Cited by 213
Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution
Roughgarden, J. E., Gilbert, S. F., ROSENBERG, E. B., Zilber‐Rosenberg, I., & Lloyd, E. A. (2017) · Biological Theory · doi:10.1007/s13752-017-0287-1 · Cited by 206
Reproducible protocols for metagenomic analysis of human faecal phageomes
Shkoporov, A. N., Ryan, F. J., Draper, L. A., Forde, A., Stockdale, S. R., Daly, K. M., McDonnell, S. A., Nolan, J. A., Sutton, T., Dalmasso, M., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0446-z · Cited by 203
Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
Brewer, T. E., Aronson, E. L., Arogyaswamy, K., Billings, S., Botthoff, J. K., Campbell, A., Dove, N. C., Fairbanks, D., Gallery, R. E., Hart, S. C., et al. (2019) · mBio · doi:10.1128/mbio.01318-19 · Cited by 198
Wang, S., Martins, R., Sullivan, M. C., Friedman, E. S., Misic, A. M., El‐Fahmawi, A., Martinis, E. C. P. D., O’Brien, K. M., Chen, Y., Bradley, C. W., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0740-4 · Cited by 208
Synthetic ecology of the human gut microbiota
Vrancken, G., Gregory, A., Huys, G. R. B., Faust, K., & Raes, J. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0264-8 · Cited by 196
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194
Self-citationBacterial RNA Biology on a Genome Scale
Hör, J., Gorski, S. A., & Vogel, J. (2018) · Molecular Cell · doi:10.1016/j.molcel.2017.12.023 · Cited by 191
Metabolite profiling of human‐originated Lachnospiraceae at the strain level
Abdugheni, R., Wang, W.-Z., Wang, Y., Du, M., Liu, F.-L., Zhou, N., Jiang, C., Wang, C., Wu, L., Ma, J., et al. (2022) · iMeta · doi:10.1002/imt2.58 · Cited by 206
Causality of small and large intestinal microbiota in weight regulation and insulin resistance
Scheithauer, T. P. M., Dallinga-Thie, G. M., de Vos, W. M., Nieuwdorp, M., & van Raalte, D. H. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.06.002 · Cited by 188
“Interestingly, recently it has been found that at least 50e60% of the bacterial genera from the intestinal microbiota produce resilient spores, which makes them more stable in an oxygen rich atmosphere and more likely to be passed from individual to individual [27].”
BackgroundForster, S. C., Liu, J., Kumar, N., Gulliver, E. L., Gould, J. A., Escobar‐Zepeda, A., Mkandawire, T. T., Pike, L. J., Shao, Y., Stares, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29096-9 · Cited by 191
Self-citationAlexa, E. A., Likotrafiti, E., Álvarez-Molina, A., Maradona, M. P., Santos, J. A., & Álvarez‐Ordóñez, A. (2018) · Genes · doi:10.3390/genes9050268 · Cited by 187
Methods in Lung Microbiome Research
Carney, S. M., Clemente, J. C., Cox, M. J., Dickson, R. P., Huang, Y. J., Kitsios, G. D., Kloepfer, K. M., Leung, J. M., LeVan, T. D., Molyneaux, P. L., et al. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2019-0273tr · Cited by 201
von Martels, J. Z. H., Sadabad, M. S., Bourgonje, A. R., Blokzijl, T., Dijkstra, G. D. H., Faber, K. N., & Harmsen, H. J. M. (2017) · Anaerobe · doi:10.1016/j.anaerobe.2017.01.001 · Cited by 186
Endometriosis induces gut microbiota alterations in mice
Yuan, M., Li, D., Zhang, Z., Sun, H., An, M., & Wang, G. (2017) · Human Reproduction · doi:10.1093/humrep/dex372 · Cited by 183
Microbial-Based and Microbial-Targeted Therapies for Inflammatory Bowel Diseases
Oka, A., & Sartor, R. B. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06090-z · Cited by 188
Roles of the intestinal microbiota in pathogen protection
Úbeda, C., Djuković, A., & Isaac, S. (2017) · Clinical & Translational Immunology · doi:10.1038/cti.2017.2 · Cited by 186
Microbiota-gut brain axis involvement in neuropsychiatric disorders
Iannone, L. F., Preda, A., Blottière, H. M., Clarke, G., Albani, D., Belcastro, V., Carotenuto, M., Cattaneo, A., Citraro, R., Ferraris, C., et al. (2019) · Expert Review of Neurotherapeutics · doi:10.1080/14737175.2019.1638763 · Cited by 177
Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target
Wang, K., Zhang, Z., Hang, J., Liu, J., Guo, F., Ding, Y., Li, M., Nie, Q., Lin, J., Zhuo, Y., et al. (2023) · Science · doi:10.1126/science.add5787 · Cited by 184
Systematic review: gastric microbiota in health and disease
Rajilić-Stojanović, M. D., Figueiredo, C., Smet, A., Hansen, R., Kupčinskas, J., Rokkas, T., Andersen, L. P., Machado, J. C., Ianiro, G., Gasbarrini, A., et al. (2020) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.15650 · Cited by 176
Human microbiome myths and misconceptions
Walker, A. W., & Hoyles, L. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01426-7 · Cited by 163
Setlow, P., & Johnson, E. A. (2019) · ASM Press eBooks · doi:10.1128/9781555819972.ch2 · Cited by 174
Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors
Colosimo, D. A., Kohn, J. A., Luo, P. M., Piscotta, F. J., Han, S. M., Pickard, A. J., Rao, A., Cross, J. R., Cohen, L. J., & Brady, S. F. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.07.002 · Cited by 176
Boertien, J. M., Pereira, P. A. B., Aho, V. T. E., & Scheperjans, F. (2019) · Journal of Parkinson s Disease · doi:10.3233/jpd-191711 · Cited by 181
Translating Immunology into Therapeutic Concepts for Inflammatory Bowel Disease
Uhlig, H. H., & Powrie, F. M. (2018) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042617-053055 · Cited by 174
The Role of the Gut Microbiota in the Pathogenesis of Parkinson's Disease
Yang, D., Zhao, D., Ali Shah, S. Z., Wu, W., Lai, M., Zhang, X., Li, J., Guan, Z., Zhao, H., Li, W., et al. (2019) · Frontiers in Neurology · doi:10.3389/fneur.2019.01155 · Cited by 162
Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review
Gardiner, G. E., Metzler-Zebeli, B. U., & Lawlor, P. G. (2020) · Microorganisms · doi:10.3390/microorganisms8121886 · Cited by 165
Keller, J. J., Ooijevaar, R. E., Hvas, C. L., Terveer, E. M., Lieberknecht-Jouy, S. C., Högenauer, C., Arkkila, P. E. T., Sokol, H., Gridnyev, O., Mégraud, F., et al. (2020) · United European Gastroenterology Journal · doi:10.1177/2050640620967898 · Cited by 168
An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species
Leviatan, S., Shoer, S., Rothschild, D., Gorodetski, M., & Segal, E. (2022) · Nature Communications · doi:10.1038/s41467-022-31502-1 · Cited by 179
Abdelfattah, A., Malacrinò, A., Wisniewski, M., Cacciola, S. O., & Schena, L. (2017) · Biological Control · doi:10.1016/j.biocontrol.2017.07.009 · Cited by 175
Medvecký, M., Čejková, D., Polanský, O., Karasová, D., Kubasová, T., Čížek, A., & Rychlı́k, I. (2018) · BMC Genomics · doi:10.1186/s12864-018-4959-4 · Cited by 157
A gut microbial signature for combination immune checkpoint blockade across cancer types
Gunjur, A., Shao, Y., Rozday, T., Klein, O., Mu, A., Haak, B. W., Markman, B., Kee, D., Carlino, M. S., Underhill, C., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-02823-z · Cited by 165
Self-citationRojo, D., Méndez–García, C., Raczkowska, B. A., Bargiela, R., Moyá, A., Ferrer, M., & Barbas, C. (2016) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw046 · Cited by 166
Liddicoat, C., Sydnor, H., Cando-Dumancela, C., Dresken, R., Liu, J., Gellie, N. J. C., Mills, J. G., Young, J. M., Weyrich, L. S., Hutchinson, M. R., et al. (2020) · Science of The Total Environment · doi:10.1016/j.scitotenv.2019.134684 · Cited by 140
The impact of nutrition on intestinal bacterial communities
Flint, H. J., Duncan, S. H., & Louis, P. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.005 · Cited by 149
The gut microbiota: An emerging risk factor for cardiovascular and cerebrovascular disease
Ascher, S., & Reinhardt, C. (2017) · European Journal of Immunology · doi:10.1002/eji.201646879 · Cited by 154
Armanhi, J. S. L., de Souza, R. S. C., Damasceno, N. E. S., de Araújo, L. M., Imperial, J., & Arruda, P. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2017.02191 · Cited by 158
Qiao, S., Li, B., Wang, K., Sun, S., Liao, M., Liu, C., Zhou, N., Ma, K., Zhang, Y., Chen, Y., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108005 · Cited by 147
Secretome of Intestinal Bacilli: A Natural Guard against Pathologies
Ilinskaya, O. N., Владимировна, У. В., Рашидовна, Я. Д., & Гатауллин, И. Г. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01666 · Cited by 149
Trait-based community assembly and succession of the infant gut microbiome
Guittar, J. L., Shade, A. L., & Litchman, E. (2019) · Nature Communications · doi:10.1038/s41467-019-08377-w · Cited by 145
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 151
Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2020) · eLife · doi:10.7554/elife.56998 · Cited by 146
Aggarwala, V., Mogno, I., Li, Z., Yang, C., Britton, G. J., Chen-Liaw, A., Mitcham, J., Bongers, G., Gevers, D., Clemente, J. C., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00966-0 · Cited by 146
Population Genetics in the Human Microbiome
Garud, N. R., & Pollard, K. S. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.10.010 · Cited by 142
A metagenomic strategy for harnessing the chemical repertoire of the human microbiome
Sugimoto, Y., Camacho, F. R., Wang, S., Chankhamjon, P., Odabas, A., Biswas, A. G., Jeffrey, P. D., & Donia, M. S. (2019) · Science · doi:10.1126/science.aax9176 · Cited by 143
Petrariu, O.-A., Barbu, I. C., Niculescu, A.-G., Constantin, M., Grigore, G. A., Cristian, R.-E., Mihăescu, G., & Vrâncianu, C. O. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1296447 · Cited by 155
Genetic innovations in animal–microbe symbioses
Perreau, J. M., & Moran, N. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00395-z · Cited by 141
Forster, S. C., Clare, S., Beresford-Jones, B. S., Harcourt, K., Notley, G., Stares, M., Kumar, N., Soderholm, A. T., Adoum, A., Wong, H. E., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01094-z · Cited by 153
Self-citationMSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
Oñate, F. P., Chatelier, E. L., Almeida, M., Cervino, A., Gauthier, F., Magoulès, F., Ehrlich, S. D., & Pichaud, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty830 · Cited by 131
Metagenomic reconstructions of gut microbial metabolism in weanling pigs
Wang, W., Hu, H., Zijlstra, R. T., Zheng, J., & Gänzle, M. G. (2019) · Microbiome · doi:10.1186/s40168-019-0662-1 · Cited by 141
The microbiota and autoimmunity: Their role in thyroid autoimmune diseases
Köhling, H.-L., Plummer, S. F., Marchesi, J. R., Davidge, K. S., & Ludgate, M. (2017) · Clinical Immunology · doi:10.1016/j.clim.2017.07.001 · Cited by 139
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 133
Specific properties of probiotic strains: relevance and benefits for the host
Bubnov, R. V., Babenko, L. P., Lazarenko, L. M., Mokrozub, V. V., & Spivak, M. Y. (2018) · The EPMA Journal · doi:10.1007/s13167-018-0132-z · Cited by 129
Notting, F., Pirovano, W., Sybesma, W., & Kort, R. (2023) · Gut Microbiome · doi:10.1017/gmb.2023.14 · Cited by 135
Fitzgerald, C. B., Shkoporov, A. N., Sutton, T., Chaplin, A. V., Velayudhan, V., Ross, R. P., & Hill, C. (2018) · BMC Genomics · doi:10.1186/s12864-018-5313-6 · Cited by 129
The landscape of microbial phenotypic traits and associated genes
Brbić, M., Piškorec, M., Vidulin, V., Kriško, A., Šmuc, T., & Supek, F. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw964 · Cited by 132
Gut microbiota regulates neuropathic pain: potential mechanisms and therapeutic strategy
Lin, B., Wang, Y., Zhang, P., Yuan, Y., Zhang, Y., & Chen, G. (2020) · The Journal of Headache and Pain · doi:10.1186/s10194-020-01170-x · Cited by 137
Multiscale Evolutionary Dynamics of Host-Associated Microbiomes
Ferreiro, A., Crook, N., Gasparrini, A. J., & Dantas, G. (2018) · Cell · doi:10.1016/j.cell.2018.02.015 · Cited by 127
Microbial transmission in the social microbiome and host health and disease
Sarkar, A., McInroy, C. J. A., Harty, S., Raulo, A., Ibata, N. G. O., Valles‐Colomer, M., Johnson, K. V. ‐., Brito, I., Henrich, J., Archie, E. A., et al. (2024) · Cell · doi:10.1016/j.cell.2023.12.014 · Cited by 143
Sporulation and Germination in Clostridial Pathogens
Shen, A., Edwards, A. N., Sarker, M. R., & Paredes‐Sabja, D. (2019) · Microbiology Spectrum · doi:10.1128/microbiolspec.gpp3-0017-2018 · Cited by 126
Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?
Quigley, E. M. M. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.29 · Cited by 125
Clavel, T., Neto, J. C. G., Lagkouvardos, I., & Ramer‐Tait, A. E. (2017) · Immunological Reviews · doi:10.1111/imr.12578 · Cited by 132
Seferovic, M. D., Pace, R. M., Carroll, M. R., Belfort, B. D. W., Major, A. M., Chu, D. M., Racusin, D., Castro, E. C. C., Muldrew, K. L., Versalovic, J. A., et al. (2019) · American Journal of Obstetrics and Gynecology · doi:10.1016/j.ajog.2019.04.036 · Cited by 124
Olm, M. R., Brown, C. T., Brooks, B., Firek, B., Baker, R., Burstein, D., Soenjoyo, K., Thomas, B. C., Morowitz, M., & Banfield, J. (2017) · Genome Research · doi:10.1101/gr.213256.116 · Cited by 121
Aranda-Díaz, A., Ng, K. M., Thomsen, T., Real-Ramírez, I., Dahan, D., Dittmar, S., Gonzalez, C. G., Chavez, T. M., Vasquez, K. S., Nguyen, T. H., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.008 · Cited by 118
Ojima, M. N., Jiang, L., Arzamasov, A. A., Yoshida, K., Odamaki, T., Xiao, J., Nakajima, A., Kitaoka, M., Hirose, J., Urashima, T., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01270-3 · Cited by 118
From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology
Nai, C., & Meyer, V. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.11.004 · Cited by 120
Dysbiotic microbiota interactions in Crohn’s disease
Caparrós, E., Wiest, R., Scharl, M. M., Rogler, G., Gutiérrez, A., Yılmaz, B., Wawrzyniak, M., & Francés, R. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1949096 · Cited by 123
Microbiome-health interactions in older people
O’Toole, P. W., & Jeffery, I. B. (2018) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2673-z · Cited by 117
Hoggard, M., Mackenzie, B. W., Jain, R., Taylor, M. W., Biswas, K., & Douglas, R. G. (2016) · Clinical Microbiology Reviews · doi:10.1128/cmr.00060-16 · Cited by 122
Evers, S. S., Sandoval, D. A., & Seeley, R. J. (2016) · Annual Review of Physiology · doi:10.1146/annurev-physiol-022516-034423 · Cited by 120
New opportunities for managing acute and chronic lung infections
Cookson, W., Cox, M. J., & Moffatt, M. F. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.122 · Cited by 122
Kim, C. Y., Lee, M., Yang, S., Kim, K., Yong, D., Kim, H. R., & Lee, I. (2021) · Genome Medicine · doi:10.1186/s13073-021-00950-7 · Cited by 120
Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids
Bartfeld, S. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.09.014 · Cited by 116
Consensus report: faecal microbiota transfer – clinical applications and procedures
König, J., Siebenhaar, A., Högenauer, C., Arkkila, P. E. T., Nieuwdorp, M., Norén, T., Ponsioen, C. Y., Rosien, U., Rossen, N., Satokari, R. M., et al. (2016) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.13868 · Cited by 115
What Is Metagenomics Teaching Us, and What Is Missed?
New, F. N., & Brito, I. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-012520-072314 · Cited by 124
Measuring and mitigating PCR bias in microbiota datasets
Silverman, J. D., Bloom, R. J., Jiang, S., Durand, H. K., Dallow, E. P., Mukherjee, S., & David, L. A. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009113 · Cited by 115
Wang, Y., Zhou, J., Ye, J., Sun, Z., He, Y., Zhao, Y., Ren, S., Zhang, G., Liu, M., Zheng, P., et al. (2023) · Microbiome · doi:10.1186/s40168-023-01635-6 · Cited by 122
García-Mauriño, C., Paes, V. M., Shao, Y., Oeser, C., Miltz, A. R., Lawley, T. D., Brocklehurst, P., Rodger, A., & Field, N. M. (2022) · The Lancet Microbe · doi:10.1016/s2666-5247(22)00184-7 · Cited by 117
Self-citationIto, T., Sekizuka, T., Kishi, N., Yamashita, A., & Kuroda, M. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1491265 · Cited by 116
Gut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention
Cani, P. D., de Hase, E. M., & Hul, M. V. (2021) · Microorganisms · doi:10.3390/microorganisms9061302 · Cited by 116
The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria
Liu, C., Zhou, N., Du, M., Sun, Y., Wang, K., Wang, Y., Li, D., Yu, H., Song, Y., Bai, B.-B., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13836-5 · Cited by 110
Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota
Ellegaard, K., & Engel, P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01475 · Cited by 113
The complexities of the diet-microbiome relationship: advances and perspectives
Leeming, E. R., Louca, P., Gibson, R., Menni, C., Spector, T. D., & Roy, C. I. L. (2021) · Genome Medicine · doi:10.1186/s13073-020-00813-7 · Cited by 116
Mother–infant transmission of human microbiota
Browne, H. P., Shao, Y., & Lawley, T. D. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102173 · Cited by 117
Self-citationQuinones are growth factors for the human gut microbiota
Fenn, K., Strandwitz, P., Stewart, E. J., Dimise, E. J., Rubin, S., Gurubacharya, S., Clardy, J., & Lewis, K. (2017) · Microbiome · doi:10.1186/s40168-017-0380-5 · Cited by 108
Podlesny, D., Durdevic, M., Paramsothy, S., Kaakoush, N. O., Högenauer, C., Gorkiewicz, G., Walter, J., & Fricke, W. F. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100711 · Cited by 111
Chen, L., Chen, D., Liu, J., Zhang, J., Vaziri, N. D., Zhuang, S., Chen, H., Feng, Y., Guo, Y. P., & Zhao, Y. (2019) · Experimental & Molecular Medicine · doi:10.1038/s12276-019-0234-2 · Cited by 105
Endocervical glandular atypia in Papanicolaou smears.
Goff, B. A., Atanassoff, P. G., Brown, E. H., Muntz, H. G., Bell, D. A., & Rice, L. W. (1992) · PubMed · Cited by 103
Cultured microbes represent a substantial fraction of the human and mouse gut microbiota
Lagkouvardos, I., Overmann, J., & Clavel, T. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1320468 · Cited by 104
CD8+ regulatory T cells are critical in prevention of autoimmune-mediated diabetes
Shimokawa, C., Kato, T., Takeuchi, T., Ohshima, N., Furuki, T., Ohtsu, Y., Suzue, K., Imai, T., Obi, S., Olia, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15857-x · Cited by 109
Commensal Koch's postulates: establishing causation in human microbiota research
Neville, B. A., Forster, S. C., & Lawley, T. D. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.001 · Cited by 107
Self-citationZhou, Y., Liu, M., & Yang, J. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127023 · Cited by 109
Fan, Y., Huang, X., Chen, J., & Han, B. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00138 · Cited by 112
Nauman, S., Bhatti, S. H., Imam, H., & Khan, M. S. (2021) · Project Management Journal · doi:10.1177/87569728211037777 · Cited by 133
A Dormant Microbial Component in the Development of Preeclampsia
Kell, D. B., & Kenny, L. C. (2016) · Frontiers in Medicine · doi:10.3389/fmed.2016.00060 · Cited by 101
The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut
Elzinga, J., John van der, O. O. S. T., de Vos, W. M., & Smidt, H. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00054-18 · Cited by 105
An Insight into Diversity and Functionalities of Gut Microbiota in Insects
Wang, S., Wang, L., Fan, X., Yu, C., Feng, L., & Li, Y. (2020) · Current Microbiology · doi:10.1007/s00284-020-02084-2 · Cited by 98
Metadata
- Authors
- Browne, H. P., Forster, S. C., Anonye, B. O., Kumar, N., Neville, B. A., Stares, M. D., Goulding, D., & Lawley, T. D.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Lawley, Trevor D.
- ORCID
- Venue
- Nature
- Published
- 2016-05-04
- Volume
- 533
- Issue
- 7604
- Pages
- 543-546
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4890681
- OpenAlex
- W2345813655
- Cited by
- 1,299
- References
- 41
- Citations by year
- 2026: 60 · 2025: 90 · 2024: 119 · 2023: 102 · 2022: 131 · 2021: 164 · 2020: 170 · 2019: 180 · 2018: 119 · 2017: 120 · 2016: 41
- FWCI
- 79.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CLOK (University of Central Lancashire) (acceptedVersion)
- Monash University Research Portal (Monash University) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust (098051)
- State Government of Victoria
- Medical Research Council (098051, PF451, MR/K000551/1)
- National Health and Medical Research Council (1091097)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- uncultured bacteria, human gut microbiome, bacterial sporulation, spore-forming bacteria, host-to-host transmission, novel bacterial taxa, Firmicutes, Bacteroidetes, anaerobic bacteria, metagenomics, whole genome sequencing
- MeSH terms
- Gastrointestinal Microbiome, Anaerobiosis, Bacteria, Feces, Health, Humans, Oxygen, Phenotype, Phylogeny, Species Specificity, Spores, Bacterial, Bacterial Typing Techniques, Genome, Bacterial, Sequence Analysis, DNA, Cell Culture Techniques, Metagenome, Metagenomics
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
