Cited by 1,299Gut microbiota and healthMicrobial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

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 access

Browne, Hilary P., Forster, Samuel C., Anonye, Blessing O., Kumar, Nitin, Neville, B. Anne, Stares, Mark D., Goulding, David, Lawley, Trevor D.·2016·Nature

DOI 10.1038/nature17645PMC PMC4890681

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1038/nature17645

Cites

41 of 41 references verified0 citation errors · 0 not checkable

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
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
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
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

Show all 41 references

Sorted by citations

Items 401–500 of 1,000

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units
de Cárcer, D. A. (2018) · Scientific Reports · doi:10.1038/s41598-018-32221-8 · Cited by 41
Metagenomics in ophthalmology: Hypothesis or real prospective?
Gallon, P., Parekh, M., Ferrari, S., Fasolo, A., Ponzin, D., & Borroni, D. (2019) · Biotechnology Reports · doi:10.1016/j.btre.2019.e00355 · Cited by 39
Benchmarking genome assembly methods on metagenomic sequencing data
Zhang, Z., Yang, C., Veldsman, W. P., Fang, X., & Zhang, L. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad087 · Cited by 39
Application of emerging technologies for gut microbiome research
Kwa, W. T., Sundarajoo, S., Toh, K. Y., & Lee, J. W. J. (2023) · Singapore Medical Journal · doi:10.4103/singaporemedj.smj-2021-432 · Cited by 40
Advances in the isolation, cultivation, and identification of gut microbes
Xu, M., Pan, F., Peng, L., & Yang, Y. (2024) · Military Medical Research · doi:10.1186/s40779-024-00534-7 · Cited by 42
Effects of Colombian oregano essential oil (Lippia origanoides Kunth) and Eimeria species on broiler production and cecal microbiota
Betancourt, L., Hume, M. E., Rodríguez, F., Nisbet, D. J., Sohail, M. U., & Téllez, G. A. (2019) · Poultry Science · doi:10.3382/ps/pez193 · Cited by 38
Genetic mechanisms governing sporulation initiation in Clostridioides difficile
Lee, C. D., Rizvi, A., Edwards, A. N., DiCandia, M. A., Vargas-Cuebas, G. G., Monteiro, M. P., & McBride, S. M. (2021) · Current Opinion in Microbiology · doi:10.1016/j.mib.2021.12.001 · Cited by 38
Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations
Rosenberg, E., & Zilber-Rosenberg, I. (2021) · Microorganisms · doi:10.3390/microorganisms10010070 · Cited by 38
SynMADE: synthetic microbiota across diverse ecosystems
Moon, T. S. (2022) · Trends in biotechnology · doi:10.1016/j.tibtech.2022.08.010 · Cited by 40
Towards microbial consortia in fermented foods for metabolic engineering and synthetic biology
Xin, Y., & Qiao, M. (2025) · Food Research International · doi:10.1016/j.foodres.2025.115677 · Cited by 39
Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics
Kubasová, T., Seidlerová, Z., & Rychlı́k, I. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115471 · Cited by 39
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 40
From Culturomics to Clinical Microbiology and Forward
Dubourg, G., Baron, S. A., Cadoret, F., Couderc, C., Fournier, P., Lagier, J., & Raoult, D. (2018) · Emerging infectious diseases · doi:10.3201/eid2409.170995 · Cited by 36
In sickness and health: Effects of gut microbial metabolites on human physiology
Glowacki, R. W. P., & Martens, E. C. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008370 · Cited by 40
Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota
Breitenwieser, F., Doll, E. V., Clavel, T., Scherer, S., & Wenning, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01557 · Cited by 37
A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone
Owens, L. A., Colitti, B., Hirji, I., Pizarro, A. I., Jaffe, J. E., Moittié, S., Bishop‐Lilly, K. A., Estrella, L. A., Voegtly, L. J., Kuhn, J. H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21012-x · Cited by 36
The interplay between Trichuris and the microbiota
Lawson, M. A., Roberts, I. S., & Grencis, R. K. (2021) · Parasitology · doi:10.1017/s0031182021000834 · Cited by 37
Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs
Wang, X., Howe, S. M., Wei, X., Deng, F., Tsai, T.-C., Chai, J., Xiao, Y., Yang, H., Maxwell, C. V. V., Li, Y., et al. (2021) · mSystems · doi:10.1128/msystems.00477-21 · Cited by 36
Research trends on the relationship between gut microbiota and colorectal cancer: A bibliometric analysis
Wu, W., Ouyang, Y., Zheng, P., Xu, X., He, C., Xie, C., Hong, J., Lü, N., Zhu, Y., & Li, N. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.1027448 · Cited by 37
Metagenomics, culturomics, and the human gut microbiota
Amrane, S., Raoult, D., & Lagier, J. (2018) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2018.1467268 · Cited by 44
A relational framework for microbiome research with Indigenous communities
Bader, A. C., Zuylen, E. M. V., Handsley‐Davis, M., Alegado, R. ʻ., Benezra, A., Pollet, R. M., Ehau‐Taumaunu, H., Weyrich, L. S., & Anderson, M. Z. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01471-2 · Cited by 35
Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces
Kim, J., Lee, K. C., Suh, M. K., Han, K. I., Eom, M. K., Lee, J. H., Park, S.-H., Kang, S. W., Park, J.-E., Oh, B. S., et al. (2018) · The Journal of Microbiology · doi:10.1007/s12275-019-8550-8 · Cited by 35
Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate
Barreto, H. C., Cordeiro, T. N., Henriques, A. O., & Gordo, I. (2020) · Scientific Reports · doi:10.1038/s41598-020-76017-1 · Cited by 35
Updating the repertoire of cultured bacteria from the human being
Diakite, A., Dubourg, G., & Raoult, D. (2020) · Microbial Pathogenesis · doi:10.1016/j.micpath.2020.104698 · Cited by 35
Gut Microbiota and Human Body Interactions; Its Impact on Health: A Review
Hajiagha, M. N., Taghizadeh, S., Asgharzadeh, M., Dao, S., Ganbarov, K., Köse, Ş., & Kafil, H. S. (2021) · Current Pharmaceutical Biotechnology · doi:10.2174/1389201022666210104115836 · Cited by 36
The Application of High-Throughput Technologies for the Study of Microbiome and Cancer
Wei, L., Cheong, I. H., Yang, G., Li, X. G., Kozlakidis, Z., Ding, L., Liu, N. N., & Wang, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.699793 · Cited by 38
Gut Dysbiosis in Pancreatic Diseases: A Causative Factor and a Novel Therapeutic Target
Zhang, T., Gao, G., Sakandar, H. A., Kwok, L., & Sun, Z. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.814269 · Cited by 39
Probiotics in health and disease: fooling Mother Nature?
Abid, M. B., & Koh, C. J. (2019) · Infection · doi:10.1007/s15010-019-01351-0 · Cited by 37
Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine
Bescucci, D. M., Moote, P. E., Polo, R. O., Uwiera, R. R. E., & Inglis, G. D. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.01569-20 · Cited by 37
Microbiology: the return of culture
Marx, V. (2016) · Nature Methods · doi:10.1038/nmeth.4107 · Cited by 34
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Bradley, P. H., Nayfach, S., & Pollard, K. S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006242 · Cited by 33
Human microbial ecology and the rising new medicine
Godoy‐Vitorino, F. (2019) · Annals of Translational Medicine · doi:10.21037/atm.2019.06.56 · Cited by 35
Optimizing ex vivo culture conditions to study human gut microbiome
Tao, X., Huang, W., Pan, L., Sheng, L., Qin, Y., Chen, L., Yu, L., Wu, G., Wan, J., & Li, H. (2023) · ISME Communications · doi:10.1038/s43705-023-00245-5 · Cited by 36
Degradation of xylan by human gut Bacteroides xylanisolvens XB1A
Zhao, T., Yue, H., Peng, J., Nie, Y., Wu, L., Li, T., Niu, W., Li, C., Zhang, Z., Li, M., et al. (2023) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2023.121005 · Cited by 35
Response, resistance, and recovery of gut bacteria to human-targeted drug exposure
de la Cuesta‐Zuluaga, J., Boldt, L., & Maier, L. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.009 · Cited by 32
A Double-blind, Randomized, Placebo-controlled Trial of Lactobacillus acidophilus for the Treatment of Acute Watery Diarrhea in Vietnamese Children
Chau, T. T. H., Chau, N. N. M., Nhat, L. T. H., The, H. C., Vinh, P. V., To, N. T. N., Ngọc, N. M., Tuấn, H. M., Ngoc, T. L. C., Kolader, M.-E., et al. (2017) · The Pediatric Infectious Disease Journal · doi:10.1097/inf.0000000000001712 · Cited by 33
Enriched Environmental Conditions Modify the Gut Microbiome Composition and Fecal Markers of Inflammation in Parkinson’s Disease
Singh, Y., El-Hadidi, M. S., Admard, J., Wassouf, Z., Schulze-Hentrich, J. M., Kohlhofer, U., Quintanilla‐Martínez, L., Huson, D. H., Rieß, O., & Casadei, N. (2019) · Frontiers in Neuroscience · doi:10.3389/fnins.2019.01032 · Cited by 33
The Route to Palatable Fecal Microbiota Transplantation
Fadda, H. M. (2020) · AAPS PharmSciTech · doi:10.1208/s12249-020-1637-z · Cited by 36
A rather dry subject; investigating the study of arid-associated microbial communities
Osborne, P., Hall, L. J., Kronfeld‐Schor, N., Thybert, D., & Haerty, W. (2020) · Environmental Microbiome · doi:10.1186/s40793-020-00367-6 · Cited by 35
Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement
Brereton, N. J. B., Pitre, F. E., & González, E. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.040 · Cited by 35
Ex vivo folate production by fecal bacteria does not predict human blood folate status: Associations between dietary patterns, gut microbiota, and folate metabolism
Malinowska, A. M., SCHMIDT, M. T., Kok, D. E. G., & Chmurzyńska, A. (2022) · Food Research International · doi:10.1016/j.foodres.2022.111290 · Cited by 35
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 34
Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation
Wang, Y., Sun, Y., Huang, K., Gao, Y., Lin, Y., Yuan, B., Wang, X., Xu, G., Nussio, L. G., Yang, F., et al. (2024) · mSystems · doi:10.1128/msystems.00682-24 · Cited by 34
Bacterial Composition, Genotoxicity, and Cytotoxicity of Fecal Samples from Individuals Consuming Omnivorous or Vegetarian Diets
Federici, E., Prete, R., Lazzi, C., Pellegrini, N., Moretti, M., Corsetti, A., & Cenci, G. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00300 · Cited by 32
Many More Microbes in Humans: Enlarging the Microbiome Repertoire
Lagier, J., Drancourt, M., Charrel, R. N., Bittar, F., Scola, B. L., Ranque, S., & Raoult, D. (2017) · Clinical Infectious Diseases · doi:10.1093/cid/cix404 · Cited by 32
Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies
Santiago-Rodríguez, T. M., Fornaciari, G., Luciani, S., Toranzos, G. A., Marota, I., Giuffra, V., & Cano, R. J. (2017) · Genes · doi:10.3390/genes8110310 · Cited by 32
Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease
Nguyen, T. T. T., Fujimura, Y., Mimura, I., Fujii, Y., Nguyen, N. L., Arakawa, K., & Morita, H. (2018) · The Journal of Microbiology · doi:10.1007/s12275-018-8297-7 · Cited by 32
Culturing the Uncultured: Risk versus Reward
Thrash, J. C. (2019) · mSystems · doi:10.1128/msystems.00130-19 · Cited by 33
Food ingredients in human health: Ecological and metabolic perspectives implicating gut microbiota function
Wu, Q., Chen, T., El-Nezami, H. S., & Savidge, T. (2020) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2020.04.007 · Cited by 31
Gut Microbiota and Disorders of the Central Nervous System
Vuotto, C., Battistini, L., Caltagirone, C., & Borsellino, G. (2020) · The Neuroscientist · doi:10.1177/1073858420918826 · Cited by 37
The Effect of Athletes’ Probiotic Intake May Depend on Protein and Dietary Fiber Intake
Son, J., Jang, L.-G., Kim, B., Lee, S., & Park, H. (2020) · Nutrients · doi:10.3390/nu12102947 · Cited by 37
Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies
López‐Moreno, A., Acuña, I., Torres-Sánchez, A., Ruiz-Moreno, Á., Cerk, K., Rivas, A., Suárez, A., Monteoliva‐Sánchez, M., & Aguilera, J. (2021) · Nutrients · doi:10.3390/nu13051617 · Cited by 35
The Age of Next-Generation Therapeutic-Microbe Discovery: Exploiting Microbe-Microbe and Host-Microbe Interactions for Disease Prevention
Cruz, N., Abernathy, G. A., Dichosa, A. E. K., & Kumar, A. (2022) · Infection and Immunity · doi:10.1128/iai.00589-21 · Cited by 34
Lactobacillus delbrueckii reduces anxiety-like behavior in zebrafish through a gut microbiome – brain crosstalk
Olorocisimo, J. P., Diaz, L. A., Co, D. E., Carag, H. M., Ibana, J. A., & Velarde, M. C. (2022) · Neuropharmacology · doi:10.1016/j.neuropharm.2022.109401 · Cited by 36
Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans
Dias, B. D. C., Lamarca, A. P., Machado, D. T., Klôh, V., de Carvalho, F. M., & de Vasconcelos, A. T. R. (2025) · Animal Microbiome · doi:10.1186/s42523-025-00379-y · Cited by 31
Neonatal oral fluid as a transmission route for bifidobacteria to the infant gut immediately after birth
Toda, K., Hisata, K., Satoh, T., Katsumata, N., Odamaki, T., Mitsuyama, E., Katayama, T., Kuhara, T., Aisaka, K., Shimizu, T., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-45198-9 · Cited by 30
Pulmonary microbiome patterns correlate with the course of disease in patients with sepsis-induced ARDS following major abdominal surgery
Schmitt, F. C. F., Lipinski, A. L., Hofer, S., Uhle, F., Nußhag, C., Hackert, T., Dalpke, A. H., Weigand, M. A., Brenner, T., & Boutin, S. (2020) · Journal of Hospital Infection · doi:10.1016/j.jhin.2020.04.028 · Cited by 31
Putative Pathobionts in HLA-B27-Associated Spondyloarthropathy
Gill, T., & Rosenbaum, J. T. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2020.586494 · Cited by 31
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections
Straub, T. J., Chou, W., Manson, A. L., Schreiber, H. L., Walker, B. J., Desjardins, C. A., Chapman, S. B., Kaspar, K. L., Kahsai, O. J., Traylor, E., et al. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02106-4 · Cited by 31
Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases
Yang, J., Qin, S., & Zhang, H. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1034727 · Cited by 31
Fecal Microbiota Transplantation: Past, Present and Future
Евдокимова, Н. В., & Chernenkaya, T. V. (2019) · Russian Sklifosovsky Journal Emergency Medical Care · doi:10.23934/2223-9022-2019-8-2-160-165 · Cited by 31
An ensemble approach to the structure-function problem in microbial communities
Gopalakrishnappa, C., Gowda, K., Prabhakara, K., & Kuehn, S. (2022) · iScience · doi:10.1016/j.isci.2022.103761 · Cited by 34
Is there a role for antibiotics in the treatment of chronic rhinosinusitis?
Smith, S. S., Kim, R., & Douglas, R. G. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2022.02.004 · Cited by 33
Biome engineering‐2020
Brüssow, H. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12391 · Cited by 31
Culturing Human Gut Microbiomes in the Laboratory
Renwick, S., Ganobis, C. M., Elder, R., Gianetto-Hill, C., Higgins, G., Robinson, A. V., Vancuren, S. J., Wilde, J., & Allen‐Vercoe, E. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-031021-084116 · Cited by 30
Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host–microbe cross talk
Steimle, A., Sciscio, A. D., Neumann, M., Grant, E. T., Pereira, G. V., Ohno, H., Martens, E. C., & Desai, M. S. (2021) · STAR Protocols · doi:10.1016/j.xpro.2021.100607 · Cited by 30
The Human Vulvar Microbiome: A Systematic Review
Pagan, L., Ederveen, R. A. M., Huisman, B. W., Schoones, J. W., Zwittink, R. D., Schuren, F. H. J., Rißmann, R., Piek, J. M. J., & van Poelgeest, M. I. E. (2021) · Microorganisms · doi:10.3390/microorganisms9122568 · Cited by 36
Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting
Dridi, L., Altamura, F., González, E., Lui, O., Kubinski, R., Pidgeon, R., Montagut, A., Chong, J., Xia, J., Maurice, C. F., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36365-8 · Cited by 32
Diabetes and gut microbiome
Fliegerova, K. O., Mahayri, T. M., Sechovcová, H., Mekadim, C., Mrázek, J., Jarošíková, R., Dubský, M., & Fejfarová, V. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1451054 · Cited by 33
A Natural Mouse Model for Neisseria Colonization
Ma, M., Powell, D. A., Weyand, N. J., Rhodes, K. A., Rendón, M. A., Frelinger, J. A., & So, M. (2018) · Infection and Immunity · doi:10.1128/iai.00839-17 · Cited by 29
Blautia hominis sp. nov., isolated from human faeces
Shin, N., Kang, W., Tak, E. J., Hyun, D., Kim, P. S., Kim, H. S., Lee, J., Sung, H., Whon, T. W., & Bae, J. (2018) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002623 · Cited by 29
Essential oils and microbiota: Implications for diet and weight control
Ünüsan, N. (2020) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2020.07.014 · Cited by 36
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’
Tan, J., Wang, S., Dick, G. J., Young, V. B., Sherman, D. H., Burns, M. A., & Lin, X. N. (2020) · Integrative Biology · doi:10.1093/intbio/zyaa021 · Cited by 27
Repertoire of Bacterial Species Cultured from the Human Oral Cavity and Respiratory Tract
Fonkou, M. D. M., Dufour, J.-C., Dubourg, G., & Raoult, D. (2018) · Future Microbiology · doi:10.2217/fmb-2018-0181 · Cited by 30
Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery
Song, H. S., Kim, Y. B., Kim, J. Y., Roh, S. W., & Whon, T. W. (2024) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2311.11024 · Cited by 31
Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health
de León, A. V.-P., Hensen, T., Hoetzinger, M., Gupta, S., Weston, B. R., Johnsen, S. M., Rasmussen, J. A., Clausen, C. G., Pless, L., Verissimo, A. R., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01830-7 · Cited by 27
Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter
Garcia‐Garcerà, M., Touchon, M., Brisse, S., & Rocha, E. P. C. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13949 · Cited by 31
A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects
Pérez, M., Ntemiri, A., Tan, H., Harris, H. M. B., Roager, H. M., Ribière, C., & O’Toole, P. W. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1919464 · Cited by 29
Toward a Biopsychosocial Ecology of the Human Microbiome, Brain-Gut Axis, and Health
Maier, K. J., & Al’Absi, M. (2017) · Psychosomatic Medicine · doi:10.1097/psy.0000000000000515 · Cited by 27
Dialister hominis sp. nov., isolated from human faeces
Sakamoto, M., Ikeyama, N., Toyoda, A., Murakami, T., Mori, H., Iino, T., & Ohkuma, M. (2019) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.003797 · Cited by 28
A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases
Qi, C., Wang, P., Fu, T., Lu, M., Cai, Y., Chen, X., & Cheng, L. (2020) · Briefings in Functional Genomics · doi:10.1093/bfgp/elaa029 · Cited by 28
Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives
Koorakula, R., Schiavinato, M., Ghanbari, M., Wegl, G., Grabner, N., Köstelbauer, A., Klose, V., Dohm, J. C., & Domig, K. J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.833790 · Cited by 27
Benchmarking microbial DNA enrichment protocols from human intestinal biopsies
Marchukov, D., Li, J., Juillerat, P., Misselwitz, B., & Yılmaz, B. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1184473 · Cited by 30
Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage
Cai, J., Auster, A., Cho, S., & Lai, Z. (2023) · Journal of Advanced Research · doi:10.1016/j.jare.2023.07.002 · Cited by 30
Microbiota, natural products, and human health: exploring interactions for therapeutic insights
Qadri, H., Shah, A. H., Almilaibary, A., & Mir, M. A. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1371312 · Cited by 31
Rapid and accurate testing for urinary tract infection: new clothes for the emperor
Moreland, R. B., Brubaker, L. T., Tinawi, L., & Wolfe, A. J. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00129-24 · Cited by 39
Gut microbiota and tuberculosis
Liu, Y., Yang, L., Meskini, M., Goel, A., Opperman, M., Shyamal, S. S., Manaithiya, A., Xiao, M., Ni, R., An, Y., et al. (2025) · iMeta · doi:10.1002/imt2.70054 · Cited by 36
The development of human gut microbiota fermentation capacity during the first year of life
Schwab, C. (2022) · Microbial Biotechnology · doi:10.1111/1751-7915.14165 · Cited by 29
The microbial dark matter and “wanted list” in worldwide wastewater treatment plants
Zhang, Y., Wang, Y., Tang, M., Zhou, J. Z., & Zhang, T. (2023) · Microbiome · doi:10.1186/s40168-023-01503-3 · Cited by 28
Cell Death Pathway That Monitors Spore Morphogenesis
Decker-Farrell, A. R., & Ramamurthi, K. S. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2017.03.005 · Cited by 27
Coordinated Assembly of the Bacillus anthracis Coat and Exosporium during Bacterial Spore Outer Layer Formation
Boone, T. J., Mallozzi, M., Nelson, A., Thompson, B. M., Khemmani, M., Lehmann, D., Dunkle, A. D., Hoeprich, P. D., Rasley, A., Stewart, G. C., et al. (2018) · mBio · doi:10.1128/mbio.01166-18 · Cited by 27
Metabolomics in the era of artificial intelligence
Coler, E., Chen, W., Melnik, A. V., Morton, J. T., & Aksenov, A. A. (2024) · Microbiota and Host · doi:10.1530/mah-23-0017 · Cited by 28
Microbiome-Based Interventions for Food Safety and Environmental Health
Simon, B. O., Nnaji, N. D., Anumudu, C. K., Aleke, J. C., Ekwueme, C. T., Uhegwu, C. C., Ihenetu, F. C., Obioha, P., Ifedinezi, O. V., Ezechukwu, P. S., et al. (2025) · Applied Sciences · doi:10.3390/app15095219 · Cited by 26
Antibiotics-induced gut microbiota dysbiosis promotes tumor initiation via affecting APC-Th1 development in mice
Xu, C., Ruan, B., Jiang, Y., Xue, T., Wang, Z., Lu, H., Wei, M., Wang, S., Ye, Z., Zhai, D., et al. (2017) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2017.05.071 · Cited by 27
Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.
Sakamoto, M., Ikeyama, N., Ogata, Y., Suda, W., Iino, T., Hattori, M., & Ohkuma, M. (2019) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.003778 · Cited by 25
Synthetic Microbiomes on the Rise—Application in Deciphering the Role of Microbes in Host Health and Disease
Bolsega, S., Bleich, A., & Basic, M. (2021) · Nutrients · doi:10.3390/nu13114173 · Cited by 28
Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megalosphaeroides sp. nov., isolated from human faeces.
Sakamoto, M., Ikeyama, N., Kunihiro, T., Iino, T., Yuki, M., & Ohkuma, M. (2018) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.003096 · Cited by 16
Cultural isolation of spore-forming bacteria in human feces using bile acids
Tanaka, M., Onizuka, S., Mishima, R., & Nakayama, J. (2020) · Scientific Reports · doi:10.1038/s41598-020-71883-1 · Cited by 25
Aggregation-induced emission: recent applications in infectious diseases
Gu, M., Chen, L., Hu, R., Chen, Q., Liu, J., Wang, L., & Chen, S. (2023) · Science China Chemistry · doi:10.1007/s11426-023-1825-7 · Cited by 26
Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella
Hu, Y. O. O., Hugerth, L. W., Bengtsson, C., Alisjahbana, A., Seifert, M., Kamal, A., Sjöling, Å., Midtvedt, T., Norin, E. L., Du, J., et al. (2018) · mSystems · doi:10.1128/msystems.00119-18 · Cited by 26

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: Browne, Hilary P.
Forster, Samuel C.
Anonye, Blessing O.
Kumar, Nitin
Stares, Mark D.
Goulding, David
Lawley, Trevor D.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-05-04
Volume: 533
Issue: 7604
Pages: 543-546
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature17645
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
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
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

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks