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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.
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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
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Pallen, M. J., & Quraishi, M. N. (2017) · Digestive Diseases · doi:10.1159/000456590 · Cited by 5
Culture and Molecular Profiling of the Respiratory Tract Microbiota
Whelan, F., Rossi, L., Stearns, J. C., & Surette, M. G. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8728-3_4 · Cited by 5
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Boutin, S., & Dalpke, A. H. (2020) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026620666200320112731 · Cited by 6
Zhang, C., Virk, A. K., KHAN, I. A., & Qin, H. (2020) · Springer eBooks · doi:10.1007/978-981-15-4759-1_2 · Cited by 5
Wongkuna, S., Ghimire, S., Janvilisri, T., Doerner, K., Chankhamhaengdecha, S., & Scaria, J. (2020) · F1000Research · doi:10.12688/f1000research.25823.1 · Cited by 5
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Marsh, A. J., Yaya, A.-M. A., Ng, S., Chandrashekhar, K., Roach, J. M., Magness, S. T., & Azcárate-Peril, M. A. (2020) · Gut Microbiome · doi:10.1017/gmb.2020.4 · Cited by 5
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Udayan, S., Stamou, P., Crispie, F., Hickey, A., Floyd, A. N., Hsieh, C., Cotter, P. D., O’Sullivan, Ó., Melgar, S., O’Toole, P. W., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2021.2007743 · Cited by 4
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Ostenfeld, L. J., Munk, P., Aarestrup, F. M., & Otani, S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0283676 · Cited by 6
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Ameen, A., Akram, M. N., Farooq, S., Fatima, M., Raza, H., Naz, R., Aziz, U., Aziz, M., Tahir, S., & Hussain, A. (2023) · Pakistan Journal of Medical and Health Sciences · doi:10.53350/pjmhs2023175311 · Cited by 6
Exploring Human Bacterial Diversity Toward Prevention of Infectious Disease and Health Promotion
Yousuf, B., & Mishra, A. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-814849-5.00029-0 · Cited by 5
Paediatrician’s perspective of infant gut microbiome research: current status and challenges
Ryan, P. M., Stanton, C., Ross, R. P., Kelly, A. L., Dempsey, E. M., & Ryan, C. A. (2019) · Archives of Disease in Childhood · doi:10.1136/archdischild-2019-316891 · Cited by 5
Achard, C. S., Dupouy, V., Siviglia, S., Arpaillange, N., Cauquil, L., Bousquet‐mélou, A., & Zemb, O. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01503 · Cited by 5
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Eghdami, S., Saeidi, M., Gunturu, S., Boroon, M., & Shalbafan, M. (2025) · Life · doi:10.3390/life15101585 · Cited by 4
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Plitt, T., & Faith, J. J. (2023) · Seminars in Immunology · doi:10.1016/j.smim.2023.101735 · Cited by 3
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Rook, G. A. W. (2022) · Progress in inflammation research · doi:10.1007/978-3-030-91051-8_2 · Cited by 4
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Boyer, R., & Freyssenet, M. (1996) · Sociologia del trabajo/Sociología del trabajo · Cited by 4
Zhu, Y., Ma, L., Wei, W., Li, X., Chang, Y., Pan, Z., Gao, H., Yang, R., Bi, Y., & Ding, L. (2022) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001523 · Cited by 4
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Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.14.422699 · Cited by 4
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Liu, C., Du, M., Abuduaini, R., Yu, H., Li, D., Wang, Y., Zhou, N., Jiang, M.-Z., Niu, P.-X., Han, S., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-168279/v1 · Cited by 4
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Chiaro, T. R., Bauer, K. M., Ost, K. S., Victor, E. S., Nelson, M. C., Hill, J. H., Bell, R. S., Harwood, M., Voth, W. P., Jackson, T., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.16.532997 · Cited by 4
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Sum, R., Lim, S. J. M., Sundaresan, A., Samanta, S., Swaminathan, M., Low, W., Ayyappan, M., Lim, T. W., Choo, M. D., Huang, G. J., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06617-4 · Cited by 3
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Ramirez, L. Y. A., Angell, I. L., Nilsen, T., & Rudi, K. (2024) · Current Microbiology · doi:10.1007/s00284-024-03869-5 · Cited by 3
Perry, E. K., Udayasuryan, B., Zegeye, E. K., Rose, C. M., Reichelt, M., & Tan, M. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00854-z · Cited by 3
Sanabria, J., Egan, S. L., Masuda, R., Lee, A. J., Gibson, G. R., Nicholson, J. K., Wist, J., & Holmes, E. C. (2022) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c03597 · Cited by 3
Huang, R., Yao, Y., Tong, X., Wang, L., Qian, W., Lu, J., Zhang, W., Liu, Y., Wang, S., Xian, S., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.00135-23 · Cited by 3
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Sakamoto, M., Hisatomi, A., & Ohkuma, M. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006381 · Cited by 3
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Imamura, Y., Motooka, D., Nakajima, Y., Ito, S., Kitakaze, M., Iida, T., & Nakamura, S. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006379 · Cited by 3
Ammar, A., Singh, V., Ilić, S., Samiksha, F., Marsh, A. E., & Rodriguez‐Palacios, A. (2024) · Microorganisms · doi:10.3390/microorganisms12061130 · Cited by 3
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Auchtung, T. A., Lerma, A. I., Schuchart, K., & Auchtung, J. M. (2025) · MicrobiologyOpen · doi:10.1002/mbo3.70030 · Cited by 3
Haute, M. J. S. V., Chacón-Vargas, K., Christensen, C. M., Yumul, S. R. P., Abdulaali, F. F., Benson, A. K., Hutkins, R. W., & Auchtung, T. A. (2025) · mSphere · doi:10.1128/msphere.00673-25 · Cited by 4
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Joshi, S. M., & Pandey, A. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-88504-1.00010-8 · Cited by 3
Defining the baseline of pulmonary microbiota in healthy populations and influencing factors
Tang, Z., Yang, S., & He, Z. (2022) · Highlights in Science Engineering and Technology · doi:10.54097/hset.v11i.1264 · Cited by 3
Bai, L., Paek, J., Shin, Y., Kim, H., Kim, S. H., Shin, J. H., Kook, J., & Chang, Y.-H. (2023) · Anaerobe · doi:10.1016/j.anaerobe.2023.102792 · Cited by 3
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Ameen, A., Amir, A., Aziz, M. N., Irshad, A., Maryam, M., & Hayat, S. (2023) · Pakistan Journal of Medical and Health Sciences · doi:10.53350/pjmhs2023175425 · Cited by 4
Guan, Y., Zhu, Z., Peng, Q., Li, M., Li, X., Yang, J., Lu, Y.-H., Wang, M., & Xie, B.-B. (2024) · Current Genomics · doi:10.2174/0113892029302230240319042208 · Cited by 3
Micati, D., Hlavca, S., Chan, W. H., & Abud, H. E. (2024) · BMC Biology · doi:10.1186/s12915-024-02092-9 · Cited by 3
Govindharaj, G., Choudhary, J. S., Panda, R. M., Gowda, G. B., Annamalai, M., Patil, N. B., Khan, R. M., Banra, S., Srivastava, K., & Mohapatra, S. D. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e42776 · Cited by 3
Fehily, S. R., Wright, E. K., Basnayake, C., Wilson-O'Brien, A. L., Stanley, A., Marks, E. P., Russell, E., Hamilton, A. L., Bryant, R. V., Costello, S. P., et al. (2025) · BMJ Open · doi:10.1136/bmjopen-2024-094714 · Cited by 4
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Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/759969 · Cited by 3
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Bernard, C., Li, Y., Lopez, P., & Bapteste, E. P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.15.452460 · Cited by 3
López‐Moreno, A., Ruiz-Moreno, Á., Pardo, J. F. J., Cerk, K., Torres-Sánchez, A., Ortíz, P., Úbeda, M., & Aguilera, J. (2021) · Research Square · doi:10.21203/rs.3.rs-754318/v1 · Cited by 3
Kiu, R., Shaw, A., Sim, K., Bedwell, H., Cornwell, E., Pickard, D., Bélteki, G., Malsom, J., Philips, S., Young, G. R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.03.454877 · Cited by 3
de León, A. V., Hoetzinger, M., Hensen, T., Gupta, S., Weston, B. R., Johnsen, S. M., Rasmussen, J. A., Clausen, C. G., Pless, L., Verissimo, A. R., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.10.570985 · Cited by 3
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Teng, N. M. Y., Kiu, R., Evans, R., Baker, D., Zenner, C., Robinson, S. D., & Hall, L. J. (2023) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005950 · Cited by 2
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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
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