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The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species
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After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.
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“These have been classified into 11 different phyla with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes comprising over 90% of the microbiome (Bilen et al., 2018;Hu-gon et al., 2015;Li et al., 2014)”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Bilen et al., 2018
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“Current combined Human Microbiome Project and MetaHIT data estimate that there are at least 2776 prokaryotic species that have been isolated from human fecal matter.”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Bilen et al., 2018
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Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Sex differences in gut microbiota
Kim, Y. S., Unno, T., Kim, B.-Y., & Park, M.-S. (2020) · The World Journal of Men s Health · doi:10.5534/wjmh.190009 · Cited by 610
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Dicks, L. M. T. (2022) · Microorganisms · doi:10.3390/microorganisms10091838 · Cited by 482
Montero, C. G., Fraile‐Μartinez, O., Gomez-Lahoz, A. M., Pekarek, L., Castellanos, A. J., Noguerales-Fraguas, F., Coca, S., Guijarro, L. G., García‐Honduvilla, N., Asúnsolo, Á., et al. (2021) · Nutrients · doi:10.3390/nu13020699 · Cited by 487
Next generation probiotics in disease amelioration
Chang, C., Lin, T., Tsai, Y., Wu, T.-R., Lai, W.-F., Lu, C., & Lai, H. (2019) · Journal of Food and Drug Analysis · doi:10.1016/j.jfda.2018.12.011 · Cited by 398
Metadata
- Authors
- Bilen, M., Dufour, J.-C., Lagier, J.-C., Cadoret, F., Daoud, Z., Dubourg, G., & Raoult, D.
- Affiliations
- University of Balamand (LB)
- Inserm (FR)
- Aix-Marseille Université (FR)
- Assistance Publique Hôpitaux de Marseille (FR)
- King Abdulaziz University (SA)
- Corresponding author
- Raoult, Didier
- ORCID
- Venue
- Microbiome
- Published
- 2018-05-24
- Volume
- 6
- Issue
- 1
- Pages
- 94-94
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC5966928
- OpenAlex
- W2807527107
- Cited by
- 231
- References
- 90
- Citations by year
- 2026: 15 · 2025: 19 · 2024: 28 · 2023: 38 · 2022: 27 · 2021: 26 · 2020: 36 · 2019: 31 · 2018: 10
- FWCI
- 2.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Microbiome (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- IHU Méditerranée Infection
- 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 › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
- Keywords
- culturomics, human microbiota, new species, Firmicutes, Proteobacteria, Bacteroidetes, actinobacteria
- MeSH terms
- Firmicutes, Bacillota, Gastrointestinal Microbiome, Archaea, Bacteria, DNA, Bacterial, Humans, DNA, Archaeal, Proteobacteria, Actinobacteria, Bacteroidetes, 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.
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