The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species
Open accessAbstract
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 species have been classified into 11 different phyla, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes comprising over 90% of the microbiome.
“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
The Abstract says the 2,776 species isolated from humans were classified into 11 phyla, mostly the four named. Table 1 in “The human bacterial repertoire: where do we stand?” lists 2,614 species in those four phyla—about 94% of the isolated-species repertoire. It does not establish that they comprise over 90% of the microbiome as a whole. (LLM, conf=0.88)
Experimental — accuracy not yet measuredCurrent combined Human Microbiome Project and MetaHIT data estimate that there are at least 2776 prokaryotic species isolated from human fecal matter.
“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
In “The human bacterial repertoire: where do we stand?” (page unavailable), the paper reports 2,776 species isolated at least once from the human body, not from fecal matter. The Conclusion says these species came from different body sites. The paper derives the total by adding its data to Hugon et al.’s 2015 repertoire, not by combining Human Microbiome Project and MetaHIT data. (LLM, conf=0.89)
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Iablokov, S. N., Klimenko, N. S., Efimova, D. A., Shashkova, T., Novichkov, P. S., Rodionov, D. A., & Tyakht, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.603740 · Cited by 18 · see citing works
Kaistha, S. D., & Deshpande, N. M. (2021) · Springer eBooks · doi:10.1007/978-981-16-2677-7_8 · Cited by 19 · see citing works
Koch Postulate: Why Should we Grow Bacteria?
Lagier, J., Dubourg, G., Amrane, S., & Raoult, D. (2017) · Archives of Medical Research · doi:10.1016/j.arcmed.2018.02.003 · Cited by 17 · see citing works
Self-citationTraore, S. I., Bilen, M., Beye, M., Diop, A., Fonkou, M. D. M., Tall, M. L., Michelle, C., Yasir, M., Azhar, E. I., Bibi, F., et al. (2019) · MicrobiologyOpen · doi:10.1002/mbo3.758 · Cited by 17 · see citing works
Self-citationThe endocannabinoid system: a bridge between alzheimer’s disease and gut microbiota
Bisogno, T., Lauritano, A., & Piscitelli, F. (2021) · Life · doi:10.3390/life11090934 · Cited by 16 · see citing works
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Culturomics: A critical approach in studying the roles of human and animal microbiota
Howe, S. M., Liu, Z., Zuo, B., & Zhao, J. (2024) · Animal Nutriomics · doi:10.1017/anr.2024.6 · Cited by 15 · see citing works
Virus and microbiota relationships in humans and other mammals: An evolutionary view
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Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis?
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- 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 · 2017: 1
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › 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
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