The DOI matches its Crossref record; 90 of the 90 references it cites were found in a registry or an index.
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 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.”
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3 retracted
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Self-citationRetractedAn obesity-associated gut microbiome with increased capacity for energy harvest
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Structure, function and diversity of the healthy human microbiome
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Human gut microbes associated with obesity
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Diversity of the Human Intestinal Microbial Flora
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Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors
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Sex differences in gut microbiota
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Next generation probiotics in disease amelioration
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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
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