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Cited by 236Gut microbiota and healthMicrobial Community Ecology and PhysiologyBacterial Identification and Susceptibility Testing

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 access
Bilen, Melhem, Dufour, Jean-Charles, Lagier, Jean-Christophe, Cadoret, Fréderic, Daoud, Ziad, Dubourg, Grégory, Raoult, Didier·2018·Microbiome
DOI 10.1186/s40168-018-0485-5PMC PMC5966928
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Abstract

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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Crossref · 10.1186/s40168-018-0485-5

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Fig. 1 All 2776 species isolated at least once from humans by culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the repertoire
Fig. 1 All 2776 species isolated at least once from humans by culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the repertoireCC BY · PubMed Central
Fig. 2 Distribution of bacterial species reported in this repertoire according to their phylum, based on the NCBI taxonomy classification with the highest category being clustered in the Firmicutes phylum. Cyanobacteria, Deferribacteres, Spirochaetes, Synergistetes, and Tenericutes represent minority phyla in this repertoire, with 1, 1, 1, 3, 3, and 3 different species, respectively
Fig. 2 Distribution of bacterial species reported in this repertoire according to their phylum, based on the NCBI taxonomy classification with the highest category being clustered in the Firmicutes phylum. Cyanobacteria, Deferribacteres, Spirochaetes, Synergistetes, and Tenericutes represent minority phyla in this repertoire, with 1, 1, 1, 3, 3, and 3 different species, respectivelyCC BY · PubMed Central
Fig. 3 All 2776 species isolated at least once from humans using culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the database. In this image, only the species name was taken into consideration, excluding the genus
Fig. 3 All 2776 species isolated at least once from humans using culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the database. In this image, only the species name was taken into consideration, excluding the genusCC BY · PubMed Central
Fig. 4 Distribution of bacterial species isolated from the gut using culturomics, according to the phylum to which they belong, based on the NCBI taxonomy classification, with the highest clustering in the Firmicutes phylum
Fig. 4 Distribution of bacterial species isolated from the gut using culturomics, according to the phylum to which they belong, based on the NCBI taxonomy classification, with the highest clustering in the Firmicutes phylumCC BY · PubMed Central
Fig. 5 Number of reported species isolated for the first time in humans by culturomics using the new species announcement format compared to the full description format
Fig. 5 Number of reported species isolated for the first time in humans by culturomics using the new species announcement format compared to the full description formatCC BY · PubMed Central

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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
Publisher
Springer Science and Business Media LLC
Published
2018-05-24
Volume
6
Issue
1
Pages
94-94
ISSN
2049-2618 (ISSN-L)
DOI
10.1186/s40168-018-0485-5
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
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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