Culturomics (microbiology) explained

Culturomics is the high-throughput cell culture of bacteria that aims to comprehensively identify strains or species in samples obtained from tissues such as the human gut or from the environment.^{[1] [2] [3]} This approach was conceived as an alternative, complementary method to metagenomics, which relies on the presence of homologous sequences to identify new bacteria. Due to the limited phylogenetic information available on bacteria, metagenomic data generally contains large amounts of "microbial dark matter", sequences of unknown origin.^[4] Culturomics provides some of the missing gaps with the added advantage of enabling the functional study of the generated cultures. Its main drawback is that many bacterial species remain effectively uncultivable until their growth conditions are better understood. Therefore, optimization of the culturomics approach has been done by improving culture conditions.^{[5] [6]}

Unlike metagenomics, which relies on direct shotgun sequencing or 16S rRNA gene sequencing, culturomics is based on matrix-assisted laser desorption/ionization–time-of-flight (MALDI-TOF) mass spectrometry. However, culturomics also uses 16S RNA sequencing to identify new species.^[7]

See also

• Genomics
• Microbiota

Further reading

• Lagier . Jean-Christophe . Hugon . Perrine . Khelaifia . Saber . Fournier . Pierre-Edouard . La Scola . Bernard . Raoult . Didier . The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota . Clinical Microbiology Reviews . January 2015 . 28 . 1 . 237–264 . 10.1128/CMR.00014-14. free . 4284300 .
• Bilen . Melhem . Dufour . Jean-Charles . Lagier . Jean-Christophe . Cadoret . Fréderic . Daoud . Ziad . Dubourg . Grégory . Raoult . Didier . The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species . Microbiome . December 2018 . 6 . 1 . 94 . 10.1186/s40168-018-0485-5. free . 5966928 .

Notes and References

1. Lagier J, Armougom F, Million M et al . Microbial culturomics: paradigm shift in the human gut microbiome study . Clinical Microbiology and Infection . December 2012 . 18 . 12 . 1185–1193 . 10.1111/1469-0691.12023. free .
2. Lagier J, Khelaifia S, Alou M et al . Culture of previously uncultured members of the human gut microbiota by culturomics . Nature Microbiology . December 2016 . 1 . 12 . 16203 . 10.1038/nmicrobiol.2016.203. free .
3. Greub . G. . Culturomics: a new approach to study the human microbiome . Clinical Microbiology and Infection . December 2012 . 18 . 12 . 1157–1159 . 10.1111/1469-0691.12032. free .
4. Rinke C, Schwientek P, Sczyrba A et al . Insights into the phylogeny and coding potential of microbial dark matter . Nature . 25 July 2013 . 499 . 7459 . 431–437 . 10.1038/nature12352. free . 10453/27467 . free .
5. Diakite A, Dubourg G, Dione N et al . Optimization and standardization of the culturomics technique for human microbiome exploration . Scientific Reports . December 2020 . 10 . 1 . 9674 . 10.1038/s41598-020-66738-8. 7295790 . free .
6. Chang Y, Hou F, Pan Z et al . Optimization of culturomics strategy in human fecal samples . Frontiers in Microbiology . 17 December 2019 . 10 . 2891 . 10.3389/fmicb.2019.02891. 6927924 . free .
7. Diakite A, Dubourg G, Dione N et al . Extensive culturomics of 8 healthy samples enhances metagenomics efficiency . PLOS ONE . 21 October 2019 . 14 . 10 . e0223543 . 10.1371/journal.pone.0223543. free . 6802823 .