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.[3] 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.[2][3] However, culturomics also uses 16S RNA sequencing to identify new species.[7]
See also
editReferences
edit- ^ Lagier J, Armougom F, Million M, et al. (December 2012). "Microbial culturomics: paradigm shift in the human gut microbiome study". Clinical Microbiology and Infection. 18 (12): 1185–1193. doi:10.1111/1469-0691.12023. PMID 23033984.
- ^ a b Lagier J, Khelaifia S, Alou M, et al. (December 2016). "Culture of previously uncultured members of the human gut microbiota by culturomics". Nature Microbiology. 1 (12): 16203. doi:10.1038/nmicrobiol.2016.203. PMID 27819657.
- ^ a b c Greub, G. (December 2012). "Culturomics: a new approach to study the human microbiome". Clinical Microbiology and Infection. 18 (12): 1157–1159. doi:10.1111/1469-0691.12032. PMID 23148445.
- ^ Rinke C, Schwientek P, Sczyrba A, et al. (25 July 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. hdl:10453/27467. PMID 23851394.
- ^ Diakite A, Dubourg G, Dione N, et al. (December 2020). "Optimization and standardization of the culturomics technique for human microbiome exploration". Scientific Reports. 10 (1): 9674. Bibcode:2020NatSR..10.9674D. doi:10.1038/s41598-020-66738-8. PMC 7295790. PMID 32541790.
- ^ Chang Y, Hou F, Pan Z, et al. (17 December 2019). "Optimization of culturomics strategy in human fecal samples". Frontiers in Microbiology. 10: 2891. doi:10.3389/fmicb.2019.02891. PMC 6927924. PMID 31921067.
- ^ Diakite A, Dubourg G, Dione N, et al. (21 October 2019). "Extensive culturomics of 8 healthy samples enhances metagenomics efficiency". PLOS ONE. 14 (10): e0223543. Bibcode:2019PLoSO..1423543D. doi:10.1371/journal.pone.0223543. PMC 6802823. PMID 31634343. (This paper currently has an expression of concern, see doi:10.1371/journal.pone.0278361, PMID 36512561, Retraction Watch)
Further reading
edit- Lagier, Jean-Christophe; Hugon, Perrine; Khelaifia, Saber; Fournier, Pierre-Edouard; La Scola, Bernard; Raoult, Didier (January 2015). "The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota". Clinical Microbiology Reviews. 28 (1): 237–264. doi:10.1128/CMR.00014-14. PMC 4284300. PMID 25567229.
- Bilen, Melhem; Dufour, Jean-Charles; Lagier, Jean-Christophe; Cadoret, Fréderic; Daoud, Ziad; Dubourg, Grégory; Raoult, Didier (December 2018). "The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species". Microbiome. 6 (1): 94. doi:10.1186/s40168-018-0485-5. PMC 5966928. PMID 29793532.