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- Title
Proof of Concept of Culturomics Use of Time of Care.
- Authors
Naud, Sabrina; Khelaifia, Saber; Mbogning Fonkou, Maxime Descartes; Dione, Niokhor; Lagier, Jean-Christophe; Raoult, Didier
- Abstract
Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including Faecalibacterium prausnitzii , Akkermansia muciniphila, Christensenella minuta , and Phascolarctobacterium faecium. Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.
- Subjects
TIME-of-flight mass spectrometry; TIME management; PROOF of concept; GUT microbiome; RUMEN fermentation
- Publication
Frontiers in Cellular & Infection Microbiology, 2020, Vol 10, pN.PAG
- ISSN
2235-2988
- Publication type
Article
- DOI
10.3389/fcimb.2020.524769