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Alcohol pretreatment of stools effect on culturomics

  • Afouda, Pamela1, 2
  • Hocquart, Marie1, 2
  • Pham, Thi-Phuong-Thao1, 2
  • Kuete, Edmond1, 2
  • Ngom, Issa Isaac1, 2
  • Dione, Niokhor1, 2
  • Valles, Camille1, 2
  • Bellali, Sara1, 2
  • Lagier, Jean-Christophe1, 2
  • Dubourg, Grégory1, 2
  • Raoult, Didier1, 2
  • 1 Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France , Marseille (France)
  • 2 IHU Méditerranée Infection, Marseille, France , Marseille (France)
Published Article
Scientific Reports
Springer Nature
Publication Date
Mar 23, 2020
DOI: 10.1038/s41598-020-62068-x
Springer Nature


Recent studies have used ethanol stool disinfection as a mean of promoting valuable species’ cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.

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