Alcohol pretreatment of stools effect on culturomics.

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.

Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections.

BACKGROUND: Irritable bowel syndrome (IBS) is a chronic and debilitating functional gastrointestinal disorder affecting 9%-23% of the population across the world. The relative efficacy of fecal microbiota transplantation (FMT) on IBS symptoms was demonstrated in a double-blind, randomized study. METHODS: We describe the case of a 73-year-old woman suffering from IBS (abdominal pain, bloating, and abundant and disabling diarrhea, with 10-15 stools a day) and repetitive urinary tract infection (UTI; 5 episodes in 6 months, including 3 the last 2 months) for several years, generating an impaired quality of life. She received an FMT with 400 mL of fecal infusion from a healthy donor via a nasogastric tube after bowel lavage. Her digestive microbiota was analyzed using culturomic and metagenomic targeting 16S rRNA sequencing methods. RESULTS: Eight months after transplantation, we observed a significant reduction in frequency and improvement in stool consistency (3-4 molded stools a day against 10-15 before the transplant) and no recurrence of urinary infection (as previously reported). Using culturomics, we found 12 bacteria present in the fecal infusion and post-transplant stool; these were absent pretransplant. Three of them (Intestinimonas massiliensis, Oscillibacter massiliensis, and Provencibacter massiliensis) were previously discovered and cultivated in our laboratory using culturomics. Using metagenomics, we also observed 12 bacteria, different from those observed during culture, that could have been transferred to the patient by FMT. CONCLUSIONS: In this case report, IBS symptoms and UTI frequency decreased after FMT UTI. Further studies involving more patients would be relevant to confirm this work and develop bacteriotherapy.

Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection.

Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.