Lutispora saccharofermentans sp. nov., a mesophilic, non-spore-forming bacterium isolated from a lab-scale methanogenic landfill bioreactor digesting anaerobic sludge, and emendation of the genus Lutispora to include species which are non-spore-forming and mesophilic.

A novel anaerobic, mesophilic, non-spore-forming bacterium (strain m25T) was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor containing anaerobic digester sludge. Cells were Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, and motile by means of a flagellum. The genomic DNA G+C content was 40.11 mol%. The optimal NaCl concentration, temperature and pH for growth were 2.5 g l-1, 35 °C and at pH 7.0, respectively. Strain m25T was able to grow in the absence of yeast extract on glycerol, pyruvate, arginine and cysteine. In the presence of 0.2 % yeast extract, strain m25T grew on carbohydrates and was able to use glucose, cellobiose, fructose, raffinose and galactose. The novel strain could utilize glycerol, urea, pyruvate, peptone and tryptone. The major fatty acids were iso-C15  :  0, C14  :  0, C16  :  0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was closely related to Lutispora thermophila EBR46T (95.02 % 16S rRNA gene sequence similarity). Genome relatedness was determined using both average nucleotide identity and amino acid identity analyses, the results of which both strongly supported that strain m25T belongs to the genus Lutispora. Based on its unique phylogenetic features, strain m25T is considered to represent a novel species within the genus Lutispora. Moreover, based on its unique physiologic features, mainly the lack of spore formation, a proposal to amend the genus Lutispora is also provided to include the non-spore-forming and mesophilic species. Lutispora saccharofermentans sp. nov. is proposed. The type strain of the species is m25T (=DSM 112749T=ATCC TSD-268T).

Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.

Altering the gut microbiota can negatively affect human health. Efforts may be sustained to predict the intended or unintended effects of molecules not naturally produced or expected to be present within the organism on the gut microbiota. Here, culture-dependent and DNA-based approaches were combined to UHPLC-MS/MS analyses in order to investigate the reciprocal interactions between a constructed Human Gut Microbiota Model (HGMM) and molecules including antibiotics, drugs, and xenobiotics. Our HGMM was composed of strains from the five phyla commonly described in human gut microbiota and belonging to Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria. Relevantly, the bacterial diversity was conserved in our constructed human gut model through subcultures. Uneven richness distribution was revealed and the sensitivity of the HGMM was mainly affected by antibiotic exposure rather than by drugs or xenobiotics. Interestingly, the constructed model and the individual cultured strains respond with the same sensitivity to the different molecules. UHPLC-MS/MS analyses revealed the disappearance of some native molecules in the supernatants of the HGMM as well as in those of the individual strains. These results suggest that biotransformation of molecules occurred in the presence of our gut microbiota model and the coupled approaches performed on the individual cultures may emphasize new bacterial strains active in these metabolic processes. From this study, the new HGMM appears as a simple, fast, stable, and inexpensive model for screening the reciprocal interactions between the intestinal microbiota and molecules of interest.

In vitro sensitivity of 30 anaerobic bacterial strains of the human intestinal core microbiota to antibiotics: Culture and LC-MS/MS approaches.

We have a vast knowledge on human intestinal microbiota but it can still be regarded incomplete. One of the objectives of scientists using so-called "omics" techniques is to be interested in the consequences that drugs can have on the composition of the intestinal microbiota and inversely. To date, few publications have reported the effects of drugs on the growth of bacteria composing this microbiota using a "culturomics" approach. We focused on antibiotics commonly prescribed for which the only published are the susceptibility of the pathogenic strains and not that of the commensal strains. The aim of our study was to determine the sensitivity of 30 strains considered to represent the intestinal core microbiota to 8 antibiotics and to study the possible modification of these molecules by bacteria. The 30 bacterial strains were cultured under anaerobic conditions in order to determine their sensitivity to the antibiotics. After 48 h of culture, the supernatants were also analyzed via UHPLC-MS/MS in order to determine if the antibiotics have been chemically modified. Under the current experimental conditions, cefpodoxime, metronidazole, erythromycin, sulfamethozaxole, trimethoprim and the trimethoprim/sulfamethozaxole combination have little impact on the core microbiota strain growth. On the contrary, moxifloxacin and amoxicillin inhibit the growth of numerous strains of our panel. Using UHPLC-MS/MS analyses, we have shown that some antibiotics can be modifed by the bacteria composing the intestinal core microbiome. The bacteria that make up the intestinal microbiota core are impacted by the antibiotics most commonly prescribed in clinics today and inversely.

Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester.

A novel, mesophilic, strictly anaerobic, sulfate-reducing and propionate-oxidizing bacterium, strain Prop6T, was enriched and isolated from a municipal anaerobic sewage sludge digester. Cells were Gram-stain-negative, catalase-positive, oval rods, motile by means of amphitrichous flagella, non-spore-forming and contained menaquinone MK-5(H2) as the major respiratory quinone. The genomic DNA G+C content was 51.7 mol%. The optimal NaCl concentration, temperature and pH were 2-5 g l-1, 35 °C and pH 7.6, respectively. Strain Prop6T could only oxidize propionate, lactate and pyruvate (weakly) with sulfate, sulfite or thiosulfate, mainly to acetate. Strain Prop6T fermented pyruvate and lactate to acetate and propionate. The predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1ω7, C16 : 1ω5, C17 : 1ω6 and C18 : 1ω7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Desulfobulbus, with Desulfobulbus elongatus DSM 2908T, Desulfobulbus propionicus DSM 2032T and Desulfobulbus rhabdoformis DSM 8777T as closest relatives among species with validly published names. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Desulfobulbus oligotrophicus sp. nov. The type strain is Prop6T (=DSM 103420T=JCM 31535T).