Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

Elucidating the mechanisms associated with the anaerobic biotransformation of the emerging contaminant nitroguanidine

Nitroguanidine (NQ) is a constituent of gas generators for automobile airbags, smokeless pyrotechnics, insecticides, propellants, and new insensitive munitions formulations applied by the military. During its manufacture and use, NQ can easily spread in soils, ground, and surface waters due to its high aqueous solubility. Very little is known about the microbial biotransformation of NQ. This study aimed to elucidate important mechanisms operating during NQ anaerobic biotransformation. To achieve this goal, we developed an anaerobic enrichment culture able to reduce NQ to nitrosoguanidine (NsoQ), which was further abiotically transformed to cyanamide. Effective electron donors for NQ biotransformation were lactate and, to a lesser extent, pyruvate. The results demonstrate that the enrichment process selected a sulfate-reducing culture that utilized lactate as its electron donor and sulfate as its electron acceptor while competing with NQ as an electron sink. A unique property of the culture was its requirement for exogenous nitrogen (e.g., from yeast extract or NH₄Cl) for NQ biotransformation since NQ itself did not serve as a nitrogen source. The main phylogenetic groups associated with the NQ-reducing culture were sulfate-reducing and fermentative bacteria, namely Cupidesulfovibrio oxamicus (63.1% relative abundance), Dendrosporobacter spp. (12.0%), and Raoultibacter massiliens (10.9%). The molecular ecology results corresponded to measurable physiological properties of the most abundant members. The results establish the conditions for NQ anaerobic biotransformation and the microbial community associated with the process, improving our present comprehension of NQ environmental fate and assisting the development of NQ remediation strategies.

New members of the family Eggerthellaceae isolated from Marmota himalayana: Xiamenia xianingshaonis gen. nov., sp. nov., from intestinal contents, and Berryella wangjianweii sp. nov., from trachea

Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886T/zg-887 and zg-1050T/zg-1084) were isolated from Marmota himalayana. Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family Eggerthellaceae : zg-1050T and zg-1084 were most closely related to Berryella intestinalis 68-1-3T (97.2 %), while zg-886T/zg-887 had the highest similarity to Slackia piriformis YIT 12062T (91.6 %), followed by Paraeggerthella hongkongensis DSM 16106T (91.4 %) and Gordonibacter urolithinfaciens DSM 27213T (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family Eggerthellaceae . The genomic G+C contents of strains zg-886T and zg-1050T were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family Eggerthellaceae were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050T, strain zg-886T contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family Eggerthellaceae are proposed, Xiamenia xianingshaonis gen. nov., sp. nov. (zg-886T=JCM 34097T=GDMCC 1.1710T) and Berryella wangjianweii sp. nov. (zg-1050T=GDMCC 1.2426T=JCM 34748T).

Raoultibacter phocaeensis sp. nov., A New Bacterium Isolated from a Patient with Recurrent Clostridioides difficile Infection

Strain Marseille-P8396^T is a new species isolated from a patient with recurrent Clostridioides difficile infection. Its optimal growth condition was observed at pH of 7.5, at a temperature of 37 °C after 72 h of incubation on Columbia agar (BioMérieux, France) with 5% sheep blood, under an anaerobic atmosphere. Strain Marseille-P8396^T cells are Gram-positive rods, nonspore-forming, and nonmotile. 9-Octadecenoic acid (41.9%), hexadecanoic acid (22.5%), and 11-Octadecenoic acid (11.0%) represent the major fatty acid of strain Marseille-P8396^T. The optimal growth condition of strain Marseille-P8396^T was observed at 37 °C after 72 h of incubation under an anaerobic atmosphere, pH ranging from 6.5 to 8.5, and salinity of 0.5 to 7.5%. Its genome (Genbank Accession Number NZ_CABDUX000000000) size was 3.86 Mb with 59.4 mol% of G+C content, and 3,124 protein-coding genes. The 16S rRNA gene sequence (Genbank accession number NR_148574.1) of strain Marseille-P8396^T shared a similarity of 98.71% with Raoultibacter timonensis strain Marseille-P3277^T (Genbank accession number NR_148574.1), currently the most closely related species. However, the OrthoANI and digital DNA-DNA hybridization values with Raoultibacter timonensis strain Marseille-P3277^T (Genbank accession number OEPT01000000) were 80.15% and 24.6 ± 4.8%, respectively. Taken together, these results clearly demonstrate that strain Marseille-P8396^T represents a new species within the genus Raoultibacter described here as Raoultibacter phocaeensis sp. nov. (type strain: Marseille-P8396^T=CSUR8396^T=CECT 30202^T).

Prokaryotic population dynamics and interactions in an AnSBBR using tequila vinasses as substrate in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse for hydrogen production

AIMS

The purpose of this study was to characterize the prokaryotic community and putative microbial interactions between H₂ -producing bacteria (HPB) and non-HPB using two anaerobic sequencing batch biofilm reactors (AnSBBRs) fed with tequila vinasses in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse (ATAB).

METHODS AND RESULTS

Two AnSBBRs were operated for H₂ production to correlate changes in physicochemical and biological variables by principal component analysis (PCA). Results indicated that H₂ yield was supported by Ethanoligenens harbinense and Clostridium tyrobutyricum through the PFOR pathway. However, only E. harbinense was able to compete for sugars against non-HPB. Competitive exclusion associated with competition for sugars, depletion of essential trace elements, bacteriocin production and resistance to inhibitory compounds could be carried out by non-HPB, increasing their relative abundances during the dark fermentation (DF) process.

CONCLUSIONS

The global scenario obtained by PCA correlated the decrease in H₂ production with the lactate:acetate molar ratio in the influent. At the beginning of co-digestion, this ratio had the minimum value considered for a net gain of ATP. This fact could cause the reduction of the relative abundance of C. tyrobutyricum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study that demonstrated the feasibility of H₂ production by Clostridiales from acid hydrolysates of ATAB in co-digestion with tequila vinasses.

Corynebacterium neomassiliense sp. nov., a new bacterium isolated in a stool sample from a healthy male pygmy

An obligate aerobic, Gram-positive, non-sporulating, rod-shaped bacterium designated Marseille P3888T was isolated from the stool sample of a healthy male pygmy. We described its main characteristics, and sequenced and annotated its genome. The 16S rRNA analysis revealed 98.10% sequence similarity with Corynebacterium terpenotabidum, the phylogenetically closest species with standing in nomenclature. The genome had a size of 3142051 bp with a guanine + cytosine content of 66.83%. We proposed the creation of the new Corynebacterium neomassiliense sp. nov. strain Marseille-P3888T.

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.