New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella

Abstract

Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella . A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.

The Antidepressant Effect of Deoiled Sunflower Seeds on Chronic Unpredictable Mild Stress in Mice Through Regulation of Microbiota–Gut–Brain Axis

“…C. scindens is actively involved in the conversion of cholate to deoxycholate, which may be important in treatment of disease associated with increased colonic secondary bile acids ( 45 ). O. massiliensis is newly found strictly anaerobic bacterium which is responsible for the production of lactic, formic, and acetic acids as fermentation products from glucose in gut ( 46 , 47 ). Taken together, these bacteria may enhance the mucosal barrier either directly or by promoting SCFA production.…”

Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

“…The type genus Atopobium was first proposed in 1992 on the basis of a re-classification of Lactobacillus minutus , Lactobacillus rimae and Streptococcus parvulus [3]. Species of the family Atopobiaceae with validly published names have been isolated from mammalian samples, such as pig faeces [4], horse pharynx [5], human vaginal crevice [6], human gingival crevice [6], human faeces [7, 8], and human blood [9]. Most of the members of the family Atopobiaceae have been reported to produce lactate as a fermentation product [3–6].…”

“…[2] and Zgheib et al . [8] with the following modifications. The cells of some genera possess intracellular granules.…”

“…The 16S rRNA gene and genome sequences have been deposited in GenBank under the accession numbers LC706268 and AP025285, respectively. The description is as given by Gupta et al [1] and emended by Nouioui et al [2] and Zgheib et al [8] with the following modifications. The cells of some genera possess intracellular granules.…”

Rapid detection of beer spoilage bacteria based on label-free SERS technology

“…As a result, identifying bacteria has become a pressing issue that must be addressed promptly in the fermentation process. Traditional methods of bacterial identification, such as colorimetric methods, 5,6 plate culture methods, 7 flow cytometry, 8 polymerase chain reaction (PCR), 9 and enzyme-linked immunosorbent assay (ELISA), 10 have accurate results but take 2–3 days to complete, which does not meet the requirement for real-time detection of beer spoilage bacteria in the beer brewing process. Bioassays with a shorter analysis time and improved sensitivity must be developed.…”