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

Abstract

Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18 : 1 cis 9 and C18 : 1 cis 9 dimethyl acetal, whereas those of TOC12T were C18 : 0 and C18 : 1 cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family Atopobiaceae , namely, Olsenella phocaeensis Marseille-P2936T (94.3 %) and Olsenella umbonata KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family Atopobiaceae . In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family Atopobiaceae , for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.

Description of an anaerobic actinobacterium, Kribbibacterium absianum gen. nov., sp. nov., a new member of the novel family Kribbibacteriaceae fam. nov., and reclassification of the genera Granulimonas and Leptogranulimonas

“…The results showed that the most closely related strain was ‘ Olsenella congonensis ’ (YH-ols2216, 92.6 %; YH-ols2217 T , 92.7 %), which was below the defined threshold for delineation of bacterial genus [23]. However, ‘ O. congonensis ’ Marseille-P3359 T was not validly published, thus, the type strain within the following type species of closely related genera were used as reference strains: Granulimonas faecalis KCTC 25474 T [7], Leptogranulimonas caecicola KCTC 25472 T [7], Paratractidigestivibacter faecalis KCTC 15699 T , Parafannyhessea umbonata KCTC 22620 T , Thermophilibacter provencensis DSM 107455 T , Tractidigestivibacter scatoligenes DSM 28304 T , Olsenella uli KCTC 5039 T , Collinsella aerofaciens JCM 10188 T [24], Coriobacterium glomerans JCM 10262 T [3], and Enorma massiliensis DSM 25476 T [25]. The similarities between isolates YH-ols2216 and YH-ols2217 T and the type species of the most closely related genus Granulimonas ( G. faecalis KCTC 25474 T ) were 92.0 and 92.5 %, respectively.…”

“…C 18 : 1 ω 6 c was only detected as the dominant whole-cell fatty acid in isolate YH-ols2216. The dominant cellular fatty acid C 18 : 1 ω 9 c , while at different percentages, was also present in G. faecalis KCTC 25474 T [7], L. caecicola KCTC 25472 T [7], O. uli KCTC 5039 T , Prf. umbonata KCTC 22620 T , Tr.…”

“…These results were different from those of the related strains. The API 50CHB/E results showed that both isolates were positive for aesculin, which differed from the related strains G. faecalis KCTC 25474 T [7], L. caecicola KCTC 25472 T [7], Th. provencensis DSM 107455 T , and Cl.…”

“…This order is the deepest lineage within Actinobacteria and clusters are closely related to the phylum Firmicutes [4,5]. To date, 10 genera of Atopobiaceae and three of Coriobacteriaceae are valid with correct names in the List of Prokaryotic Names with Standing in Nomenclature (LPSN; https://lpsn.dsmz.de), including Atopobium, Fannyhessea, Lancefieldella, Olsenella, Paratractidigestivibacter, Parolsenella, Thermophilibacter, Tractidigestivibacter, Collinsella, Coriobacterium, and Enorma, in addition to the recently described genera Granulimonas and Leptogranulimonas that were proposed in 2022 [6,7]. Members of the order Coriobacteriales are strictly or facultatively anaerobic, non-motile, non-spore-forming, Gram-stain-positive, rod-or cocci-shaped bacteria that frequently ferment glucose into lactic acid as an end-product [2].…”

“…Cellular fatty acid profiles of isolates and closely related species.Strains: 1, YH-ols2216; 2, YH-ols2217 T ; 3, Granulimonas faecalis KCTC 25474 T[7]; 4, Leptogranulimonas caecicola KCTC 25472 T[7]; 5, Paratractidigestivibacter faecalis KCTC 15699 T ; 6, Olsenella uli KCTC 5039 T ; 7, Parafannyhessea umbonata KCTC 22620 T ; 8, Tractidigestivibacter scatoligenes DSM 28304 T ; 9, Thermophilibacter provencensis DSM 107455 T ; 10, Atopobium minutum DSM 20586 T[26]; 11, Coriobacterium aerofaciens ATCC 25986 T[24]. Values are percentage of total fatty acid detected.…”