Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow

Abstract

A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131T, which grew at 20–40 °C (optimum 30 °C), pH 3.0–11.0 (optimum pH 4.0) and in the presence of 0–18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131T formed a group within the genus Peribacillus , and showed the highest sequence similarity with Peribacillus endoradicis DSM 28131T (96.9 %), following by Peribacillus butanolivorans DSM 18926T (96.6 %). The genome of AGMB 02131T comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA–DNA hybridization revealed that AGMB 02131T displayed 21.4 % genomic DNA relatedness with the most closely related strain, P. butanolivorans DSM 18926T. AGMB 02131T contains all of the conserved signature indels that are specific for members of the genus Peribacillus . The major cellular fatty acids (>10 %) of AGMB 02131T were C18 : 1ω9c, C18:0 and C16 : 0. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131T represents a novel species of the genus Peribacillus , for which the name Peribacillus faecalis sp. nov. is proposed. The type strain is AGMB 02131T (=KCTC 43221T=CCTCC AB 2020077T).

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

“…Due to their group (taxon)-specificity and predictive ability to be found in other members of the indicated group, the identified CSIs have provided important means for the demarcation of prokaryotic taxa of different ranks in molecular terms, thus aiding in the development of more robust classification schemes for prokaryotic organisms [38, 39, 47, 48, 50, 52, 53, 58]. The CSIs have now been identified for numerous prokaryotic taxa [38, 39, 47, 48, 50, 52, 53, 58, 63, 93, 94] and several investigators have used them for the classification of newly described species into specific taxa [54–56, 62, 67–74]. However, the lack of a convenient method for determining the presence or absence of known CSIs in genome sequences has limited the use of these molecular markers for taxonomic and diagnostic studies.…”

“…In the new classification scheme for Bacillus species, all newly described genera were reliably distinguished from each other (and other prokaryotic taxa) based on multiple identified CSIs which were specific for each of these genera [52,58]. Because of the predictive ability of the CSIs to be present in other members of these genera, the described CSIs have also been used by other investigators to assign newly described Bacillaceae species, as well as other species, into different genera [54][55][56][67][68][69][70][71][72][73][74]. Although the CSIs provide a very useful means for the circumscription of taxa of different ranks (specifically the genus-level clades), and for the assignment of new species into these genera based on the shared presence of CSIs, there is no convenient method available for determining the presence or absence of known taxon-specific CSIs in genome sequences.…”

Genome Sequence and Characterisation of Peribacillus sp. Strain AS_2, a Bacterial Endophyte Isolated from Alectra sessiliflora

“…Strain AS_2 tested positive for eleven sugars in API 50CH, while some of the type strain species could not produce acids from the sugars tested. In contrast, AS_2 grew in a wider range of pH (4)(5)(6)(7)(8)(9)(10)(11)(12) and NaCl (1-7%) and it tested negative for hydrolysis of gelatine, arginine dihydrolase, indole production, and tryptophan deaminase.…”

“…Members of the genus Peribacillus have been isolated from various sources including soil [11], cow faeces [12], plant tissues [13,14], and river water [15]. Currently, within the genus Peribacillus there are 17 species which have been validly published [16,17].…”

Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain

“…At the time of writing, the genus Peribacillus comprises 17 species with validly published names (https://lpsn.dsmz.de/ genus/peribacillus); most of them have been isolated from a variety of ecological niches, including soil (Yumoto et al, 2004;Lim et al, 2007;Kuisiene et al, 2008;Zhang et al, 2011;Li et al, 2014;Feng et al, 2016;Liu et al, 2016;Ma et al, 2018), plant tissues (Zhang et al, 2012;Kämpfer et al, 2015), and cow feces (Jiang et al, 2019). The species of this genus are Gram-positive, the cells are motile, aerobic, or facultatively anaerobic, and the growth occurs at the temperature range between 3 and 45 • C. The whole-genome sequences are available only for 11 species with validly published names and range in sizes from 4.1 to 5.7 Mbp.…”