Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces

Abstract

A strictly anaerobic, motile bacterium, designated as strain NSJ-9T, was isolated from human faeces. Cells were Gram-negative, non-spore-forming, non-pigmented, and spiral-shaped or slightly curved rods with flagella. Optimal growth in M2GSC medium was observed at 37 °C (growth range 30–45 °C) and pH 6.5–7.0 (growth range 6.5–7.5) under anaerobic conditions. Phylogenetic analysis of the 16S rRNA gene revealed that strain NSJ-9T formed a distinct phylogenetic lineage that reflects a new genus in the family Lachnospiraceae , with high levels of similarity to Roseburia hominis A2-183T (95.2 %), Roseburia cecicola ATCC 33874T (95.2 %), Pseudobutyrivibrio ruminis DSM 9787T (95.2 %), Pseudobutyrivibrio xylanivorans MZ 5T (94.8%) and Roseburia faecis M72/1T (94.4 %). Genomic similarity (average nucleotide identity and digital DNA–DNA hybridization) values between strain NSJ-9T and its phylogenetic neighbours were below 71 and 31 %, respectively, indicating that strain NSJ-9T represented a novel species. The average amino acid identity and the percentage of conserved proteins between strain NSJ-9T and other related members of the family Lachnospiraceae were below 63 and 50 %, respectively, supporting that strain NSJ-9T was a member of a new genus. The predominant cellular fatty acids of strain NSJ-9T were C16 : 0 and C17 : 0 2-OH, and major polar lipids were glycolipids. The end products of glucose fermentation were acetate, propionate, iso-butyrate, butyrate and valerate. Phylogenetic and phylogenomic lineage, pairwise determined genome identity analysis suggested that strain NSJ-9T represents a novel genus in the family Lachnospiraceae . The genome size of strain NSJ-9T is 2.56 Mbp with 44.9 mol% G+C content. Collectively, the genotypic and phenotypic differences between phylogenetic relatives suggested strain NSJ-9T represented a novel species of a new genus, for which the name Pararoseburia lenta gen. nov., sp. nov. is proposed. The type strain of Pararoseburia lenta is NSJ-9T (=CGMCC 1.32469T=KCTC 15957T).

Metabolite profiling of human‐originated Lachnospiraceae at the strain level

“…By modification of culturing methods, we newly cultured 114 Lachnospiraceae strains. Together with our previous Lachnospiraceae culture collections [51,52], we collected 77 species representing 33 genera of the Lachnospiraceae family, and provided taxonomic descriptions of nine novel species and five genera (humanoriginated Lachnospiraceae species [hLchsp], https:// hgmb.nmdc.cn/subject/lachnospiraceae). In total 242 metabolites comprised 17 major categories were detected for Lachnospiraceae strains (https://hgmb.nmdc.cn/ subject/lachnospiraceae/metabolites).…”

Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human

“…The 16S rRNA gene of the pure culture was amplified by using universal primers 27F (5′-AGAGTTTGATCCTGG CTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) according to the following procedure: DNA of cultured bacteria was extracted using a Wizard Genomic DNA Purification Kit (catalogue number A1120, Promega) and used as the template for PCR amplification of the 16S rRNA gene, as described previously [19]. After that, PCR products were sequenced by Sanger dideoxy DNA sequencing (Tianyi Huiyuan Biotechnology, Beijing, PR China).…”

“…The donor was without any diagnosed chronic or malignant disease. Fresh faeces were collected and immediately transferred to an anaerobic workstation (AW400SG workstation, Electrotek) filled with a CO 2 /H 2 /N 2 (5 %/10 %/85 %) gas mix, and all the subsequent operations of faecal treatment and cultivation were also conducted in an anaerobic workstation according to methods described in our previous report [19]. The generated faecal filtrate was re-suspended in phosphate buffer solution (pH 7.2-7.4; catalogue number P1022, Solarbio) and subsequently serially diluted tenfold over a range of 10 −1 to 10 −7 , and the suspension of 10 −5 to 10 −7 was spread on Petri plates of 1.5 % (w/v) agar and subsequently incubated at 37 °C anaerobically for 3-7 days.…”

Comparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus

“…Four R. gnavus strains, namely RSHDN_120, RSHDN_121, RSHDN_122 and RSHDN_123, were isolated from the faeces of four healthy Chinese adults, during a massive cultivation of human gut microbes. Fresh faecal samples were collected and immediately transferred into an anaerobic workstation (AW 500SG; Electrotek) filled with 85 % N 2 , 5 % CO 2 and 10 % H 2 , and isolation, culturing, purification, identification and preservation of micro-organisms were conducted according to our previous methods [24]. Genomic DNA was extracted from overnight bacterial cultures using a Wizard genomic DNA purification kit (Promega), following the manufacturer's protocol, and assembled according to our previous report [25].…”