Characterization and description of Gabonibacter chumensis sp. nov., isolated from feces of a patient with non-small cell lung cancer treated with immunotherapy

Abstract

A polyphasic taxonomic approach, incorporating analysis of phenotypic features, cellular fatty acid profiles, 16S rRNA gene sequences, and determination of average nucleotide identity (ANI) plus digital DNA-DNA hybridization (dDDH), was applied to characterize an anaerobic bacterial strain designated KD22^T isolated from human feces. 16S rRNA gene-based phylogenetic analysis showed that strain KD22^T was found to be most closely related to species of the genus Gabonibacter. At the 16S rRNA gene level, the closest species from the strain KD22^T corresponded with Gabonibacter massiliensis GM7^T, with a similarity of 97.58%. Cells of strain KD22^T were Gram-negative coccobacillus, positive for indole and negative for catalase, nitrate reduction, oxidase, and urease activities. The fatty acid analysis demonstrated the presence of a high concentration of iso-C_{15: 0} (51.65%). Next, the complete whole-genome sequence of strain KD22^T was 3,368,578 bp long with 42 mol% of DNA G + C contents. The DDH and ANI values between KD22^T and type strains of phylogenetically related species were 67.40% and 95.43%, respectively. These phylogenetic, phenotypic, and genomic results supported the affiliation of strain KD22^T as a novel bacterial species within the genus Gabonibacter. The proposed name is Gabonibacter chumensis and the type strain is KD22^T (= CSUR Q8104^T = DSM 115208 ^T).

Keywords: Bacteria; Cancer; Gabonibacter chumensis; Gut microbiota; Immunotherapy; Non-small cell lung cancer.

Fig. 1

Phylogenetic tree, based on the 16S rRNA gene sequence of strain KD22^T and closest related taxa, constructed using the neighbor-joining method with the maximum composite likelihood model. Branch supports were evaluated by generating 100 bootstraps replicates. 16S rRNA gene GenBank accession numbers are shown in parentheses. The scale bar represented 0.02 substitutions per nucleotide position

Fig. 2

Graphical circular map of the chromosome of strain KD22.^T. From the outside to the center: genes on the forward strand colored by Clusters of Orthologous Groups of proteins (COG) categories (only genes assigned to COG), genes on the reverse strand colored by COG categories (only gene assigned to COG), RNA genes (tRNAs green and rRNAs red), GC content (dark), and GC skew (negative values purple and positive values olive green)

Fig. 3

Core-genome phylogenetic tree between strain KD22^T and other related species. Phylogenetic tree built with a concatenated alignment of 108 single copy genes present in all the analyzed genomes, using the maximum-likelihood method with GTR model. Percentage bootstrap support values above 99% are shown for each node. The bar is nucleotide substitutions per site