Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of
Brachybacterium equifaecis
sp. nov. isolated from horse feces
Authors: Farooq Adeel , Lee Myunglip , Han Saem , Jung Gi-Yong , Kim So-Jeong , Jung Man-Young 
Published: September 2023

ABSTRACT

Brachybacterium species have been identified in various ecological niches and belong to the family
Dermabacteriaceae
within the phylum
Actinobacteria
. In this study, we isolated a novel
Brachybacterium equifaecis
JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other
Brachybacterium
strains. Moreover, comparative genomic analysis using publicly available
Brachybacterium
genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5–82.5%), average amino acid identity (66.7–75.8%), and
in silico
DNA-DNA hybridization (23.7–27.9) using closely related strains. This study also presents the first report of the kinetic properties of
Brachybacterium
species. Most of the
Brachybacterium
strains displayed high oxygen (
K
m(app)
=1.6–24.2 µM) and glucose (
K
m(app)
=0.73–1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of
Brachybacterium
species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of
Brachybacterium
species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation.

IMPORTANCE

Basic physiological and genomic properties of most of the
Brachybacterium
isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel
Brachybacterium
strain through physiological and comparative genomic analysis. In addition, we presented the first report examining
Brachybacterium
kinetics, indicating that all strains of
Brachybacterium
, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.