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Microbiology spectrum2023; 11(5); e0504822; doi: 10.1128/spectrum.05048-22

Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces.

Abstract: Brachybacterium species have been identified in various ecological niches and belong to the family within the phylum . In this study, we isolated a novel JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other strains. Moreover, comparative genomic analysis using publicly available 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 DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of species. Most of the strains displayed high oxygen ( =1.6-24.2 µM) and glucose ( =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 species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of 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 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 strain through physiological and comparative genomic analysis. In addition, we presented the first report examining kinetics, indicating that all strains of , 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.
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Publication Date: 2023-09-14 PubMed ID: 37707449PubMed Central: PMC10581053DOI: 10.1128/spectrum.05048-22Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article deals with the identification and study of a new strain of bacterium, Brachybacterium equifaecis sp. nov., found in horse feces, understanding its ecological adaptations, genetic features, and metabolic potential. The study also provides the debut reporting of kinetic properties of Brachybacterium species, with insights into their adaptability and defensive mechanisms.

Introduction

  • The research focuses on a newly isolated strain of Brachybacterium (JHP9) found in horse feces. Brachybacterium species have been found in several ecological niches but their adaptability to inhabit different environments is less explored.
  • The objective is to understand the bacterium’s kinetic, biochemical, genomic characteristics, and compare them with other Brachybacterium strains. Also, the ambition is to discover properties that help in their eco-adaptation and metabolic potential via genomic analysis.

Methodology

  • The study distinguishes the novel species through 16S rRNA gene similarity and other genetic benchmarks such as average nucleotide identity, average amino acid identity, and DNA-DNA hybridization with related strains.
  • A comparative genomic examination involving publicly available Brachybacterium genomes was carried out to understand their ecological adaptation and metabolic potential.

Findings

  • The novel species JHP9 and others revealed high oxygen and glucose affinities, indicating potential niche adaptations.
  • The researchers identified various properties through genotypic and/or phenotypic analysis that provided insights into their adaptability. These included different carbohydrate metabolic pathways under both aerobic and anaerobic conditions, resistance to antibiotics, presence of mobile genetic elements, and carbohydrate-active enzymes. Plus, attributes such as lactic acid production and defense mechanisms like the Clustered Regularly Interspaced Short Palindromic Repeats-Cas and bacteriophage exclusion systems were also noted.
  • These findings suggest significant genome flexibility in Brachybacterium species that equip them with defense mechanisms and adaptability, supporting their survival and growth in diverse environments.

Conclusion

  • The research enhances understanding about novel Brachybacterium equifaecis sp. nov. strain (JHP9) and the kinetic, physiological, and genomic properties of Brachybacterium species in general.
  • The newly discovered strain, along with the others, exhibit high affinities towards oxygen and glucose potentially aiding their environmental adaptation. Diverse genomic properties further provide these bacteria with competitive advantages.
  • Comprehensive genotypic and phenotypic analysis, along with kinetic properties at the species level, support the differential characteristics of Brachybacterium species that allow them to inhabit varied eco niches. Hence, this study provides a solid foundation for further ecological and microbiological analysis.

Cite This Article

APA
Farooq A, Lee M, Han S, Jung GY, Kim SJ, Jung MY. (2023). Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces. Microbiol Spectr, 11(5), e0504822. https://doi.org/10.1128/spectrum.05048-22

Publication

Microbiology spectrum
ISSN: 2165-0497
NlmUniqueID: 101634614
Country: United States
Language: English
Volume: 11
Issue: 5
Pages: e0504822
PII: e05048-22

Researcher Affiliations

Farooq, Adeel
  • Research Institute for Basic Sciences (RIBS), Jeju National University , Jeju, South Korea.
Lee, Myunglip
  • Department of Marine Life Science, Jeju National University , Jeju, South Korea.
Han, Saem
  • Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University , Jeju, South Korea.
Jung, Gi-Yong
  • Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources , Daejeon, South Korea.
  • Department of Biological Sciences and Biotechnology, Chungbuk National University , Cheongju, South Korea.
Kim, So-Jeong
  • Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources , Daejeon, South Korea.
Jung, Man-Young
  • Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University , Jeju, South Korea.
  • Department of Science Education, Jeju National University , Jeju, South Korea.
  • Jeju Microbiome Center, Jeju National University , Jeju, South Korea.

Conflict of Interest Statement

The authors declare no conflict of interest.

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