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Comparative genomics reveals genetic diversity and differential metabolic potentials of the species of Arachnia and suggests reclassification of Arachnia propionica E10012 (=NBRC_14587) as novel species

March 2025
Archives of Microbiology 207(4)

DOI:10.1007/s00203-025-04302-6

Authors:

Roja Suresh

Sri Balaji Vidyapeeth University

Susanthika Jayachandiran

Sri Balaji Vidyapeeth University

Pratebha Balu

Sri Balaji Vidyapeeth University

The genus Arachnia, including Arachnia propionica and Arachnia rubra, are part of the normal oral and respiratory microbiota but can act as opportunistic pathogens in humans. This study investigates the functional, phylogenomic and taxonomic characteristics of 10 completely sequenced Arachnia strains, to elucidate their evolutionary relationships and divergence patterns, focusing on genomic variability and functional diversity. Phylogenetic analyses revealed distinct patterns, with Arachnia propionica strains showing significant divergence compared to the conserved Arachnia rubra strains. Notably, E10012 (=NBRC 14587) emerged as a distinct lineage with unique adaptations, while NCTC11666 exhibited a unique phylogenetic position, suggesting subspecies-level classification. Functional analyses highlighted variability among Arachnia propionica strains, with E10012 (=NBRC 14587) showing genes linked to choline metabolism and metal resistance, and NCTC11666 enriched in carbohydrate-active enzymes like GH179. In contrast, Arachnia rubra demonstrated genomic conservation, indicative of evolutionary specialization. This study reveals that strains E10012 (=NBRC 14587) and NCTC11666 displayed unique genomic features and distinct phylogenetic positioning, suggesting their reclassification as potential novel species and subspecies respectively. This underscores the balance between genomic conservation and diversification in Arachnia, reflecting their ecological adaptability and functional roles in the oral microbiome.

Phylogenetic analysis based on the 10 complete 16S rRNA gene sequences of Arachnia: the phylogenetic tree based on the 16S rRNA gene sequences of 10 Arachnia strains, revealing three distinct clusters. The phylogram was constructed using the maximum likelihood method and MUSCLE alignment with 1000 bootstrap replicates to assess the robustness of the tree topology

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Comparative analysis of whole genome sequence data: a heat plot that visualizes the comparative analysis of whole genome sequence data for 10 A. propionica strains performed using Gegenees software. The heatmap is based on a fragmented alignment using BLASTN with settings 50/25

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Phylogenetic analysis based on the whole-genome sequences of A. propionica strains: the maximum likelihood (ML) phylogenetic tree was constructed using concatenated core genes from the whole-genome sequences of 10 A. propionica strains. The tree is rooted, displayed with branch lengths, and scaled appropriately

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Distribution of COG functional categories: the distribution of COG functional categories across the 10 Arachnia strains. COG function classification of consensus sequences is presented graphically, with categories on the horizontal axis and strains on the vertical axis, using colour coding to highlight functional groupings

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Heatmap illustrating antimicrobial resistance (AMR) profiles: a heatmap illustrating the antimicrobial resistance profiles of 10 Arachnia strains, based on the number of resistance genes identified in each strain. The heatmap was generated using data from RAST, showing the resistance to antibiotics and toxic compounds for each strain across different subsystem groups, reflecting the variability in antimicrobial resistance among the strains

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Vol.:(0123456789)

Archives of Microbiology (2025) 207:93

https://doi.org/10.1007/s00203-025-04302-6

ORIGINAL PAPER

Comparative genomics reveals genetic diversity anddiﬀerential

metabolic potentials ofthespecies ofArachnia andsuggests

reclassiﬁcation ofArachnia propionica E10012 (=NBRC_14587)

asnovel species

RojaSuresh1· SusanthikaJayachandiran1· PratebhaBalu2· DhamodharanRamasamy1

Received: 11 January 2025 / Revised: 1 March 2025 / Accepted: 9 March 2025 / Published online: 18 March 2025

Abstract

The genus Arachnia, including Arachnia propionica and Arachnia rubra, are part of the normal oral and respiratory micro-

biota but can act as opportunistic pathogens in humans. This study investigates the functional, phylogenomic and taxonomic

characteristics of 10 completely sequenced Arachnia strains, to elucidate their evolutionary relationships and divergence pat-

terns, focusing on genomic variability and functional diversity. Phylogenetic analyses revealed distinct patterns, with Arach-

nia propionica strains showing signiﬁcant divergence compared to the conserved Arachnia rubra strains. Notably, E10012

(=NBRC 14587) emerged as a distinct lineage with unique adaptations, while NCTC11666 exhibited a unique phylogenetic

position, suggesting subspecies-level classiﬁcation. Functional analyses highlighted variability among Arachnia propionica

strains, with E10012 (=NBRC 14587) showing genes linked to choline metabolism and metal resistance, and NCTC11666

enriched in carbohydrate-active enzymes like GH179. In contrast, Arachnia rubra demonstrated genomic conservation,

indicative of evolutionary specialization. This study reveals that strains E10012 (=NBRC 14587) and NCTC11666 displayed

unique genomic features and distinct phylogenetic positioning, suggesting their reclassiﬁcation as potential novel species

and subspecies respectively. This underscores the balance between genomic conservation and diversiﬁcation in Arachnia,

reﬂecting their ecological adaptability and functional roles in the oral microbiome.

Keywords Arachnia· Arachnia propionica· Arachnia rubra· Phylogenomic analysis· Comparative genomics· Novel

species

Abbreviations

ABC transporters ATP-binding cassette transporters

Alr Alanine racemase

AMR Antimicrobial resistance

ANI Average nucleotide identity

BGCs Biosynthetic gene clusters

BLASTn Basic Local Alignment Search Tool

for nucleotides

BPGA Bacterial pan genome analysis

CARD Comprehensive Antibiotic Resistance

Database

CAZYME Carbohydrate active enzyme

CBM Carbohydrate-binding module

CDs Coding sequences

CE Carbohydrate esterase

COG Clusters of Orthologous Groups

Dbcan Database of Carbohydrate-Active

Enzymes

DDH DNA–DNA hybridization

Ddl D-Alanine-

-alanine ligase

DNA Deoxyribonucleic acid

EF-G Elongation factor G

EGGNOG Evolutionary genealogy of genes: non-

supervised orthologous groups

Communicated by Huayue Li.

* Dhamodharan Ramasamy

rbdhamu@gmail.com

1 Mahatma Gandhi Medical Advanced Research Institute

(MGMARI), Sri Balaji Vidyapeeth (Deemed tobe

University), Pondicherry607402, India

2 Indira Gandhi Institute ofDental Sciences (IGIDS),

Sri Balaji Vidyapeeth (Deemed tobe University),

Pondicherry607402, India

Content courtesy of Springer Nature, terms of use apply. Rights reserved.

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