Food and Fermentation Industries >

2026 , Vol. 52 >Issue 5: 111 - 120

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.042154

Comparative genomics analysis of different isolates of Pediococcus acidilactici revealed its habitat adaptive evolution

  • YUAN Ruijun ,
  • LI Weicheng ,
  • SUN Jiaqi ,
  • JIAO Yangbo ,
  • XIN Yi ,
  • SUN Zhihong
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  • 1(Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China)
    2(Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China)
    3(Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China)
    4(Collaborative Innovative Center of Lactic Acid Bacteria and Fermented Dairy Products of Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China)

Received date: 2025-01-15

  Revised date: 2025-07-10

  Online published: 2026-03-25

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Abstract

Pediococcus acidilactici is extensively utilized in the food and feed industries due to its diverse origins and probiotic properties.In this study, we conducted whole-genome sequencing and assembly of nine P.acidilactici strains isolated from the feces of piglets.Additionally, we performed a comparative genomic analysis by integrating genomic data from 275 P.acidilactici strains available in the NCBI database.Our findings indicated that the pan-genome of these 284 P.acidilactici strains followed an open-state trend.Phylogenetic analysis and average nucleotide identity (ANI) clustering produced consistent results, classifying the strains into two major genetic clades.Notably, human- and animal-derived strains exhibited a relatively clustered distribution within the phylogenetic tree, whereas plant-derived strains were interspersed.Comparative genomic analysis revealed that human-derived P.acidilactici strains possessed significantly smaller genomes, lower GC content, and fewer coding sequences (CDSs) than their animal- and plant-derived counterparts (P<0.05).Furthermore, animal-derived strains exhibited significantly higher copy numbers of carbohydrate-active enzyme (CAZy) families, such as GH2 and CBM50, than human-derived strains (P<0.05).Functional annotation further demonstrated that genes associated with information storage and processing were significantly more abundant in animal-derived strains than in human-derived strains (P<0.000 1), whereas genes involved in cell growth and signal transduction displayed the opposite pattern (P<0.000 1).No significant differences (P>0.05) were observed between pig-derived strains and other animal-derived strains regarding fundamental genomic characteristics and Clusters of Orthologous Groups (COG) functional classifications.However, pig-derived strains exhibited significantly higher copy numbers of GT2, GT4, and GT26 family genes than other animal-derived strains (P<0.05), whereas CE10 and GH43 family genes were significantly less abundant (P>0.05).Additionally, 44.4% of animal-derived strains contained bacteriocin gene clusters, with a higher prevalence than those in human- or plant-derived strains.This study provides a comprehensive genomic characterization of P.acidilactici strains from diverse sources, offering valuable insights into their genetic diversity and evolutionary adaptations to distinct ecological niches.

Key words： Pediococcus acidilactici; comparative genomics; habitat adaptation evolution; carbohydrate-active enzymes; bacteriocin gene cluster

Cite this article

YUAN Ruijun , LI Weicheng , SUN Jiaqi , JIAO Yangbo , XIN Yi , SUN Zhihong . Comparative genomics analysis of different isolates of Pediococcus acidilactici revealed its habitat adaptive evolution[J]. Food and Fermentation Industries, 2026 , 52(5) : 111 -120 . DOI: 10.13995/j.cnki.11-1802/ts.042154

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