Description and comparative genome analysis of Hallella absiana sp. nov., isolated from pig feces

Anaerobe. 2023 Jun:81:102735. doi: 10.1016/j.anaerobe.2023.102735. Epub 2023 May 16.


Objective: The genus Hallella was described within Bacteroidaceae, and then reclassified within Prevotellaceae based on its phenotypic and phylogenetic description. It is associated with degradation of carbohydrate. However, some species of Hallella have pathobiotic properties, and are involved in infections and chronic inflammatory disorders.

Methods: Here, we used a polyphasic taxonomic approach to characterize the two strains: YH-C38T and YH-C4B9b. A detailed metabolic analysis was conducted to compare the two novel isolates with related strains within the genus Hallella.

Result: Analysis of 16S rRNA gene sequences revealed that the isolates were most closely related to Hallella mizrahii JCM 34422T with 98.5% and 98.6% similarities, respectively. Analysis of the multi-locus species tree based on whole genome sequences of the isolates and related strains revealed that the isolates formed a sub-cluster adjacent to H. mizrahii JCM 34422T. The average nucleotide identity values for YH-C38T and YH-C4B9b, and the most closely related strain H. mizrahii JCM 34422T, were 93.5% and 93.8%, respectively. The main fatty acids were iso C17:0 3OH and anteiso C15:0. The predominant menaquinones were MK-12, MK-11, and MK-13. The cell wall contained the peptidoglycan of meso-diaminopimelic acid. Analysis of comparative metabolic analysis revealed that isolates YH-C38T and YH-C4B9b each contained 155 carbohydrate-active enzymes, and glycoside hydrolase was the largest family.

Conclusion: Two rod-shaped, obligately anaerobic, Gram-stain-negative bacteria, isolated from pig feces, were designated as strains YH-C38T and YH-C4B9b. Based on the chemotaxonomic, phenotypic, and phylogenetic properties, YH-C38T (=KCTC 25103T = JCM 35423T) and YH-C4B9b (=KCTC 25104 = JCM 35609) represent a novel taxon. The name Hallella absiana sp. nov. is proposed.

Keywords: Comparative metabolic analysis; Genomic analysis; Hallella; Hallella absiana; New species; Pig feces.

MeSH terms

  • Animals
  • Bacterial Typing Techniques
  • Bacteroidetes*
  • Base Composition
  • DNA, Bacterial / genetics
  • Fatty Acids* / analysis
  • Feces / microbiology
  • Nucleic Acid Hybridization
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Swine


  • RNA, Ribosomal, 16S
  • Fatty Acids
  • DNA, Bacterial