Actinomyces lilanjuaniae sp. nov., isolated from the faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Characterization of isolates of members of the genus Actinomyces from Marmota himalayana: description of Actinomyces faecalis sp. nov., Actinomyces respiraculi sp. nov., and Actinomyces trachealis sp. nov

Six novel strains (ZJ34^T, ZJ561, ZJ750^T, ZJ1629, zg-993^T and zg-987) isolated from faeces and respiratory tracts of Marmota himalayana from the Qinghai-Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus Actinomyces, and are closely related to Actinomyces urogenitalis DSM 15434^T (16S rRNA gene sequences similarities, 94.9-98.7 %), Actinomyces weissii CCUG 61299^T (95.6-96.6 %), Actinomyces bovis CCTCC AB2010168^T (95.7 %) and Actinomyces bowdenii DSM 15435^T (95.2-96.4 %), with values of digital DNA-DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34^T/ZJ561, ZJ750^T/ZJ1629 and zg-993^T/zg-987). All the novel strains had C_18 : 1 ω9c and C_16 : 0 as the two most abundant major fatty acids. MK-9(H₄) or MK-8(H₄) was the sole or predominant respiratory quinone of strains ZJ34^T, ZJ750^T and zg-993^T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750^T shared identical peptidoglycan amino acid profile with ZJ34^T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993^T (glucose, rhamnose and ribose). Strain zg-993^T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34^T was ribose. The DNA G+C contents of the novel strains were within the range of 65.8-70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus Actinomyces, for which the names Actinomyces faecalis sp. nov. [type strain ZJ34^T (=GDMCC 1.1952^T=JCM 34355^T)], Actinomyces respiraculi sp. nov. [type strain ZJ750^T (=GDMCC 1.1950^T=JCM 34356^T)] and Actinomyces trachealis sp. nov. [type strain zg-993^T (=GDMCC 1.1956^T=JCM 34357^T)] were proposed, respectively.

Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. isolated from wild animals and reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively

Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325^T, zg329, dk561^T and dk752) were isolated from the respiratory tract of marmot (Marmota himalayana) and the faeces of Tibetan gazelle (Procapra picticaudata) from the Qinghai-Tibet Plateau of PR China. The results of 16S rRNA gene sequence-based phylogenetic analyses indicated that strains zg-325^T and dk561^T represent members of the genus Actinomyces, most similar to Actinomyces denticolens DSM 20671^T and Actinomyces ruminicola B71^T, respectively. The DNA G+C contents of strains zg-325^T and dk561^T were 71.6 and 69.3 mol%, respectively. The digital DNA-DNA hybridization values of strains zg-325^T and dk561^T with their most closely related species were below the 70 % threshold for species demarcation. The four strains grew best at 35 °C in air containing 5 % CO₂ on brain heart infusion (BHI) agar with 5 % sheep blood. All four strains had C_18:1ω9c and C_16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325^T while MK-10 was predominant in dk561^T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325^T and dk561^T represent novel species of the genus Actinomyces, for which the name Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. are proposed. The type strains are zg-325^T (=GDMCC 1.1724^T=JCM 34091^T) and dk561^T (=CGMCC 4.7566^T=JCM 33484^T). We also propose, on the basis of the phylogenetic results herein, the reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.

Actinomyces wuliandei sp. nov., Corynebacterium liangguodongii sp. nov., Corynebacterium yudongzhengii sp. nov. and Oceanobacillus zhaokaii sp. nov., isolated from faeces of Tibetan antelope in the Qinghai-Tibet plateau of China

Eight Gram-stain-positive, rod-shaped bacterial strains were isolated from faeces of Tibetan antelopes on the Tibet-Qinghai Plateau of China. Genomic sequence analysis showed that the strains belong to the genera Actinomyces (strains 299^T and 340), Corynebacterium (strains 2184^T, 2185, 2183^T and 2189) and Oceanobacillus (strains 160^T and 143), respectively, with a percentage of similarity for the 16S rRNA gene under the species threshold of 98.7 % except for strains 160^T and 143 with Oceanobacillus arenosus CAU 1183^T (98.8 %). The genome sizes (and genomic G+C contents) were 3.1 Mb (49.4 %), 2.5 Mb (64.9 %), 2.4 Mb (66.1 %) and 4.1 Mb (37.1 %) for the type strains 299^T, 2183^T, 2184^T and 160^T, respectively. Two sets of the overall genome relatedness index values between our isolates and their corresponding closely related species were under species thresholds (95 % for average nucleotide identity, and 70 % for digital DNA-DNA hybridization). These results, together with deeper genotypic, genomic, phenotypic and biochemical analyses, indicate that these eight isolates should be classified as representing four novel species. Strain 299^T (=CGMCC 1.16320^T=JCM 33611^T) is proposed as representing Actinomyces wuliandei sp. nov.; strain 2184^T (=CGMCC 1.16417^T=DSM 106203^T) is proposed as representing Corynebacterium liangguodongii sp. nov.; strain 2183^T (=CGMCC 1.16416^T=DSM 106264^T) is proposed as representing Corynebacterium yudongzhengii sp. nov.; and strain 160^T (=CGMCC 1.16367^T=DSM 106186^T) is proposed as representing Oceanobacillus zhaokaii sp. nov.