Actinomyces tangfeifanii sp. nov., isolated from the vulture Aegypius monachus

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.

Nanchangia anserum gen. nov., sp. nov., isolated from feces of greater white-fronted geese (Anser albifrons)

Two rod-shaped and Gram-stain-positive bacteria (strains C64^T and C62) were isolated in 2020 from faeces of greater white-fronted geese (Anser albifrons) from Poyang Lake, PR China. Their optimal growth conditions were at 37 °C, pH 7.0 and with 0.5 % (w/v) NaCl. The two isolates showed a highest 16S rRNA gene sequence similarity to Bowdeniella nasicola DSM 19116^T (92.1 %). Phylogenetic/phylogenomic analyses indicated that strains C64^T and C62 clustered independently in the vicinity of the genera Varibaculum, Winkia and Mobiluncus within the family Actinomycetaceae, but could not be classified clearly as members of any of these known genera. The average amino acid identity values between our isolates and available genomes of members of the family Actinomycetaceae were around the genus threshold value (45-65 %). The major cellular fatty acids of the strains were C_18 : 1ω9c and C_16 : 0. The predominant polar lipids were phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine, diacylglycerol, triacylglycerol and cardiolipin. The amino acid composition of peptidoglycan contained alanine, glutamic acid and glycine. The major respiratory menaquinones were MK-8(H₄) and MK-9(H₄). The whole cell sugars included galactose, arabinose and glucose. On the basis of the results of the 16S rRNA gene sequences comparison, whole-genome phylogenomic analysis, phenotypic and chemotaxonomic characteristics, we propose that strains C64^T and C62 represent a novel species belonging to a novel genus within the family Actinomycetaceae, for which the name Nanchangia anserum gen. nov., sp. nov. is proposed. The type strain is Nanchangia anserum C64^T (=CGMCC 1.18410^T=GDMCC 1.1969^T=KCTC 49511^T=KACC 22143^T).

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.

Nocardioides jishulii sp. nov.,isolated from faeces of Tibetan gazelle (Procapra picticaudata)

Two novel Gram-stain-positive, irregular rod-shaped bacterial strains, dk3136^T and dk3543, were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) in the Qinghai-Tibet Plateau of PR China. The cells were aerobic, oxidase-negative and catalase-positive. Colonies were yellowish, circular without any observable aerial mycelium after culturing at 28 ℃ for 3 days on brain-heart infusion (BHI) agar with 5 % sheep blood. The cells grew optimally at 28 °C, pH 7.5 and with 1 % (w/v) NaCl on BHI agar supplemented with 5 % sheep blood. Phylogenetic analysis of the 16S rRNA gene sequences revealed that their nearest phylogenetic relative was Nocardioides solisilvae Ka25^T (97.9 % similarity). The results of 16S rRNA gene sequence and phylogenetic/phylogenomic analyses illustrated that N. solisilvae Ka25^T, Nocardioides gilvus XZ17^T, Nocardioides houyundeii 78^T and Nocardioides daphniae D287^T were their nearest phylogenetic neighbours. The DNA G+C contents of strains dk3136^T and dk3543 were 70.3 mol% and 70.4 mol%, respectively. Their genomes exhibit lower than threshold (95-96 %) average nucleotide identity to known species of the genus Nocardioides. ll-2,6-diaminopimelic acid was the diagnostic diamino acid and MK-8(H₄) was the predominant respiratory quinone. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The two strains had C_18 : 1 ω9c, iso-C_16 : 0 and C_17 : 1 ω8c as the major fatty acids, and rhamnose and galactose as the main whole-cell sugars. On the basis of the results of our genotypic, phenotypic and biochemical analyses, we conclude that strains dk3136^T and dk3543 represent a novel species in genus Nocardioides, for which the name Nocardioides jishulii sp. nov. is proposed. The type strain is dk3136^T (=CGMCC 4.7570^T=JCM 33496^T=KCTC 49314^T).

Actinomyces qiguomingii sp. nov., isolated from the Pantholops hodgsonii

Two previously undescribed, Gram-stain-positive, rod-shaped strains, 410^T and 553, were isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) from the Tibet-Qinghai Plateau, PR China. The optimum growth conditions of the two novel strains were 1 % (w/v) NaCl, 37 °C and pH 7. The end products from glucose fermentation included ethanol and lactic acid. Based on results of 16S rRNA gene sequence comparison and phylogenetic and phylogenomic analyses, strains 410^T and 553 were classified into the genus Actinomyces, and were closely related to Actinomyces ruminicola (97.6 %), Actinomyces oricola (93.5 %) and Actinomyces dentalis (90.8 %). The genomic G+C content of strain 410^T was 67.4 mol%. Digital DNA-DNA hybridization values between strain 410^T and each of the closely related species were under 70 %. The respiratory quinones were MK-10 (68 %) and MK-9 (32 %). The main cellular fatty acids of the isolates were C_16 : 0, followed by C_18 : 1 ω9c. The major polar lipids were diphosphatidylglycerol and phosphatidylinositol-mannoside. The whole-cell sugars contained rhamnose, ribose and glucose. The diagnostic amino acids of cell-wall peptidoglycan included alanine, glutamic acid, lysine and ornithine. The results of biochemical, chemotaxonomic and genotypic analyses revealed that the two novel strains represent a novel species of genus Actinomyces, for which the name Actinomyces qiguomingii sp. nov. is proposed. The type strain is 410^T (=CGMCC 1.16361^T= DSM 106201^T).

Actinomyces Produces Defensin-Like Bacteriocins (Actifensins) with a Highly Degenerate Structure and Broad Antimicrobial Activity

We identified a strain of Actinomyces ruminicola which produces a potent bacteriocin with activity against a broad range of Gram-positive bacteria, many of which are pathogenic to animals and humans. The bacteriocin was purified and found to have a mass of 4,091 ± 1 Da with a sequence of GFGCNLITSNPYQCSNHCKSVGYRGGYCKLRTVCTCY containing three disulfide bridges. Surprisingly, near relatives of actifensin were found to be a series of related eukaryotic defensins displaying greater than 50% identity to the bacteriocin. A pangenomic screen further revealed that production of actifensin-related bacteriocins is a common trait within the genus, with 47 being encoded in 161 genomes. Furthermore, these bacteriocins displayed a remarkable level of diversity with a mean amino acid identity of only 52% between strains/species. This level of redundancy suggests that this new class of bacteriocins may provide a very broad structural basis on which to deliver and design new broad-spectrum antimicrobials for treatment of animal and human infections.IMPORTANCE Bacteriocins (ribosomally produced antimicrobial peptides) are potential alternatives to current antimicrobials given the global challenge of antimicrobial resistance. We identified a novel bacteriocin from Actinomyces ruminicola with no previously characterized antimicrobial activity. Using publicly available genomic data, we found a highly conserved yet divergent family of previously unidentified homologous peptide sequences within the genus Actinomyces with striking similarity to eukaryotic defensins. These actifensins may provide a potent line of antimicrobial defense/offense, and the machinery to produce them could be used for the design of new antimicrobials given the degeneracy that exists naturally in their structure.

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

Two novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod-shaped bacteria (strains 2129^T and 2119) were isolated from the faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed highest similarity values to Actinomyces timonensis DSM 23838^T (92.9 and 92.8 %, respectively), and phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that strains 2129^T and 2119 represent a new lineage. Strains 2129^T and 2119 could ferment d-adonitol and d-xylose, but were unable to utilize d-mannose and d-melibiose nor produce esterase (C4) and proline arylamidase. The G+C contents of the two strains were both 69.0 mol%. Their genomes exhibited less than 40.4 % relatedness in DNA-DNA hybridization tests (below 70 % as the recommended threshold for new species) with all available genomes of the genus Actinomyces in the NCBI database. The major fatty acids of the two strains were C_18 : 1ω9c and C_16 : 0, and the major polar lipids were diphosphatidylglycerol, glycolipid, phosphatidylinositol, phosphatidyl inositol mannoside and phosphoglycolipid. Based on the results of genotypic, phenotypic and biochemical analyses, it is proposed that the two unidentified bacteria be classified as representing a novel species, Actinomyces lilanjuaniae sp. nov. The type strain is 2129^T (=CGMCC 4.7483^T=DSM 106426^T).