Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae)

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.

Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China

Four novel bacterial strains (ST-M6^T, L-033, L-031^T and Z-333) were isolated from the intestinal contents of plateau pikas (Ochotona curzoniae) collected on the Qinghai-Tibet Plateau, PR China. Cells were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, capsuled and short-rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequences and 387 core genes indicated that the four isolates belong in the genus Microbacterium and clearly separate from recognized species. The two type strains (ST-M6^T and L-031^T) shared low 16S rRNA similarity, average nucleotide identity values and digital DNA-DNA hybridization relatedness with their phylogenetic neighbours (Microbacterium ginsengisoli DSM 18659^T, Microbacterium hatanonis DSM 19179^T, Microbacterium rhizomatis JCM 30598^T, Microbacterium radiodurans CCTCC M208212^T, Microbacterium oleivorans DSM 16091^T and Microbacterium arborescens DSM 20754^T). The genomic DNA G+C contents of strains ST-M6^T and L-031^T were 70.4 and 70.7 mol%, respectively. The major cellular fatty acids of strain ST-M6^T were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0, in contrast to anteiso-C_17 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 1  ω9c of strain L-031^T. Both type strains (ST-M6^T and L-031^T) were glycolate test positive and shared the following common features: MK-11 and MK-12 as major menaquinones; rhamnose, ribose, mannose and galactose as major cell-wall sugars; diphosphatidylglycerol, phosphatidylglycerol and two glycolipids as polar lipids; and ornithine, alanine, glycine and glutamic acid as cell-wall amino acids. Comparing the phenotypic, phylogenetic and chemotaxonomic features of the four strains and their related taxa, strains ST-M6^T and L-031^T represent two novel species of the genus Microbacterium, for which the names Microbacterium caowuchunii sp. nov. (type strain ST-M6^T=CGMCC 1.16364^T=DSM 104058^T) and Microbacterium lushaniae sp. nov. (type strain L-031^T =CGMCC 1.16363^T=DSM 106170^T) are proposed.

Pelistega ratti sp. nov. from Rattus norvegicus of Hainan island

Two strains (NLN63^T and NLN82) of Gram-stain-negative, oxidase- and catalase-positive, bacilli-shaped organisms were isolated from the faecal samples of two separate Rattus norvegicus in Baisha county of Hainan Province, Southern PR China. Phylogenetic analysis based on the near full-length 16S rRNA sequences revealed that strain NLN63^T belongs to the genus Pelistega, having maximum similarity to Pelistega suis CCUG 64465^T (97.1 %), Pelistega europaea CCUG 39967^T (96.2 %) and Pelistega indica DSM 27484^T (96.2 %), respectively. The phylogenomic tree built on 553 core genes from genomes of 20 species in the genus Pelistega and other adjacent genera further confirmed that strains NLN63^T and NLN82 form a distinct subline and exhibit specific phylogenetic affinity with P. europaea CCUG 39967^T. In digital DNA-DNA hybridization analyses, strain NLN63^T showed low estimated DNA reassociation values (21.4-22.6 %) with the type strains of the species in the genus Pelistega. The DNA G+C contents of strains NLN63^T and NLN82 were 37.3 and 37.1 mol%, respectively. Strain NLN63^T had a unique MALDI-TOF MS profile, contained Q-8 as the major quinone and C_16 : 0, summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c or both) and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c or both) as the dominant fatty acids. Based upon these polyphasic characterization data obtained from the present study, a novel species of the genus Pelistega, Pelistega ratti sp. nov., is proposed with NLN63^T (=GDMCC 1.1697^T=JCM 33788^T) as the type strain.

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.

Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai-Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785^T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391^T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA-DNA hybridization values illustrated that the two type strains, 785^T and J391^T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter. These strains had DNA G+C contents of 66.0-66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785^T and J391^T were in line with those of the genus Arthrobacter: anteiso-C_15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H₂) (65.8 %) or MK-9(H₂) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785^T=CGMCC 1.16725^T=GDMCC 1.1592^T=JCM 33491^T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391^T=CGMCC 1.17382^T=GDMCC 1.1667^T=JCM 33841^T).

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).

Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111^T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111^T belong to the genus Luteimonas, and are closest to Luteimonas rhizosphaerae 4-12^T (98.02 % similarity), Luteimonas aestuarii B9^T (97.8 %) and Luteimonas terrae THG-MD21^T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111^T and its closely related species was 83.34 %, well below the threshold of 95-96 %. The major cellular fatty acids were iso-C_11 : 0, iso-C_15 : 0 and iso-C_17 : 1  ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35-37 °C, pH 7.0-8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111^T represent a novel species in genus Luteimonas, for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111^T=DSM 104077^T=CGMCC 1.16429^T) is proposed.

Georgenia wutianyii sp. nov. and Georgenia yuyongxinii sp. nov. isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet plateau of China

Four novel bacterial strains, designated Z294^T, Z311, Z443^T and Z446, were isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of China. Cells were Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four isolates belong to the genus Georgenia, but clearly separate from the currently recognized species. Both type strains (Z294^T and Z443^T) shared low 16S rRNA gene sequence similarity, digital DNA-DNA hybridization relatedness and average nucleotide identity values with Georginia satyanarayanai NBRC 107612^T, G. subflava JCM 19765^T, G. ruanii JCM 15130^T and G. thermotolerans DSM 21501^T and against each other. The genomic DNA G+C contents of strains Z294^T and Z443^T were 73.3 and 70 %, respectively. The major cellular fatty acids of strain Z294^T were anteiso-C_15 : 0, anteiso-C_15 : 1 A and C_16 : 0, in contrast to anteiso-C_15 : 0 and anteiso-C_15 : 1 A for strain Z443^T. Both type strains (Z294^T and Z443^T) shared the following common features: glucose, rhamnose and ribose as cell-wall sugars; MK-8(H₄) as major menaquinone; alanine, glutamic acid and lysine as cell-wall amino acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phosphoglycolipid as polar lipids. Comparing the phenotypic and phylogenetic features among the four strains and their related organisms, strains Z294^T and Z443^T represent two novel species within the genus Georgenia, for which the names Georgenia wutianyii sp. nov. (type strain Z294^T=CGMCC 1.16428^T=DSM 106344^T) and Georgenia yuyongxinii sp. nov. (type strain Z443^T=CGMCC 1.16435^T=DSM 106174^T) are proposed.

Microbacterium wangchenii sp. nov., isolated from faeces of Tibetan gazelles (Procapra picticaudata) on the Qinghai-Tibet Plateau

Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512^T and dk508) were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) collected from the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed the highest identity to Microbacterium saccharophilum K-1^T (98.0 and 97.9 % similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512^T and dk508 were members of the genus Microbacterium, and most closely related to strains Microbacterium mitrae M4-8^T and Microbacterium hatanonis FCC-01^T. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0 % (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0 % (w/v) NaCl. The genome of type strain dk512^T was 3.8 Mb with a G+C content of 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain dk512^T and previously characterized Microbacterium species were <95 and <70 %, respectively. In strain dk512^T, the detected primary cellular fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0, the main respiratory quinones were MK-9 (37.9 %) and MK-10 (35.7 %), and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. The major cell-wall sugars were rhamnose, ribose and galactose. Alanine, glutamic acid, glycine and ornithine were in the cell-wall peptidoglycan. Based on phenotypic data and phylogenetic inference, these two strains represent a novel species of the genus Microbacterium, named here as Microbacterium wangchenii sp. nov, where dk512^T is designated the type strain (=CGMCC 1.16590^T=JCM 33494^T=KCTC 49313^T).

Mumia zhuanghuii sp. nov., isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350^T and Z527) were isolated from intestinal contents of plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau, PR China. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Z350^T belongs to the genus Mumia (family Nocardioidaceae) but clearly differs from the currently recognized species Mumia xiangluensis DSM 101040^T (98.4 % similarity) and Mumia flava DSM 27763^T (97.4 %). Strain Z350^T had a DNA G+C content of 70.7 mol% and shared 80.4 and 76.7 % average nucleotide identity values and 23.4 and 20.6 % in silico DNA-DNA hybridization relatedness with M. xiangluensis DSM 101040^T and M. flava DSM 27763^T, respectively. Further phylogenetic analyses based on 497 core genes indicated that our isolates were members of the genus Mumia but separated from all existing genera within the family Nocardioidaceae. The major cellular fatty acids were C_{18 : 1} ω9c and 10-methyl C_{18 : 0}. The cell wall contained ll-diaminopimelic acid as the diamino acid, and rhamnose, ribose and glucose as whole cell-wall sugars. MK-9(H₄) was detected as the major menaquinone. Polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phospholipid. Based on distinct differences in the genotypic and phenotypic data from the two Mumia species, a novel species, Mumia zhuanghuii sp. nov., is proposed. The type strain is Z350^T (=CGMCC 4.7464^T=DSM 106288^T).

Agromyces badenianii sp. nov., isolated from plateau pika (Ochotona curzoniae)

Two aerobic, Gram-stain-positive, catalase-positive, non-motile and rod-shaped bacterial strains, designated MF30-A^T and MF845, were isolated from the intestinal contents of plateau pika collected from the Qinghai-Tibet Plateau. Optimal growth of these two strains was observed under aerobic conditions at pH 7.0 and 28 °C. The 16S rRNA gene sequences of the isolates had highest similarities of 98.5 and 98.4 % to Agromyces fucosus, respectively. In the 16S rRNA gene and polygenetic trees, strains MF30-A^T and MF845 were clearly distinct from other species. The two strains could not produce acid from arbutin, d-fructose, D-sucrose, glycogen, salicin or starch. Production of β-glucosidase by these strains was negative. The major fatty acids of these strains were anteiso-C_{15 : 0}, anteiso-C_{17 : 0} and iso-C_{16 : 0}. Strain MF30-A^T contained galactose, rhamnose and ribose as cell wall sugars and MK-12 and MK-11 as predominant menaquinones. The major polar lipids in strain MF30-A^T were diphosphatidylglycerol, phosphatidylglycerol and a glycolipid, while the peptidoglycan contained alanine, glutamic acid, glycine and 2,4-diaminobutyric acid. The G+C contents of the DNA of strains MF30-A^T and MF845 were 69.8 mol% and 69.7 mol%, respectively. The average nucleotide identity and digital DNA-DNA relatedness values of the two strains with all available genomes of the genus Agromyces were far below the respective thresholds of 95 and 70 %, respectively. All genotypic and phenotypic data indicated that strains MF30-A^T and MF845 should be classified as novel members of the genus Agromyces, for which the name Agromyces badenianii sp. nov. is proposed. The type strain is MF30-A^T (=CGMCC 1.16469^T=DSM 106183^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).

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

A novel, Gram-stain-positive, catalase-positive, non-spore-forming, short rod-shaped strain (VUL4_3^T) was isolated from rectal swabs of Old World vultures (Aegypius monachus) from the Tibet-Qinghai Plateau, China. Based on the results of biochemical tests and 16S rRNA gene sequence comparison, strain VUL4_3^T was determined to be a member of the genus Actinomyces that is closely related to the type strains of Actinomyces liubingyangii (97.7 % 16S rRNA gene sequence similarity) and Actinomyces marimammalium (96.5 %). Optimal growth occurred at 37 °C, pH 6-7 and with 1 % (w/v) NaCl. The typical major cellular fatty acids of strain VUL4_3^T were C18 : 1ω9c, C16 : 0 and C18 : 0. The VUL4_3^T genome contained 2 207 832 bp with an average G+C content of 51.9 mol%. DNA-DNA hybridization values between strain VUL4_3^T and the above two species of the genus Actinomyces showed less than 32 % DNA-DNA relatedness, supporting a novel species status of strain VUL4_3^T. Based on the phenotypic data and phylogenetic inference, the novel species Actinomycestangfeifanii sp. nov. is proposed. The type strain is VUL4_3^T (=CGMCC 4.7369^T=DSM 103436^T).