Search

Four novel bacterial strains (zg-ZUI122 T /zg-ZUI10 and zg-ZUI227 T /zg-ZUI100) were isolated from the intestinal contents of Marmota himalayana and characterized using a polyphasic approach. Cells were Gram-stain- and catalase-positive, urease- and oxidase-negative. Strains grew optimally at 28-30 °C, pH 7.0, with 0.5 % NaCl (w/v). A comparative analysis of 16S rRNA gene sequences revealed that strain pairs zg-ZUI122 T /zg-ZUI10 and zg-ZUI227 T /zg-ZUI100 belonged to the genus Arthrobacter and were most closely related to Arthrobacter citreus DSM 20133 T , with similarities of 99.6 and 99.5 %, respectively. This was further confirmed by phylogenetic analyses based on the 16S rRNA gene and genome sequences. The digital DNA-DNA hybridization and average nucleotide identity values between the two new type strains (zg-ZUI122 T and zg-ZUI227 T ) and other species in the genus Arthrobacter were 20.0-24.4/77.2-83.4% and 19.9-25.1/77.1-83.4%, all below the thresholds. The major cellular fatty acids detected in the two novel species included iso -C 15 : 0 and anteiso -C 15 : 0 ; the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. MK-8(H 2 ) (77.3%) was the predominant respiratory quinone detected in strain zg-ZUI122 T , while MK-8(H 2 ) (53.7%) and MK-9(H 2 ) (46.3%) were detected in strain zg-ZUI227 T . The shared cell-wall amino acids detected in the two novel species were alanine, glutamic acid and lysine; the shared whole cell wall sugars consisted of galactose, mannose and ribose. All these analyses concluded that these four strains represent two different novel species in the genus Arthrobacter , for which the names Arthrobacter sunyaminii sp. nov. (zg-ZUI122 T = GDMCC 1.2502 T = KCTC 49677 T ) and Arthrobacter jiangjiafuii sp. nov. (zg-ZUI227 T = GDMCC 1.2500 T = KCTC 49676 T ) are proposed.

Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546 T and 573) and respiratory tracts of marmots (strains 1318 T and 1311). The 16S rRNA gene sequencing revealed that strains 546 T and 573 were 97.8% identical to Roseomonas wenyumeiae Z23 T , whereas strains 1311 and 1318 T were 98.3% identical to Roseomonas ludipueritiae DSM 14915 T . In addition, a 98.0% identity was observed between strains 546 T and 1318 T . Phylogenetic and phylogenomic analyses revealed that strains 546 T and 573 clustered with R. wenyumeiae Z23 T , whereas strains 1311 and 1318 T grouped with R. ludipueritiae DSM 14915 T . The average nucleotide identity between our isolates and members of the genus Roseomonas was below 95%. The genomic G+C content of strains 546 T and 1318 T was 70.9% and 69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the major polar lipids, with Q-10 as the predominant respiratory quinone. According to all genotypic, phenotypic, phylogenetic, and phylogenomic analyses, the four strains represent two novel species of the genus Roseomonas, for which the names Roseomonas haemaphysalidis sp. nov. and Roseomonas marmotae sp. nov. are proposed, with 546 T (= GDMCC 1.1780 T = JCM 34187 T ) and 1318 T (= GDMCC 1.1781 T = JCM 34188 T ) as type strains, respectively., (© 2021. The Microbiological Society of Korea.)

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320 T /zg-336, zg-917 T /zg-910 and zg-913 T /zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320 T /zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353 T (97.51 %), zg-917 T /zg-910 to Corynebacterium coyleae DSM 44184 T (98.68 %), and zg-913 T /zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500 T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2-64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320 T vs. Corynebacterium auriscanis CIP 106629 T , Corynebacterium resistens DSM 45100 T and Corynebacterium suicordis DSM 45110 T ); 24.4/82.3% and 23.7/81.3 % (zg-917 T vs. C. coyleae DSM 44184 T and Corynebacterium jeddahense JCB T ); 26.8/83.7% and 27.7/84.4 % (zg-913 T vs. Corynebacterium mucifaciens ATCC 700355 T and C. afermentans subsp. lipophilum CCUG 32105 T ). The three novel species had C 16 : 0 , C 18 : 0 , C 18 : 1  ω 9 c and C 18 : 0 ante/C 18 : 2  ω 6,9 c as the major cellular fatty acids; MK-8(H 2 ) in strain zg-917 T and MK-9(H 2 ) in strains zg-320 T and zg-913 T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso -DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35-37 °C, 0.5 % (w/v) NaCl and pH 7.0-8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320 T = GDMCC 1.1719 T = JCM 34106 T ), Corynebacterium lujinxingii sp. nov. (zg-917 T = GDMCC 1.1707 T = JCM 34094 T ) and Corynebacterium wankanglinii sp. nov. (zg-913 T = GDMCC 1.1706 T = JCM 34398 T ).

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 ω 9 c and C 16 : 0 as the two most abundant major fatty acids. MK-9(H 4 ) or MK-8(H 4 ) 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.

Four Gram-stain-positive, non-motile and asporous bacilli (strains ZJ-599 T , ZJ-621, MC1420 T and MC1482), isolated from animal tissue and environmental samples collected on the Qinghai-Tibet Plateau, PR China, were taxonomically characterized. Based on the results of 16S rRNA gene sequence analyses, the closest relatives of strains ZJ-599 T and ZJ-621 were Corynebacterium endometrii LMM-1653 T (97.5 %), Corynebacterium phocae M408/89/1 T (96.5 %) and Corynebacterium flavescens OJ8 T (96.3 %), whereas strains MC1420 T and MC1482 were closest to Corynebacterium sanguinis CCUG 58655 T (98.9 %), Corynebacterium mycetoides DSM 20632 T (98.4 %) and Corynebacterium lipophiloflavum DSM 44291 T (97.9 %). The results of rpoB gene sequence similarity analysis indicated that C. phocae M408/89/1 T and C. sanguinis CCUG 58655 T were closest to strains ZJ-599 T /ZJ-621 (83.5 %) and MC1420 T /MC1482 (91.8 %), respectively. The two novel type strains shared a similarity of 95.2 % in 16S rRNA and 81.3 % in rpoB gene sequences. The TAP-PCR DNA fingerprint and MALDI-TOF MS spectrum patterns clearly differentiated the novel isolates within and between each pair of strains. Strain ZJ-599 T had 21.9-22.4 % digital DNA-DNA hybridization (dDDH) scores with C. endometrii LMM-1653 T , C. phocae M408/89/1 T and C. flavescens OJ8 T , and 72.3-72.9 % of average nucleotide identity (ANI) with them. Similarly, strain MC1420 T had 22.9-23.7 % dDDH values with C. sanguinis CCUG 58655 T , C. mycetoides DSM 20632 T and C. lipophiloflavum DSM 44291 T , and 80.4-81.3 % ANI scores with them. Strain ZJ-599 T had a 23.1 % dDDH value and 70.5 % ANI score with strain MC1420 T , both below the corresponding thresholds for species delineation. Strains ZJ-599 T and MC1420 T both contain mycolic acids and have MK-8(H 2 ) and MK-9(H 2 ) as the predominant respiratory quinones, meso -diaminopimelic acid as the diagnostic diamino acid, and C 18 : 1  ω 9 c as the main fatty acid. C 17 : 1  ω 8 c and C 15 : 1  ω 8 c were predominant in strain ZJ-599 T in contrast to C 17 : 1  ω 7 c being predominant in strain MC1420 T . The main polar lipids in strain ZJ-599 T were diphosphatidylglycerol, phosphatidylinositol and one unidentified glycolipid, while strain MC1420 T had diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid as the major components. Since the two pairs of novel strains (ZJ-599 T /ZJ-621, MC1420 T /MC1482) distinctly differ from each other and from their nearest relatives, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium lizhenjunii (type strain ZJ-599 T =GDMCC 1.1779 T =JCM 34341 T ) and Corynebacterium qintianiae (type strain MC1420 T =GDMCC 1.1783 T =JCM 34340 T ), respectively.

Two novel strains (HT111-2 T and HT170-2) of the genus Lactobacillus were isolated from Marmota himalayana faecal samples collected on the Qinghai-Tibet Plateau, PR China. The isolates were Gram-stain-positive, rod-shaped, non-spore-forming bacteria with irregular circular colonies. Phylogenetic analysis and comparison of the 16S rRNA gene sequences demonstrated that the two strains form a subcluster and are closest to Lactobacillus hamsteri JCM 6256 T (97.3 %) and Lactobacillus amylolyticus DSM 11664 T (97.2 %). Phylogenetic analysis of two housekeeping genes ( rpoA and pheS ) found that strains HT111-2 T and HT170-2 had the same closest relatives as the 16S rRNA gene sequence analysis did. The G+C content of strains HT111-2 T and HT170-2 were 38.8 mol%. The values of in silico DNA-DNA hybridization with known Lactobacillus species were lower than the threshold (70%). Average nucleotide identity values of strain HT111-2 T with L. hamsteri JCM 6256 T and L. amylolyticus DSM 11664 T were 77.84 % and 76.85 %, respectively. The major fatty acids of strains HT111-2 T and HT170-2 were C 16 : 0 , C 18 : 1 ω 9c and C 18 : 0 . Results of phenotypic, chemotaxonomic and phylogenetic analyses suggest strains HT111-2 T and HT170-2 represent a novel species of the genus Lactobacillus , for which the name Lactobacillus xujianguonis sp. nov. is proposed with HT111-2 T (=CGMCC 1.13855 T =KCTC 15803 T ) as the type strain.

Two bacterial strains were individually isolated from Marmota himalayana respiratory tracts; the animals were from the Tibet-Qinghai Plateau, PR China. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of 16S rRNA gene sequences indicated that the type strain HTS25 T shared 98.0, 97.4, 97.2 and 97.1 % similarity with Streptococcus cuniculi, Streptococcus acidominimus, Streptococcus marmotae and Streptococcus himalayensis respectively. Sequence analysis of the sodA and rpoB genes indicated that HTS25 T was closely related to S. marmotae (similarities of 94.7 and 91.4 % respectively). Analysis of groEL sequences showed interspecies similarity of 84.8 % between HTS25 T and S. himalayensis. A whole-genome phylogenetic tree reconstructed from 81 core genes from the genomes of 17 members of the genus Streptococcus was used to validate that HTS25 T forms a distinct subline from other recognized species of the genus Streptococcus. DNA-DNA hybridization of HTS25 T showed a maximum estimated DNA reassociation value of 32.1 % to Streptococcus cuniculi CCUG 65085 T . On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two isolates be classified as representing a novel species of the genus Streptococcus, named Streptococcus respiraculi sp. nov. The type strain is HTS25 T (=DSM 101998 T =CGMCC 1.15531 T ). The genome of Streptococcus respiraculi sp. nov. strain HTS25 T (2 067 971 bp) contains 2001 genes with an average DNA G+C content of 42.7 mol%.

Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five Marmota himalayana animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus Streptococcus, being phylogenetically closest to Streptococcus marmotae DSM 101995T (98.4 % similarity). The groEL, sodA and rpoB sequence analysis showed interspecies similarity values between HTS2T and Streptococcus. marmotae DSM 101995T, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus Streptococcus validated that HTS2T forms a distinct subline and exhibits specific phylogenetic affinity with S. marmotae. In silico DNA-DNA hybridization of HTS2T showed an estimated DNA reassociation value of 40.5 % with Streptococcus. marmotae DSM 101995T. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus Streptococcus, Streptococcus himalayensis sp. nov. The type strain is HTS2T (=DSM 101997T=CGMCC 1.15533T). The genome of Streptococcus himalayensis sp. nov. strain HTS2T contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.