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

Author(s):  
Caixin Yang ◽  
Yibo Bai ◽  
Kui Dong ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  

Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325T, zg329, dk561T 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-325T and dk561T represent members of the genus Actinomyces , most similar to Actinomyces denticolens DSM 20671T and Actinomyces ruminicola B71T, respectively. The DNA G+C contents of strains zg-325T and dk561T were 71.6 and 69.3 mol%, respectively. The digital DNA–DNA hybridization values of strains zg-325T and dk561T 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 C18:1ω9c and C16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325T while MK-10 was predominant in dk561T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325T and dk561T 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-325T (=GDMCC 1.1724T=JCM 34091T) and dk561T (=CGMCC 4.7566T=JCM 33484T). 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.

Author(s):  
Jiao Huang ◽  
Ying Huang

A novel filamentous Actinobacterium, designated strain FXJ1.1311T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea . The genome-wide average nucleotide identity between strain FXJ1.1311T and L. guizhouensis DHS C013T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis . Based on the evidence presented here, strain FXJ1.1311T represents a novel species of the genus Lentzea , for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311T (=CGMCC 4.7383T=DSM 104975T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2493-2498 ◽  
Author(s):  
Yajun Ge ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Gui Zhang ◽  
Dong Jin ◽  
...  

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai–Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49T was closely related to Vagococcus elongatus CCUG 51432T (96.5 % similarity), Vagococcus fluvialis NCFB 2497T (96.0 %) and Vagococcus lutrae CCUG 39187T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp). The major cellular fatty acids (>10 %) were C16 : 0 (35.6 %), C14 : 0 (17.3 %), C18 : 1 ω9c (16.2 %) and C16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA–DNA hybridization of strain CF-49T with V. fluvialis DSM 5731T, V. elongatus CCUG 51432Tand V. lutrae CCUG 39187T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus , with the name Vagococcus xieshaowenii. The type strain is CF-49T (=CGMCC 1.6436T=GDMCC 1.1588T=JCM 33477T).


Author(s):  
Yanpeng Cheng ◽  
Yifan Jiao ◽  
Sihui Zhang ◽  
Jing Yang ◽  
Shan Lu ◽  
...  

In the present study, four bacterial strains, two (S-713 T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531 T and 1598) from leaves of dandelion collected on the Qinghai–Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713 T /406 and S-531 T /1598 form two independent branches belonging to the genus Nocardioides , and are closest to Nocardioides lianchengensis , Nocardioides dokdonensis , Nocardioides salarius , Nocardioides marinisabuli , Nocardioides psychrotolerans and Nocardioides szechwanensis . Although sharing MK8-(H 4 ) as their major isoprenoid quinone, strains S-713 T and S-531 T contained C 18 : 1  ω 9 c (24.64 and 16.34 %) and iso-C 16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713 T and S-531 T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides , for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713 T (=JCM 33698 T =CGMCC 4.7660 T ) and S-531 T (=JCM 33468 T =CGMCC 4.7659 T ) as the respective type strains.


Author(s):  
Yanpeng Cheng ◽  
Wenjing Lei ◽  
Xiaoxia Wang ◽  
Zhi Tian ◽  
Haican Liu ◽  
...  

Four bacterial strains (LJ126T/S18 and Z-34T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai–Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium . Strains LJ126T/S18 and Z-34T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667T, Mycobacterium aurum NCTC 10437T, Mycobacterium pyrenivorans DSM 44605T, Mycobacterium monacense JCM 15658T, Mycolicibacterium sarraceniae JCM 30395T, Mycolicibacterium tokaiense JCM 6373T and Mycobacterium murale JCM 13392T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4–84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126T (=CGMCC 1.1992T=KCTC 49535T) and Z-34T (=CGMCC 1.1993T=DSM 106172T) as the respective type strains.


2019 ◽  
Vol 69 (4) ◽  
pp. 1237-1243 ◽  
Author(s):  
Zhi Tian ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Ji Pu ◽  
...  

Three Gram-stain-positive, catalase-negative, α-haemolytic, chain-forming and coccus-shaped microorganisms (strains Z15T, Z1 and Z2) were isolated from feces of Tibetan antelopes collected from the Qinghai–Tibet plateau, PR China. The results of 16S rRNA gene sequence studies indicated that Z15T shared 94.5, 93.1 and 92.2 % similarity with Streptococcus pantholopis DSM 102135T, Streptococcus ursoris NUM 1615T and Streptococcus dentapri NUM 1529T, respectively. rpoB and groEL-based sequence analysis of our three novel isolates revealed interspecies divergence of 16.7 and 14.3 % from Streptococcus pantholopis DSM 102135T. The genomic DNA G+C content of Z15T is 42.48 mol%. Z15T has an average nucleotide identity (ANI) value of 81.19 % with S. pantholopis DSM 102135T and a DNA–DNA relatedness value of less than 70 % in the in-silico DNA–DNA hybridization (isDDH) with other species of genus Streptococcus deposited in the GenBank database. A whole-genome phylogenetic tree based on 246 core genes of 78 genomes of members of the genus Streptococcus indicated that Z15T represents a member of genus Streptococcus but one well separated from the currently recognized species. Z15T contains C18 : 1ω7c (25.5 %), C18 : 1ω9c (19.6 %), C16 : 0 (17.5 %) and C16 : 1ω9c (13.3 %) as its major cellular fatty acids. According to the morphological, biochemical and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus , and Streptococcus chenjunshii sp. nov. is thus proposed. The type strain is Z15T (=CGMCC 1.16529=DSM 106182).


2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2204-2210 ◽  
Author(s):  
Zhi Tian ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Ji Pu ◽  
...  

Two Gram-stain-positive, catalase-positive and oxidase-negative, aerobic, non-motile, cellobiose-utilizing, short-rod-shaped strains (Z28T and Z29) were isolated from faeces of Tibetan antelope (Pantholops hodgsonii) collected on the Qinghai–Tibet Plateau. Strain Z28T shared 98.1, 98.0, 97.8 and 97.4 % 16S rRNA gene similarity, 24.1, 22.8, 23.2 and 26.3 % digital DNA–DNA hybridization relatedness and 80.8, 80.0, 80.7 and 80.9 % average nucleotide identity values with Cellulomonas oligotrophica DSM 24482T, Cellulomonas flavigena DSM 20109T, Cellulomonas iranensis DSM 14785T and Cellulomonas terrae JCM 14899T, respectively. Results from further phylogenetic analyses based on the 16S rRNA gene and 148 core genes indicated that strains Z28T and Z29 were closest to C. oligotrophica DSM 24482T and C. flavigena DSM 20109T, but clearly separated from the currently recognized species of the genus Cellulomonas . The genomic DNA G+C content of strain Z28T was 75.3 mol%. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A, C16 : 0 and anteiso-C17 : 0. Ribose and mannose were detected as the whole-cell sugars. The major respiratory quinone was MK-9(H4) and ornithine was the diamino acid of the cell wall. The polar lipids present in strain Z28T were phosphatidylethanolamine, five phospholipids, two aminophospholipids, aminolipid and three unidentified lipids. Comparison of phenotypic and phylogenetic features between the two strains and the related organisms revealed that Z28T and Z29 represent a novel species of the genus Cellulomonas , for which the name Cellulomonas shaoxiangyii sp. nov. is proposed. The type strain is Z28T (=CGMCC 1.16477T=DSM 106200T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3234-3240 ◽  
Author(s):  
Sihui Zhang ◽  
Xiaoxia Wang ◽  
Jing Yang ◽  
Shan Lu ◽  
Xin-He Lai ◽  
...  

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner’s 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718T (98.4 %), Nocardioides rubriscoriae DSM 23986T (98.2%) and Nocardioides plantarum DSM 11054T (97.8 %). The genome of strain S-1144T showed less than 70 % digital DNA–DNA hybridization and < 95–96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144T was 73.5 mol%. MK-8(H4) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1  ω8c, C17 : 0 and C18 : 1  ω9c. On the basis of obtained data, strain S-1144T represented a novel species of the genus Nocardioides , for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144T (=CGMCC 4.7568T=JCM 33469T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2233-2238 ◽  
Author(s):  
Zhi Tian ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Ji Pu ◽  
...  

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350T 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 Z350T belongs to the genus Mumia (family Nocardioidaceae ) but clearly differs from the currently recognized species Mumia xiangluensis DSM 101040T (98.4 % similarity) and Mumia flava DSM 27763T (97.4 %). Strain Z350T 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 101040T and M. flava DSM 27763T, 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 C18 : 1 ω9c and 10-methyl C18 : 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 Z350T (=CGMCC 4.7464T=DSM 106288T).


Author(s):  
Piyanat Charoenyingcharoen ◽  
Ji-Sun Kim ◽  
Gunjana Theeragool ◽  
Keun-Chul Lee ◽  
Pattaraporn Yukphan ◽  
...  

Two novel Gram-stain-negative, rod-shaped and non-motile bacterial strains, designated B5-SW-15T and C2-DW-16, were isolated from water collected in mangrove forests in Ranong Province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains B5-SW-15T and C2-DW-16 belonged to the genus Donghicola and were most closely related to Donghicola tyrosinivorans DSM 100212T (98.2 and 98.1 %, respectively) and Donghicola eburneus DSM 29127T (97.7 and 97.6 %, respectively). The average nucleotide identity and digital DNA–DNA hybridization values between strain B5-SW-15T, strain C2-DW-16 and related species were 95.8 and 71.6 % (to strain C2-DW-16), 76.8 and 21.3 % (to D. tyrosinivorans DSM 100212T) and 80.3 and 24.2 % (to D. eburneus DSM 29127T), respectively. The predominant cellular fatty acids (>5 %) were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c), C16 : 0 and C12 : 1 3-OH. Ubiquinone Q-10 was the sole respiratory quinone. DNA G+C contents of the isolates were 61.0 and 61.2 mol% based on whole genome sequences. Strains B5-SW-15T and C2-DW-16 contained aminolipid, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. On the basis of the results from phenotypic, chemotaxonomic and phylogenetic analyses, strains B5-SW-15T and C2-DW-16 constitute a novel species of the genus Donghicola in the family Rhodobacteraceae for which the name Donghicola mangrovi sp. nov. is proposed. The type strain is B5-SW-15T (=BCC 56522T=TBRC 9562T=KCTC 72743T).


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