Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces

International Journal of Systematic and Evolutionary Microbiology

et al. 2020

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Four novel strains (592T, S592, MF47T and SMF47) were isolated from Tibetan antelopes (Pantholops hodgsonii) and plateau pikas (Ochotona curzoniae), respectively. The cells were aerobic, non-motile, Gram-stain- and catalase-positive, rod-shaped bacteria. The 16S rRNA gene sequences of the four strains showed highest similarities to Aeromicrobium fastidiosum DSM 10552T (98.1, 98.6, 98.7 and 98.7 %, respectively), and the phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that strains 592T and MF47T represent two novel species. The four isolates produced acid from l-rhamnose, d-xylose and cellobiose, but were unable to reduce nitrate. The DNA G+C contents of strains 592T and MF47T were 70.3 and 69.8 mol%, respectively. The digital DNA–DNA hybridization value between strains 592T and MF47T was 32.6 %, lower than the threshold of 70 %, indicating they belong to different species. The four strains’ genomes displayed less than 24.6 % DNA–DNA relatedness with all available genomes of the genus Aeromicrobium in the NCBI database, including Aeromicrobium fastidiosum NBRC 14897T and Aeromicrobium ginsengisoli JCM 14732T. The major fatty acids of the four strains were C18 : 1 ω9c and C18 : 0 10-methyl, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant respiratory quinones were MK-9(H4) and MK-8(H4). The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on these genotypic, phenotypic and biochemical analyses, it is proposed that the four unidentified bacteria be classified as two novel species, Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov. The type strains are 592T (=CGMCC1.16526T=DSM 106289T) and MF47T (=CGMCC 1.17444T=JCM 33790T), respectively.

Section: Introductionmentioning

confidence: 99%

Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively

Lei

International Journal of Systematic and Evolutionary Microbiology

et al. 2020

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“…net/ identify) [18]. Strains dk3136 T and dk3543 were identical (99.8 %) in their 16S rRNA gene sequences and showed a high similarity to Nocardioides solisilvae Ka25 T (97.9 %) [19], Nocardioides gilvus XZ17 T (97.7 %) [11], Nocardioides houyundeii 78 T (97.6 %) [13], Nocardioides daphniae D287 T (97.5 %) [12], Nocardioides yefusunii HY056 T (97.5 %) [20] and other species of the genus Nocardioides (<97.4 %), indicating that they are very likely to represent a novel species of the genus Nocardioides [21]. Fig.…”

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confidence: 96%

“…The initial pH of culture medium was adjusted with a buffer system [Na 2 HPO 4 /citric acid (for pH ≤7.0), Tris/HCl (for pH 8.0-9.0) and Na 2 CO 3 / NaHCO 3 (for pH ≥10.0)] as described by Borsodi et al [31], and determined by a benchtop pH meter (FE20K; Mettler). Bacterial growth at various temperatures (4,8,12,16,20,28,35,37, 42 or 50 ℃) was also tested in BHI broth with different NaCl concentrations (0.5-6.0 %, w/v, at intervals of 0.5 %). Growth of the strains at 28 ℃ on different media (BHI, BHI with 5 % sheep blood, Reasoner's 2A, MacConkey or tryptic soy agar) was monitored for 2 weeks.…”

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confidence: 99%

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

Dong

International Journal of Systematic and Evolutionary Microbiology

et al. 2020

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Two novel Gram-stain-positive, irregular rod-shaped bacterial strains, dk3136T 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 Ka25T (97.9 % similarity). The results of 16S rRNA gene sequence and phylogenetic/phylogenomic analyses illustrated that N. solisilvae Ka25T, Nocardioides gilvus XZ17T, Nocardioides houyundeii 78T and Nocardioides daphniae D287T were their nearest phylogenetic neighbours. The DNA G+C contents of strains dk3136T 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 C18 : 1 ω9c, iso-C16 : 0 and C17 : 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 dk3136T and dk3543 represent a novel species in genus Nocardioides , for which the name Nocardioides jishulii sp. nov. is proposed. The type strain is dk3136T (=CGMCC 4.7570T=JCM 33496T=KCTC 49314T).

“…The phylogenomic tree was reconstructed as described previously [27], based on 314 core genes [28] of 42 genomes of the genus Nocardioides (including five new genomes from this study and 37 Nocardioides genomes available from the NCBI GenBank database) and the Aeromicrobium erythreum AR18 T genome as an outgroup. The phylogenomic tree was visualized in Dendroscope 3 [29].…”

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confidence: 99%

Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau

Zhang

Wang

International Journal of Systematic and Evolutionary Microbiology

et al. 2020

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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).