ABSTRACT
Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65â% 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89â% 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5âmol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5â% as well as digital DNA-DNA hybridization values between 20.1 and 40.8â%, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16â:â0, C17â:â1 ω8c or C18â:â1 ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).
Subject(s)
Antelopes , Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Feces , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Soil Microbiology , RNA, Ribosomal, 16S/genetics , Tibet , Fatty Acids/analysis , Fatty Acids/chemistry , DNA, Bacterial/genetics , Feces/microbiology , Antelopes/microbiology , Animals , China , Actinomycetales/genetics , Actinomycetales/isolation & purification , Actinomycetales/classification , Peptidoglycan , Phospholipids/analysisABSTRACT
In recent decades, Saiga antelope (Saiga t. tatarica) mass die-offs have become more common. The mass die-off of 2015 in central Kazakhstan, recorded 140,000 individual deaths across multiple herds. Previously, research has shown atmospheric humidity, the bacterium Pasteurella multocida serotype B, and resultant haemorrhagic septicaemia, were the primary cause. However, other synergistic factors may have impacted this process. Here we use a multivariate compositional data analysis (CoDA) approach to assess what other factors may have been involved. We show a pollutant linkage mechanism where relative humidity and dewpoint temperature combine with environmental pollutants, potentially toxic elements (e.g., Hg, As), complex carbon compounds (e.g., Acetone, Toluene), and inorganic compounds (e.g., CHx, SO2) which affected the Saiga during the calving season (start and peak) and at the onset of the mass die-off. We suggest a mechanism for this process. Upon arrival at their carving grounds, the Saiga experienced a sudden precipitation event, a spike in temperatures, and resultant high humidity occurs. The infectious bacterium P. multocida serotype B then spreads. Further, environmental pollutants contained within steppe soils are released to the air, forming localised smog events, these synergistically combine, and mass die-off occurs.
Subject(s)
Antelopes , Environmental Pollutants , Animals , Antelopes/microbiology , Climate Change , KazakhstanABSTRACT
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 (74.4-84.9â%). 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.
Subject(s)
Antelopes/microbiology , Mycobacteriaceae/classification , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Feces/microbiology , Mycobacteriaceae/isolation & purification , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , TibetABSTRACT
In the present study, four bacterial strains, two (S-713T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531T 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-713T/406 and S-531T/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-(H4) as their major isoprenoid quinone, strains S-713T and S-531T contained C18â:â1 ω9c (24.64 and 16.34â%) and iso-C16â:â0 (9.74 and 29.38â%), 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-713T and S-531T were 4â207â844 bp (G+C content, 73.0 mol%) and 4â809â817 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-713T (=JCM 33698T=CGMCC 4.7660T) and S-531T (=JCM 33468T=CGMCC 4.7659T) as the respective type strains.
Subject(s)
Antelopes/microbiology , Nocardioides/classification , Phylogeny , Taraxacum/microbiology , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Nocardioides/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , Plant Leaves/microbiology , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
The anaerobic gut fungi (AGF; phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from faecal samples of a wild blackbuck (Indian Antelope, Antilope cervicapra) from Sutton County, Texas, USA. The isolates displayed medium sized (2-4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D1/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5 and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyonii strain D3A (D1/D2 LSU) and Joblinomyces apicalis strain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3T) demonstrated growth capabilities on a wide range of mono-, oligo- and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the name Paucimyces polynucleatus gen. nov., sp. nov. is proposed.
Subject(s)
Antelopes/microbiology , Feces/microbiology , Neocallimastigomycota/classification , Phylogeny , Anaerobiosis , Animals , DNA, Fungal/genetics , DNA, Ribosomal Spacer/genetics , Neocallimastigomycota/isolation & purification , Ribosome Subunits, Large , Sequence Analysis, DNA , TexasABSTRACT
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 98.7â%, 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 32.6â%, lower than the threshold of 70â%, indicating they belong to different species. The four strains' genomes displayed less than 24.6â% 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 C18â:â1 ω9c and C18â:â0 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.
Subject(s)
Actinobacteria/classification , Antelopes/microbiology , Lagomorpha/microbiology , Phylogeny , Actinobacteria/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Feces/microbiology , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612T and Georgenia subflava CGMCC 1.12782T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612T and Georgenia wutianyii Z294. The predominant cellular fatty acids were anteiso-C15:0, anteiso-C15:1A and C16:0. The major menaquinone was MK-8(H4). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA-DNA hybridization value between strains ZLJ0423T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423T (= CGMCC 1.13681T = JCM 33470T).
Subject(s)
Actinobacteria/classification , Antelopes/microbiology , Actinobacteria/genetics , Actinobacteria/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition/genetics , DNA, Bacterial/genetics , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , TibetABSTRACT
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 299T and 340), Corynebacterium (strains 2184T, 2185, 2183T and 2189) and Oceanobacillus (strains 160T and 143), respectively, with a percentage of similarity for the 16S rRNA gene under the species threshold of 98.7â% except for strains 160T and 143 with Oceanobacillus arenosus CAU 1183T (98.8â%). The genome sizes (and genomic G+C contents) were 3.1 Mb (49.4â%), 2.5 Mb (64.9â%), 2.4 Mb (66.1â%) and 4.1 Mb (37.1â%) for the type strains 299T, 2183T, 2184T and 160T, respectively. Two sets of the overall genome relatedness index values between our isolates and their corresponding closely related species were under species thresholds (95â% for average nucleotide identity, and 70â% 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 299T (=CGMCC 1.16320T=JCM 33611T) is proposed as representing Actinomyces wuliandei sp. nov.; strain 2184T (=CGMCC 1.16417T=DSM 106203T) is proposed as representing Corynebacterium liangguodongii sp. nov.; strain 2183T (=CGMCC 1.16416T=DSM 106264T) is proposed as representing Corynebacterium yudongzhengii sp. nov.; and strain 160T (=CGMCC 1.16367T=DSM 106186T) is proposed as representing Oceanobacillus zhaokaii sp. nov.
Subject(s)
Actinomyces/classification , Antelopes/microbiology , Bacillaceae/classification , Corynebacterium/classification , Feces/microbiology , Phylogeny , Actinomyces/isolation & purification , Animals , Bacillaceae/isolation & purification , Bacterial Typing Techniques , Base Composition , China , Corynebacterium/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , TibetABSTRACT
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 â for 3 days on brain-heart infusion (BHI) agar with 5â% sheep blood. The cells grew optimally at 28 °C, pH 7.5 and with 1â% (w/v) NaCl on BHI agar supplemented with 5â% sheep blood. Phylogenetic analysis of the 16S rRNA gene sequences revealed that their nearest phylogenetic relative was Nocardioides solisilvae Ka25T (97.9â% 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 (95-96â%) 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 C18â:â1 ω9c, iso-C16â:â0 and C17â:â1 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).
Subject(s)
Actinobacteria/classification , Antelopes/microbiology , Feces/microbiology , Phylogeny , Actinobacteria/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Peptidoglycan/chemistry , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
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 97.4â% 16S rRNA gene similarity, 24.1, 22.8, 23.2 and 26.3â% digital DNA-DNA hybridization relatedness and 80.8, 80.0, 80.7 and 80.9â% 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-C15â:â0, anteiso-C15â:â1 A, C16â:â0 and anteiso-C17â:â0. 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).
Subject(s)
Antelopes/microbiology , Cellulomonas/classification , Feces/microbiology , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , Cellulomonas/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Ornithine/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512T 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-1T (98.0 and 97.9â% similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512T and dk508 were members of the genus Microbacterium, and most closely related to strains Microbacterium mitrae M4-8T and Microbacterium hatanonis FCC-01T. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0â% (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0â% (w/v) NaCl. The genome of type strain dk512T 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 dk512T and previously characterized Microbacterium species were <95 and <70â%, respectively. In strain dk512T, the detected primary cellular fatty acids were anteiso-C15â:â0 and anteiso-C17â:â0, the main respiratory quinones were MK-9 (37.9â%) 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 dk512T is designated the type strain (=CGMCC 1.16590T=JCM 33494T=KCTC 49313T).
Subject(s)
Actinobacteria/classification , Antelopes/microbiology , Phylogeny , Actinobacteria/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Glycolipids/chemistry , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/chemistryABSTRACT
Two previously undescribed, Gram-stain-positive, rod-shaped strains, 410T 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 1â% (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 410T and 553 were classified into the genus Actinomyces, and were closely related to Actinomyces ruminicola (97.6â%), Actinomyces oricola (93.5â%) and Actinomyces dentalis (90.8â%). The genomic G+C content of strain 410T was 67.4 mol%. Digital DNA-DNA hybridization values between strain 410T and each of the closely related species were under 70â%. The respiratory quinones were MK-10 (68â%) and MK-9 (32â%). The main cellular fatty acids of the isolates were C16â:â0, followed by C18â:â1 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 410T (=CGMCC 1.16361T= DSM 106201T).
Subject(s)
Actinomyces/classification , Antelopes/microbiology , Phylogeny , Actinomyces/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/chemistryABSTRACT
Two strains, designated 2251T and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan antelopes on the Qinghai-Tibet Plateau. The results of phylogenetic analyses of 16S rRNA gene sequences indicated that strains 2251T and 3058 represent a new species within the genus Paracoccus and are most similar to 'Paracoccus gahaiensis' CUG00006T (98.9 and 99.3â%), Paracoccus nototheniae I-41R45T (98.3 and 98.7â%) and Paracoccus hibiscisoli THG-T2.31T (97.6 and 97.8â%). Results of genomic sequence-based phylogenomic analysis agreed with those from 16S rRNA gene sequence analysis. Optimal growth was achieved at pH 7.0-7.5 and 28 °C with marine medium. Cells contained C18â:â1 ω7c as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and an unidentified lipid. The cell-wall peptidoglycan amino acids were meso-2,6-diaminopimelic acid, alanine and glutamic acid; the major cell-wall sugar was galactose. The G+C content of strain 2251T was 66.5 mol%. Both strains (2251T and 3058) had DNA-DNA relatedness values less than 50â% with all available genomes of the genus Paracoccus in the ncbi database. Differential genotypic inferences, together with phenotypic and biochemical characteristics, demonstrated that strains 2251T and 3058 should be classified as a novel species of the genus Paracoccus, for which the name Paracoccus liaowanqingii sp. nov. is suggested. The type strain is 2251T (=CGMCC 1.16490T=DSM 106269T).
Subject(s)
Antelopes/microbiology , Paracoccus/classification , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Feces/microbiology , Nucleic Acid Hybridization , Paracoccus/isolation & purification , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Ubiquinone/analogs & derivatives , Ubiquinone/chemistryABSTRACT
Two novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod-shaped bacteria (strains 2129T 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 23838T (92.9 and 92.8â%, respectively), and phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that strains 2129T and 2119 represent a new lineage. Strains 2129T 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 40.4â% relatedness in DNA-DNA hybridization tests (below 70â% 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 C18â:â1ω9c and C16â:â0, 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 2129T (=CGMCC 4.7483T=DSM 106426T).
Subject(s)
Actinomyces/classification , Antelopes/microbiology , Phylogeny , Actinomyces/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , TibetABSTRACT
Two hitherto unknown bacteria (strains 313T and 352) were recovered from the faeces of Tibetan antelopes on the Tibet-Qinghai Plateau, PR China. Cells were rod-shaped and Gram-stain-positive. The optimal growth conditions were at 37 °C and pH 7. The isolates were closely related to Actinotignum sanguinis (92.6â% 16S rRNA gene sequence similarity), Arcanobacterium haemolyticum (92.5â%), Actinotignum schaalii (92.4â%), Actinobaculum massiliense (92.2â%) and Flaviflexus huanghaiensis (91.6â%). Phylogenetic analyses showed that strains 313T and 352 clustered independently in the vicinity of the genera Actinotignum, Actinobaculum and Flaviflexus, but could not be classified clearly as a member of any of these genera. Phylogenomic analysis also indicated that strains 313T and 352 formed an independent branch in the family Actinomycetaceae. The major cellular fatty acids of the strains were C16â:â0 and C18â:â1ω9c. The polar lipids comprised diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylglycerol, phosphatidylinositol and five unidentified components. The peptidoglycan contained lysine, alanine and glutamic acid. The respiratory quinone was absent. The whole-cell sugars included glucose and rhamnose. The DNA G+C content of strain 313T was 60.6 mol%. Based on the low 16S rRNA gene sequence similarities, its taxonomic position in the phylogenetic and phylogenomic trees and its unique lipid pattern, we propose that strains 313T and 352 represent members of a novel species in a new genus, for which the name Fudania jinshanensis gen. nov., sp. nov. is proposed. The type strain is 313T (=CGMCC 4.7453T=DSM 106216T).
Subject(s)
Actinomycetaceae/classification , Antelopes/microbiology , Phylogeny , Actinomycetaceae/isolation & purification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , TibetABSTRACT
Limited is known about role of gut microbiota in the metabolism of high-altitude-living herbivores, and potential co-evolution between gut microbiome and host genome during high altitude adaptation were not fully understood. Here, DNA from faecal samples was used to investigate the gut microbial compositions and diversity in three host species endemic to the high-altitude Tibetan plateau, the Tibetan antelope (Pantholops hodgsonii, T-antelope, 4300â¯m) and the Tibetan wild ass (Equus kiang, T-ass, 4300â¯m), and in the Tibetan sheep (Ovis aries, T-sheep) collected from two different altitudes (T-sheep [k], 4300â¯m and T-sheep [l] 3000â¯m). Ordinary sheep (O. aries, sheep) from low altitudes (1800â¯m) were used for comparison. 16S rRNA gene sequencing revealed that the genera Ruminococcus (22.78%), Oscillospira (20.00%), and Clostridium (10.00%) were common taxa in all high-altitude species (T-antelope, T-ass and T-sheep [k]). Ruminococcaceae, Clostridiales, Clostridia, and Firmicutes showed greater enrichment in the T-antelopes' gut microbiota than in the microbiota of lower-altitude sheep (T-sheep [l] and sheep). The T-antelopes' gut microbiota displayed a higher ratio of Firmicutes to Bacteroidetes than lower-altitude sheep (T-sheep [l] and sheep). A functional capacity analysis of the paired-end metagenomics sequences of the gut metagenomes of high-altitude T-antelopes and T-sheep annotated over 80% of the unique genes to metabolism (especially carbohydrate metabolism pathways) and genetic information processing in the Kyoto Encyclopedia of Genes and Genomes database. The gut metagenome of the T-antelope may have co-evolved with the host genomes (e.g. glycolysis and DNA repair). The higher-altitude herbivores tended to have similar gut microbial compositions, with similar functional capacities, suggesting that their gut microbiota could involved in their high-altitude adaptation.
Subject(s)
Antelopes/microbiology , Equidae/microbiology , Gastrointestinal Microbiome , Sheep/microbiology , Acclimatization , Altitude , Animals , Antelopes/physiology , Equidae/physiology , Feces/microbiology , Metagenome , Sheep/physiology , TibetABSTRACT
Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23T and Z24) were isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau, PR China. Results of the morphological, biochemical, and phylogenetic studies indicated that they were similar to each other, but distinct from existing species of the genus Roseomonas. The proposed type strain, Z23T, had 97.8, 97.1 and 96.8â% 16S rRNA similarity to Roseomonas ludipueritiae DSM 14915T, Roseomonas aerofrigidensis JCM 31878T and Roseomonas aerophila KACC 16529T. Results from further phylogenetic analyses based on the 16S rRNA gene and 857 core genes indicated that the two strains were members of Roseomonas, but clearly separated from the currently recognized species. Strains Z23T had 43.8â%, 25.0â% DNA-DNA relatedness and 91.2, 81.3â% ANI values with R. ludipueritiae DSM 14915T and R. aerophila KACC 16529T. The genomic DNA G+C content of strain Z23T was 68.6 mol%. The major cellular fatty acids of strain Z23T were C18â:â1ω7c and/or C18â:â1ω6c and C19â:â0cyclo ω8c. The cell-wall sugars included glucose, rhamnose and ribose. Q-10 was the sole respiratory quinone, and spermidine was the major polyamine component. Polar lipids present in strain Z23T were phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, three aminolipids, two phospholipids and two unidentified lipids. Based on the distinct differences from other Roseomonas species judged from the genotypic and phenotypic data, a novel species represented by Z23T and Z24, Roseomonas wenyumeiae sp. nov., is proposed. The type strain is Z23T (=CGMCC 1.16540T=DSM 106207T).
Subject(s)
Antelopes/microbiology , Methylobacteriaceae/classification , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Methylobacteriaceae/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Ubiquinone/analogs & derivatives , Ubiquinone/chemistryABSTRACT
In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.
Subject(s)
Animal Diseases/mortality , Antelopes , Animal Diseases/epidemiology , Animal Diseases/history , Animal Diseases/microbiology , Animals , Antelopes/microbiology , Bacterial Infections/veterinary , Female , Gammaproteobacteria/classification , Gammaproteobacteria/genetics , Geography, Medical , History, 21st Century , Kazakhstan/epidemiology , Male , Metagenomics , RNA, Ribosomal, 16S/geneticsABSTRACT
Two rod-shaped, slightly halophilic and extremely halotolerant bacterial strains (X-1125T and X-1174), which were Gram-stain-positive, facultatively anaerobic and motile with peritrichous flagella, were isolated from the faeces of Tibetan antelopes. Their optimal temperature, NaCl concentration and pH for growth were 28 °C, 3â% (w/v) NaCl and pH 7.5, respectively. Based on the results of 16S rRNA gene sequences, and phylogenetic and phylogenomic analyses, their nearest phylogenetic neighbours were Paraliobacillussediminis KCTC 33762T (98.4â% similarity), Paraliobacillusquinghaiensis CGMCC 1.6333T (96.9â%) and Paraliobacillusryukyuensis NBRC 100001T (95.9â%) while the 16S rRNA genes of strains X-1125T and X-1174 were highly similar (99.7â%) to each other. The polar lipids comprised diphosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. MK-7 was the sole menaquinone (100â%). The cell wall contained alanine, glycine, glutamic acid and meso-diaminopimelic acid. The major fatty acids (>9â%) were anteiso-C15â:â0, anteiso-C17â:â0 and C16â:â1ω11c. The in silico DNA-DNA hybridization value between strains X-1125T and X-1174 was 97.8â% (well above the species threshold), but their values were lower than the 70â% threshold with the three closely related type strains. Strains X-1125T and X-1174 had DNA G+C contents (mol%) of 35.2 and 35.1â%, respectively. Based on the presented data, strains X-1125T and X-1174 hereby represent a novel species of the genus Paraliobacillus, for which the name Paraliobacillus zengyii sp. nov. is proposed. The type strain is X-1125T (=DSM 107811T=CGMCC 1.16464T).
Subject(s)
Antelopes/microbiology , Bacillaceae/classification , Phylogeny , Animals , Bacillaceae/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Feces/microbiology , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
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 92.2â% 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 14.3â% 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 81.19â% with S. pantholopis DSM 102135T and a DNA-DNA relatedness value of less than 70â% 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 Streptococcusindicated that Z15T represents a member of genus Streptococcus but one well separated from the currently recognized species. Z15T contains C18â:â1ω7c (25.5â%), C18â:â1ω9c (19.6â%), C16â:â0 (17.5â%) and C16â:â1ω9c (13.3â%) 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).