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  • 1
    In: Journal of Microbiology, Springer Science and Business Media LLC, Vol. 60, No. 2 ( 2022-02), p. 147-155
    Type of Medium: Online Resource
    ISSN: 1225-8873 , 1976-3794
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 2
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 5 ( 2023-05-25)
    Abstract: Six facultative anaerobic, Gram-stain-positive, oxidase-negative, rod-shaped bacteria (strains zg-B89 T , zg-B12, zg-Y338 T , zg-Y138, zg-Y908 T and zg-Y766), were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. The 16S rRNA gene sequence analysis showed that zg-B89 T showed highest similarity to Cellulomonas iranensis NBRC 101100 T (99.5 %), zg-Y338 T to Cellulomonas cellasea DSM 20118 T (98.7 %), and zg-Y908 T to Cellulomonas flavigena DSM 20109 T (99.0 %). Phylogenetic and phylogenomic analysis based on 16S rRNA gene and 881 core genes revealed that these six strains formed three separate clades in the genus Cellulomonas . Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between these three novel species and all members of the genus Cellulomonas were below species thresholds (95–96 % for ANI and 70 % for dDDH). The DNA G+C contents of zg-B89 T , zg-Y338 T and zg-Y908 T were 73.6, 72.9 and 74.5 %, respectively. Strains zg-B89 T and zg-Y908 T had anteiso-C 15 : 0 , C 16 : 0 and anteiso-C 15 : 1 A, and zg-Y338 T had anteiso-C 15 : 0 , C 16 : 0 and iso-C 16 : 0 as the main fatty acids. All novel type strains had MK-9 (H 4 ) as the predominant respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as the major polar lipids, and rhamnose, ribose and glucose as the cell-wall sugars. The peptidoglycan amino acids of zg-B89 T , zg-Y338 T and zg-Y908 T contained ornithine, alanine, glutamic acid and aspartic acid (except for zg-Y338 T ). Based on genotypic, phenotypic, phylogenetic and biochemical properties, the six uncharacterized strains represent three novel species in the genus Cellulomonas , for which the names Cellulomonas xiejunii sp. nov. (type strain zg-B89 T =GDMCC 1.2821 T =KCTC 49756 T ), Cellulomonas chengniuliangii sp. nov. (type strain zg-Y338 T =GDMCC 1.2829 T =KCTC 49754 T ) and Cellulomonas wangsupingiae sp. nov. (type strain zg-Y908 T =GDMCC 1.2820 T =KCTC 49755 T ) are proposed, respectively.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 3
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 7 ( 2021-07-12)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
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    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 4
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 10 ( 2022-10-07)
    Abstract: Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313 T , ZJ1307, MC1495 T , Y192, 603 T and X2025) were isolated from the Qinghai–Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides , and strains ZJ1313 T and ZJ1307 were most closely related to N. solisilvae JCM 31492 T (16S rRNA gene sequence similarity, 98.0 %), MC1495 T and Y192 to N. houyundeii 78 T (98.5 %), and 603 T and X2025 to N. dokdonensis JCM 14815 T (97.6 %). The digital DNA–DNA hybridization values of strains ZJ1313 T , MC1495 T and 603 T among each other and with type strains of their closest relatives were all below the 70 % cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C 16 : 0 , C 17 : 1  ω 8 c or C 18 : 1  ω 9 c . MK-8(H 4 ) was the predominant respiratory menaquinone and ʟʟ−2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313 T , MC1495 T and 603 T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313 T /ZJ1307, MC1495 T /Y192 and 603 T /X2025 represent three new species of genus Nocardioides , for which the names Nocardioides ochotonae sp. nov. (ZJ1313 T =GDMCC 4.177 T =KCTC 49537 T =JCM 34185 T ), Nocardioides campestrisoli sp. nov. (MC1495 T =GDMCC 4.176 T =KCTC 49536 T =JCM 34307 T ) and Nocardioides pantholopis sp. nov. (603 T =CGMCC 4.7510 T =DSM 106494 T ) are proposed accordingly.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
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    detail.hit.zdb_id: 2056611-6
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  • 5
    Online Resource
    Online Resource
    Frontiers Media SA ; 2023
    In:  Frontiers in Cellular and Infection Microbiology Vol. 13 ( 2023-2-14)
    In: Frontiers in Cellular and Infection Microbiology, Frontiers Media SA, Vol. 13 ( 2023-2-14)
    Abstract: Four Gram-staining-positive, aerobic, non-motile, circle-shaped bacteria were isolated from the faeces of bats ( Rousettus leschenaultia and Taphozous perforates ) collected from Guangxi autonomous region (E106°49′20″, N22°20′54″) and Yunnan province (E102°04′39″, N25°09′10″) of South China. Strains HY006 T and HY008 shared highly 16S rRNA gene sequence similarity to those of Ornithinimicrobium pratense W204 T (99.3%) and O. flavum CPCC 203535 T (97.3%), while the strains HY1745 and HY1793 T were closest to the type strains O. ciconiae H23M54 T (98.7%), O. cavernae CFH 30183 T (98.3%), and O. murale 01-Gi-040 T (98.1%). Furthermore, when compared to the other members of the genus Ornithinimicrobium , the digital DNA-DNA hybridization and average nucleotide identity values of the four novel strains were within the ranges of 19.6–33.7% and 70.6–87.4%, respectively, both of which were below the respective recommended cutoff values of 70.0% and 95–96%. Significantly, strain HY006 T was resistant to chloramphenicol and linezolid whereas strain HY1793 T was resistant to erythromycin, clindamycin (intermediately), and levofloxacin (intermediately). The main cellular fatty acids ( & gt;20.0%) of our isolates were iso -C 15:0 and iso -C 16:0 . Strains HY006 T and HY1793 T contained ornithine as the diagnostic diamino acid, also along with the alanine, glycine and glutamic acid in their cell wall. Based on phylogenetic, chemotaxonomic and phenotypic analyses, these four strains could be classified as two novel species of the genus Ornithinimicrobium , for which the names Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. are proposed. The type strains are HY006 T (=CGMCC 1.16565 T =JCM 33397 T ) and HY1793 T (=CGMCC 1.19143 T =JCM 34881 T ), respectively.
    Type of Medium: Online Resource
    ISSN: 2235-2988
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
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  • 6
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 11, No. 3 ( 2023-06-15)
    Abstract: Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as “microbial dark matter,” may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika ( Ochotona curzoniae ) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a “core microbiota.” They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema , the families Muribaculaceae , Lachnospiraceae , and Oscillospiraceae , and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika ( Ochotona curzoniae ) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
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  • 7
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 10 ( 2022-10-20)
    Abstract: Six Gram-stain-positive, aerobic or facultative anaerobic, catalase-positive, urease- and oxidase-negative, rod-shaped bacteria (zg-ZUI157 T /zg-ZUI40, zg-ZUI222 T /zg-ZUI199 and zg-ZUI188 T / zg-ZUI168) were characterized by a polyphasic approach. Optimal growth of the six strains was observed at pH 7.0 and 28 °C. Phylogenetic analyses based on the 16S rRNA gene and 247 core genes revealed that they belong to genus Cellulomonas . The three type strains have low digital DNA-DNA hybridization (19.3–30.1%) and average nucleotide identity values (78.0-85.5%) with all available genomes in the genus Cellulomonas , and a DNA G+C content range of 73.0-74.6 mol%. The major fatty acids detected in strain pairs zg-ZUI157 T /zg-ZUI40 and zg-ZUI 222 T /zg-ZUI199 were C 16:0 , anteiso-C 15:0 and anteiso A-C 15:1 , and C 16:0 , anteiso-C 15:0 , anteiso A-C 15:1 and anteiso-C 17:0 in strain pair zg-ZUI188 T /zg-ZUI168. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides were the major polar lipids detected in the three novel species. MK-9(H 4 ) was the predominant quinone detected in strains zg-ZUI222 T (87.4 %) and zg-ZUI188 T (91.4 %), and MK-9(H 4 ) (49.1 %) and MK-8 (43.4 %) in strain zg-ZUI157 T . The cell-wall sugars detected in the three novel species mainly contained rhamnose. The cell-wall peptidoglycan type of the three novel species was A4 β , with an inferred l -Orn –d -Asp interpeptide bridge for strains zg-ZUI157 T and zg-ZUI222 T , and l -Orn –d -Glu for strain zg-ZUI188 T . Based on the results of the phenotypic, phylogenetic, genomic hybridization, average nucleotide identity and chemotaxonomic analyses, the six strains should be classified as belonging to three novel Cellulomonas species, for which the names Cellulomonas dongxiuzhuiae sp. nov. (zg-ZUI157 T =GDMCC 1.2559 T =KCTC 49678 T ), Cellulomonas wangleii sp. nov. (zg-ZUI222 T =GDMCC 1.2501 T =KCTC 49675 T ) and Cellulomonas fengjieae sp. nov. (zg-ZUI188 T =GDMCC 1.2563 T =KCTC 49674 T ) are proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
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    SSG: 12
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  • 8
    In: Systematic and Applied Microbiology, Elsevier BV, Vol. 45, No. 2 ( 2022-04), p. 126294-
    Type of Medium: Online Resource
    ISSN: 0723-2020
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
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    detail.hit.zdb_id: 2046331-5
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  • 9
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 9 ( 2022-09-20)
    Abstract: Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886 T /zg-887 and zg-1050 T /zg-1084) were isolated from Marmota himalayana . Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family Eggerthellaceae : zg-1050 T and zg-1084 were most closely related to Berryella intestinalis 68-1-3 T (97.2 %), while zg-886 T /zg-887 had the highest similarity to Slackia piriformis YIT 12062 T (91.6 %), followed by Paraeggerthella hongkongensis DSM 16106 T (91.4 %) and Gordonibacter urolithinfaciens DSM 27213 T (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family Eggerthellaceae . The genomic G+C contents of strains zg-886 T and zg-1050 T were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family Eggerthellaceae were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050 T , strain zg-886 T contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family Eggerthellaceae are proposed, Xiamenia xianingshaonis gen. nov., sp. nov. (zg-886 T =JCM 34097 T =GDMCC 1.1710 T ) and Berryella wangjianweii sp. nov. (zg-1050 T =GDMCC 1.2426 T =JCM 34748 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 10
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 4 ( 2023-04-12)
    Abstract: Six aerobic or facultative anaerobic, motile, Gram-stain-positive, catalase-positive and oxidase-negative strains (zg-Y453 T , zg-Y324, zg-Y462 T , zg-Y411, zg-Y809 T and zg-Y786) were isolated from different faecal samples of Marmota himalayana from the Qinghai–Tibet Plateau. Pale yellow, round, raised and moist colonies appeared 48 h after incubation at 28 °C on brain–heart infusion plates supplemented with 5 % defibrinated sheep blood. According to the 16S rRNA gene sequence alignment, two strain pairs (zg-Y453 T /zg-Y324 and zg-Y462 T /zg-Y411) shared the highest similarities to Arthrobacter luteolus (99.5 and 99.2 %), and the other one (zg-Y809 T /zg-Y786) to Arthrobacter citreus (99.5 %). Results of phylogenetic analysis based on the 16S rRNA gene and genome sequences showed that these six strains represented three separate species within the genus Arthrobacter . The average nucleotide identity and digital DNA–DNA hybridization values between the three novel type strains (zg-Y453 T /zg-Y462 T /zg-Y809 T ) and other known species in this genus were all below respective thresholds (70.2–81.5/19.6–24.2 %, 70.6–81.8/19.8–25.0 %, and 70.4–88.2/19.9–35.3 %). Although phylogenetically related, there were obvious chemotaxonomic and phenotypic differences: strain pair zg-Y462 T /zg-Y411 had anteiso- C 15 : 0 as the only major fatty acid; the three novel species had different dominant quinones, MK-8(H 2 ) in strains zg-Y462 T /zg-Y809 T (74.8/81.1 %) and MK-8(H 2 )/MK-9(H 2 ) (43.1/53.0 %) in zg-Y453 T ; similarly, the ability to reduce nitrate in strains zg-Y453 T and zg-Y462 T could differentiate them from zg-Y809 T . All strains had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, but differed slightly in the types of unidentified glycolipids, phospholipids and lipids. Based on the results of these polyphasic taxonomic analyses, three novel species within the genus Arthrobacter are proposed, namely Arthrobacter caoxuetaonis sp. nov. (type strain, zg-Y453 T =GDMCC 1.2809 T =JCM 35173 T ), Arthrobacter zhangbolii sp. nov. (type strain, zg-Y462 T =GDMCC 1.2880 T =JCM 35170 T ) and Arthrobacter gengyunqii sp. nov. (type strain, zg-Y809 T =GDMCC 1.2808 T =JCM 35168 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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