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1.
Nat Commun ; 12(1): 4191, 2021 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-34234149

RESUMO

The vaginal and uterine microbiota play important roles in the health of the female reproductive system. However, the interactions among the microbes in these two niches and their effects on uterine health remain unclear. Here we profile the vaginal and uterine microbial samples of 145 women, and combine with deep mining of public data and animal experiments to characterize the microbial translocation in the female reproductive tract and its role in modulating uterine health. Synchronous variation and increasing convergence of the uterine and vaginal microbiome with advancing age are shown. We also find that transplanting certain strains of vaginal bacteria into the vagina of rats induces or reduces endometritis-like symptoms, and verify the damaging or protective effects of certain vaginal bacteria on endometrium. This study clarifies the interdependent relationship of vaginal bacterial translocation with uterine microecology and endometrial health, which will undoubtedly increase our understanding of female reproductive health.


Assuntos
Translocação Bacteriana , Endometrite/microbiologia , Microbiota , Saúde Reprodutiva , Vagina/microbiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Doença Crônica , Estudos de Coortes , DNA Bacteriano/isolamento & purificação , Modelos Animais de Doenças , Endometrite/epidemiologia , Endometrite/patologia , Endométrio/microbiologia , Endométrio/patologia , Feminino , Humanos , Pessoa de Meia-Idade , Fatores de Proteção , RNA Ribossômico 16S/genética , Ratos , Fatores de Risco , Saúde da Mulher , Adulto Jovem
2.
Artigo em Inglês | MEDLINE | ID: mdl-34283014

RESUMO

A Gram-stain-positive, yellow-pigmented, non-motile actinobacterial strain, designated as BIT-GX5T, was isolated from a sesame husks compost collected in Beijing, PR China. This bacterium was found to be able to grow in the temperature range from 16 to 50 °C and had an optimal growth temperature at 45 °C. Its taxonomic position was analysed using a polyphasic approach. The 16S rRNA gene sequence (1482 bp) of strain BIT-GX5T was most similar to Cellulosimicrobium funkei ATCC BAA-886T (99.45%), Cellulosimicrobium cellulans LMG 16121T (99.17%) and Cellulosimicrobium marinum RS-7-4T (98.75%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (gyrB, rpoB, recA, atpD and trpB) and genome sequences, placed strain BIT-GX5T in a separate lineage among the genus Cellulosimicrobium within the family Promicromonosporaceae. The major polar lipids of strain BIT-GX5T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The major isoprenoid quinone was MK-9(H4), while the cell-wall sugars were galactose, rhamnose, glucose and mannose. The peptidoglycan type was A4α l-Lys-d-Ser-d-Asp. The major fatty acids were anteiso-C15:0 and iso-C15: 0, which were similar to other members in the genus Cellulosimicrobium. Results of in silico DNA-DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-GX5T from the other members of the genus Cellulosimicrobium. Therefore, strain BIT-GX5T is considered to represent a novel species within the genus Cellulosimicrobium, for which the name Cellulosimicrobium composti sp. nov. is proposed. The type strain is BIT-GX5T (= CGMCC 1.17687T = KCTC 49391T).


Assuntos
Actinobacteria/isolamento & purificação , Compostagem/métodos , Actinobacteria/genética , Técnicas de Tipagem Bacteriana/métodos , DNA Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos
3.
Artigo em Inglês | MEDLINE | ID: mdl-34252019

RESUMO

A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1-0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20-37 °C, at pH 5.0-8.5 and at 0-2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2-83.2 % and 22.1-27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA-DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus Niastella, for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.


Assuntos
Bacteroidetes/isolamento & purificação , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/metabolismo , Composição de Bases , DNA Bacteriano/genética , Diospyros/crescimento & desenvolvimento , Diospyros/microbiologia , Ácidos Graxos/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Rizosfera , Árvores/crescimento & desenvolvimento , Árvores/microbiologia
4.
Artigo em Inglês | MEDLINE | ID: mdl-34252020

RESUMO

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842T (96.9 %), and Facklamia hominis CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10-40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l-1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.


Assuntos
Aerococcaceae/isolamento & purificação , Leite/microbiologia , Aerococcaceae/classificação , Aerococcaceae/genética , Aerococcaceae/metabolismo , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Bovinos , DNA Bacteriano/genética , Ácidos Graxos/metabolismo , Glicolipídeos/metabolismo , Fosfolipídeos/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
5.
Artigo em Inglês | MEDLINE | ID: mdl-34252022

RESUMO

Six novel strains (ZJ34T, ZJ561, ZJ750T, ZJ1629, zg-993T 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 15434T (16S rRNA gene sequences similarities, 94.9-98.7 %), Actinomyces weissii CCUG 61299T (95.6-96.6 %), Actinomyces bovis CCTCC AB2010168T (95.7 %) and Actinomyces bowdenii DSM 15435T (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 (ZJ34T/ZJ561, ZJ750T/ZJ1629 and zg-993T/zg-987). All the novel strains had C18 : 1 ω9c and C16 : 0 as the two most abundant major fatty acids. MK-9(H4) or MK-8(H4) was the sole or predominant respiratory quinone of strains ZJ34T, ZJ750T and zg-993T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750T shared identical peptidoglycan amino acid profile with ZJ34T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993T (glucose, rhamnose and ribose). Strain zg-993T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34T 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 ZJ34T (=GDMCC 1.1952T=JCM 34355T)], Actinomyces respiraculi sp. nov. [type strain ZJ750T (=GDMCC 1.1950T=JCM 34356T)] and Actinomyces trachealis sp. nov. [type strain zg-993T (=GDMCC 1.1956T=JCM 34357T)] were proposed, respectively.


Assuntos
Actinomyces/isolamento & purificação , Marmota/microbiologia , Actinomyces/classificação , Actinomyces/genética , Actinomyces/metabolismo , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/metabolismo , Fosfolipídeos/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Artigo em Inglês | MEDLINE | ID: mdl-34198553

RESUMO

Few studies have exhaustively assessed relationships among polymorphisms, the microbiome, and periodontitis. The objective of the present study was to assess associations simultaneously among polymorphisms, the microbiome, and periodontitis. We used propensity score matching with a 1:1 ratio to select subjects, and then 22 individuals (mean age ± standard deviation, 60.7 ± 9.9 years) were analyzed. After saliva collection, V3-4 regions of the 16S rRNA gene were sequenced to investigate microbiome composition, alpha diversity (Shannon index, Simpson index, Chao1, and abundance-based coverage estimator) and beta diversity using principal coordinate analysis (PCoA) based on weighted and unweighted UniFrac distances. A total of 51 single-nucleotide polymorphisms (SNPs) related to periodontitis were identified. The frequencies of SNPs were collected from Genome-Wide Association Study data. The PCoA of unweighted UniFrac distance showed a significant difference between periodontitis and control groups (p < 0.05). There were no significant differences in alpha diversity and PCoA of weighted UniFrac distance (p > 0.05). Two families (Lactobacillaceae and Desulfobulbaceae) and one species (Porphyromonas gingivalis) were observed only in the periodontitis group. No SNPs showed significant expression. These results suggest that periodontitis was related to the presence of P. gingivalis and the families Lactobacillaceae and Desulfobulbaceae but not SNPs.


Assuntos
Microbiota , Periodontite , Estudo de Associação Genômica Ampla , Humanos , Microbiota/genética , Periodontite/epidemiologia , Periodontite/genética , RNA Ribossômico 16S/genética , Fatores de Risco , Saliva
7.
Int J Mol Sci ; 22(13)2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34202141

RESUMO

Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.


Assuntos
Microbioma Gastrointestinal , Lepidópteros/microbiologia , Análise de Variância , Animais , Biologia Computacional/métodos , Interações Hospedeiro-Parasita , Metagenômica/métodos , Plantas/parasitologia , RNA Ribossômico 16S/genética
8.
Curr Microbiol ; 78(8): 3334-3341, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34259886

RESUMO

Two novel Gram-stain-negative, non-motile, aerobic, rod-shaped, circular, convex, red-colored and UV-tolerant strains BT594T and BT646T were isolated from soil collected in Guri city (37° 36' 0″ N, 127° 9' 0″ E) and Gwangju city (37° 22' 0″ N, 127° 17' 0″ E), respectively, South Korea. 16S rDNA sequence analysis indicated that strains BT594T and BT646T belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes, kingdom Bacteria). The 16S rDNA gene sequence similarity between the two strains BT594T and BT646T was 96.2%. The strain BT594T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (97.0% 16S rDNA gene similarity) and Hymenobacter tibetensis XTM003T (96.3%). The strain BT646T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (98.6%), Hymenobacter kanuolensis T-3 T (96.8%) and Hymenobacter perfusus LMG 26000 T (96.7%). The two strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strains BT594T and BT646T were phosphatidylethanolamine (PE) and aminophospholipids (APL). The major cellular fatty acids of strain BT594T were anteiso-C15:0 (17.9%), iso-C15:0 (16.1%) and summed feature 3 (C16:1 ω6c / C16:1 ω7c) (10.0%). The major cellular fatty acids of strain BT646T were summed feature 3 (C16:1 ω6c / C16:1 ω7c) (18.3%), C16:0 (17.2%) and summed feature 4 (iso-C17:1 I / anteiso-C17:1 B) (14.5%). Based on the polyphasic analysis, strains BT594T and BT646T can be suggested as two novel bacterial species within the genus Hymenobacter and the proposed names are Hymenobacter guriensis and Hymenobacter duratus, respectively. The type strain of Hymenobacter guriensis is BT594T (= KCTC 21863 T = NBRC 114853 T) and the type strain of Hymenobacter duratus is BT646T (= KCTC 21915 T = NBRC 114854 T).


Assuntos
Cytophagaceae , Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes , Composição de Bases , Cytophagaceae/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Filogenia , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Microbiologia do Solo , Tibet
9.
Microbiome ; 9(1): 152, 2021 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-34193273

RESUMO

BACKGROUND: The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission, six crewmembers lived completely isolated from the outer world for 520 days following standardized diet regimes. The mission constitutes the first spaceflight simulation to Mars and was a unique experiment to determine, in a longitudinal study design, the composition and importance of the resident vs. a more variable microbiota-the fraction of the human microbiota that changes in time and according to environmental conditions-in humans. METHODS: Here, we report the characterization of the salivary microbiota from 88 samples taken during and after Mars500 mission for a total of 720 days. Amplicon sequencing of the V3-V4 regions of 16S rRNA gene was performed, and results were analyzed monitoring the diversity of the microbiota while evaluating the effect of the three main variables present in the experimental system: time, diet, and individuality of each subject. RESULTS: Results showed statistically significant effects for either time, diet, and individuality of each subject. The main contribution came from the individuality of each subject, emphasizing salivary microbiota-personalized features, and an individual-based resilience of the microbiota. CONCLUSIONS: The uniqueness of Mars500 mission, allowed to dampen the effect of environmental variables on salivary microbiota, highlighting its pronounced personalization even after sharing the same physical space for more than a year. Video abstract.


Assuntos
Microbiota , Voo Espacial , Dieta , Humanos , Estudos Longitudinais , RNA Ribossômico 16S/genética
10.
BMC Genomics ; 22(1): 527, 2021 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-34246242

RESUMO

BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol. RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data. CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.


Assuntos
Microbioma Gastrointestinal , Benchmarking , Microbioma Gastrointestinal/genética , Genes de RNAr , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Japão , RNA Ribossômico 16S/genética
11.
Artigo em Inglês | MEDLINE | ID: mdl-34196604

RESUMO

An actinobacterium, strain CH5-8T, which formed spiral chains of spore arising from the aerial mycelium, was isolated from rhizosphere soil of Musa spp. The organism exhibited vivid greenish yellow substrate mycelium and easily produced the medium grey aerial spore mass on ISP2 medium. The typical chemotaxonomic properties of members of the genus Streptomyces were observed for strain CH5-8T, e.g. ll-diaminopimelic acid in cell peptidoglycan, MK-9(H8), MK-9(H6), and MK-9(H4) as major menaquinones and anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside were detected in the cells. A combination of morphological and chemotaxonomic data supported the assignment to the genus Streptomyces. The analysis result obtained for the 16S rRNA gene sequence confirmed the taxonomic affiliation at the genus level of this strain. The novel strain CH5-8T showed the highest 16S rRNA gene sequence values to Streptomyces echinatus NBRC 12763T (98.9 %), followed by Streptomyces actinomycinicus RCU-197T (98.9 %). The average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization values between CH5-8T and its closest relatives, S. echinatus CECT 3313T and S. actinomycinicus RCU-197T, were ≤91.6 % and ≤47.4 %, respectively. The digital DNA G+C content of genomic DNA was 72.1 mol%. On the basis of these phenotypic and genotypic data, strain CH5-8T represents a novel species, for which the name Streptomyces musisoli sp. nov. is proposed. The type strain is CH5-8T (=TBRC 9950T=NBRC 113997T).


Assuntos
Musa , Filogenia , Rizosfera , Microbiologia do Solo , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Micélio , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/isolamento & purificação , Tailândia , Vitamina K 2/análogos & derivados , Vitamina K 2/química
12.
Int J Mol Sci ; 22(11)2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-34205981

RESUMO

Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.


Assuntos
Microbioma Gastrointestinal/genética , Trato Gastrointestinal/microbiologia , Microbiota/genética , Animais , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Dieta Ocidental/efeitos adversos , Fezes/microbiologia , Firmicutes/genética , Firmicutes/isolamento & purificação , Humanos , Camundongos , RNA Ribossômico 16S/genética
13.
Artigo em Inglês | MEDLINE | ID: mdl-34214024

RESUMO

Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of the isolates were Gram-reaction-negative, facultatively anaerobic, motile and rod-shaped and showed growth at 4-30 °C, pH 4.0-9.0 and with 0-6 (w/v) NaCl. In phylogenomic analysis based on 92 single-copy core genes, it was shown that the isolates belonged to the genus Rahnella and formed three distinct sublines within the genus. The isolates shared 16S rRNA gene sequence similarities of 97.9-100 % with one another. The isolates contained ubiquinone-8 was as the major isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were C16 : 0 and C17 : 0 cyclo. The G+C content of their genomic DNA was 52.8-53.1 %. Average nucleotide identity and digital DNA-DNA hybridization values supported that strains SAP-17T and Lac-M11T represented two new species of the genus Rahnella, whereas strain SAP-10 was a strain of Rahnella victoriana. Based on the results obtained here, Rahnella laticis sp. nov. (type strain SAP-17T=KCTC 72960T=NBRC 114723T=CCM 9079T) and Rahnella contaminans sp. nov. (type strain Lac-M11T=KACC 21743T=NBRC 114406T) are proposed. Also, an emended description of the genus Rahnella is given on the basis of our physiological and chemotaxonomic results.


Assuntos
Filogenia , Rahnella/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rahnella/isolamento & purificação , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-34214025

RESUMO

A strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain R1DC9T, was isolated from sediments of a mangrove stand on the Red Sea coast of Saudi Arabia via diffusion chamber cultivation. Strain R1DC9T grew at 20-40 °C (optimum, 37 °C), pH 6-10 (optimum, pH 8) and 3-11 % NaCl (optimum, 7-9 %) in the cultivation medium. The genome of R1DC9T was 4 661 901 bp long and featured a G+C content of 63.1 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis using 120 concatenated single-copy genes revealed that R1DC9T represents a distinct lineage in the order Cytophagales and the phylum Bacteroidetes separated from the Roseivirgaceae and Marivirgaceae families. R1DC9T displayed 90 and 89 % 16S rRNA gene sequence identities with Marivirga sericea DSM 4125T and Roseivirga ehrenbergii KMM 6017T, respectively. The predominant quinone was MK7. The polar lipids were phosphatidylethanolamine, two unknown phospholipids and two unknown lipids. The predominant cellular fatty acids were the saturated branch chain fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 0, along with a low percentage of the monounsaturated fatty acid C16 : 1 ω5c. Based on differences in phenotypic, physiological and biochemical characteristics from known relatives, and the results of phylogenetic analyses, R1DC9T (=KCTC 72349T=JCM 33609T=NCCB 100698T) is proposed to represent a novel species in a new genus, and the name Mangrovivirga cuniculi gen. nov., sp. nov. is proposed. The distinct phylogenetic lineage among the families in the order Cytophagales indicates that R1DC9T represents a new family for which the name Mangrovivirgaceae fam. nov. is proposed.


Assuntos
Bacteroidetes/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Rhizophoraceae , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Arábia Saudita , Água do Mar/microbiologia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Artigo em Inglês | MEDLINE | ID: mdl-34214026

RESUMO

A novel actinomycete, designated strain KK5PA1T, was isolated from a soil sample collected from Kuan Kreng peat swamp forest, Nakhon Si Thammarat Province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. Strain KK5PA1T was most closely related to Streptomyces bryophytorum NEAU-HZ10T (98.0 %) and Streptomyces guanduensis 701T (97.6 %). The G+C content of the genomic DNA was 72.3 mol%. Digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain KK5PA1T and those of S. bryophytorum DSM 42138T(25.1 and 79.1 %) and S. guanduensis DSM 41944T(25.1 and 79.7%) were below the thresholds of 70 and 96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain KK5PA1T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, mannose and ribose as whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside, two unidentified aminolipids, five unidentified phospholipids and an unidentified lipid. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and C16 : 0. On the basis of these genotypic and phenotypic data, it is proposed that strain KK5PA1T represents a novel species of the genus Streptomyces, for which the name Streptomyces acididurans sp. nov. is proposed. The type strain is strain KK5PA1T (=TBRC 13094T=NBRC 114802T).


Assuntos
Filogenia , Microbiologia do Solo , Streptomyces/classificação , Áreas Alagadas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Florestas , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/isolamento & purificação , Tailândia , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Artigo em Inglês | MEDLINE | ID: mdl-34214027

RESUMO

A previously unrecognized Rickettsia species was isolated in 1976 from a pool of Ixodes pacificus ticks collected in 1967 from Tillamook County, Oregon, USA. The isolate produced low fever and mild scrotal oedema following intraperitoneal injection into male guinea pigs (Cavia porcellus). Subsequent serotyping characterized this isolate as distinct from recognized typhus and spotted fever group Rickettsia species; nonetheless, the isolate remained unevaluated by molecular techniques and was not identified to species level for the subsequent 30 years. Ixodes pacificus is the most frequently identified human-biting tick in the western United States, and as such, formal identification and characterization of this potentially pathogenic Rickettsia species is warranted. Whole-genome sequencing of the Tillamook isolate revealed a genome 1.43 Mbp in size with 32.4 mol% G+C content. Maximum-likelihood phylogeny of core proteins places it in the transitional group of Rickettsia basal to both Rickettsia felis and Rickettsia asembonensis. It is distinct from existing named species, with maximum average nucleotide identity of 95.1% to R. asembonensis and maximum digital DNA-DNA hybridization score similarity to R. felis at 80.1%. The closest similarity at the 16S rRNA gene (97.9%) and sca4 (97.5%/97.6% respectively) is to Candidatus 'Rickettsia senegalensis' and Rickettsia sp. cf9, both isolated from cat fleas (Ctenocephalides felis). We characterized growth at various temperatures and in multiple cell lines. The Tillamook isolate grows aerobically in Vero E6, RF/6A and DH82 cells, and growth is rapid at 28 °C and 32 °C. Using accepted genomic criteria, we propose the name Rickettsia tillamookensis sp. nov., with the type strain Tillamook 23. Strain Tillamook 23 is available from the Centers for Disease Control and Prevention Rickettsial Isolate Reference Collection (WDCM 1093), Atlanta, GA, USA (CRIRC accession number RTI001T) and the Collection de Souches de l'Unité des Rickettsies (WDCM 875), Marseille, France (CSUR accession number R5043). Using accepted genomic criteria, we propose the name Rickettsia tillamookensis sp. nov., with the type strain Tillamook 23 (=CRIRC RTI001=R5043).


Assuntos
Ixodes/microbiologia , Filogenia , Rickettsia/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Cobaias , Masculino , Oregon , RNA Ribossômico 16S/genética , Rickettsia/isolamento & purificação , Análise de Sequência de DNA
17.
Artigo em Inglês | MEDLINE | ID: mdl-34214029

RESUMO

Strain MaA-C15T, a Gram-stain-negative, non-spore-forming and strictly aerobic bacterium, was isolated from a xenic culture of Microcystis aeruginosa in the Republic of Korea. Cells were motile rods showing positive reactions in catalase and oxidase tests. Growth was observed between 15 and 37 °C (optimum, 30 °C), between pH 6.0 and pH 11.0 (optimum, pH 7.5) and in the presence of 0-2.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-C15T contained C16 : 0, 11-methyl-C18 : 1 ω7c, cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) as the major cellular fatty acids and ubiquinone-10 as the sole respiratory quinone. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids were detected as the major polar lipids. The G+C content of the genomic DNA was 64.1 mol%. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences revealed that strain MaA-C15T formed a phyletic lineage with Mesorhizobium sediminum YIM M12096T within the family Phyllobacteriaceae. Strain MaA-C15T was most closely related to Mesorhizobium albiziae DSM 21822T with a 98.2 % 16S rRNA sequence similarity. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-C15T and M. albiziae DSM 21822T were 75.4 and 20.1 %, respectively. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain MaA-C15T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium microcysteis sp. nov. is proposed. The type strain is MaA-C15T (=KACC 21226T=JCM 33503T).


Assuntos
Mesorhizobium/classificação , Microcystis , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Mesorhizobium/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
18.
Artigo em Inglês | MEDLINE | ID: mdl-34224346

RESUMO

Two bacterial strains, designated as 1-4-3T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4-37 °C, pH 7.0-9.0, and 0-7% NaCl. The predominant fatty acids of the novel strains were C18 : 1 ω7c, C19 : 0 cyclo ω8c, C18 : 0, and C16 : 0. A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas, with closest sequence similarity to A. populi 4M3-2T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3T was 66.80 mol%. Strain 1-4-3T displayed low DNA-DNA relatedness to A. populi 4M3-2T, with an average nucleotide identity value of 77.47 % and digital DNA-DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3T and 1-4-4 represent a novel species of the genus Aureimonas, for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3T (=LMG 31693T=CGMCC 1.18507T).


Assuntos
Alphaproteobacteria/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tailândia , Áreas Alagadas
19.
Artigo em Inglês | MEDLINE | ID: mdl-34228608

RESUMO

A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073T, was isolated from the sea sponge Aplysina fistularis, collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073T grew optimally at 30-37 °C, pH 6-7, and with 2-3 % (w/v) NaCl. The predominant fatty acids of RKSG073T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073T in a clade with its closest relative Aestuariispira insulae AH-MY2T (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Hwanghaeella grinnelliae Gri0909T, Marivibrio halodurans ZC80T and type species of the genera Kiloniella, Thalassospira and Terasakiella. The DNA G+C content calculated from the genome of RKSG073T was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073T (culture deposit numbers: ATCC collection = TSD-74T, BCCM collection = LMG 29869T) represents the type strain of a novel genus and species within the family Kiloniellaceae, order Rhodospirillales and class Alphaproteobacteria, for which the name Curvivirga aplysinae gen. nov., sp. nov. is proposed.


Assuntos
Alphaproteobacteria/classificação , Filogenia , Poríferos/microbiologia , Alphaproteobacteria/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Bahamas , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
20.
Artigo em Inglês | MEDLINE | ID: mdl-34228609

RESUMO

The genus Flavobacterium (family Flavobacteriaceae) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium. None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium. Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95-96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).


Assuntos
Flavobacterium/classificação , Camada de Gelo/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tibet
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