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1.
Food Chem ; 368: 130890, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34438182

RESUMO

Dietary supplements containing vitamin K2 are often used to prevent osteoporosis, vascular calcification and coronary heart disease. It has been shown that some of these products contain a mixture of menaquinone-7 geometric isomers. Since the geometric shape may influence biological activity, there was a need for a semipreparative method to isolate single compounds for further studies. Here, we present an argentation chromatographic method for the separation of menaquinone-7 isomers and an nuclear magnetic resonance (NMR) methodology for the configuration assignment of isoprenoid side chain. The DFT calculations were performed to determine more energetically favorable complexes between the cis or trans menaquinone-7 isomers and the silver cation. Seventeen components were resolved, and fractions were collected and subjected to NMR study. Structures and chemical shifts for thirteen new compounds were assigned, and the identity of three known compounds was confirmed.


Assuntos
Prata , Cromatografia Líquida de Alta Pressão , Espectroscopia de Ressonância Magnética , Vitamina K 2/análogos & derivados
2.
Int J Syst Evol Microbiol ; 71(10)2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34668849

RESUMO

This paper presents a polyphasic taxonomic study of a Gram-stain-negative bacterium designated GA093T, a soil isolate capable of benzo(α)pyrene degradation. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GA093T is a member of the genus Flavobacterium, and formed an independent phylogenetic line while clustering with the type strains of Flavobacterium hibernum, Flavobacterium branchiarum and Flavobacterium hydatis. Strain GA093T was facultatively anaerobic, and could grow at 4-33 °C (optimum, 30 °C), at pH 6-11 (optimum, pH 7) and in the presence of 0-2 % (w/v) NaCl (optimum, 0 %). Strain GA093T was capable of producing acid from various carbon sources, which was comparable to other related species of Flavobacterium. The strain contained MK-6 as the only isoprenoid quinone, iso-C15 : 0 as the major cellular fatty acid, phosphatidylethanolamine and phosphatidylinositol as diagnostic polar lipids, and sym-homospermidine as the major polyamine. The chemotaxonomic properties of strain GA093T were consistent with the general properties of Flavobacterium except the presence of phosphatidylinositol, which distinguished it from other related species. The total stretch of the obtained genome of GA093T was 5.05 Mbp, and the DNA G+C content was 34.79 mol%. The genome contained genes potentially related to the degradation of aromatic hydrocarbons. On the basis of the present polyphasic analysis, strain GA093T was found to have properties that distunguished it as representing a novel species of the genus Flavobacterium, for which the name Flavobacterium hydrocarbonoxydans sp. nov. is proposed. The type strain is GA093T (=KCTC 72594T=LMG 31760T).


Assuntos
Ácidos Graxos , Flavobacterium , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo , Vitamina K 2
3.
Artigo em Inglês | MEDLINE | ID: mdl-34590995

RESUMO

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae. Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10-37 °C (optimum at 30 °C), pH 6-8 (optimum at pH 7) and with 0-2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter, for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602-396T=KCTC 82079T=JCM 34181T).


Assuntos
Pedobacter , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pedobacter/genética , Filogenia , RNA Ribossômico 16S/genética , Rios , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2
4.
Artigo em Inglês | MEDLINE | ID: mdl-34582326

RESUMO

The actinomycetes strains KRD168T and KRD185T were isolated from sediments collected from the deep Southern Ocean and, in this work, they are described as representing two novel species of the genus Pseudonocardia through a polyphasic approach. Despite sharing >99 % 16S rRNA gene sequence similarity with other members of the genus, comparative genomic analysis allowed species delimitation based on average nucleotide identity and digital DNA-DNA hybridization. The KRD168T genome is characterized by a size of 6.31 Mbp and a G+C content of 73.44 mol%, while the KRD185T genome has a size of 6.82 Mbp and a G+C content of 73.98 mol%. Both strains contain meso-diaminopimelic acid as the diagnostic diamino acid, glucose as the major whole-cell sugar, MK-8(H4) as a major menaquinone and iso-branched hexadecanoic acid as a major fatty acid. Biochemical and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their status as distinct species. The names Pseudonocardia abyssalis sp. nov. (type strain KRD168T=DSM 111918T=NCIMB 15270T) and Pseudonocardia oceani (type strain KRD185T=DSM 111919T=NCIMB 15269T) are proposed.


Assuntos
Actinobacteria , Actinobacteria/genética , Actinomyces , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceanos e Mares , Filogenia , Pseudonocardia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análise
5.
Arch Microbiol ; 203(9): 5783-5792, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34515811

RESUMO

During a study aiming at isolation and genomic characterization of non-pathogenic fish symbionts, strain F-328T was isolated from skin mucus of healthy-seeming rainbow trout (Oncorhynchus mykiss) and subjected to polyphasic characterization, including a comprehensive genome analysis. Strain F-328T was Gram stain negative, none-gliding, strictly aerobic, and rod shaped. The 16S rRNA gene sequence of strain F-328T exhibited the highest level of identity (98.9%) with F. turcicum F-339T. The major fatty acids were iso-C15:0, C15:1 ω6c, and summed feature 3 (C16:1 ω7c, C16:1 ω6c). The polar lipid profile consisted mainly of phosphatidylethanolamine and aminolipids, while the predominant menaquinone was MK-6. The DNA G + C content and genome size of the strain were 35.3% and 3.4 Mb, respectively. Strain F-328T shows 93.8% average nucleotide identity and 53% digital DNA-DNA hybridization identity with the closest type strain F. turcicum F-339T. In addition, strain F-328T was found to carry antimicrobial resistance genes, which confer resistance to several antimicrobials, including aminoglycoside, macrolides, and streptogramin. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain F-328T should be classified as a novel species of the genus Flavobacterium for which the name Flavobacterium erciyesense sp. nov. is proposed, with F-328T as the type strain (= JCM 34201T = KCTC 82261T).


Assuntos
Ácidos Graxos , Flavobacterium , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacterium/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
6.
Eur J Epidemiol ; 36(10): 1005-1014, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34591201

RESUMO

Reported associations between vitamin K1 and both all-cause and cause-specific mortality are conflicting. The 56,048 participants from the Danish Diet, Cancer, and Health prospective cohort study, with a median [IQR] age of 56 [52-60] years at entry and of whom 47.6% male, were followed for 23 years, with 14,083 reported deaths. Of these, 5015 deaths were CVD-related, and 6342 deaths were cancer-related. Intake of vitamin K1 (phylloquinone) was estimated from a food-frequency questionnaire (FFQ), and its relationship with mortality outcomes was investigated using Cox proportional hazards models. A moderate to high (87-192 µg/d) intake of vitamin K1 was associated with a lower risk of all-cause [HR (95%CI) for quintile 5 vs quintile 1: 0.76 (0.72, 0.79)], cardiovascular disease (CVD)-related [quintile 5 vs quintile 1: 0.72 (0.66, 0.79)], and cancer-related mortality [quintile 5 vs quintile 1: 0.80 (0.75, 0.86)], after adjusting for demographic and lifestyle confounders. The association between vitamin K1 intake and cardiovascular disease-related mortality was present in all subpopulations (categorised according to sex, smoking status, diabetes status, and hypertension status), while the association with cancer-related mortality was only present in current/former smokers (p for interaction = 0.002). These findings suggest that promoting adequate intakes of foods rich in vitamin K1 may help to reduce all-cause, CVD-related, and cancer-related mortality at the population level.


Assuntos
Doenças Cardiovasculares/mortalidade , Mortalidade , Neoplasias/mortalidade , Vitamina K/administração & dosagem , Doenças Cardiovasculares/metabolismo , Doenças Cardiovasculares/prevenção & controle , Causas de Morte , Dinamarca/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias/metabolismo , Neoplasias/prevenção & controle , Avaliação Nutricional , Estudos Prospectivos , Fatores de Risco , Inquéritos e Questionários , Vitamina K 1/administração & dosagem , Vitamina K 2/administração & dosagem
7.
Artigo em Inglês | MEDLINE | ID: mdl-34495823

RESUMO

The novel, anaerobic, Gram-positive, rod-shaped bacterial strain, ResAG-91T, was isolated from a faecal sample of a male human volunteer. Analysis of the 16S rRNA gene sequence revealed that strain ResAG-91T showed high similarity to the type strains of Adlercreutzia equolifaciens subsp. equolifaciens and Adlercreutzia equolifaciens subsp. celatus. Analysis of the whole draft genome sequences, i.e. digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), of strain ResAG-91T and the type strains of Adlercreutzia species revealed that strain ResAG-91T represents a novel species of the genus Adlercreutzia. The genome size of strain ResAG-91T is 2.8 Mbp and the G+C content is 63.3 mol%. The major respiratory quinone of strain ResAG-91T was MMK-5 (methylmenaquinone). Major cellular fatty acids were C15 : 0 anteiso, C14 : 0 iso and C14 : 0 2-OH. Galactose and ribose were detected as major whole cell sugars. Furthermore, the peptidoglycan type of strain ResAG-91T was A1γ with meso-diaminopimelic acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and five unidentified glycolipids. Strain ResAG-91T was able to metabolize the stilbene resveratrol into dihydroresveratrol. On the basis of this polyphasic approach, including phenotypical, molecular (16S rRNA gene and whole genome sequencing) and biochemical (fatty acids, quinones, polar lipids, peptidoglycan, whole cell sugars, Rapid ID32A and API20A) analyses, we propose the novel species Adlercreutzia rubneri sp. nov. with the type and only strain ResAG-91T (=DSM 111416T=JCM 34176T=LMG 31897T).


Assuntos
Actinobacteria/classificação , Fezes/microbiologia , Resveratrol , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Alemanha , Humanos , Masculino , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
8.
Artigo em Inglês | MEDLINE | ID: mdl-34499595

RESUMO

A novel cellulase-producing actinomycete, designated strain NEAU-H7T, was isolated from coconut palm rhizosphere soil collected from Wenchang City, Hainan Province, PR China. A polyphasic taxonomic study was carried out to establish the status of this strain. Results of 16S rRNA gene sequence analysis indicated that strain NEAU-H7T belonged to the genus Actinoplanes, with highest similarity to Actinoplanes hulinensis NEAU-M9T (99.2 % 16S rRNA gene sequence similarity). The diagnostic sugars in cell hydrolysates were determined to be ribose, galactose and mannose. The major fatty acids (>10%) were C16 : 0, C18 : 1 ω9c and C18 : 0. The predominant menaquinones were identified as MK-9(H4) and MK-9(H6). The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and two phosphatidylinositol mannosides. The amino acid of the cell-wall peptidoglycan was determined to be meso-diaminopimelic acid. The DNA G+C content was 71.2 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain NEAU-H7T formed a stable phyletic line with A. hulinensis NEAU-M9T. However, whole-genome phylogeny showed strain NEAU-H7T formed a stable phyletic line with A. hulinensis NEAU-M9T (99.2%), Actinoplanes campanulatus DSM 43148T (98.6%), Actinoplanes capillaceus DSM 44859T (98.3%) and Actinoplanes lobatus DSM 43150T (97.6%). The digital DNA-DNA hybridization (dDDH) results between them were 53.6 (50.9-56.2), 54.1 (51.3-56.9), 53.1 (50.3-55.9) and 52.9 % (50.1-55.6 %), and whole-genome average nucleotide identity (ANI) values between them were 93.7, 93.6, 93.5 and 93.5 %. The low dDDH and ANI values demonstrated that strain NEAU-H7T could be distinguished from its reference strains. Moreover, genomic analysis indicated that the strain NEAU-H7T had the potential to decompose cellulose and produce bioactive compounds. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, strain NEAU-H7T is proposed to represent a novel species of the genus Actinoplanes, with the name Actinoplanes flavus sp. nov. The type strain is NEAU-H7T (=CCTCC AA 2020034T=DSM 112042T).


Assuntos
Actinoplanes , Cocos/microbiologia , Filogenia , Rizosfera , Microbiologia do Solo , Actinoplanes/classificação , Actinoplanes/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Celulase , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
9.
Artigo em Inglês | MEDLINE | ID: mdl-34516364

RESUMO

An aerobic, Gram-stain-negative, rod-shaped and non-motile strain (XY-359T) was isolated from the mouth of a marine invertebrate Onchidium species from the South China Sea. It grew at pH 6.0-8.5 (optimum, pH 7.5), at 15-37 °C (optimum, 30 °C) and in the presence of 0.5-4.5 % (w/v) NaCl (optimum, 2.5 %). It could not hydrolyse Tweens 20, 40, 60 or 80 and no flexirubin-type pigments were produced. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, six unidentified phospholipids and two unidentified polar lipids. The major fatty acids were iso-C17:0 3-OH, iso-C15:1 G and iso-C15:0 3-OH. The respiratory quinone was MK-6. Strain XY-359T showed the greatest degree of 16S rRNA sequence similarity to Flagellimonas algicola AsT0115T (96.54 %), followed by Muricauda flava DSM 22638T (96.27 %). Phylogenetic analysis based on 16S rRNA gene sequences and 31 core genes indicated that strain XY-359T belongs to the genus Muricauda. The genome size of strain XY-359T was 4 207 872 bp, with 39.1 mol% of DNA G+C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain XY-359T and F. algicola AsT0115T were 74.58 % and 18.5 %, respectively, and those between strain XY-359T and M. flava DSM 22638T were 74.2 % and 18.3 %. The combined phenotypic, chemotaxonomic and phylogenetic data suggest that strain XY-359T represents a novel species of the genus Muricauda, for which the name Muricauda onchidii sp. nov. is proposed. The type strain is XY-359T (=MCCC 1K03658T =KCTC 72218T). Moreover, based on the proposal of nesting Spongiibacterium and Flagellimonas within Muricauda by García (Validation List No. 193) and the analyses of phylogenetic trees and average amino acid identities in this study, the transfers of F. algicola, F. pacifica and F. maritima to the genus Muricauda as Muricauda algicola comb. nov., Muricauda parva nom. nov. and M. aurantiaca nom. nov., respectively, are proposed, with an emended description of the genus Muricauda.


Assuntos
Ácidos Graxos , Gastrópodes , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
10.
Artigo em Inglês | MEDLINE | ID: mdl-34559623

RESUMO

A Gram-positive, aerobic, heterotrophic, non-endospore-forming, rod-shaped and indole-acetic acid-producing strain, designated NEAU-184T, was isolated from marine sand collected in Sanya, PR China, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NEAU-184T should be assigned to the genus Agromyces and formed a distinct branch with its closest neighbour, Agromyces iriomotensis NBRC 106452T (99.1 %). 2,4-Diaminobutyric acid, d-alanine, d-glutamic acid and glycine were detected in cell-wall hydrolysate and glucose, rhamnose and xylose were detected in whole-cell hydrolysate. The polar lipids were found to contain diphosphatidylglycerol, glycolipid, phosphatidylglycerol and two unidentified lipids. The major menaquinone was MK-12 and the minor menaquinones were MK-13 and MK-11. The predominant fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 71.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, the strain has the ability to produce indole-acetic acid (0.334mg ml-1). Therefore, strain NEAU-184T represents a novel species of the genus Agromyces, for which the name Agromyces mariniharenae sp. nov. is proposed, with strain NEAU-184T (=CGMCC 4.7505T=JCM 32546T) as the type strain.


Assuntos
Ácidos Graxos , Areia , Acetatos , Actinobacteria , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Indóis , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
11.
Artigo em Inglês | MEDLINE | ID: mdl-34559624

RESUMO

A yellow bacterial strain, designated LRZ-2T, was isolated from High Arctic tundra near the settlement Ny-Ålesund in the Svalbard Archipelago, Norway. The cells were Gram-stain-positive, aerobic and non-sporulating. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain LRZ-2T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Luteimicrobium, with 16S rRNA gene sequence similarity of 95.3-96.9 %. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain LRZ-2T and its closely related strains were 77.4-74.3 % and 21.4-19.6 %, respectively. The DNA G+C content was 72.4 mol%. The peptidoglycan type of the isolate was A4ß with an interpeptide bridge comprising l-ornithine and d-glutamic acid. The predominant menaquinone was MK-9 (H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0, anteiso-C15 : 1 A, anteiso-C17 : 0 and iso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylinositol dimannoside, unidentified phosphoglycolipid, four unidentified phospholipids and two unidentified polar lipids. Strain LRZ-2T showed a 16S rRNA gene signature pattern consisting of nucleotides at positions 120 (A), 131-231 (C-G), 196 (C), 342-347 (C-G), 444-490 (A-U), 580-761 (C-G), 602-636 (C-G), 670-736 (A-U), 822-878 (G-C), 823-877 (G-C), 826-874 (C-G), 827 (U), 843 (C), 950-1231 (U-A), 1047-1210 (G-C), 1109 (C), 1145 (G), 1309-1328 (G-C), 1361 (G) and 1383 (C), which clearly distinguished it from all genera previously reported in the suborder Micrococcineae. On the basis of the phylogenetic, phenotypic and chemotaxonomic data, strain LRZ-2T is considered to represent a novel species of a new genus, for which the name Pengzhenrongella sicca gen. nov., sp. nov. is proposed. The type strain of Pengzhenrongella sicca is LRZ-2T (=CCTCC AB 2012163T=DSM 100332T).


Assuntos
Ácidos Graxos , Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tundra , Vitamina K 2
12.
Artigo em Inglês | MEDLINE | ID: mdl-34550061

RESUMO

Endophytic actinobacterial strain 3R004T was isolated from a root of Justicia subcoriacea collected in Thailand. In this report, the taxonomic position of this strain is described using a polyphasic approach. Based on the morphological characteristics and chemical composition of its cells, strain 3R004T was identified as a member of the genus Streptomyces. It produced a long chain of cylindrical spores on aerial mycelia. ll-Diaminopimelic acid was detected in the cell wall peptidoglycan. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0 were detected as the major cellular fatty acids. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and one unidentified lipid. Strain 3R004T showed the highest 16S rRNA gene similarity of 99.45 % to Streptomyces cyaneochromogenes MK-45T. The phylogenomic results indicated that strain 3R004T was close to Streptomyces aquilus GGCR-6T and Streptomyces antibioticus DSM 40234T. The DNA-DNA hybridization and average nucleotide identity values among strain 3R004T and closely related Streptomyces species were 35.5-63.1 % and 82.7-94.3 %, respectively. The type strain produced actinomycin D antibiotic as the major secondary metabolite. The maximum productivity of the actinomycin D (378 mg l-1) was observed when the strain was grown in 301 broth at 30 °C, 180 r.p.m. for 12 days. On the basis of phenotypic and genotypic evidence, strain 3R004T represents a novel species of the genus Streptomyces, for which the name Streptomyces justiciae is proposed. The type strain is 3R004T (=LMG 32138T=TBRC 13128T=NBRC 115065T).


Assuntos
Justicia, Planta , Streptomyces , Antibacterianos , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/genética , Vitamina K 2
13.
Nat Commun ; 12(1): 5236, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34475399

RESUMO

New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme.


Assuntos
Grupo dos Citocromos b/química , Grupo dos Citocromos d/química , Complexo de Proteínas da Cadeia de Transporte de Elétrons/química , Mycobacterium tuberculosis/enzimologia , Proteínas de Bactérias/química , Sítios de Ligação , Microscopia Crioeletrônica , Simulação de Dinâmica Molecular , Oxirredutases/química , Conformação Proteica , Subunidades Proteicas , Vitamina K 2/análogos & derivados , Vitamina K 2/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-34542390

RESUMO

A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1T (98.9 %), Flavobacterium sharifuzzamanii A7.6T (98.6 %), Flavobacterium zhairuonense A5.7T (98.3 %) and Flavobacterium anhuiense D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16  : 1 ω6c and/or C16  :  1 ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.


Assuntos
Flavobacterium , Tagetes , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/genética , Humanos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ureia , Vitamina K 2
15.
Artigo em Inglês | MEDLINE | ID: mdl-34542393

RESUMO

An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces of a 2-week-old piglet raised at the National Institute of Animal Science in Wanju, Republic of Korea. Growth of strain AGMB03916T occurred at 30-45 °C (optimum, 37 °C), at pH 6-9 (optimum, pH 8) and in the presence of 0.5-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence analyses, strain AGMB03916T was closely related to two validly published species of the genus Phocaeicola, Phocaeicola plebeius and Phocaeicola coprocola. The 16S rRNA gene sequence similarity of strain AGMB03916T compared to P. plebeius M12T (=KCTC 5793T) and P. coprocola M16T (=KCTC 5443T) were 96.3 and 95.0 %, respectively. The genomic DNA G+C content of strain AGMB03916T was 46.4 mol%. The average nucleotide identity values between strain AGMB03916T and the reference strains were 74.9-78.5 %. Cells were able to utilize d-glucose, lactose, sucrose, maltose, salicin, aesculin hydrolysis, cellobiose and raffinose. The major end product of metabolism was acetate. The major cellular fatty acids (>10 %) of the isolate were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, C16 : 0 3-OH and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA). On the basis of the genotypic, biochemical, chemotaxonomic, phenotypic and phylogenetic data, strain AGMB03916T represents a novel species of the genus Phocaeicola, for which the name Phocaeicola faecicola sp. nov. is proposed. The type strain is AGMB03916T (=KCTC 25014T=GDMCC 1.2574T).


Assuntos
Ácidos Graxos , Fosfolipídeos , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suínos , Vitamina K 2
16.
Arch Microbiol ; 203(8): 5249-5255, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34373934

RESUMO

A Gram-stain-positive, aerobic, nonmotile actinobacterium, designated strain YIM 93776T, was isolated from a saline sediment sample collected from Aiding Lake in Xinjiang Uygur Autonomous Region, Northwest China. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain YIM 93776T was affiliated to the genus Glycomyces and was closely related to Glycomyces albus TRM 49136T (97.6% sequence similarity), Glycomyces lacisalsi XHU 5089T (97.0%) and Glycomyces anabasis EGI 6500139T (96.2%). The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates sugars were galactose, mannose, arabinase, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-10 (H4). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two phosphatidylglyceride, two unidentified phospholipids and two unidentified polar lipids were detected in the polar lipid extracts. Major fatty acids were anteiso-C17:0, iso-C15:0, iso-C16:0, anteiso-C15:0 and anteiso C17:1 A. The draft genome sequence of strain YIM 93776T was 5.37 Mbp in size with 69.5% DNA G + C content. The dDDH and ANI values between strain YIM 93776T and related neighbours were 25.0-34.3% and 77.3-79.8%, respectively. On the basis of morphological, chemotaxonomic and phylogenetic evidence, strain YIM 93776T; therefore, represents a novel species, for which the name Glycomyces salinus sp. nov. is proposed. The type strain is YIM 93776T (= KCTC 49430T = CGMCC 4.7685T).


Assuntos
Actinobacteria , Actinobacteria/genética , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ecossistema , Ácidos Graxos/análise , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
17.
Arch Microbiol ; 203(9): 5363-5371, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34386827

RESUMO

A novel mycelium-forming actinomycete strain, designated YIM S01255T were isolated from a salt lake. Optimal growth occurred in the presence of 0-5.0% (w/v) NaCl, at pH 7.0-8.0, and at 37 °C. Strain YIM S01255T contained meso-diaminopimelic acid as the diagnostic diamino acid, and glucose, galactose and arabinose as the whole-cell sugars. The major fatty acid (> 5.0%) were iso-C16:0, iso-C16:1H and iso-C15:0. The major menaquinone were MK-9(H4) and MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylinositolmannoside and phosphatidylinositol. The DNA G + C content was 70.7 mol%. The 16S rRNA gene sequence of the strain showed high similarity to members of genera in the family Pseudonocardiaceae with values less than 95.8%, and most closely related to the genus Amycolatopsis. Both of phylogenetic analysis based on 16S rRNA gene sequences and the up-to-date bacterial genome sequences analysis revealed that strains YIM S01255T and Prauserella shujinwangii XJ46T formed a distinct monophyletic clade and was separated from the other members within the family Pseudonocardiaceae. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) between the two strains were 81.0% and 40.6%, respectively. The distinctive polyphasic evidences differentiated YIM S01255T from members of the family Pseudonocardiaceae, so strain YIM S01255T is considered to represent a novel species of a novel genus of the family Pseudonocardiaceae, for which the name Qaidamihabitans albus gen. nov., sp. nov. is proposed. The type strain of genus Qaidamihabitans is YIM S01255T (= KCTC 49476T = CGMCC 4.7684T). Moreover, Prauserella shujinwangii is also proposed to being transferred into the genus Qaidamihabitans as Qaidamihabitans shujinwangii comb. nov. (type strain XJ46T = CGMCC 4.7125T = JCM 19736T).


Assuntos
Ácidos Graxos , Fosfolipídeos , Actinobacteria , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
18.
Arch Microbiol ; 203(9): 5381-5386, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34392381

RESUMO

A Gram-stain-negative, rod-shaped (0.3-0.6 × 0.9-2.2 µm), facultatively aerobic, non-motile and yellow-coloured bacterium, designated strain F6397T, was isolated from a marine sediment in Weihai, PR China. Growth of strain F6397T occurred at 4-37 °C (optimum, 30-33 °C), pH 6.0-9.0 (optimum, 7.5) and in the presence of 1-12% (optimum, 3.0%) (w/v) NaCl. Strain F6397T showed oxidase- and catalase-positive activities. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain was assigned to the genus Winogradskyella. Strain F6397T exhibited 95.5-98.1% sequence similarities to recognized species of the genus Winogradskyella. The average nucleotide identity (ANI) scores with Winogradskyella ludwigii HL116T, Winogradskyella litoriviva KMM 6491 T and Winogradskyella thalassocola KMM 3907 T were 80.1, 78.9 and 82.6%, respectively. The digital DNA-DNA hybridization (dDDH) scores were 23.5, 22.9 and 25.7%, respectively. The genomic DNA G + C content was 33.5 mol%. Strain F6397T contained iso-C15:0, iso-C15:1G, iso-C15:0 3-OH and iso-C17:0 3-OH as the predominant fatty acid and MK-6 as the predominant menaquinone. The polar lipid profiles contained phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. On the basis of the evidence presented in this study, strain F6397T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella marina sp. nov. is proposed. The type strain is F6397T (= KCTC 82422 T = MCCC 1H00438T).


Assuntos
Sedimentos Geológicos , Água do Mar , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2
19.
Artigo em Inglês | MEDLINE | ID: mdl-34346863

RESUMO

Two Gram-stain-negative, motile, facultatively anaerobic, rod-shaped strains, FJAT-53720T and FJAT-53726, were isolated from rhizosphere sediment of plant Cyperus malaccensis. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that strains FJAT-53720T and FJAT-53726 were affiliated to the genus Shewanella (forming an independent cluster) with the highest sequence similarity to the type strain of Shewanella algae. Optimum growth of both strains was observed at 30 °C and pH 7. The respiratory quinones were Q-7, Q-8 and MK-7. The polar lipid profile included phosphatidylmethyl ethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminophospholipid and four unknown phospholipids. The major fatty acids of strains FJAT-53720T and FJAT-53726 were iso-C15:0, C17 : 1 ω8c and summed feature 3. The genomic DNA G+C content of strain FJAT-53720T was 55.6 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between FJAT-53720T and FJAT-53726 were 97.4 and 77.9 %, confirming that they were similar species and hence FJAT-53720T was selected for further analysis. The ANI and dDDH values between FJAT-53720T and other members of the genus Shewanella were below the cut-off level (95-96 %; 70 %) for species delineation. Based on the above results, FJAT-53720T represents a novel species of the genus Shewanella, for which the name Shewanella cyperi sp. nov. is proposed. The type strain is FJAT-53720T (=KCTC 82444T=GDMCC 1.2207T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rizosfera , Shewanella , Anaerobiose , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Cyperus/microbiologia , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Shewanella/classificação , Shewanella/isolamento & purificação , Vitamina K 2/química , Áreas Alagadas
20.
Artigo em Inglês | MEDLINE | ID: mdl-34382925

RESUMO

A novel Gram-stain-negative strain, WQ 117T, isolated from the faeces of Rhinopithecus bieti collected at Yunnan Snub-nosed Monkey National Park, Yunnan province, PR China, was subjected to a polyphasic taxonomic study. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate represented a member of the genus Faecalibacter, sharing 97.64 % sequence similarity with the type strain Faecalibacter macacae YIM 102668T. The G+C content of the genomic DNA of WQ117T was 30.5 mol%. The predominant isoprenoid quinone was MK-6. The major cellular fatty acids was iso-C15 : 0. The whole genome average nucleotide identity (gANI) values and the digital DNA-DNA hybridization values between WQ 117T and YIM 102668T were 79.66 % and 22.20 %, respectively. Growth occurred at 0-50 °C (optimally at 28-35 °C), pH 7.0-9.0 (optimally at pH 8.0) and with 0-2 % (w/v) NaCl (optimally without NaCl). On the basis of the taxonomic evidence, a novel species, Faecalibacter rhinopitheci sp. nov., is proposed. The type strain is WQ 117T (=KCTC 82394T=CCTCC AA 2020027T).


Assuntos
Bacteroidetes/classificação , Filogenia , Presbytini , Animais , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Hibridização de Ácido Nucleico , Presbytini/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
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