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1.
Aquat Toxicol ; 227: 105591, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32853898

RESUMO

The effects of allelopathy and the potential harm of several isolated allelochemicals have been studied in detail. Microorganisms in the phycosphere play an important role in algal growth, decay and nutrient cycling. However, it is unknown and often neglected whether allelochemicals affect the phycosphere. The present study selected a phenolic acid protocatechuic acid (PA) - previously shown to be an allelochemical. We studied PA at a half maximal effective concentration of 0.20 mM (30 mg L-1) against Scrippsiella trochoidea to assess the effect of PA on its phycosphere in an acute time period (48 h). The results showed that: 1) OTUs (operational taxonomic units) in the treatment groups (31.4 ± 0.55) exceeded those of the control groups (28.2 ± 1.30) and the Shannon and Simpson indices were lower than the control groups (3.31 ± 0.08 and 0.84 ± 0.02, 3.45 ± 0.09 and 0.88 ± 0.01); 2) Gammaproteobacteria predominated in the treatment groups (44.71 ± 2.13 %) while Alphaproteobacteria dominated in the controls (67.17 ± 3.87 %); 3) Gammaproteobacteria and Alphaproteobacteria were important biomarkers in the treatment and control groups respectively (LDA > 4.0). PA improved the relative abundance of Alteromonas significantly and decreased the one of Rhodobacteraceae. PICRUSt analysis showed that the decrease of Rhodobacterceae was closely related with the decline of most functional genes in metabolism such as amino acid, carbohydrate, xenobiotics, cofactors and vitamins metabolism after PA-treated.


Assuntos
Alelopatia/efeitos dos fármacos , Dinoflagelados/efeitos dos fármacos , Proliferação Nociva de Algas/efeitos dos fármacos , Hidroxibenzoatos/farmacologia , Microbiota/efeitos dos fármacos , Feromônios/farmacologia , Alelopatia/genética , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Dinoflagelados/genética , Dinoflagelados/crescimento & desenvolvimento , Microbiota/genética , Proteobactérias/efeitos dos fármacos , Proteobactérias/genética , Proteobactérias/isolamento & purificação
2.
Int J Syst Evol Microbiol ; 70(8): 4616-4622, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32667873

RESUMO

Two Gram-stain-negative, facultative anaerobic and non-motile bacteria, strains R11T and S1162T, were isolated from soil in the Republic of Korea. Both strains were catalase- and oxidase-positive and contained menaquinone-7 as the major isoprenoid quinone. Strain R11T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, C16:0 and iso-C17:0 3-OH as major fatty acids and phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified aminolipid as major polar lipids; while strain S1162T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, iso-C17:0 3-OH, C16:0 and summed feature 9 (10-methyl C16:0 and/or iso-C17:1 ω9c) as major fatty acids and phosphatidylethanolamine and an unidentified aminophospholipid as major polar lipids. The DNA G+C contents of strains R11T and S1162T calculated from their whole genomes were 42.7 and 42.9 mol%, respectively. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain R11T formed a phylogenetic lineage with Mucilaginibacter jinjuensis YC7004T and strain S1162T formed a distinct phyletic lineage from closely related type strains within the genus Mucilaginibacter. Strains R11T and S1162T were most closely related to M. jinjuensis YC7004T and Mucilaginibacter panaciglaebae BXN5-31T with 97.78 and 97.23% 16S rRNA gene sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and molecular analysis, strains R11T and S1162T represent two novel species of the genus Mucilaginibacter, for which the names Mucilaginibacter agri sp. nov. and Mucilaginibacter humi sp. nov. are proposed, respectively. The type strains of M. agri and M. humi are R11T (=KACC 21228T=JCM 33472T) and S1162T (=KACC 21669T=JCM 33916T), respectively.


Assuntos
Bacteroidetes/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
3.
Int J Syst Evol Microbiol ; 70(8): 4725-4729, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32687462

RESUMO

An anaerobic bacterial strain, named TLL-A4T, was isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of the 16S rRNA gene indicated that the strain belongs to the phylum Bacteroidetes and, more specifically, to the recently proposed Muribaculaceae (also known as S24-7 clade or Candidatus Homeothermaceae). Strain TLL-A4T's 16S rRNA gene shared 92.8 % sequence identity with the type strain of the only published species of the genus Muribaculum, Muribaculum intestinale DSM 28989T. Genome-sequencing of TLL-A4T was performed to compare average amino acid identity (AAI) value and percentage of conserved proteins (POCP) between both strains. The AAI analysis revealed that strain TLL-A4T had high identity (69.8 %) with M. intestinale DSM 28989T, while the POCP was 56 %. These values indicate that strain TLL-A4T could be considered a member of the genus Muribaculum but not belonging to the species M. intestinale. Quinone analysis indicated MK10 (63 %) and MK11 (32 %) as major quinones in the membrane, while MK9 was only present as a minor component (5 %). The main cellular fatty acid was anteiso-C15 : 0 (42.8 %); summed feature 11 (17.5 %), C15 : 0 iso (13.4 %), C18 : 1 ω9c (5.6 %), C16.0 3-OH (4.5 %) and C15 : 0 (4.2 %) were detected in minor amounts. Analysis of enzyme activities using the API 32A and API 20A kits indicated major differences between strain TLL-A4T and Muribaculum intestinale DSM 28989T. Based on genotypic, phylogenetic and phenotypic differences, strain TLL-A4T is considered to represent a novel species of the genus Muribaculum, for which the name Muribaculum gordoncarteri sp. nov. is proposed. The type strain is TLL-A4T (=DSM 108194T=KCTC 15770T).


Assuntos
Bacteroidetes/classificação , Fezes/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Camundongos , Camundongos Endogâmicos C57BL , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
4.
Int J Syst Evol Microbiol ; 70(8): 4808-4815, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32701428

RESUMO

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, O9T, was isolated from a forest soil sample collected at Dai, Xishuangbanna, Yunnan Province, PR China. Strain O9T grew optimally at pH 7.0, at 28‒30 °C and in the absence of NaCl. 16S rRNA gene sequence analysis placed strain O9T within the genus Chitinophaga of the family Chitinophagaceae, with Chitinophaga terrae KP01T (97.8 %), Chitinophaga jiangningensis JN53T (97.7 %), Chitinophaga niastensis JS16-4T (97.4 %), Chitinophaga qingshengii JN246T (97.3 %) and Chitinophaga dinghuensis DHOC24T (97.3 %) as its closest relatives. Strain O9T hydrolysed casein, gelatin and Tween 80. It could not assimilate l-arabinose, l-rhamnose, sucrose, melibiose, gentiobiose or d-fructose as a carbon source. It was negative for esterase lipase (C8) and ß-glucosidase. Phosphatidylethanolamine was the predominant polar lipid. The major respiratory quinone of strain O9T was MK-7. Its major fatty acids were iso-C15:0 (34.2 %), C16:1 ω5c (20.9 %) and iso-C17:0 3-OH (12.6 %). The genomic DNA G+C content of strain O9T was 49.0 mol% based on total genome calculations. The average nucleotide identity score between the genomic sequence of strain O9T and that of Chitinophaga terrae KP01T was 72.9%. The Genome-to-Genome Distance Calculator showed that DNA‒DNA hybridization values for strain O9T and Chitinophaga terrae KP01T were 13.6, 21.1 and 14.4%, respectively. Based on the polyphasic taxonomic data, strain O9T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga solisilvae sp. nov. is proposed. The type strain is O9T (=CGMCC 1.12462T=KCTC 32404T).


Assuntos
Bacteroidetes/classificação , Florestas , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
5.
Int J Syst Evol Microbiol ; 70(8): 4816-4821, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32706333

RESUMO

A marine bacterial strain, designated GM2-18T, was isolated from mangrove sediment sampled at Luoyang River estuary, Quanzhou, PR China. Cells were Gram-stain-negative, slightly curved long rod-shaped and facultatively anaerobic with no flagellum. Catalase activity was found to be weak-positive and oxidase-positive. It had no ability to degrade or hydrolyse substrates including skimmed milk, cellulose, starch and Tweens (40, 60 and 80). The 16S rRNA gene sequence of strain GM2-18T had maximum similarity values to 'Draconibacterium filum' F2T, Draconibacterium sediminis JN14CK-3T and Draconibacterium orientale FH5T of 98.0, 97.8 and 97.4 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GM2-18T was affiliated to the genus Draconibacterium and formed a clade with an uncultured bacterium clone identified from mangrove environment. Average nucleotide identity values and DNA-DNA hybridization estimates of strain GM2-18T compared to its Draconibacterium relatives strongly supported that it belonged to a new species. The respiratory quinone was menaquinone MK-7. The major fatty acids (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and C17 : 1 ω6c. The polar lipids were phosphatidylethanolamine, a phospholipid and several unidentified lipids. The genomic size of strain GM2-18T was 5.9 Mb and the G+C content was 40.8 mol%. Gene prediction and annotation of strain GM2-18T indicated that there was a nitrogen-fixing gene cluster encoding nitrogenase molybdenum-iron protein and related proteins responsible for nitrogen fixation. Based on the above characteristics, strain GM2-18T represents a novel species within the genus Draconibacterium. Thus, Draconibacterium mangrovi sp. nov. is proposed with type strain GM2-18T (=MCCC 1K04382T=KCTC 72879T), isolated from mangrove sediment.


Assuntos
Bacteroidetes/classificação , Estuários , Sedimentos Geológicos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
PLoS One ; 15(7): e0218636, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32639969

RESUMO

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.


Assuntos
Osso e Ossos/microbiologia , Microbiota , Antropologia , Ascomicetos/genética , Ascomicetos/isolamento & purificação , Autopsia , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , DNA/química , DNA/metabolismo , Humanos , Masculino , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Dente/microbiologia
7.
Int J Syst Evol Microbiol ; 70(6): 3639-3646, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32501783

RESUMO

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191FT, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191FT and Pseudoflavitalea rhizosphaerae T16R-265T and Pseudobacter ginsenosidimutans Gsoil 221T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191FT was MK-7 and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191FT calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191FT represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191FT (=DSM 104999T=ATCC BAA-2857T = CCUG 72691T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.


Assuntos
Bacteroidetes/classificação , Neoplasias Peritoneais/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Baltimore , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Humanos , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
8.
Int J Syst Evol Microbiol ; 70(8): 4502-4507, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32598276

RESUMO

An alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7T, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7T were 0.4-0.6 µm wide and 1.0-8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7T could grow at 10-37 °C (optimum, 25-28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0.5-6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7T belonged to the genus Mangrovibacterium of the family Prolixibacteraceae. It showed the highest similarity to Mangrovibacterium diazotrophicum JCM 19152T (96.8 %), followed by Mangrovibacterium marinum KCTC 42253T (96.1%). The values of average nucleotide identity and DNA-DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7T with M. diazotrophicum JCM 19152T and M. marinum KCTC 42253T, respectively. The major respiratory quinone of strain BM_7T was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C15 : 0, anteiso-C15 : 0, C15 : 1 ω6c, iso-C17 : 0 3-OH, C17 : 1 ω6c, C17 : 0 3-OH and C17 : 0. The genome size of strain BM_7T is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7T was considered to represent a novel species of the genus Mangrovibacterium, and the name Mangrovibacterium lignilyticum sp. nov. is proposed. The type strain is BM_7T (=MCCC 1A15882T=KCTC 72696T).


Assuntos
Bacteroidetes/classificação , Estuários , Sedimentos Geológicos/microbiologia , Lignina/metabolismo , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
9.
Int J Syst Evol Microbiol ; 70(6): 3859-3864, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32501195

RESUMO

A novel bacterial strain, designated ysch24T, was isolated from a forest soil sample collected from the Cat Tien National Park, southern Vietnam. Cells were Gram-stain-negative, aerobic, gliding, filamentous or rod-shaped. The results of 16S rRNA gene analyses revealed that strain ysch24T belongs to the genus Chitinophaga, and was most closely related to Chitinophaga silvisoli GDMCC 1.1411T (97.4 %), followed by Chitinophaga oryziterrae JCM 16595T (97.3 %) and Chitinophaga sancti NBRC 15057T (96.9 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain ysch24T and closely related type strains were 72.0-74.0 % and 19.1-19.4 %, respectively. Major fatty acids were iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH and the predominant respiratory quinone was menaquinone 7. Polar lipids consisted of phosphatidylethanolamine, four unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. The genomic DNA G+C content was 45.6 mol%. The study clearly showed that strain ysch24T should represent a novel species of the genus Chitinophaga, for which the name Chitinophaga tropicalis sp. nov. is proposed. The type strain is ysch24T (=GDMCC 1.1355T=KACC 21527T).


Assuntos
Bacteroidetes/classificação , Florestas , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vietnã , Vitamina K 2/análogos & derivados , Vitamina K 2/química
10.
Int J Syst Evol Microbiol ; 70(6): 3749-3754, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32519941

RESUMO

Three strains representing the previously uncultured human oral Tannerella taxon HMT-286 were recently isolated from the subgingival plaque of a patient with chronic periodontitis. The phenotypic and genetic features of strain SP18_26T were compared to those of the type species of Tannerella, Tannerella forsythia. A genome size of 2.97 Mbp (G+C content 56.5 mol%) was previously reported for SP18_26T, compared to a size of 3.28 Mbp (47.1 mol%) in T. forsythia ATCC 43037T. 16S rRNA gene sequence comparisons also revealed 94.3 % sequence identity with T. forsythia ATCC 43037T. Growth was stimulated by supplementation of media with N-acetyl muramic acid, as seen with T. forsythia, but the cells displayed a distinctive snake-like morphology. Fatty acid methyl ester analysis revealed a profile differing from T. forsythia, chiefly in the amount of 3-OH-16 : 0 (four-fold lower in SP18_26T). Overall, metabolic enzyme activity also differed from T. forsythia, with enzyme activity for indole present, but the complement of glycoside hydrolase enzyme activity was smaller than T. forsythia, for example, lacking sialidase and N-acetyl-ß-glucosaminidase - evidence backed up by analysis of its gene content. On the basis of these results, a new species Tannerella serpentiformis is proposed for which the type strain is SP18_26T (=DSM 102894T=JCM 31303T).


Assuntos
Bacteroidetes/classificação , Boca/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Feminino , Humanos , Londres , Ácidos Murâmicos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Int J Syst Evol Microbiol ; 70(7): 4139-4144, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32501784

RESUMO

Strains of Echinicola, thought to play vital roles in the environment for their high enzyme production capacity during decomposition of polysaccharides, are ubiquitous in hypersaline environments. A Gram-negative, non-spore forming, gliding, aerobic bacterial strain, designated LN3S3T, was isolated from alkaline saline soil sampled in Tumd Right Banner, Inner Mongolia, northern PR China. Strain LN3S3T grew at 10-40 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 8.0) and with 0-12.5 % NaCl (optimum, 2.0 %). A phylogenetic tree based on the 16S rRNA gene sequences showed that strain LN3S3T clustered with Echinicola rosea JL3085T and Echinicola strongylocentroti MEBiC08714T, sharing 97.0, 96.7 and <96.50 % of 16S rRNA gene sequence similarities to E. rosea JL3085T, E. strongylocentroti MEBiC08714T and all other type strains. MK-7 was the major respiratory quinone, while phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminophospholipid, an unidentified lipid and two unidentified aminolipids were the major polar lipids. Its major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The genome consisted of a circular 5 550 304 bp long chromosome with a DNA G+C content of 44.0 mol%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values of strain LN3S3T to E. rosea JL3085T and E. strongylocentroti MEBiC08714T were 82.5 and 81.5 %, 87.5 and 86.0 %, and 39.1 and 35.1 %, respectively. Based on physiological, genotypic and phylogenetic analyses, strain LN3S3T could be discriminated from its phylogenetic relatives. Echinicola soli sp. nov. is therefore proposed with strain LN3S3T (=CGMCC 1.17081T=KCTC 72458T) as the type strain.


Assuntos
Álcalis , Bacteroidetes/classificação , Filogenia , Salinidade , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química
12.
Int J Syst Evol Microbiol ; 70(7): 4186-4192, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32538740

RESUMO

A Gram-stain-negative, facultative anaerobic, red-pigmented, rod-shaped and non-motile strain (RC1_OXG_1FT) was isolated from deep sea water of the Indian Ocean. It was able to grow at pH 5-8 (optimum, pH 7), at 5-37 °C (optimum, 30 °C), and at salinity (% NaCl, w/v) of 0.5-5 % (optimum, 1-2 %). Catalase- and oxidase-positive. It had highest 16S rRNA gene similarity (96.7 %) to 'Sunxiuqinia dokdonensis' DH1T, followed by Sunxiuqinia faeciviva JAM-BA0302T (96.6 %), Sunxiuqinia elliptica CGMCC 1.9156T (96.2 %), Sunxiuqinia rutila HG677T (96.0 %) and species (less than 92.3 %) of other genera. It belongs to the genus Sunxiuqinia within the phylum Bacteroidetes, based on the phylogenetic analysis. The results of digital DNA-DNA hybridization and average nucleotide identity analyses indicated that the strain belonged to a novel species. Its genome size is 5,250, 885 bp, with DNA G+C content of 40.5 mol%. Genome analysis revealed that the strain possessed many genes involved in polysaccharide degradation, especially hemicellulose degradation, indicating that the strain could maintain its normal metabolism by using recalcitrant organic matter in the oligotrophic deep sea environment. Its principal fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the major polar lipids were phosphatidylethanolamine, two unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. The isoprenoid quinone was MK-7. Based on the phenotypic, chemotaxonomic and genotypic data, the strain represents a novel species within the genus Sunxiuqinia, for which the name Sunxiuqinia indica sp. nov. is proposed. The type strain is RC1_OXG_1FT (=MCCC 1A13858T=KCTC 62805T).


Assuntos
Bacteroidetes/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Oceano Índico , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
Int J Syst Evol Microbiol ; 70(7): 4245-4249, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32568032

RESUMO

A Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10-45 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0) and with 0.5-9.0 % (w/v) NaCl (optimum, 2-5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).


Assuntos
Bacteroidetes/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
14.
World J Microbiol Biotechnol ; 36(6): 90, 2020 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-32524202

RESUMO

A chitinolytic bacterium Chitinophaga sp. S167 producing extracellular chitinases was isolated from a soil sample in India. The extracellular chitinases produced by S167 were concentrated by ammonium sulphate precipitation (AS70) and seven bands corresponding to chitinases were observed by zymography. Optimum temperature and pH of AS70 were between 40 and 45 °C and pH 6.0 respectively with high stability at 20-40 °C and pH 5-7. AS70 inhibited the growth of Fusarium oxysporum, Alternaria alternata and Cladosporium sp. in vitro. The culture conditions for the high level production of extracellular chitinases were optimized resulting in 48-folds higher chitinase production. As the combination of chitinases could be more potent in biocontrol of plant diseases, it was checked if AS70 could control postharvest fungal infection caused by Fusarium oxysporum on tomatoes. AS70 treated tomatoes showed significant lower incidence of infection (11%) by F. oxysporum as compared with 100% in the control at 5 days post inoculation. Further, AS70 caused significant mortality in second stage juveniles of root knot nematode, Meloidogyne incognita, a major agriculture pest responsible for economic losses in agriculture. This study highlights the antifungal and nematicidal activity of chitinases produced by Chitinophaga sp. S167. To the best of our knowledge, this is the first report of the biocontrol potential of the chitinases produced by Chitinophaga sp.


Assuntos
Antifúngicos/farmacologia , Bacteroidetes/isolamento & purificação , Quitinases/farmacologia , Doenças das Plantas/prevenção & controle , Alternaria/efeitos dos fármacos , Sulfato de Amônio , Bacteroidetes/enzimologia , Precipitação Química , Quitinases/metabolismo , Cladosporium/efeitos dos fármacos , Estabilidade Enzimática , Fusarium/efeitos dos fármacos , Concentração de Íons de Hidrogênio , Microbiologia do Solo , Temperatura
15.
Int J Syst Evol Microbiol ; 70(6): 3785-3793, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32463784

RESUMO

Two novel strains, designated SYSU L10167T and SYSU L10180T, were isolated from sediment sampled at Dabancheng saline lake in Xinjiang, PR China. A polyphasic approach was used to clarify the taxonomic positions of the two strains. Cells of the isolates were curved ring-like, horseshoe-shaped or rod-shaped, non-motile and non-spore-forming. Cells were Gram-stain-negative, aerobic, heterotrophic and rose-pigmented. The phylogenetic trees based on 16S rRNA gene sequences showed that strains SYSU L10167T and SYSU L10180T formed a distinct lineage within the genus Cyclobacterium. Strains SYSU L10167T and SYSU L10180T showed highest similarities to Cyclobacterium jeungdonense KCTC 23150T (98.0 and 97.4%, respectively). Results of genomic analyses (including average nucleotide identity, digital DNA-DNA hybridization and the marker gene tree) and pan-genome analysis further confirmed that strains SYSU L10167T and SYSU L10180T were separate from each other and other species of the genus Cyclobacterium. The draft genomes of the isolates had sizes of 5.5-5.7 Mb and reflected their major physiological capabilities. Based on phenotypic, physiological, chemotaxonomic and genotypic characterization, we propose that the isolates represent two novel species, for which the names Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov. are proposed. The type strains of the species are SYSU L10167T (=KCTC 72390T=CGMCC 1.17521T) and SYSU L10180T (=KCTC 72391T=CGMCC 1.17278T).


Assuntos
Bacteroidetes/classificação , Sedimentos Geológicos/microbiologia , Lagos/microbiologia , Filogenia , Águas Salinas , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
16.
Int J Syst Evol Microbiol ; 70(3): 1758-1768, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32228771

RESUMO

We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15T of 97.42 %. Their predominant fatty acid is iso-C15 : 0 (73.8 % for strain BD 01T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01T was chosen as type strain of C. vietnamensis sp. nov.


Assuntos
Bacteroidetes/classificação , Farmacorresistência Bacteriana Múltipla , Filogenia , Bacteriemia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Diabetes Mellitus Tipo 2 , Ácidos Graxos/química , Humanos , Abscesso Pulmonar/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vietnã
17.
Int J Syst Evol Microbiol ; 70(5): 3105-3110, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32250242

RESUMO

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae, and shared 91.6-99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA-DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae (Muribaculum intestinale DSM 28989T , Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella, for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).


Assuntos
Bacteroidetes/classificação , Fezes/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Camundongos , Camundongos Endogâmicos C57BL , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
18.
Int J Syst Evol Microbiol ; 70(4): 2766-2781, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32238229

RESUMO

Two Gram-stain-negative, strictly aerobic, marine bacteria, designated as strains RKSG066T and RKSG123T, were isolated from a sponge Aplysina fistularis collected at a depth of 15 m off the west coast of San Salvador, The Bahamas. Investigation of nearly full-length 16S rRNA gene and whole genome-based phylogenies revealed that both strains belong to the order Cytophagales within the class Cytophagia and phylum Bacteroidetes. Strain RKSG066T formed a monophyletic clade with described members of the genus Fulvivirga, while strain RKSG123T formed a well-supported paraphyletic branch apart from this and other related genera within the family Flammeovirgaceae. For both RKSG066T and RKSG123T, optimal growth parameters were 30-37 °C, pH 7-8 and 2-3 % (w/v) NaCl; cells were catalase- and oxidase-positive, and flexirubin-type pigments were absent. The predominant fatty acids were iso-C15 : 0, C16 : 0, C18 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C18 : 1 ω9c and iso-C15 : 1 G for RKSG066T, and iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0, C16 : 0 3-OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) for RKSG123T. Menaquinone-7 was the major respiratory quinone for both strains. The DNA G+C contents of RKSG066T and RKSG123T were 39.5 and 36.7 mol%, respectively. On the basis of phylogenetic distinctiveness and polyphasic analysis, the type strain RKSG066T (=TSD-73T=LMG 29870T) is proposed to represent a novel species of the genus Fulvivirga, for which the name Fulvivirga aurantia sp. nov. is proposed. The type strain RKSG123T (=TSD-75T=LMG 30075T) is proposed to represent the type species of a novel genus and species with the proposed name Xanthovirga aplysinae gen. nov., sp. nov. Additionally, the genus Fulvivirga is emended to include strains of orange-pigmented colonies that contain the predominant cellular fatty acids C16 : 0, C18 : 0, C16  :  1 ω5c and C18  :  1 ω9c.


Assuntos
Bacteroidetes/classificação , Filogenia , Poríferos/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Bahamas , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
19.
Exp Appl Acarol ; 80(3): 363-380, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32072355

RESUMO

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.


Assuntos
Bacteroidetes/isolamento & purificação , Dermatophagoides farinae/microbiologia , Genoma Bacteriano , Animais , China , Dermatophagoides pteronyssinus/microbiologia , Europa (Continente) , Feminino , Masculino , Microbiota , Simbiose , Estados Unidos , Sequenciamento Completo do Genoma
20.
PLoS One ; 15(2): e0228133, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32023276

RESUMO

The neonatal period, during which the initial gut microbiota is acquired, is a critical phase. The healthy development of the infant's microbiome can be interrupted by external perturbations, like antibiotics, which are associated with profound effects on the gut microbiome and various disorders later in life. The aim of this study was to investigate the development of intestinal microbiota and the effect of antibiotic exposure during the first three months of life in term infants. Fecal samples were collected from healthy infants and infants who received antibiotics in the first week of life at one week, one month, and three months after birth. Microbial composition was analyzed using IS-pro and compared between antibiotics-treated and untreated infants. In total, 98 infants, divided into four groups based on feeding type and delivery mode, were analyzed. At one week of age, samples clustered into two distinct groups, which were termed "settler types", based on their Bacteroidetes abundance. Caesarean-born infants belonged to the low-Bacteroidetes settler type, but vaginally-born infants were divided between the two groups. The antibiotics effect was assessed within a subgroup of 45 infants, vaginally-born and exclusively breastfed, to minimize the effect of other confounders. Antibiotics administration resulted in lower Bacteroidetes diversity and/or a delay in Bacteroidetes colonization, which persisted for three months, and in a differential development of the microbiota. Antibiotics resulted in pronounced effects on the Bacteroidetes composition and dynamics. Finally, we hypothesize that stratification of children's cohorts based on settler types may reveal group effects that might otherwise be masked.


Assuntos
Antibacterianos/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Fezes/microbiologia , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Análise de Componente Principal , RNA Ribossômico 16S/isolamento & purificação , RNA Ribossômico 16S/metabolismo
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