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1.
Syst Appl Microbiol ; 43(1): 126051, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892483

RESUMO

A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H4), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6T and M. italicus BC 501T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6T (=DSM 107535T =PCM 3004T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.


Assuntos
Actinobacteria/classificação , Actinobacteria/fisiologia , Clima Desértico , Microbiologia do Solo , Actinobacteria/química , Actinobacteria/citologia , Altitude , DNA Bacteriano/genética , Ácidos Graxos/análise , Genoma Bacteriano/genética , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Estresse Fisiológico/genética , Vitamina K 2/química
2.
mSphere ; 5(1)2020 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-31996419

RESUMO

We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.


Assuntos
Actinobacteria/classificação , Bacteroidetes/classificação , Biodiversidade , Cianobactérias/classificação , Proteobactérias/classificação , Microbiologia da Água , Ásia , DNA Bacteriano/genética , Europa (Continente) , Água Doce/microbiologia , Aprendizado de Máquina , Microbiota , Filogeografia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Navios , Estados Unidos
3.
Gene ; 733: 144379, 2020 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-31972312

RESUMO

An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.


Assuntos
Actinobacteria/efeitos dos fármacos , Actinobacteria/genética , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Genoma Bacteriano , Metais Pesados/farmacologia , Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Mineração , Família Multigênica , Filogenia , Microbiologia do Solo
4.
Int J Syst Evol Microbiol ; 70(1): 636-647, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31693475

RESUMO

Five actinobacteria isolates, KC201T, KC401, KC310T, KC712T and 6K102T, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus Nonomuraea. The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus Nonomuraea. Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201T, KC310T, KC712T and 6K102T showed that these strains belonged to novel Nonomuraea species, the names proposed for these taxa are Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov., with the type strains KC310T (=CGMCC 4.7331T =DSM 102919T =KCTC 39774T), KC712T (=CGMCC 4.7334T =DSM 102925T =KCTC 39776), KC201T (=CGMCC 4.7339T =DSM 102917T =KCTC 39781T) and 6K102T (=CGMCC 4.7541T =JCM 32916), respectively.


Assuntos
Actinobacteria/classificação , Clima Desértico , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Turcomenistão , Vitamina K 2/química
5.
Int J Syst Evol Microbiol ; 70(1): 675-679, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31671046

RESUMO

A taxonomic study was performed on strain GCJ02T, which was isolated from forest soil from Baishan City, PR China. The bacterium was Gram-stain-positive, catalase-positive and weakly oxidase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0-6.0 % and at temperatures of 4-26 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that GCJ02T represented a member of the genus Cryobacterium, with the highest sequence similarity to Cryobacterium arcticum SK1T (99.5 %) and Cryobacterium zongtaii TMN-42T (99.5 %), followed by Cryobacterium psychrotolerans CGMCC 1.5382T (97.7 %), and other species of the genus Cryobacterium (96.4-96.9 %). The ANI and the DNA-DNA hybridization estimate values between GCJ02T and all type strains of species of the genus Cryobacterium were 72.5-84.5 % and 19.6-28.7 %, respectively. The principal fatty acids (>10 %) of GCJ02T were anteiso-C15 : 0(53.0 %) and anteiso-C17 : 0 (18.8 %). The G+C content of the chromosomal DNA was 68.4 mol%. The respiratory quinone was determined to be MK-10. Phosphatidylglycerol, diphosphatidylglycerol, glycolipid, and one unidentified phospholipid and three unidentified polar lipid were present. The combined genotypic and phenotypic data indicated that strain GCJ02T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium soli sp. nov. is proposed, with the type strain GCJ02T (=MCCC 1K03549T=JCM 32391T).


Assuntos
Actinobacteria/classificação , Florestas , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
6.
Int J Syst Evol Microbiol ; 70(1): 693-699, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31671049

RESUMO

A Gram-staining-positive, aerobic, rod-shaped, non-spore-forming actinobacterium, designated strain M2KJ-4T, was isolated from a surface-sterilized bark of Melia azedaeach L. collected from Xinpu in Guizhou, PR China and characterized using a polyphasic approach to determine its taxonomic position. M2KJ-4T grew optimally with 1 % (w/v) NaCl at 25 °C and pH 8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on 16S rRNA gene sequence indicated that M2KJ-4Trepresented a member of the genus Aeromicrobium and shared the highest 16S rRNA gene sequence similarity with Aeromicrobium fastidiosum DSM 10552T (Z78209) (98.95 %). The DNA G+C content of M2KJ-4T was 70.6 mol%. The average nucleotide identity value and estimated DDH value between M2KJ-4T and the type strain of A. fastidiosum were 86.1 % and 30.2 %, respectively. The cell-wall peptidoglycan contained ll-diaminopimelic acid and MK-9(H4) was the predominant menaquinone. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids and unidentified lipids. The major fatty acids were C16 : 0, 10-methyl C18 : 0, C16 : 0 2-OH and C18 : 1ω9c. On the basis of the results from phylogenetic, phenotypic and chemotaxonomic analysis, strain M2KJ-4T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium endophyticum sp. nov. is proposed. The type strain is M2KJ-4T (=KCTC 49174T=CGMCC 1.13666T).


Assuntos
Actinobacteria/classificação , Filogenia , Casca de Planta/microbiologia , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Melia , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
Int J Syst Evol Microbiol ; 70(1): 380-387, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31671051

RESUMO

A Gram-strain positive, mycelium-forming actinomycete, YIM 121212T, was isolated from an alkaline soil sample collected in Yunnan province, PR China. Classification using a polyphasic approach indicated that YIM 121212T represents a member of the genus Prauserella, and is closely related to Prauserella coralliicola SCSIO 11529T (99.31 %), Prauserella endophytica SP28S-3T (99.17 %), Prauserella soli 12-833T (97.43 %), Prauserella oleivorans RIPIT (97.03 %), Prauserella marina MS498T (96.74 %), Prauserella rugosa DSM 43194T (96.54 %) and Prauserella muralis 05-Be-005T (95.92 %). Average nucleotide identity values (ANI) of YIM 121212T to P. coralliicola DSM 45821T and P. endophytica CGMCC 4.7182T were 93.1 and 92.8 %, respectively, which were lower than the threshold of 95 %. The digital DNA-DNA hybridization (dDDH) values between YIM 121212T and these two species were 50.8 and 49.9 %, respectively and thus were also well below the cut off value (>70 %) for species delineation. The DNA G+C content of YIM 121212T is 70.8 mol%. Major fatty acids are iso-C16 : 0, iso-C16 : 1H, C16 : 1ω7c/iso-C15 : 0 2OH, C17 : 1ω6c, and C17 : 1ω8c. The predominant menaquinone is MK-9(H4). The polar lipid profile consists of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmethylethanolamine (PME), phosphatidylinositol (PI), and phosphatidylinositol mannoside (PIM). The draft genomes were further analyzed for the presence of secondary metabolite biosynthesis (SMB) gene clusters. On the basis of the above observations, YIM121212T can be distinguished from closely related species belonging to the genus Prauserella. Thus, YIM121212T represents a novel species of the genus Prauserella, for which the name Prauserella flavalba sp. nov. is proposed. The type strain is YIM121212T (=CCTCC AA 2013011T=DSM 45973T).


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , 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
8.
Int J Syst Evol Microbiol ; 70(1): 77-82, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31535960

RESUMO

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5T grew at 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5T formed a distinct lineage within the genus Nocardioides and had the highest similarity to Nocardioides albidus THG-S11.7T (97.30 %), followed by Nocardioides kongjuensis A2-4T (97.22 %), Nocardioides nitrophenolicus NSP 41T (97.15 %) and Nocardioides caeni MN8T (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed ll-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H4) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0 and 10-methyl C18 : 0. The genome length of strain 21Sc5-5T was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5T represents a novel species of the genus Nocardioides, for which the name Nocardioides vastitatis sp. nov. is proposed. The type strain is 21Sc5-5T (=JCM 33365T=CGMCC 4.7608T).


Assuntos
Actinobacteria/classificação , Clima Desértico , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Peptidoglicano/química , 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(1): 112-119, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31535964

RESUMO

A Gram-positive, aerobic, non-spore-forming, non-pigmented and non-motile actinobacterial strain was isolated from a soil sample collected in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 130T is most closely related to the type strain Nocardioides iriomotensis NBRC 105384T, with a sequence similarity of 97.69 %. The isolate was distinguished from this phylogenetically related type strain by DNA-DNA hybridization (33.3 %), digital DNA-DNA hybridization (21.2 %), average nucleotide identity (75.7 %) and by a range of physiological and biochemical characteristics. Strain 130T contained MK-8(H4) and MK-7 as the major menaquinones, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol as the main polar lipids, and iso-C16 : 0, C17 : 1ω8c, anteiso-C17 : 0, C18 : 1ω9c, C17 : 0 and iso-C14 : 0 as the major cellular fatty acids. The novel strain grew at 20-36 °C, at pH 6.0-8.0 and in the presence of 0-6 % (w/v) NaCl. The genomic DNA G+C content was 72.9 mol%. The genome contained 4817 putative protein-coding sequences, and 45 tRNA and three rRNA genes. Phylogenomic analysis confirmed that strain 130T belongs to the genus Nocardioides and distinguished it from recognized Nocardioides species with available genomes. Based on these polyphasic taxonomic data, strain 130T represents a new species of the genus Nocardioides, for which the name Nocardioidesguangzhouensis sp. nov. is proposed. The type strain is 130T (=CICC 24668T=JCM 33269T).


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , 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/química
10.
Int J Syst Evol Microbiol ; 70(1): 89-92, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31535965

RESUMO

A genome-based phylogeny of the publicly available genomes of the genus Nocardiopsis reveals that Nocardiopsis baichengensis YIM 90130T is closely related to Nocardiopsis halophila DSM 44494T. Overall genome relatedness indices between the genomes of the two species were above the threshold values necessary for defining a new species (dDDH, 82.9 %; ANIb, 97.8 %; ANIm, 98.3 %; AAI, 97.7 %). Both species showed a similar G+C content of 73.6 mol% in their genomes. Considering the high similarity between the genomes of the two species, we propose that Nocardiopsisbaichengesis Li et al. 2006 should be reclassified as a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994.


Assuntos
Actinobacteria/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Genes Bacterianos , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Int J Syst Evol Microbiol ; 70(1): 16-22, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31513005

RESUMO

Strain KUDC5002T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25-37°C and pH 5.0-12.0, and showed optimal growth at 30 °C and pH 7.0-8.0. Strain KUDC5002T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C18 : 1 ω9c (17.3 %), iso-C16 : 0 (16.0 %) and iso-C17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002T should be considered a novel species in the genus Nocardioides, for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002T (=KCTC 39855T=DSM 106604T).


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Ilhas , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA
12.
Int J Syst Evol Microbiol ; 70(2): 1259-1265, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31851604

RESUMO

An actinobacterial strain, designated FW100M-8T, was isolated from a gut sample of larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, South Korea. Cells were Gram-stain-positive, microaerophilic to aerobic, non-spore forming and non-motile. It grew at pH 7.0-9.0 (optimum, pH 8.0), at 15-35 °C (optimum, 28 °C) and 0-3.0 % (w/v) NaCl (optimum, 0 %). According to the 16S rRNA gene analysis, strain FW100M-8T shared the highest sequence similarity with Agromyces mediolanus DSM 20152T (98.4 %), Agromyces ulmi XIL01T (98.3 %), Agromyces indicus NIO-1018T (98.3 %), Agromyces soli MJ21T (98.3 %), and Agromyces arachidis AK-1T (97.9 %). Phylogenetic trees showed that strain FW100M-8T fell into the lineage of the genus Agromyces. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The menaquinones of strain FW100M-8T were MK-12 (46 %), MK-11 (36 %), MK-10 (14 %) and MK-13 (4 %). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The peptidoglycan type was supposed to be the type B1, comprising d-Ala, d-Glu, Gly and l-A2bu. The G+C content of the genomic DNA is 70.5 mol%. On the basis of the genotypic and phenotypic data, we conclude that strain FW100M-8T represents a novel species of the genus Agromyces, for which the name Agromyces protaetiae sp. nov. is proposed with strain FW100M-8T (=KACC 19308T=NBRC 113048T) as the type strain.


Assuntos
Actinobacteria/classificação , Besouros/microbiologia , Trato Gastrointestinal/microbiologia , Filogenia , Actinobacteria/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Larva/microbiologia , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/química
13.
Parasit Vectors ; 12(1): 504, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31665056

RESUMO

BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.


Assuntos
Bactérias/classificação , Doença de Chagas/transmissão , Insetos Vetores/microbiologia , Microbiota , Rhodnius/microbiologia , Actinobacteria/classificação , Actinobacteria/genética , Análise de Variância , Animais , Bactérias/genética , Bacteroidetes/classificação , Bacteroidetes/genética , Biodiversidade , Código de Barras de DNA Taxonômico , Ecossistema , Firmicutes/classificação , Firmicutes/genética , Biblioteca Gênica , Humanos , Insetos Vetores/fisiologia , Panamá , Filogeografia , Reação em Cadeia da Polimerase , Proteobactérias/classificação , Proteobactérias/genética , RNA Ribossômico 16S/química , Rhodnius/fisiologia
14.
Int J Syst Evol Microbiol ; 69(12): 3710-3715, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31665101

RESUMO

A pale-yellow bacterial strain, designated S14-144T, was isolated from tundra soil sampled near the Antarctic Peninsula, South Shetland Islands (62° 22' 34″ S, 59° 42' 34″ W). The cells were strictly aerobic, Gram-stain-positive, non-motile and coccoid-shaped. Growth occurred at 4-28 °C, at pH 5.0-9.0 and in the presence of 0-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S14-144T formed a lineage within the genus Nakamurella and shared the highest 16S rRNA gene sequence similarity with Nakamurella deserti 12Sc4-1T (96.5 %) and Nakamurella silvestrisS20-107T (96.4 %). The average nucleotide identity value between the genomes of strain 14-144T and the type strain of the species, N. deserti, was 72.0 % . The DNA G+C content of strain S14-144T was 61.6 mol% . The major cellular fatty acids of strain S14-144T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. The strain contained MK-8(H4) as the predominant respiratory quinone, phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids, rhamnose, ribose and glucose as the major whole-cell sugars, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. On the basis of the phylogenetic, phenotypic and chemotaxonomic analysis, strain S14-144T is considered to represent a novel species of the genus Nakamurella, for which the name Nakamurella antarctica sp. nov. is proposed. The type strain is S14-144T (=CCTCC AB 2015345T=KCTC 39796T).


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Ilhas , Peptidoglicano/química , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tundra
15.
Microbiology ; 165(11): 1169-1180, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31592756

RESUMO

Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare A ctinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.


Assuntos
Actinobacteria/genética , Actinobacteria/metabolismo , Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Regiões Antárticas , Regiões Árticas , Biodiversidade , Produtos Biológicos/classificação , Produtos Biológicos/metabolismo , DNA Bacteriano/genética , Evolução Molecular , Sedimentos Geológicos/microbiologia , Metagenômica , Microbiota/genética , Filogenia , RNA Ribossômico 16S/química
16.
Nat Biotechnol ; 37(11): 1314-1321, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31570900

RESUMO

Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea; however, while 'omics can be used to infer physiological or ecological roles for species in a community, most of these hypothetical roles remain unvalidated. Here, we report an approach to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria (TM7). Using our pure cultures, we show that all three Saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.


Assuntos
Actinobacteria/metabolismo , Anticorpos/metabolismo , Proteínas de Membrana/imunologia , Boca/microbiologia , Análise de Célula Única/métodos , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/imunologia , Genômica , Humanos , Proteínas de Membrana/química , Proteínas de Membrana/genética , Modelos Moleculares , Filogenia , Conformação Proteica , Genética Reversa , Análise de Sequência de DNA
17.
World J Microbiol Biotechnol ; 35(10): 153, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31576426

RESUMO

Karst caves, considering to be the "arks" of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.


Assuntos
Actinobacteria/isolamento & purificação , Cavernas/microbiologia , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/crescimento & desenvolvimento , Animais , Ásia , Biodiversidade , Quirópteros/microbiologia , DNA Bacteriano/genética , Ecossistema , Sedimentos Geológicos/microbiologia , Filogenia , RNA Ribossômico 16S/genética , Microbiologia do Solo
18.
Int J Syst Evol Microbiol ; 69(12): 3792-3799, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31532356

RESUMO

A novel actinobacterium, designated strain CFH 30434T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive, non-motile and coccoid or short rods. The strain was found to be oxidase-positive and weakly catalase-positive. Strain CFH 30434T grew optimally at 28 °C, pH 7.0-9.0 and in the presence of up to 0-1.5 % NaCl (w/v). The whole-cell sugars were glucose, mannose and rhamnose. The major isoprenoid quinone was MK-9(H8) and the major fatty acids (>10 % of the total fatty acids compositions) were anteiso-C15 : 0, iso-C15:0 and iso-C14 : 0. The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The genomic DNA G+C content was determined to be 72.3 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that CFH 30434T clustered within the family Promicromonosporaceae, and closely with the type strains of Xylanimicrobium pachnodae DSM 12657T, Myceligenerans crystallogenes DSM 17134T and Promicromonospora xylanilytica CCTCC AA 208046T (97.3 %, 96.2 and 95.9 % sequence similarities, respectively). Phylogenetic analysis showed that strain CFH 30434T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae. Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain CFH 30434T represents a novel genus of the family Promicromonosporaceae, for which the name Antribacter gilvus gen. nov., sp. nov. is proposed. The type strain is CFH 30434T (=CGMCC 1.13856T=KCTC 49093T).


Assuntos
Actinobacteria/classificação , Cavernas/microbiologia , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Actinomycetales/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
19.
Int J Syst Evol Microbiol ; 69(12): 3946-3954, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31535962

RESUMO

Three actinobacterial strains, 27D-LEPIT, 1B-Mac and 36A-HELLB, were isolated from small standing and running freshwater habitats located in Salzburg, Austria. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome based on concatenated amino acid sequences of 119 single-copy genes referred the three strains within the family Microbacteriaceae to the genus Rhodoluna. The strains showed 100 % 16S rRNA gene sequence similarities to the previously described Candidatus Rhodoluna limnophila. Cells were very small, approximately 0.5×0.3 µm, and showed a red pigmentation in liquid nutrient broth-soyotone-yeast extract medium as well as on agar plates. The strains assimilated a broad variety of substrates; however, the patterns differed a great deal between the three investigated strains. For strain 27D-LEPIT, the major fatty acids were iso-C14 : 0 and anteiso-C15 : 0; the identified polar lipids were phosphatidylglycerol and diphosphatidylglycerol; the major respiratory quinone was MK-11; and analysis of the peptidoglycan structure indicated the presence of type B2ß (typeB10). The genomic DNA of the three strains was very small (1.4 Mbp) and had a DNA G+C content of 54 mol%. The investigated traits suggested that strains 36A-HELLB (=DSM 107805=JCM 32927), 1B-Mac (=DSM 107802=JCM 32925) and 27D-LEPIT (=JCM 32926T =DSM 107804T) represent a new species for which the name Rhodolunalimnophila sp. nov. is proposed, with strain 27D-LEPIT as the type strain.


Assuntos
Actinobacteria/classificação , Água Doce/microbiologia , Filogenia , Actinobacteria/isolamento & purificação , Áustria , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Tamanho do Genoma , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
20.
Int J Syst Evol Microbiol ; 69(11): 3629-3635, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31511125

RESUMO

Two Gram-stain-positive, irregular rod-shaped (0.2-0.5×1.3-2.5 um) strains, HY056T and HY057, were isolated from the faeces of Equus kiang (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056T and HY057 belong to the genus Nocardioides by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with Nocardioides daphniae JCM 16608T, Nocardioides houyundeii 78T, Nocardioides solisilvae Ka25T and Nocardioides gilvus XZ17T. The digital DNA-DNA hybridization value of strain HY056T was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H4) was the predominant (91.6 %) respiratory quinone. The cell wall contained ll-2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were C18 : 1ω9c and iso-C16:0. The DNA G+C contents of strains HY056T and HY057 were 68.9 and 69.1 mol%, respectively. ß-Glucosidase expression was positive, and acid was produced from d-fructose. Strain HY056T (=CGMCC 4.7563T=JCM 33399T) is assigned as the type strain of a novel species within the genus Nocardioides, for which the name Nocardioidesyefusunii sp. nov is proposed.


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