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1.
BMC Bioinformatics ; 22(1): 312, 2021 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-34107881

RESUMO

BACKGROUND: Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limited numbers of non-bacterial species in their databases compared to available genomic sequences and their methodologies do not favour classification of rare sequences which may represent only a small fraction of their parent genome. In seeking to optimise identification of non-bacterial species, we evaluated five widely-used metagenome classifier programs (BURST, Kraken2, Centrifuge, MetaPhlAn2 and CCMetagen) for their ability to correctly assign and count simulations of bacterial, viral and eukaryotic DNA sequence reads, including the effect of taxonomic order of analysis of bacteria, viruses and eukaryotes and the effect of sequencing depth. RESULTS: We found that the precision of metagenome classifiers varied significantly between programs and between taxonomic groups. When classifying viruses and eukaryotes, ordering the analysis such that bacteria were classified first significantly improved classification precision. Increasing sequencing depth decreased classification precision and did not improve recall of rare species. CONCLUSIONS: Choice of metagenome classifier program can have a marked effect on results with respect to precision of species assignment in different taxonomic groups. The order of taxonomic classification can markedly improve precision. Increasing sequencing depth can decrease classification precision and yields diminishing returns in probability of species detection.


Assuntos
Metagenoma , Vírus , Bactérias/genética , Biologia Computacional , Humanos , Metagenômica , Análise de Sequência de DNA , Vírus/genética
2.
BMC Genomics ; 22(1): 430, 2021 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-34107894

RESUMO

BACKGROUND: Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target for diseases like cancer. In recent years, the detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method to supersede existing single-molecule methods such as DNA fibre analysis: ONT sequencing yields long reads with high throughput, and sequenced molecules can be mapped to the genome using standard sequence alignment software. RESULTS: This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-nucleotide resolution. DNAscent v2 also comes equipped with an autoencoder that interprets the pattern of BrdU incorporation on each ONT-sequenced molecule into replication fork direction to call the location of replication origins termination sites. DNAscent v2 surpasses previous versions of DNAscent in BrdU calling accuracy, origin calling accuracy, speed, and versatility across different experimental protocols. Unlike NanoMod, DNAscent v2 positively identifies BrdU without the need for sequencing unmodified DNA. Unlike RepNano, DNAscent v2 calls BrdU with single-nucleotide resolution and detects more origins than RepNano from the same sequencing data. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent . CONCLUSIONS: This paper shows that DNAscent v2 is the new state-of-the-art in the high-throughput, single-molecule detection of replication fork dynamics. These improvements in DNAscent v2 mark an important step towards measuring DNA replication dynamics in large genomes with single-molecule resolution. Looking forward, the increase in accuracy in single-nucleotide resolution BrdU calls will also allow DNAscent v2 to branch out into other areas of genome stability research, particularly the detection of DNA repair.


Assuntos
Aprendizado Profundo , Sequenciamento por Nanoporos , Nanoporos , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , Software
3.
Int J Mol Sci ; 22(11)2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-34073702

RESUMO

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins-AlkB and FTO-biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.


Assuntos
Bacteriófagos/genética , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Biblioteca de Peptídeos , Mutação INDEL , Análise de Sequência de DNA
4.
Int J Mol Sci ; 22(11)2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-34073818

RESUMO

Approximately 23% of metastatic castration-resistant prostate cancers (mCRPC) harbor deleterious aberrations in DNA repair genes. Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) therapy has shown improvements in overall survival in patients with mCRPC who harbor somatic and/or germline alterations of homology recombination repair (HRR) genes. Peripheral blood samples are typically used for the germline mutation analysis test using the DNA extracted from peripheral blood leucocytes. Somatic alterations can be assessed by extracting DNA from a tumor tissue sample or using circulating tumor DNA (ctDNA) extracted from a plasma sample. Each of these genetic tests has its own benefits and limitations. The main advantages compared to the tissue test are that liquid biopsy is a non-invasive and easily repeatable test with the value of better representing tumor heterogeneity than primary biopsy and of capturing changes and/or resistance mutations in the genetic tumor profile during disease progression. Furthermore, ctDNA can inform about mutation status and guide treatment options in patients with mCRPC. Clinical validation and test implementation into routine clinical practice are currently very limited. In this review, we discuss the state of the art of the ctDNA test in prostate cancer compared to blood and tissue testing. We also illustrate the ctDNA testing workflow, the available techniques for ctDNA extraction, sequencing, and analysis, describing advantages and limits of each techniques.


Assuntos
DNA Tumoral Circulante/sangue , Mutação , Proteínas de Neoplasias/genética , Neoplasias de Próstata Resistentes à Castração/diagnóstico , Reparo de DNA por Recombinação , Proteínas Mutadas de Ataxia Telangiectasia/genética , Proteína BRCA1/genética , Proteína BRCA2/genética , Humanos , Biópsia Líquida , Masculino , Neoplasias de Próstata Resistentes à Castração/sangue , Neoplasias de Próstata Resistentes à Castração/genética , Análise de Sequência de DNA
5.
Artigo em Inglês | MEDLINE | ID: mdl-34085922

RESUMO

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae, respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1-98.4 and 97.3-98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0-83.2 and 20.7-27.1 % and 79.4-81.5 and 22.3-23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya, respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya, respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
Artigo em Inglês | MEDLINE | ID: mdl-34100698

RESUMO

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621T, was isolated from rhizosphere soil of Spartina alterniflora in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621T was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 7.0) and in the presence of 0-5% NaCl (w/v) (optimum 1-3%). The main menaquinones were MK-9 (H4) (92.2 %) and MK-10 (7.8 %). The major cellular fatty acids were anteiso-C15 : 0 and C14 : 0. The peptidoglycan was the type A4α (l-Lys-Ser-d-Glu). The polar lipids included four phosphoglycolipids, four glycolipids, an unidentified lipid and six unidentified phospholipids. The DNA G+C content of the type strain was 71.7 mol%. On the basis of the results of 16S rRNA gene analysis, the type strain of a species with a validly published name with the highest similarity to GY 10621T was Flavimobilis soli KCTC 13155T (97.16 %), followed by Sanguibacter suarezii NBRC 16159T (96.39 %). The calculated results indicated that compared with GY 10621T, the average nucleotide identity (ANI) values of three strains closely related to GY 10621T (the two aforementioned type strains and 'S. massiliensis' Marseille-P3815) were 74.18-94.97 %, and the digital DNA-DNA hybridization (dDDH) values were 20.3-60.6 %. The results of 16S rRNA-based and genome-based phylogenetic tree analysis indicated that GY 10621T should be assigned to the genus Flavimobilis. On the basis of evidence from polyphasic studies, GY 10621T should be designated as representing a novel species of the genus Flavimobilis, for which the name Flavimobilis rhizosphaerae sp. nov. is proposed. The type strain is GY 10621T (=CGMCC 1.17411T=KCTC 49515T).


Assuntos
Actinobacteria/classificação , Filogenia , Poaceae/microbiologia , Rizosfera , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
7.
Int J Mol Sci ; 22(10)2021 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-34069990

RESUMO

The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.


Assuntos
Código de Barras de DNA Taxonômico/estatística & dados numéricos , Metagenômica/estatística & dados numéricos , Microbiota/genética , Software , Algoritmos , Análise por Conglomerados , Biologia Computacional/métodos , Interpretação Estatística de Dados , Sequenciamento de Nucleotídeos em Larga Escala , Metadados , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
8.
BMC Bioinformatics ; 22(Suppl 6): 427, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078257

RESUMO

BACKGROUND: The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is a short-read de novo metagenome assembler that partitions a multi-species de Bruijn graph into single-species sub-graphs. This study aimed to improve the performance of MetaVelvet-SL by using a deep learning-based model to predict the partition nodes in a multi-species de Bruijn graph. RESULTS: This study showed that the recent advances in deep learning offer the opportunity to better exploit sequence information and differentiate genomes of different species in a metagenomic sample. We developed an extension to MetaVelvet-SL, which we named MetaVelvet-DL, that builds an end-to-end architecture using Convolutional Neural Network and Long Short-Term Memory units. The deep learning model in MetaVelvet-DL can more accurately predict how to partition a de Bruijn graph than the Support Vector Machine-based model in MetaVelvet-SL can. Assembly of the Critical Assessment of Metagenome Interpretation (CAMI) dataset showed that after removing chimeric assemblies, MetaVelvet-DL produced longer single-species contigs, with less misassembled contigs than MetaVelvet-SL did. CONCLUSIONS: MetaVelvet-DL provides more accurate de novo assemblies of whole metagenome data. The authors believe that this improvement can help in furthering the understanding of microbiomes by providing a more accurate description of the metagenomic samples under analysis.


Assuntos
Aprendizado Profundo , Metagenoma , Algoritmos , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Análise de Sequência de DNA , Software
9.
BMC Bioinformatics ; 22(Suppl 6): 142, 2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078284

RESUMO

BACKGROUND: Genomic reads from sequencing platforms contain random errors. Global correction algorithms have been developed, aiming to rectify all possible errors in the reads using generic genome-wide patterns. However, the non-uniform sequencing depths hinder the global approach to conduct effective error removal. As some genes may get under-corrected or over-corrected by the global approach, we conduct instance-based error correction for short reads of disease-associated genes or pathways. The paramount requirement is to ensure the relevant reads, instead of the whole genome, are error-free to provide significant benefits for single-nucleotide polymorphism (SNP) or variant calling studies on the specific genes. RESULTS: To rectify possible errors in the short reads of disease-associated genes, our novel idea is to exploit local sequence features and statistics directly related to these genes. Extensive experiments are conducted in comparison with state-of-the-art methods on both simulated and real datasets of lung cancer associated genes (including single-end and paired-end reads). The results demonstrated the superiority of our method with the best performance on precision, recall and gain rate, as well as on sequence assembly results (e.g., N50, the length of contig and contig quality). CONCLUSION: Instance-based strategy makes it possible to explore fine-grained patterns focusing on specific genes, providing high precision error correction and convincing gene sequence assembly. SNP case studies show that errors occurring at some traditional SNP areas can be accurately corrected, providing high precision and sensitivity for investigations on disease-causing point mutations.


Assuntos
Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Genômica , Análise de Sequência de DNA
10.
BMC Bioinformatics ; 22(1): 304, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090332

RESUMO

BACKGROUND: The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats. RESULTS: We introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves higher accuracy than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome sequencing data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease. CONCLUSIONS: We developed a mapping-free protocol for variant calling between matched DNA-seq samples. Our protocol is suitable for variant detection in unmappable genome regions or in the absence of a reference genome.


Assuntos
Genômica , Sequenciamento de Nucleotídeos em Larga Escala , DNA , Genoma Humano , Humanos , Análise de Sequência de DNA
11.
BMC Bioinformatics ; 22(1): 303, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090340

RESUMO

BACKGROUND: Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking. RESULTS: We tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups. CONCLUSIONS: We provide a thorough evaluation of popular assemblers on a non-model eukaryote genome with variable levels of heterozygosity. Our study highlights several strategies using pre and post-processing approaches to generate haploid assemblies with high continuity and completeness. This benchmark will help users to improve haploid assemblies of non-model organisms, and evaluate the quality of their own assemblies.


Assuntos
Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Genoma , Haplótipos , Análise de Sequência de DNA
12.
Artigo em Inglês | MEDLINE | ID: mdl-33999788

RESUMO

A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.


Assuntos
Irrigação Agrícola , Listeria/classificação , Filogenia , Microbiologia da Água , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Listeria/isolamento & purificação , New York , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
Artigo em Inglês | MEDLINE | ID: mdl-33999789

RESUMO

Two Gram-negative, aerobic, motile bacteria strains were isolated from leaf spot disease of Quercus mongolica. Strain hsmgli-8T has 99.86 % 16S rRNA gene sequence similarity to LY10J, and the highest 16S rRNA gene sequence similarity to Pseudomonas cerasi 58T (97.2 %), then Pseudomonas ficuserectae JCM 2400T (97.18 %), Pseudomonas meliae CFBP 3225T, Pseudomonas tremae CFBP 6111T and Pseudomonas congelans DSM 14939T (all 97.12 %), and less than 97.1 % similarity to other recognized species. In phylogenetic trees based on 16S rRNA gene and multilocus sequence data, the two novel strains form a separate branch, indicating that they do not belong to any Pseudomonas group and subgroup, and should belong to a novel species within the genus Pseudomonas. This assertion is also supported by the results of genome average nucleotide identity analysis. The major fatty acids are C16 : 0, C18 : 1 ω7c and/or C18 : 1 ω6c, C16 : 1 ω7c and/or C16 : 1 ω6c. Polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, aminolipid and seven uncharacterized phospholipids. The predominant respiratory quinone is Q-9. The DNA G+C content is 59.45-59.50 mol%. Based on these data, we propose that the two novel strains should be assigned as a novel species within the genus Pseudomonas. We propose that the novel strains be named Pseudomonas quercus sp. nov. The type strain is hsmgli-8T (=CFCC 15739T=LMG 31544T).


Assuntos
Filogenia , Doenças das Plantas/microbiologia , Pseudomonas/classificação , Quercus/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-33999790

RESUMO

A novel Gram-reaction-negative bacterial strain, designated Ka43T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (97.1 %) to Cellvibrio diazotrophicus E50T. Cells of strain Ka43T are aerobic, motile, short rods. The major fatty acids are summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C18 : 1 ω7c and C16 : 0. The only isoprenoid quinone is Q-8. The polar lipid profile includes phosphatidylethanolamine, phosphatidylglycerol, four phospholipids, two lipids and an aminolipid. The assembled genome of strain Ka43T has a total length of 4.2 Mb and the DNA G+C content is 51.6 mol%. Based on phenotypic data, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain Ka43T represents a novel species in the genus Cellvibrio, for which the name Cellvibrio polysaccharolyticus sp. nov. is proposed. The type strain of the species is strain Ka43T (=LMG 31577T=NCAIM B.02637T).


Assuntos
Agricultura , Cellvibrio/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Cellvibrio/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hungria , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
15.
Artigo em Inglês | MEDLINE | ID: mdl-33999791

RESUMO

The taxonomic relationships and genome features of the type strains in the Streptomyces aurantiacus clade, including Streptomyces aurantiacus, Streptomyces ederensis, Streptomyces glomeroaurantiacus, Streptomyces umbrinus, Streptomyces phaeochromogenes, Streptomyces dioscori and Streptomyces tauricus, were investigated. Type strains of these species shared high 16S rRNA gene sequence similarity to each other. Multilocus sequence analysis (MLSA) based on atpD, gyrB, recA, rpoB and trpB genes revealed that S. ederensis and S. umbrinus belong to the same species. Also, S. aurantiacus and S. glomeroaurantiacus belong to the same species, but the remaining species are not closely related to each other. MLSA results were verified by the results average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses; while the ANI and dDDH values between S. ederensis and S. umbrinus are 98.1 and 85.4 %, respectively, these values between S. aurantiacus and S. glomeroaurantiacus are 98.9 and 90.7 %, respectively. The presence of almost the same set of biosynthetic gene clusters and highly consistent phenotypic test results also supported the synonymy between S. ederensis and S. umbrinus, as well as between S. aurantiacus and S. glomeroaurantiacus. Therefore, S. ederensis should be reclassified as a later heterotypic synonym of S. umbrinus and S. glomeroaurantiacus should be reclassified as a later heterotypic synonym of S. aurantiacus.


Assuntos
Filogenia , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Genes Bacterianos , Genômica , Tipagem de Sequências Multilocus , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
16.
Artigo em Inglês | MEDLINE | ID: mdl-33999792

RESUMO

Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.


Assuntos
Camelídeos Americanos/microbiologia , Bovinos/microbiologia , Filogenia , Leões-Marinhos/microbiologia , Streptococcus/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Sequência de Bases , California , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Florida , Maryland , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Sistema Respiratório/microbiologia , Análise de Sequência de DNA , Streptococcus/isolamento & purificação
17.
Artigo em Inglês | MEDLINE | ID: mdl-33999794

RESUMO

A haloalkaliphilic hydrolytic actinobacterium, strain ACPA22T, was enriched and isolated in pure culture from saline alkaline soil (soda solonchak) in northeastern Mongolia. The isolate was facultatively alkaliphilic, growing at pH 6.5-10.5 (optimum at 7.3-9.0) and highly salt-tolerant, tolerating up to 3 M total Na+ as carbonates. The hydrolytic nature of ACPA22T was confirmed by two different growth-dependent methods and by the presence of multiple glycosidase-encoding genes in the genome. The 16S rRNA gene-based phylogenetic analysis demonstrated that strain ACPA22T formed a deep-branching lineage within the family Glycomycetaceae, with the highest sequence similarity value to Glycomyces buryatensis 18T (92.1 %) and Salininema proteolyticum Miq-4T (91.8 %). The average amino acid identity values (56.1-61.5 %) between ACPA22T and other Glycomycetaceae members with available genomes did not exceed the threshold reported for different genera. The cell wall of ACPA22T contained meso-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars included mannose, galactose, arabinose, ribose and xylose. The major menaquinones were MK-10(Н4) and MK-11(Н4). The identified polar lipids were represented by phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. In addition, the strain had a few unidentified characteristic polar lipids, including an amine-containing phospholipid with chromatographic mobility similar to that of phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C17 : 0 and iso-C16 : 0. The genome included a chromosome of 3.94 Mbp (G+C content 61.5 mol%) encoding 3285 proteins and two plasmids of 59.8 and 14.8 kBp. Based on the data obtained in this study, a new genus and species, Natronoglycomyces albus gen. nov., sp. nov, is proposed with the type strain ACPA22T (=DSM 106290T=VKM Ac-2771T).


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Álcalis , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Mongólia , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , Vitamina K 2/química
18.
Artigo em Inglês | MEDLINE | ID: mdl-33999795

RESUMO

We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1 ω7c and/or C18 : 1 ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).


Assuntos
Alphaproteobacteria/classificação , Filogenia , Rhizophoraceae/microbiologia , Áreas Alagadas , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Arábia Saudita , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
19.
Artigo em Inglês | MEDLINE | ID: mdl-33999796

RESUMO

The actinobacterial strain 15G-AUS-rotT was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rotT to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rotT were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C16 : 0, antiso-C15 : 0 and iso-C14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rotT (=DSM 107803T=JCM 32974T).


Assuntos
Actinobacteria/classificação , Água Doce/microbiologia , Filogenia , Actinobacteria/isolamento & purificação , Áustria , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , Ácidos Graxos/química , Tamanho do Genoma , Peptidoglicano/química , Pigmentação , Lagoas/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
20.
Artigo em Inglês | MEDLINE | ID: mdl-34003738

RESUMO

A novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated strain LB2T, grew at 25-50 °C (optimum, 37 °C) and pH 8.2-10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0-1 %) but was tolerated up to 7 %. Strain LB2T utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C15 : 0 and C16 : 0. The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Proteinivoraceae, order Clostridiales within the phylum Firmicutes. Strain LB2T was most closely related to the thermophilic Anaerobranca gottschalkii LBS3T (93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain LB2T with A. gottschalkii LBS3T showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2T is proposed to represent the first species of a novel genus, for which the name Alkalicella caledoniensis gen. nov., sp. nov. is proposed (type strain LB2T=DSM 100588T=JCM 30958T).


Assuntos
Clostridiales/classificação , Fontes Termais/microbiologia , Filogenia , Anaerobiose , Bactérias Anaeróbias/classificação , Bactérias Anaeróbias/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridiales/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Fermentação , Nova Caledônia , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
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