scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology

2018 ◽  
Author(s):  
Douglas Eduardo Valente Pires ◽  
Francislon Silva Oliveira ◽  
Felipe Borim Correa ◽  
Daniel Kumazawa Morais ◽  
Gabriel Rocha Fernandes
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genetic Markers ◽  
Microbial Community Composition ◽  
Classification Model ◽  
Marker Genes ◽  
Rrna Gene ◽  
Specific Method ◽  
Taxonomic Assignment ◽  
Sequence Identity

1.AbstractBackgroundSequencing of amplified genetic markers, such as the 16S rRNA gene, have been extensively used to characterize microbial community composition. Recent studies suggested that Amplicon Sequences Variants (ASV) should replace the Operational Taxonomic Units (OTU), given the arbitrary definition of sequence identity thresholds used to define units. Alignment-free methods are an interesting alternative for the taxonomic classification of the ASVs, preventing the introduction of biases from sequence identity thresholds.ResultsHere we present TAG.ME, a novel alignment-independent and amplicon-specific method for taxonomic assignment based on genetic markers. TAG.ME uses a multilevel supervised learning approach to create predictive models based on user-defined genetic marker genes. The predictive method can assign taxonomy to sequenced amplicons efficiently and effectively. We applied our method to assess gut and soil sample classification, and it outperformed alternative approaches, identifying a substantially larger proportion of species. Benchmark tests performed using the RDP database, and Mock communities reinforced the precise classification into deep taxonomic levels.ConclusionTAG.ME presents a new approach to assign taxonomy to amplicon sequences accurately. Our classification model, trained with amplicon specific sequences, can address resolution issues not solved by other methods and approaches that use the whole 16S rRNA gene sequence. TAG.ME is implemented as an R package and is freely available at http://gabrielrfernandes.github.io/tagme/

Nonomuraea montanisoli sp. nov., isolated from mountain forest soil

2021 ◽  
Author(s):  
Suchart Chanama ◽  
Chanwit Suriyachadkun ◽  
Manee Chanama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Mountain Forest ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
A Genome

A novel actinomycete, strain SMC 257T, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257T formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257T belonged to the genus Nonomuraea , and the closest phylogenetically related species were Nonomuraea roseoviolacea subsp. carminata JCM 9946T (98.9 % 16S rRNA gene sequence similarity), Nonomuraea rhodomycinica TBRC 6557T (98.4 %), and Nonomuraea roseoviolacea subsp. roseoviolacea JCM 3145T (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA–DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95–96 % and 70 %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H4). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C17 : 0 10-methyl and iso-C16 : 0. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257T is considered to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea montanisoli is proposed. The type strain is SMC 257T (=TBRC 13065T=NBRC 114772T).

scholarly journals Hansschlegelia quercus sp. nov., a novel methylotrophic bacterium isolated from oak buds

2020 ◽  
Vol 70 (8) ◽  
pp. 4646-4652 ◽  
Author(s):  
Nadezhda V. Agafonova ◽  
Elena N. Kaparullina ◽  
Denis S. Grouzdev ◽  
Nina V. Doronina
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Content Type ◽  
Link Type ◽  
A Genome

Novel aerobic, restricted facultatively methylotrophic bacteria were isolated from buds of English oak (Quercus robur L.; strain DubT) and northern red oak (Quercus rubra L.; strain KrD). The isolates were Gram-negative, asporogenous, motile short rods that multiplied by binary fisson. They utilized methanol, methylamine and a few polycarbon compounds as carbon and energy sources. Optimal growth occurred at 25 °C and pH 7.5. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phoshatidylglycerol. The major cellular fatty acids of cells were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The major ubiquinone was Q-10. Analysis of 16S rRNA gene sequences showed that the strains were closely related to the members of the genus Hansschlegelia : Hansschlegelia zhihuaiae S113T(97.5–98.0 %), Hansschlegelia plantiphila S1T (97.4–97.6 %) and Hansschlegelia beijingensis PG04T(97.0–97.2 %). The 16S rRNA gene sequence similarity between strains DubT and KrD was 99.7 %, and the DNA–DNA hybridization (DDH) result between the strains was 85 %. The ANI and the DDH values between strain DubT and H. zhihuaiae S113T were 80.1 and 21.5  %, respectively. Genome sequencing of the strain DubT revealed a genome size of 3.57 Mbp and a G+C content of 67.0 mol%. Based on the results of the phenotypic, chemotaxonomic and genotypic analyses, it is proposed that the isolates be assigned to the genus Hansschlegelia as Hansschlegelia quercus sp. nov. with the type strain DubT (=VKM B-3284T=CCUG 73648T=JCM 33463T).

scholarly journals GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

2022 ◽  
Vol 12 ◽  
Author(s):  
Ilona A. Ruhl ◽  
Andriy Sheremet ◽  
Chantel C. Furgason ◽  
Susanne Krause ◽  
Robert M. Bowers ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Hot Spring ◽  
Gc Content ◽  
Gene Copy ◽  
Marker Genes ◽  
Rrna Gene ◽  
Separate Species ◽  
Distinct Subgroup

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.

Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 251-259 ◽  
Author(s):  
Patricia L. Tavormina ◽  
Roland Hatzenpichler ◽  
Shawn McGlynn ◽  
Grayson Chadwick ◽  
Katherine S. Dawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Sequence Identity ◽  
Link Type

We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1T, ‘whale fall 1’) that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina . Strain WF1T represents the first cultivar from the ‘deep sea-1’ clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1T were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1T was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1T, a capacity that had not been functionally demonstrated previously in members of Methylobacter . On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1T ( = LMG 28393T = ATCC BAA-2619T).

scholarly journals Development of a Universal Microarray Based on the Ligation Detection Reaction and 16S rRNA Gene Polymorphism To Target Diversity of Cyanobacteria

2004 ◽  
Vol 70 (12) ◽  
pp. 7161-7172 ◽  
Author(s):  
Bianca Castiglioni ◽  
Ermanno Rizzi ◽  
Andrea Frosini ◽  
Kaarina Sivonen ◽  
Pirjo Rajaniemi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Samples ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Culture Collections ◽  
Reliable Identification ◽  
Ligation Detection Reaction ◽  
Universal Array ◽  
Axenic Strains

ABSTRACT The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring.

scholarly journals Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.

2018 ◽  
Author(s):  
Hugo R Barajas de la Torre ◽  
Miguel Romero ◽  
Shamayim Martínez-Sánchez ◽  
Luis D Alcaraz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Core Genome ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Phylogeny ◽  
The Core ◽  
Sequence Identity ◽  
Core Proteins ◽  
Genomic Similarity

Background. Comparative genomics between closely related bacterial strains can distinguish important features determining pathogenesis, antibiotic resistance, and phylogenetic structure. The Streptococcus genus is relevant to public health and food safety and it is well-represented (>100 genomes) in databases of publicly available databases. Streptococci are cosmopolitan, with multiple sources of isolation, from humans to dairy products. The Streptococcus genus has been classified by morphology, serotypes, 16S rRNA gene, and Multi Locus Sequence Types (MLST). The Genomic Similarity Score (GSS) is proposed as a tool to quantify genome level relatedness between species of Streptococcus. The Streptococcus core genome can be used to assess strain specific abundances in metagenomic sequences. Methods. A 16S rRNA gene phylogeny was calculated for 108 strains, belonging to 16 Streptococcus species and compared to a dendrogram using GSS pairwise distances for the same genomes. The core and pan-genome were calculated for these 108 genomes. The core genome sequences were analyzed and used as a resource to discriminate homologous fragment reads from closely related strains in metagenomic samples. Results. A total of 404 proteins are shared by all 108 Streptococcus genomes, which is the core genome. The pairwise amino acid identity values of the core proteins for all the compared strains and outgroups are reported. Lower sequence identity variation (90-100%) is predominantly found in core clusters containing ribosomal and translation-related proteins. For 48 core proteins (11.8%) no functional assignment could be made and those proteins have larger sequence identity variations than other core proteins. The sequence identity of the core genome diminishes as GSS score between species decreases. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). Finally, the core genome was used to distinguish between closely related species within human oral metagenomes. Discussion. The Streptococcus genus provides a benchmark dataset for comparative genomic studies due to the breath depth of genomic coverage. Comparing metagenomic shotgun fragment reads to the core genome using rapid alignment tools allows species-specific abundance estimates in metagenomic samples. Understanding of genomic variability and strains relatedness is the goal of tools like GSS, which make use of both pairwise shared core and pan-genomic homologous shared sequences for its calculation.

scholarly journals Roseovarius gahaiensis sp. nov., isolated from Gahai Saline Lake, PR China

2020 ◽  
Vol 70 (10) ◽  
pp. 5330-5336 ◽  
Author(s):  
Xia Sun ◽  
Fang Wang ◽  
Yang Liu ◽  
Ying Lu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Saline Lake ◽  
Qaidam Basin ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
A Genome ◽  
Pr China

A Gram-stain-negative, aerobic, non-motile and ovoid- to rod-shaped bacterial strain, designated GH877T, was isolated from a water sample of Gahai saline lake in Qaidam Basin,PR China. The isolate grew at 5–45 °C, pH 6.0–9.0 (optima, 37 °C and pH 7.5) and with 0.5–20 % (w/v) NaCl (optimum, 2.0 %). The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain GH877T belonged to the genus Roseovarius , and had highest 16S rRNA gene sequence similarity of 97.7 % to Roseovarius pacificus 81-2T, followed by Roseovarius halotolerans HJ50T (97.5 %) and Roseovarius litoreus GSW-M15T (96.8 %). Genome sequencing revealed a genome size of 3 378 519 bp and a G+C content of 59.8 mol %. Up-to-date bacterial core gene set analysis indicated that strain GH877T represents one independent lineage with R. pacificus DSM29589T. The average nucleotide identity values of GH877T with R. pacificus 81-2T and R. halotolerans HJ50T are 80.7 and 77.3 %, respectively. In silico DNA–DNA hybridization values between strain GH877T and R. pacificus 81-2T and R. halotolerans HJ50T are 23.2 and 20.0 %, respectively. Q-10 was the predominant respiratory quinone and summed feature 8 (C18  :  1 ω7c and/or C18  :  1 ω6c) and C16  :  0 were the major cellular fatty acids. The polar lipids of strain GH877T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified phosphoglycolipids. Based on polyphasic taxonomic analysis, strain GH877T is proposed to represent a novel species of the genus Roseovarius , for which the name Roseovarius gahaiensis sp. nov. is proposed. (type strain GH877T=CGMCC 1.13971T=KCTC 72576T).

scholarly journals ‘Candidatus Mycoplasma haematoparvum’, a novel small haemotropic mycoplasma from a dog

2005 ◽  
Vol 55 (1) ◽  
pp. 27-30 ◽  
Author(s):  
Jane E. Sykes ◽  
Louise M. Ball ◽  
Nathan L. Bailiff ◽  
Michael M. Fry
Keyword(s):  
Nucleotide Sequence ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Nucleotide Sequence Identity ◽  
Rrna Gene ◽  
Sequence Identity ◽  
Gene Nucleotide Sequence ◽  
Blood Smears ◽  
Candidate Species

A novel small haemoplasma was detected following cytological examination of blood smears from a splenectomized dog with haemic neoplasia. The 16S rRNA and rnpB genes of the organism were partially sequenced and a phylogenetic tree constructed. The organism was most closely related to the small feline haemoplasma, ‘Candidatus Mycoplasma haemominutum’ (94 % 16S rRNA gene nucleotide sequence identity; 75 % rnpB) and was only distantly related to Mycoplasma haemocanis (78 % 16S rRNA gene nucleotide sequence identity; 65 % rnpB). As this organism has not been cultured in vitro, the candidate species name ‘Candidatus Mycoplasma haematoparvum’ is proposed.

scholarly journals Towards a Genome-Based Taxonomy for Prokaryotes

2005 ◽  
Vol 187 (18) ◽  
pp. 6258-6264 ◽  
Author(s):  
Konstantinos T. Konstantinidis ◽  
James M. Tiedje
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Content ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
The 16S Rrna Gene

ABSTRACT The ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R 2 > 0.69 for the protein-coding genes versus R 2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.

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