scholarly journals Paenibacillus Piscarius Sp. Nov., a Novel Nitrogen-Fixing Species Isolated from the Gut of the Armored Catfish Parotocinclus Maculicauda

2021 ◽  
Author(s):  
Mariana Barbalho Farias da silva ◽  
Ericka Arregue Lemos ◽  
Renata E. Vollú ◽  
Fernanda Abreu ◽  
Alexandre S. Rosado ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Distinct Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Closely Related Species ◽  
A Genome ◽  
Encoding Gene ◽  
Encoding Genes

Abstract A gram-positive, nitrogen-fixing and endospore-forming strain, designated P121T, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA encoding gene, rpoB, gyrB and nifH genes and phenotypic analyses. The most closely related species to strain P121T were Paenibacillus rhizoplanae DSM 103993T, Paenibacillus silagei DSM 101953T and Paenibacillus borealis DSM 13188T, with similarity values of 98.9%, 98.3% and 97.6%, respectively, based on 16S rRNA gene sequences. Genome sequencing revealed a genome size of 7,513,698 bp, DNA G + C content of 53.9 mol% and the presence of the structural nitrogenase encoding genes (nifK, nifD and nifH) necessary for nitrogen fixation. Digital DNA-DNA hybridization (dDDH) experiments and average nucleotide identity (ANI) analyses between strain P121T and the type strains of the closest species demonstrated that the highest values were below the thresholds of 70% dDDH (42.3% with P. borealis) and 95% ANI (84.28% with P. silagei) for bacterial species delineation, indicating that strain P121T represents a distinct species. Its major cellular fatty acid was anteiso-C15:0 (42.4%), and the major isoprenoid quinone was MK-7. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain P121T represents a novel species for which the name Paenibacillus piscarius sp. nov. is proposed (type strain = DSM 25072 = LFB-Fiocruz 1636).

scholarly journals Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere

2007 ◽  
Vol 57 (3) ◽  
pp. 620-624 ◽  
Author(s):  
Samina Mehnaz ◽  
Brian Weselowski ◽  
George Lazarovits
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Morphological Characterization ◽  
Major Fatty Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Closely Related Species ◽  
Gene Sequence Analysis ◽  
Biolog Analysis

A free-living diazotrophic strain, DS2T, was isolated from corn rhizosphere. Polyphasic taxonomy was performed including morphological characterization, Biolog analysis, and 16S rRNA, cpn60 and nifH gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain DS2T was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (DNA G+C content 67.9 mol%; Q-10 quinone system; major fatty acid 18 : 1ω7c) were also similar to those of the genus Azospirillum. In all the analyses, including phenotypic characterization using Biolog analysis and comparison of cellular fatty acids, this isolate was found to be different from the closely related species Azospirillum lipoferum, Azospirillum oryzae and Azospirillum brasilense. On the basis of these results, a novel species is proposed for this nitrogen-fixing strain. The name Azospirillum canadense sp. nov. is suggested with the type strain DS2T (=NCCB 100108T=LMG 23617T).

scholarly journals Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

2010 ◽  
Vol 76 (12) ◽  
pp. 3886-3897 ◽  
Author(s):  
Anna Y. Pei ◽  
William E. Oberdorf ◽  
Carlos W. Nossa ◽  
Ankush Agarwal ◽  
Pooja Chokshi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Operational Definition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Thermoanaerobacter Tengcongensis ◽  
A Genome ◽  
Prokaryotic Genomes

ABSTRACT Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp ). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ± 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ± 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2° structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in “Candidatus Protochlamydia amoebophila.” Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.

scholarly journals Methylibium aquaticum sp. nov., a betaproteobacterium isolated from a eutrophic freshwater pond

2007 ◽  
Vol 57 (9) ◽  
pp. 2125-2128 ◽  
Author(s):  
Jaeho Song ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Closely Related Species ◽  
Freshwater Pond ◽  
Phyletic Line ◽  
Utilization Patterns

A freshwater bacterium, designated IMCC1728T, was isolated from a eutrophic pond. The strain was Gram-negative, chemoheterotrophic and facultatively aerobic, forming non-motile rods that contained poly-β-hydroxybutyrate granules. Based on 16S rRNA gene sequence comparisons, the most closely related species to strain IMCC1728T was Methylibium petroleiphilum (97.0 % similarity). Phylogenetic trees generated using 16S rRNA gene sequences showed that this isolate formed an independent phyletic line of the genus Methylibium clade of the class Betaproteobacteria. The DNA G+C content of the strain was 66.2±0.4 mol%. The predominant cellular fatty acid constituents were C16 : 1 ω7c and/or iso-C15 : 0 2-OH (43.1 %), C16 : 0 (20.3 %), C12 : 0 (13.4 %) and C10 : 0 3-OH (7.3 %). The strain contained Q-8 as the predominant ubiquinone. Several phenotypic characteristics, including flagellation, temperature range for growth and carbon source utilization patterns, differentiated strain IMCC1728T from species of the genus Methylibium. Therefore, it is proposed that strain IMCC1728T represents a novel species, Methylibium aquaticum sp. nov. The type strain is IMCC1728T (=KCCM 42364T=NBRC 102349T).

scholarly journals A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria,Paenibacillus larvaeandBrevibacillus laterosporus

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
Jordan A. Berg ◽  
Bryan D. Merrill ◽  
Donald P. Breakwell ◽  
Sandra Hope ◽  
Julianne H. Grose
Keyword(s):  
Molecular Markers ◽  
16S Rrna ◽  
Related Species ◽  
Ecological Niche ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Closely Related Species ◽  
Content Type

ABSTRACTPaenibacillus larvaeandBrevibacillus laterosporusare two bacteria that are members of thePaenibacillaceaefamily. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published asP. larvaeand provide the phylogenetic evidence that supported the GenBank reassignment of the sequences asB. laterosporus. We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguishP. larvaefromB. laterosporusand other closely related species within thePaenibacillusgenus and a third set that distinguishesB. laterosporusfromP. larvaeand other closely related species within theBrevibacillusgenus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains ofP. larvaeandB. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studyingBrevibacillus,Paenibacillus, and other disease-relevant bacteria commonly found in beehives.

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 Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces

2008 ◽  
Vol 74 (13) ◽  
pp. 3969-3976 ◽  
Author(s):  
Jingrang Lu ◽  
Jorge W. Santo Domingo ◽  
Regina Lamendella ◽  
Thomas Edge ◽  
Stephen Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Diversity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Environmental Waters ◽  
Potential Risks ◽  
Species Specific ◽  
Gut Microbial Community

ABSTRACT In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.

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 Amplification of 16S rRNA gene sequences to differentiate two highly related bradyrhizobia species

2007 ◽  
Vol 42 (9) ◽  
pp. 1361-1364 ◽  
Author(s):  
Adriana Giongo ◽  
Adriana Ambrosini ◽  
João Ruy Jardim Freire ◽  
Maria Helena Bodanese Zanettini ◽  
Luciane Maria Pereira Passaglia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bradyrhizobium Japonicum ◽  
Diagnostic Method ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Reference Strains ◽  
Commercial Inoculants

A 16S rRNA gene PCR-based assay was developed aiming at a fast molecular diagnostic method to differentiate the two phylogenetically closely related species Bradyrhizobium japonicum and B. elkanii, isolated from soybean nodules, in order to identify those more competitive and comprising greater nitrogen fixation ability for use in the formulation of commercial inoculants. The assay used was able to discriminate ten reference strains belonging to these two Bradyrhizobium species, as well as to efficiently identify 37 strains isolated from fields cultivated with soybean.

scholarly journals 16S rRNA Long-Read Sequencing of the Granulation Tissue from Nonsmokers and Smokers-Severe Chronic Periodontitis Patients

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Rebecca Chowdhry ◽  
Neetu Singh ◽  
Dinesh Kumar Sahu ◽  
Ratnesh Kumar Tripathi ◽  
Archana Mishra ◽  
...  
Keyword(s):  
16S Rrna ◽  
Granulation Tissue ◽  
Ketone Bodies ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Streptobacillus Moniliformis ◽  
Increased Risk ◽  
Long Read ◽  
Significant Enrichment

Smoking has been associated with increased risk of periodontitis. The aim of the present study was to compare the periodontal disease severity among smokers and nonsmokers which may help in better understanding of predisposition to this chronic inflammation mediated diseases. We selected deep-seated infected granulation tissue removed during periodontal flap surgery procedures for identification and differential abundance of residential bacterial species among smokers and nonsmokers through long-read sequencing technology targeting full-length 16S rRNA gene. A total of 8 phyla were identified among which Firmicutes and Bacteroidetes were most dominating. Differential abundance analysis of OTUs through PICRUST showed significant (p>0.05) abundance of Phyla-Fusobacteria (Streptobacillus moniliformis); Phyla-Firmicutes (Streptococcus equi), and Phyla Proteobacteria (Enhydrobacter aerosaccus) in nonsmokers compared to smokers. The differential abundance of oral metagenomes in smokers showed significant enrichment of host genes modulating pathways involving primary immunodeficiency, citrate cycle, streptomycin biosynthesis, vitamin B6 metabolism, butanoate metabolism, glycine, serine, and threonine metabolism pathways. While thiamine metabolism, amino acid metabolism, homologous recombination, epithelial cell signaling, aminoacyl-tRNA biosynthesis, phosphonate/phosphinate metabolism, polycyclic aromatic hydrocarbon degradation, synthesis and degradation of ketone bodies, translation factors, Ascorbate and aldarate metabolism, and DNA replication pathways were significantly enriched in nonsmokers, modulation of these pathways in oral cavities due to differential enrichment of metagenomes in smokers may lead to an increased susceptibility to infections and/or higher formation of DNA adducts, which may increase the risk of carcinogenesis.

scholarly journals Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

2021 ◽  
Vol 9 (8) ◽  
pp. 1721
Author(s):  
Christian O’Dea ◽  
Roger Huerlimann ◽  
Nicole Masters ◽  
Anna Kuballa ◽  
Cameron Veal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Surface Waters ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Faecal Contamination ◽  
Hypervariable Regions ◽  
Geographical Regions ◽  
V3 Region

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

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