Characterization of oral bacteria in the tongue coating of patients with halitosis using 16S rRNA analysis

2020 ◽  
Vol 78 (7) ◽  
pp. 541-546 ◽  
Author(s):  
Akiko Oshiro ◽  
Takashi Zaitsu ◽  
Masayuki Ueno ◽  
Yoko Kawaguchi
Keyword(s):  
16S Rrna ◽  
Oral Bacteria ◽  
Tongue Coating ◽  
16S Rrna Analysis

scholarly journals Functional Metagenomics Characterization of an Anaerobic Saltwater Bioreactor

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
D. Derilus ◽  
A. Forestil ◽  
J. Fortuné ◽  
O. Polyanska ◽  
C. Louime ◽  
...  
Keyword(s):  
Renewable Energy ◽  
16S Rrna ◽  
Microbial Communities ◽  
Common Property ◽  
Marine Macroalgae ◽  
Functional Metagenomics ◽  
16S Rrna Analysis ◽  
Potential Applications ◽  
Tree Building

Methanogens are restricted to a few genera of Archaea, however they have great importance in the carbon cycle, impacting climactic considerations, and also find a role in renewable energy in the form of biogas. Here, we examine the microbial contribution to the production of methane in a sargassum fed anaerobic saltwater bioreactor, which are poorly characterized compared to fresh water bioreactors, using a comprehensive functional metagenomics approach. Despite abundant production of methane, we detected a low proportion of Archaea in the system using 16S rRNA community profile analyses. We address the low representation using an additional 16S rRNA analysis of shotgun data and a consideration of CO2:CH4production. Using a novel network alignment and tree building approach, we measured similarity between the meta-metabolic capabilities of different anaerobic microbial communities. The saltwater bioreactor samples clustered together, validating the approach and providing a method of determining meta-metabolic similarity between microbial communities, with a range of potential applications. We also introduce a number of additional approaches for examining and interpreting meta-metabolic network topology. The low abundance of methanogens appears as a common property of such anaerobic systems and likely reflects the relatively poor energetics of methanogens, while examination of key enzymes confirms that hydrogen producing bacteria are the major fermentative guild. Our results indicate that the use of readily available seawater and marine macroalgae is a promising approach to the production of biogas as a source of renewable energy.

scholarly journals Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis

Microbiology ◽  
1995 ◽  
Vol 141 (2) ◽  
pp. 513-521 ◽  
Author(s):  
M. Schuppler ◽  
F. Mertens ◽  
G. Schon ◽  
U. B. Gobel
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Molecular Characterization ◽  
16S Rrna Analysis

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

Functional and Structural Characterization of Acquired Pan-Aminoglycoside Resistance 16S rRNA Methyltransferase NpmB1

2021 ◽  
Author(s):  
Akito Kawai ◽  
Masahiro Suzuki ◽  
Kentaro Tsukamoto ◽  
Yusuke Minato ◽  
Yohei Doi
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Amino Acid Identity ◽  
Single Amino Acid ◽  
Aminoglycoside Resistance ◽  
E Coli ◽  
The United Kingdom ◽  
Amino Acid Variant ◽  
A Site

Post-translational methylation of the A site of 16S rRNA at position A1408 leads to pan-aminoglycoside resistance encompassing both 4,5- and 4,6-disubstituted 2-deoxystreptamine (DOS) aminoglycosides. To date, NpmA is the only acquired enzyme with such function. Here, we present function and structure of NpmB1 whose sequence was identified in Escherichia coli genomes registered from the United Kingdom. NpmB1 possesses 40% amino acid identity with NpmA1 and confers resistance to all clinically relevant aminoglycosides including 4,5-DOS agents. Phylogenetic analysis of NpmB1 and NpmB2, its single amino acid variant, revealed that the encoding gene was likely acquired by E. coli from a soil bacterium. The structure of NpmB1 suggests that it requires a structural change of the β6/7 linker in order to bind to 16S rRNA. These findings establish NpmB1 and NpmB2 as the second group of acquired pan-aminoglycoside resistance 16S rRNA methyltransferases.

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