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16S rRNA - PubAg

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Last Updated: 15 October 2021

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Phylogenetic Relationships of Flounders from the Family Pleuronectidae (Ostichties: Pleuronectiformes) Based on 16S rRNA Gene

In complete 62 specimens of 14 types of our own collections were sent to the GenBank/BOLD databases and studied. If the people Microstomini is omitted from it and genus Lepidopsetta is moved into the people Pleuronectini, the subfamily Pleuronectinae can be taken into consideration monophyletic. One set included all the obtained 16S rRNA genetics series, the second set consisted of an example of longer 16S rRNA sequences, and the third set was composed of 3 gene sequences: 16S co-1, cyt-b, and rrna.

Source link: https://pubag.nal.usda.gov/catalog/7331221


Impact of DNA extraction methods on 16S rRNA-based profiling of bacterial communities in cheese

Numerous factors related to example prep work, DNA extraction, primer option, sequencing platform and information evaluation can influence the accuracy of 16S rRNA sequencing outcomes. DNA was isolated from Mozzarella as a model cheese utilizing enhanced bead-based homogenization complied with by various removal treatments. Six out of seven DNA removal treatments were discovered to be able to offer amplifiable microbial DNA ideal for 16S rRNA series analysis, but private extraction procedures led to variable outcomes. Particularly, lysis supported with bead-beating resulted in a greater percentage of G+ germs in relative wealth profiles, possibly due to the a lot more effective cell wall disruption. The results demonstrated a threat in contrasting the information on microbial areas in cheese when various DNA removal procedures are utilized and highlighted the requirement to pick a standard strategy when contrast throughout numerous sequencing runs is required.

Source link: https://pubag.nal.usda.gov/catalog/7327909


16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys

The presence of several copies of this genetics makes the community abundance data distorted and genetics duplicate normalization required for modification. Also though GCN of 16S data offered a picture closer to the metagenome before, it needs to be contrasted with neighborhoods of well-known make-up due to the fact that library preparation is prone to methodological biases. Right here, we process 16S rRNA gene amplicon data from eleven easy mock communities with DADA2 and estimate the impact of GCN. Our approach provides empirical proof that GCN does not boost the 16S target sequencing analyses in real situations.

Source link: https://pubag.nal.usda.gov/catalog/7255051


Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis

Human milk is the perfect food for infants because of its one-of-a-kind dietary and immune properties, and more lately human milk has been identified as an essential resource of microorganisms for babies. A considerable amount of essential human milk microbiome info continues to be uncertain, such as the beginning, structure and function of the community and its members.

Source link: https://pubag.nal.usda.gov/catalog/7200994


Microbial communities in field-scale oil-polluted soil remediation using 16S rRNA amplicon sequencing

This investigation utilized 16S rRNA amplicon sequencing to comprehend microbial dynamics throughout a 2-month field-scale oil-impacted soil removal in the N.... Delta. Surface area soil had extractable overall petroleum hydrocarbons focus of 6231 mg/kg and subsurface samples from 1. 0 m, 1. 5 m and 2. 0 m depths had 4836 mg/kg, 9112 mg/kg and 7273 mg/kg, respectively. Proteobacteria controlled the bacterial community of the oil-polluted soil and made up primarily Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Principal coordinate analysis indicated that the community framework continually altered complying with variants in the ETPH concentrations.

Source link: https://pubag.nal.usda.gov/catalog/7358082


Gut microbiome of the White Sea fish revealed by 16S rRNA metabarcoding

Because of high phylogenetic diversity and broad circulation understanding of gut microbiota of fish is uncertain. We clarify previously undescribed variety of bacteria in the White Sea fish posterior intestinal tract based on 16S rRNA metabarcoding: shorthorn sculpin, lumpfish frozen flounder, cod, and herring. The datasets of G. morhua and Cl. pallasii were enriched by reviews of Shewanella; the datasets of G. morhua and M. scorpius consisted of high variety of Mycoplasma, which remains in line with previous records on the microbiome of marine fish intestine from other geographical regions. Collectively, on the one hand, the research study is a confirmation of well-known data on marine fish intestine microbiome, on the other hand, it reveals some particular patterns of White Sea fish intestine microbiota, e. g.

Source link: https://pubag.nal.usda.gov/catalog/7184695


Evaluation of microbial diversity of three recreational water bodies using 16S rRNA metagenomic approach

Surface water plays a significant duty in world advancement by advertising financial growth and health and wellness advantages to animals and people whose lives rely on great water quality in the ecological community. The results gotten recommend that the water resources met the recommended entertainment water quality criteria basic for clean water. Pressure, conductivity, temperature, liquified oxygen, and pH made up 74. 2% of the variation in the distribution of the microbial community in the three locations, while 58. 2% of the variant in the microbial community circulation was accounted for by pressure and conductivity. The arise from this research show that the microbial areas in both lakes are different from the fish pond and all the environmental variables accounted for a significant part of the overall variant, however temperature level, pressure, and conductivity are more crucial aspects as a result of considerable relationship with the circulation of the microbial areas.

Source link: https://pubag.nal.usda.gov/catalog/7258917


Bacterial association observations in Lucilia sericata and Lucilia cuprina organs through 16S rRNA gene sequencing

Blowfly types Lucilia sericata and related species Lucilia cuprina are essential farming bugs, help in forensic fields and additionally have a restorative duty in medication. Conversely, larvae of L. cuprina feed invasively, as major initiators of lamb myiasis in Australia, New Zealand, and the UK, amongst various other regions. Comparison of bait attractions to example sequence read result of insect samplings showed no relationship with genera such as Pseudomonas existing in insects, while lacking from wild lure, and in lowered quantities from fleece lure accounts. ESSENTIAL POINTS: Genera Pseudomonas appears consistently in the microbiome of Lucilia varieties. Salivary glands and women spermathecae reveal the highest possible microbial variety. Microbial profiles of L. sericata and L. cuprina have comparable make-up.

Source link: https://pubag.nal.usda.gov/catalog/7257349


Comparison of different hypervariable regions of 16S rRNA for taxonomic profiling of vaginal microbiota using next-generation sequencing

The research aimed to identify vaginal microbiota from medical samples using NGS targeting the 16S rRNA gene and to identify the efficiency of specific and concatenated hypervariable area series to generate the taxonomic accounts of the genital microbiota. Fifty-one vaginal DNA samples were subjected to 16S rRNA gene NGS based on the Ion Torrent PGM platform with making use of two guide collections covering seven hypervariable regions of the 16S rRNA gene. Our analysis disclosed that the predominant microbial category were Lactobacillus, Gardnerella and Atopobium, which accounted for 78%, 14% and 2%, specifically, of sequences from all vaginal microbial category. At the varieties degree, Lactobacillus iners, Gardnerella vaginalis and Atopobium vaginae made up 72%, 10% and 6%, specifically, of the bacterial cells present. Evaluations using the V3 region usually indicated the greatest microbial variety adhered to by the V6-- V7 and V4 regions, while the V9 area gave the most affordable microbial resolution.

Source link: https://pubag.nal.usda.gov/catalog/7311239


Simple assay for colorimetric quantification of unamplified bacterial 16S rRNA in activated sludge using gold nanoprobes

Domestic and industrial wastewater treatment systems are vital in the security of natural ecological communities and human wellness. Identification of microbial communities in the systems is vital to secure treatment performance. The present tools of microbial community evaluation are labor extensive and time consuming, and call for costly tools. We established a simple assay for colorimetric quantification of microbial 16S rRNA extracted from ecological samples. We achieved ample capture DNA density by setting the capture DNA probe focus at 10 μM throughout the functionalization action. Making use of the calibration curve, the bacterial 16S rRNA focus in triggered sludge samples could be measured with variances between 48% and 208% against those figured out by RT-qPCR. The findings of our study present a cutting-edge tool for the metrology of 16S rRNA concentration as the task of essential germs in wastewater treatment processes, accomplishing stable treatment performance.

Source link: https://pubag.nal.usda.gov/catalog/7131686

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions