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Metagenomics - DOAJ

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Last Updated: 23 April 2022

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Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

Bone and joint infections are extremely infectious infections that necessitate precise microbiological information to optimize antibiotic therapy. We compared the results of CMg in 34 patients with suspected BJIs, as well as culture and 16S rDNA sequencing in the present study. Based on the sequencing results of negative controls, 414 out of 539 out of 539 bacterial species detected by CMg were classified as contaminants and 125 as present. For monomicrobial infections, the sensitivity of CMg was 83. 3% higher than culture, and 100% as compared to 16S rDNA. CMg detected 11 bacteria in ten samples from five different patients, including samples that were negative in culture. CMg performed a microbiological diagnosis where traditional treatments failed in 5/34 patients, and in 16/34 patients, CMg provided additional details. In conclusion, our review found that the CMg provides additional and potentially useful data to conventional BJIs diagnosis methods.

Source link: https://doi.org/10.3389/fmicb.2022.863777


Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique

Beside HLB In Pakistan, citrus groves host several other bacterial species. For diversity analysis, grapefruit, C. aurantifolia, and C. reticulata Blanco leaf samples were used. Using PCR amplicons of 16S rDNA sequences with Illumina Hi seq, this high-throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves. Both C. aurantifolia and C. paradisi displayed nearly equal diversity, although C. reticulata Blanco had a larger proportion of Prothrobacteria and Cyanobacteria in their leaves. Microbiota in plant tissues was successfully captured by NGS technology, which can enable us to learn more about plant-microbe interactions. This paper is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina Technology.

Source link: https://doaj.org/article/0c6d06a4aca94cedb8ef682efc81edac


Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water

Therefore, we seek to assess the effectiveness of our municipal wastewater treatment plant process in producing pathogen-free water by analyzing the microbial composition of influent and effluent water sites in this report. The influent and effluent samples of six separate WWTP sites located in Johore, Malaysia, were processed using the Illumina platform using the Illumina platform. As compared to tightly clustered influent samples, effluent sites showed significant variation in the genetic composition due to loosely clustered sample plots, as well as tight clustered influent samples. Despite the closeness of the top three abundant phyla in influent and effluent locations, the ARG composition heat map and drug class plot bar displays a general trend of a downward trend, revealing WWTP's effectiveness in reducing opportunistic pathogens.

Source link: https://doi.org/10.3389/fmicb.2022.779196


´╗┐Comparative metagenomics of phytoplankton blooms after nutrient enrichment of oligotrophic marine waters

The coastal marine environments are being affected by a variety of factors, including increasing algal blooms and increasing nutrient loading. We use a metagenomics approach to examine the neomic and functional changes of the microbial community during a bloom of nutrient-rich mesocosm phytoplanktons. For the first two weeks of the experiment, we tested four different nutrient treatments, composed of either nitrate and phosphate, and silicate. A remarkable improvement of the dissimilatory nitrate reduction pathway in the post-bloom period was shown by changes within energy metabolism pathways. During the bloom, the Eukaryotic oxidative phosphorylation and photosynthetic antenna proteins were more abundant, especially in the continuous treatment with silicate. Our findings indicate that continued nutrient enrichment has a larger effect on marine systems' functioning relative to a single addition.

Source link: https://doi.org/10.3897/mbmg.6.79208


Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

Abstract Background Improving knowledge of biodiversity could improve conservation biology, enhance bioremediation methods, and lead to new medical treatments. First, integrative metagenomic studies, aimed at simultaneous examination of findings based on a large number of genes, functions, and evolutionary processes documented by multiple markers' frequent sequence of sequences, should be preferred over DNA barcoding schemes and metagenomic studies based on a single marker. Testing the hypothesis We arrived these results by a comparison of the theoretical bases of two molecular approaches trying to document biodiversity: metagenomics and DNA barcoding, as well as pragmatic evaluations of the challenges posed by the'species problem' in biodiversity research. The hypothesis of producing biodiversity estimates with low explanatory ability, biased either by unequal numbers of LGT or impossible to interpret due to the challenges posed by type I and type II grey zones, which were difficult to interpret due to the difficulties posed by type I and type II grey zones.

Source link: https://doi.org/10.1186/1745-6150-5-47


Assessing intragenomic variation of the internal transcribed spacer two: Adapting the Illumina metagenomics protocol.

The green algae's primary and secondary structure data from the internal transcribed spacer two have been used extensively for diversity research of many species of eukaryotic plants, including the green algae. In selected isolates of the green algal genus, Haematococcus, we have the results from our modification of the 16S Metagenomics Sequencing Library Preparation/Illumina protocol for deep sequencing of the ITS2 genes. In addition, a conservative review of these results revealed a spectrum of three to six ITS2 sequence haplotypes throughout taxon sampling. From 0. 35 to 0. 98, the frequency of the most common haplotype varied. In all but two instances, the haplotype with the highest frequency corresponded to a sequence obtained by the Sanger method using PCR templates. The results of this research will enable us to start testing hypotheses regarding the preservation of homogeneity across multi-copy genes in addition to improving our understanding of ribosomal RNA variations.

Source link: https://doi.org/10.1371/journal.pone.0181491

* 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