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Metagenomics - Europe PMC

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Last Updated: 23 April 2022

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Relative species abundance estimation in artificial mixtures of insects using mito‐metagenomics and a correction factor for the mitochondrial DNA copy number

Mitometagenomics is a viable alternative to amplicon metabarcoding for the determination of biodiversity in complicated biological samples using high-throughput sequencing. As the reads are gathered from shotgun sequencing, a small number of reads map to the mitogenomes, so a high sequencing effort is required. The relative species abundance in a mixture could be inaccurate, as the number of mitogenomes per cell can vary among species. We created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to determine the RSA using fresh specimens of these species. The method was also able to determine the number of species of a species from different samples, but it was also unable to determine RSA within a single sample unless a adjustment factor accounted for the variable number of mitogenomes per cell.

Source link: https://europepmc.org/article/MED/IND607601463


Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions

We used metagenomics technologies to comprehensively investigate the metabolic function and taxonomic diversity of the microbial confederation of the microbial confederations CS and FP. The microbial consortia CS and FP's taxonomic affiliations revealed substantial variations in the taxonomic composition and carbohydrate-active enzymes profiles. In CS and Cellvibrio and Pseudomonas in FP, a much larger distribution of lignocellulose degradative activity. When the relatively simple substrate filter paper was used as the carbon source, the enzymes for more lignocellulose degradative enzymes were discovered. These results reveal how microorganisms and enzyme synergism occur during the degradative process of lignocellulose under various substrates, indicating the potential microbial resources.

Source link: https://europepmc.org/article/MED/IND607715610


Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis.

Phoxim is one of the most common organophosphorus pesticides used in agricultural production. The presence of aquatic microbial communities was significantly altered by seven days of phoxim exposure, obliterating the interactions between microorganisms and microorganisms, thereby reducing the complexity and stability of the microbial community. The zebrafish gut microbial community also recovered from a temporary biological disturbance of aquatic microbiota, but phoxim has continued to influence zebrafish growth and swimming habits. Overall, our findings found that phoxim exposure significantly improved the structure and function of the microbial community, as well as showing a negative effect on freshwater ecosystems in a short exposure time.

Source link: https://europepmc.org/article/MED/35449330


Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.

Centenarians' gut microbiota profile shows some unusual characteristics from young adults, and the gut microbiota profile shows some important differences in human longevity. Most microbial studies on longevity are now based on metagenomic sequencing, which may lack details about the functional microbes in a low number. To discover a Chinese longevity population's unique gut microbial community and longevity, we combined in-depth metagenomic sequencing and large-scale culturomics. From a individual fecal sample, an average of 51. 1 Gb raw sequencing results were obtained. The elderly cohort in Hainan province displayed a significant decrease in butyrate-producing bacteria and a large number of Escherichia coli, Desulfovibrio piger, and Methanobacter smithii. The Hainan extreme decades population's uniquely enriched gut microbes may help to improve health and longevity.

Source link: https://europepmc.org/article/MED/35440640


Short- and long-read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing.

Short-read metabarcoding of variable regions of the 18S rRNA gene with amplicons is currently the go-to test for determining microbial eukaryotes. It determines whether community members are included, if they can be identified at a high taxonomic level, and if the collected community profile is representative. 177,934 and 21,072 database sequences were used to develop new primers for 18S and 28S rRNA. The primers were tested in silico, as well as published primers on reference sequence databases and marine metagenomics datasets. A subset of the primers for short- and long-read sequencing of environmental samples in vitro was further tested by the researchers, who compared the estimated community profile with primer-unbiased metagenomic sequencing. Good results were obtained in silico and in vitro, among the short-read pair, a new V6-V8 pair and the V4_Balzano pair using a simplified PCR protocol.

Source link: https://europepmc.org/article/MED/35437888


Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting.

Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can raise the effectiveness of composting. To improve manure composting, we show an approach that integrates 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria. Firmicutes and Actinobacteria were predominant in the composting mixture, according to a 16S RNA amplicon sequencing report, and that different microbial hubs thrived during the thermophilic stage. The amplicon sequencing revealed that these isolated thermophilic bacteria were divided into 11 phylotypes, which shared >99% sequence identity to 0. 15 to 5. 3 percent of 16S rRNA reads by the amplicon sequencing. Five out of seven of five of the microbial inoculants improved composting's thermophilic stage by 16. 9% to 52. 2%. In conclusion, 16S rRNA amplicon metagenomics is a useful device for the production of microbial inoculants that can improve manure composting.

Source link: https://europepmc.org/article/MED/35436715


Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique.

Beside HLB There are several other bacterial species in citrus groves in Pakistan. For diversity analysis, Grapefruit, C. aurantifolia, and C. reticulata Blanco were grown on sick leaf samples of Grapefruit, C. aurantifolia, and C. reticulata Blanco were used. Using PCR amplicons of 16S rDNA sequences with Illumina Hi seq, a high throughput NGS technique was used to access both cultivable and non-cultivable bacterial endophytes from citrus leaves. Both C. aurantifolia and C. paradisi displayed nearly equal abundance, while C. reticulata Blanco had a higher number of Procobacteria and Cyanobacteria in their leaves, although C. reticulata Blanco had a higher proportion of Proseobacteria and Cyanobacteria in their leaves. According to the inverse Simpson diversity survey, the microbial population in six different citrus samples was 0. 48, 0. 6, and 0. 63 percent, respectively. Microbiota in plant tissue was successfully captured by NGS technology, which may help us learn more about plant-microbe interactions.

Source link: https://europepmc.org/article/MED/35417473


Ultra-high-throughput microbial single-cell whole genome sequencing for genome-resolved metagenomics

However, less than 1% of microorganism species have been found so far, and more than 99% of microorganisms have remain unknown, which is described as microbial dark matter. Unraveling microbial dark matter is not only useful for investigating the unknown microbial world, but also of utmost importance for human health research. When studying rare and unknown microbial species, traditional population-based metagenomic analysis methods are lacking single microbial resolution, and they are becoming more restricted.

Source link: https://europepmc.org/article/PPR/PPR479619

* 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