What is the purpose of metagenomic sequencing?
What is Shotgun Metagenomic Sequencing? Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments.
What is whole metagenomic sequencing?
Whole Metagenome sequencing (WMS), or shotgun metagenome sequencing, is a relatively new and powerful sequencing approach that provides insight into community biodiversity and function. The choice of shotgun or 16S approaches is usually dictated by the nature of the studies being conducted.
How is a metagenome analyzed?
Metagenomics is defined as the direct genetic analysis of genomes contained with an environmental sample. The field initially started with the cloning of environmental DNA, followed by functional expression screening [1], and was then quickly complemented by direct random shotgun sequencing of environmental DNA [2,3].
How do you analyze metagenomic data?
Understand the advantages and limitations of metagenomic data analysis. Devise an appropriate bioinformatics workflow for processing and analyzing metagenomic sequence data (marker-gene, shotgun metagenomic, and metatranscriptomic data) Apply appropriate statistics to undertake rigorous data analysis.
What is metagenomic assembly?
Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks.
What is a metagenomic library?
Metagenomic libraries are useful in exploration of microbial diversity in unculturable systems and they form the basis for genomic studies that link the phylogenetic and functional relationships within the system and with the environment.
How metagenomic sequence reads can be analyzed to assign Otus?
Each taxonomic group consists of multiple 16S rRNA gene sequences to which a read may have multiple hits. The nearest neighbor approach assigns each read to the taxonomic group with the highest BLAST score, or, if two or more groups have the same score, to all of those with equal weights summing up to 1.
Where are microbiota found?
gut
The human body is inhabited by millions of tiny living organisms, which, all together, are called the human microbiota. Bacteria are microbes found on the skin, in the nose, mouth, and especially in the gut.
Can whole-metagenome shotgun sequencing characterize bird microbiomes and resistomes?
Rapid, high-throughput metagenomics have recently been used to annotate functional pathways and identify ARGs in the microbiota of humans and soil samples. Here, we collected fresh samples from 10 bird species and their associated environments and used whole-metagenome shotgun sequencing to characterize their microbiomes and resistomes.
How common are mcr-1 and β-lactamase genes in birds?
Interestingly, we found that the mcr-1 resistance gene is widespread among different birds, accounting for 50% of the total samples. Meanwhile, a large number of novel β-lactamase genes are also reconstructed from bird metagenomic assemblies based on fARGene software.
Is the resistome related to microbial community structure in migratory birds?
Procrustes analysis indicated that microbial community structure is not correlated with the resistome in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate from Proteobacteria.
Is the gut microbiota a reservoir of antibiotic resistance genes in humans?
Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated.