Metagenomics is a rapidly growing field of research that permits direct investigation of viruses, bacteria, and fungi irrespective of their taxonomic and culturability identities. Metagenomic analysis method can infer functional and taxonomic information for the complex microbial community, guiding the studies aimed at understanding its role in human health.
In a new study by researchers at EMBL’s European Bioinformatics Institute and Wellcome Sanger Institute with the help of computational method have identified around 2,000 bacterial species in the human gut. The researchers have reconstructed nearly 92,000 bacterial genomes from around 12,000 human gut metagenomic datasets, corresponding to 1,952 uncultured bacterial species.
The results published in the Nature journal highlighted that although researchers are getting closer to creating a list of common microbes found in the European and North American population, there is still a lack of data from other parts of the world. Hence, researchers are calling for more data from Africa, South America, and Asia in order to achieve a comprehensive blueprint of the human gut.
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Reconstructing the Genomes of Gut Bacteria
There are a number of reasons as to why microbial species in the gut have remained unknown for so long. However, by using computational methods, researchers successfully reconstructed the genomes of these bacteria. According to Robert Finn, group leader at EMBL-EBI, using metagenomics to reconstruct the bacterial genomes is a bit tuff. However, researchers are now at the position where a variety of computational tools can be used to expose new insights in the human gut.
In order to conduct the study, Finn and his colleagues collected around 13,133 human gut metagenomic datasets from 75 studies. Majority of these samples, nearly 88% were collected from Europe and North America. Researchers assembled the metagenomes using genome assembler SPAdes and they also used software tool MetaBAT to efficiently reconstruct single genomes from complex microbial communities.
Researchers also generated 40,029 metagenomes assembled genomes (MAGs) with over 90% completeness. In the study, researchers leveraged a comprehensive public database of gastrointestinal bacteria in order to identify new bacterial species. According to Trevor Lawley, group leader at Wellcome Sanger Institute, the analysis methods used in the study can be applied to the more diverse dataset in the future for further discovery. This research is also helping scientists to create a blueprint of human gut that can help in better understanding of diseases and can even guide in the treatment of gastrointestinal diseases.
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Genetic information is being used on a large scale to identify new diseases and development of a novel test for disease diagnosis. Many new bioinformatics and biotechnology tools are being developed by manufacturers, thereby driving the growth in metagenomics market. With various types of metagenomics products available, library preparation kits are being frequently used as it influences functional and genomic predictions in human microbiome research.
A recent study on the metagenomics has also found that next-gen sequencing of metagenomes is now widely used in various applications including clinical diagnostics, forensic genetics, infectious disease surveillance and pathogen outbreaks. Meanwhile, advances in the next-gen sequencing technology, it is resulting in various library preparation products in the metagenomics market.