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Metagenomics

Personalized gut microbiome variants

Nature Reviews Genetics volume 14, pages 80–81 (2013)Cite this article

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Schloissnig et al. developed a pipeline for the identification of genetic variants within metagenomic data and applied this to the human gut microbiome. To generate reference genomes, they first assigned the genome sequences of 1,497 published bacterial and archaeal genomes to 929 genome clusters, each of which represented a different species. The reference from each genome cluster was then defined as being the genome that recruited the highest number of reads within each cluster.

Metagenomic reads from 252 stool samples from 207 individuals from North America and Europe (most from previous large microbiome projects) were then mapped to these reference genomes, and variants were called in the 101 most abundant genomes. A total of 10.3 million SNPs were identified in addition to 107,991 indels and 1,051 structural variants. Annotation of the genes revealed that genes relating to conjugal transfer of antibiotic resistance genes had the highest SNP density.

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ORIGINAL RESEARCH PAPER

  1. Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 5 Dec 2012 (doi:10.1038/nature11711)

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  1. Hannah Stower
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Stower, H. Personalized gut microbiome variants. Nat Rev Genet 14, 80–81 (2013). https://doi.org/10.1038/nrg3408

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