Open AccessA breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems
Author(s) -
Gabriele Andrea Lugli,
Marco Ventura
Publication year - 2022
Publication title -
microbiome research reports
Language(s) - English
Resource type - Journals
ISSN - 2771-5965
DOI - 10.20517/mrr.2021.07
Subject(s) - metagenomics , microbiome , shotgun sequencing , computational biology , shotgun , biology , dna sequencing , data science , computer science , ecology , bioinformatics , genetics , gene
Next-generation sequencing technologies allow accomplishing massive DNA sequencing, uncovering the microbial composition of many different ecological niches. However, the various strategies developed to profile microbiomes make it challenging to retrieve a reliable classification that is able to compare metagenomic data of different studies. Many limitations have been overcome thanks to shotgun sequencing, allowing a reliable taxonomic classification of microbial communities at the species level. Since numerous bioinformatic tools and databases have been implemented, the sequencing methodology is only the first of many choices to make for classifying metagenomic data. Here, we discuss the importance of choosing a reliable methodology to achieve consistent information in uncovering microbiomes.