Abstract
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms in a single experiment, with the possibility of de novo reconstruction of the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. However, we demonstrate that-for some applications-it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. Here we compared the results obtained on full size, real datasets with results obtained by randomly extracting a fixed number of reads. The main statistics that were compared are alpha diversity estimates, species abundance, and ability of reconstructing the metagenome in terms of length and completeness. Our results show that a classification of the communities present in a complex matrix can be accurately performed even using very low number of reads. With samples of 100,000 reads, the alpha diversity estimates were in most cases comparable to those obtained with the full sample, and the estimation of the abundance of all the present species was in excellent agreement with those obtained with the full sample. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1M reads). The length of the reconstructed assembly was sensibly smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct de novo-even partially-the metagenome.
Highlights
Shotgun metagenomics offers the possibility to assess the complete taxonomic composition of biological matrices and to estimate the relative abundances of each species in an unbiased way[1,2]
Metagenome shotgun high-throughput sequencing has progressively gained popularity in parallel with the advancing of next-generation sequencing technologies[8,9], which provide more data in less time at a lower cost than previous sequencing techniques
The aim of the present work was to assess the reliability of lowdepth shotgun metagenome sequencing for the characterization of complex matrices, as follows: 1) determining diversity and species richness in complex matrices; 2) estimating abundance of the species present in the complex matrix, and 3) reconstructing de novo the genome of the species present in the samples
Summary
Shotgun metagenomics offers the possibility to assess the complete taxonomic composition of biological matrices and to estimate the relative abundances of each species in an unbiased way[1,2]. Metagenome shotgun high-throughput sequencing has progressively gained popularity in parallel with the advancing of next-generation sequencing technologies[8,9], which provide more data in less time at a lower cost than previous sequencing techniques This allows the extensive application to study the most various biological mixtures such as environmental samples[10,11], gut samples[12,13,14], skin samples[15], clinical samples for diagnostics and surveillance purposes[16,17,18,19], food ecosystems[20,21] and drugs manufactured using biological sources as vaccines[22]. The approach has been used to analyze the ensemble of genes that may encode antibiotic resistance in various microbial ecosystems (i.e. soil), which are defined as the resistome[24]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
