# Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

## TL;DR

This study examines how different DNA library preparation methods and input DNA amounts affect the accuracy of metagenomic reconstructions in low biomass microbial communities.

## Contribution

The study provides benchmarking insights and recommendations for minimizing bias in metagenomic sequencing of low biomass environments.

## Key findings

- Lower input DNA quantities led to increased GC content and more unmapped low-quality reads.
- Library preparation methods significantly influenced metagenomic community composition and assembly quality.
- Recommendations are provided for creating representative metagenome shotgun sequencing libraries.

## Abstract

The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation.

Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition.

This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.

The online version of this article (doi:10.1186/s12864-015-2063-6) contains supplementary material, which is available to authorized users.