Synergistic effect of short- and long-read sequencing on functional meta-omics

Abstract

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only, and hybrid assembly approaches on four different metagenomic samples of varying complexity and demonstrate how they affect gene and protein inference which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.

Metatranscriptomics of cheese microbial communities: Efficiency of RNA extraction from various cheese types and of mRNA enrichment

“…We also tested the recently released FastSelect kits that use oligonucleic acids that selectively block the reverse transcription of rRNA. The bacterial version (5S/16S/23S) of this kit was used in a recent study for the metatranscriptomic analysis of a fecal sample (Galata et al, 2021). When we performed RNA sequencing on samples with no mRNA enrichment, approximately 99% of the reads corresponded to rRNA.…”