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

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 assessment 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.Here we include the short-read (sr) and long-read (lr) metagenomic (metag) and metatranscriptomic (metat) read files, after removing any human-associated sequences.