1 Data set overview

Traditionally, viruses were considered solely pathogens; however, growing evidence suggests a more dynamic relationship between the virome and host, essentially through direct interactions with the bacterial microbiome. Much as the virome, intestinal fungi have only recently been acknowledged as a small but potentially important part of the intestinal ecosystem. As these findings provide clues that specific cross-kingdom interactions potentially contribute to or exacerbate disease, there remains a large paucity on the composition, interactions and function of fungi and viruses. Hence, there is an increasing need for unsupervised integrative computational frameworks that can robustly and systematically identify underlying patterns of variation across these communities in health and disease.

To examine the extent of these transkingdom interactions during critical illness, we collected faecal samples from 33 patients admitted to the Intensive Care Unit (ICU). Of these patients, 24 were admitted with sepsis while nine patients had a non-infectious diagnosis (non-septic ICU). All patients were treated with broad-spectrum antibiotics. In addition. 13 healthy volunteers were evaluated as controls. 6 healthy subjects received oral broad-spectrum antibiotics for 7 days, whereas 7 volunteers did not receive antibiotics. Subjects were asked to collect faecal samples before antibiotic treatment and one day after the course of antibiotics.
We performed parallel sequencing of bacterial 16S ribosomal RNA, and the fungal ITS rDNA gene and sought to examine community compositions by characterizing fungal and bacterial sequences into exact amplicon-sequencing variants. In addition, we also obtained Virus composition using VIDISCA-NGS.

An overview of the data set is shown below. Link to the paper