Microbial species abundances from public project PRJEB6337 on liver cirrhosis

In the context of the GuildBuilder, this dataset was created to assess the performances of network inference methods for liver cirrhosis risk gut microbiome alterations. This dataset corresponds to stool samples from 216 Chinese individuals sequenced using whole-metagenome sequencing techniques, a dataset deposited in the European Nucleotide Archive (ENA) under accession number PRJEB6337. Among this population, 102 individuals are healthy and 114 are suffering from liver cirrhosis. Abundances of all microbial species (metagenomic species or MSP) detected using 10.4 million IGC2 gut gene catalogue are extracted using the Meteor software suite that create a gene count table by mapping high quality reads onto the gene catalogue, using Bowtie2. Abundance of each MSP is computed as the mean abundance of 100 marker genes selected for each MSP, where the gene abundance is the read count normalized by gene length. The final table of size 1990 MSP by 216 individuals records all the normalized abundances.