In contrast, in the metasecretome of the xylose-driven consortium, 86%% of the proteins were classifiable based on the KEGG orthology system, the most abundant functions being related with carbohydrate metabolism (30 %), environmental information (16 %) and genetic information processing (13 %).
We list in Additional file 1: Table S9 the influential pathways in which multiple genes in a cluster were involved whereas in Additional file 1: Table S10 we present the abundant functions, processes, and pathways in the individual gene clusters.
Moreover, a GO Slim Mapper functional analysis showed that the third most abundant functional group (after molecular function unknown and transmembrane transporter activity) was oxidoreductase activity, including the genes ADI1, ARI1, CTT1, ERG27, GRE2, HBN1, MPD2, and PUT1.
Members of the order Strongylida are considered to be relatively closely related to Caenorhabditis elegans, being within clade V [ 34], such that it is considered appropriate to infer gene function from the abundant functional genomic data (including a whole genome RNAi knockdown) that exist for C. elegans [ 26, 35, 36].
The most-abundant functions among DEG that were more highly-expressed in MFP vs. PAR are reported in Table 3. Complete details of the functional analysis and associated genes are reported in the Additional file 3. Metabolic functions related to transport and lipid synthesis and oxidation were among the most significantly-enriched.
The results showed that binding and catalytic functions were the most abundant GO function items (>10%), both from L5D6 to PP and PP to P0 developmental stages.
However, some trends can be observed: (i) the most abundant molecular function is "protein binding" (21.57% of all annotated molecular functions in the dataset) followed by "transferase activity" (9.80%).
The second most abundant general function category was the metabolism category, encompassing 17% of all predicted genes, followed by general function (15%), regulation (15%), intracellular processes (13%), information (4%), extracellular processes (2%), and "other" (1%).
The most abundant molecular function category was "catalytic activity", which is consistent with the role of modifying enzymes.
