Authors
Subrata Kumar Ghosh, Mai A Wassel, Marty Kwok-Shing Wong, Susumu Hyodo, Koji Hamasaki
Published in
Environmental microbiology. Volume 28. Issue 10. Pages e70448.
Abstract
The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.
PMID:
42885240
Bibliographic data and abstract were imported from PubMed on 16 Oct 2026.
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