Time from feeding impacts farmed Atlantic salmon (Salmo salar) gut microbiota and faecal score

In intensive Atlantic salmon aquaculture, faecal score potentially serves as a generalised indicator of gut microbiome diversity and composition and as a proxy for gut transit time. There is also the possible application to detect dysbiosis. The utility of using faecal scoring for assessing commercially farmed fish populations may, however, be impacted by rapid temporal changes in digestive status following feeding that, as yet, has not been considered. To help inform sampling strategies and better understand the utility of faecal scoring for farmed fish, this study documented Atlantic salmon faecal scores and gut bacterial 16S rRNA amplicon sequence profiles over 24 h following a feeding event. Samples were collected from two marine cohorts of salmon in different seasons (summer and winter), and comparisons were also made between non-destructive stripped hindgut faeces (HS) and destructive sampling of hindgut digesta (HD) and hind gut mucosa (HM). Average hindgut faecal scores and microbiome diversity were largely consistent over a normal (6 to 8 h) sampling day in winter, but were much more variable in summer, potentially associated with faster faecal passage and dynamic gut microbial changes in the hours after feeding. HS samples were determined to be a valid non-destructive method to obtain material for assessing the diversity and composition of transient bacterial communities in the distal intestine. For an accurate representation of both the transient and resident bacterial communities, both sample types should be considered. It is recommended that studies comparing treatment cohorts, or between individuals in large sample sets, should be designed to capture temporal and seasonal effects that are associated with changes in digestive status and gut microbiome.