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\begin{document}

\title{Gut microbial assembly among freshwater Atlantic salmon reared in a
natural stream system during a simulated farm escape and introgression
event}



\author[1]{Patrick Schaal}%
\author[2]{Bachar Cheaib}%
\author[2]{Chloe Heys}%
\author[1]{Joshka Kaufmann}%
\author[1]{Karl Phillips}%
\author[1]{Liz Ryder}%
\author[1]{Philip McGinnity}%
\author[2]{Martin  Llewellyn}%
\affil[1]{University College Cork}%
\affil[2]{University of Glasgow}%


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  \date{May 29, 2024}


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\begin{abstract}
Intestinal microbial communities are influenced by a confluence of
ecological forces. Understanding the dynamics between environment,
microbiota and host is essential to gain insights into microbial
community assembly processes. However, few studies systematically assess
the contribution of different environmental sources to gut microbial
community composition. We used a common garden experiment to determine
the roles of biotic, abiotic and stochastic processes shaping gut
microbial communities in Atlantic salmon (\emph{Salmo salar}) in a
natural river during a simulated 10-month farm escape scenario. Most of
the taxa found in the salmon intestine originated from
macroinvertebrates (the potential food source) rather than the water
column, indicating that diet is an important factor in community
assembly. The contribution of food sources to the fish gut community was
lowest in winter and increased over March and May, reflecting
seasonality in fish appetite. Previous work in salmon has hinted at a
role for maternal effects in driving inter-generational sharing of
microbial taxa. Our results suggest a possible host and/or maternal
genetic effect affecting inter-individual differences in gut microbial
community composition, whereby distinct assemblages were noted between
farmed, wild and hybrid fish. Neutral modelling estimated that the
majority (86\%) of taxa present in the gut are transient. Overall, our
data highlight the significance of both deterministic and stochastic
drivers influencing the seasonal fluctuations of gut microbial
communities in young Atlantic Salmon and hint at potential genetic or
maternal effects on fish microbiota. These findings greatly enhance our
understanding of the complex interactions between hosts, their living
environment and associated microbiota.%
\end{abstract}%



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