Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale

Abstract

Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.

Influence of Seaweed Supplements on the Intestinal Bacteria in the Rabbitfish Siganus Fuscescens: Evidence for a Core Microbiome

“…Although this bacterium is generally associated with freshwater sh such as the grass carp, Ctenopharyngodon idellus, its detection could be related to the presence of functional genes associated with protein digestion within the genome of Cetobacterium spp. [86], which support host responses to dietary change [87]. Since our sh were wild-caught and, prior to capture, presumably browsed mainly on seaweed, Cetobacterium sp.…”

Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products

“…Numerous molecular studies have found a link between the microbiome of the host and that of the rearing environment (Chen et al, 2017;Zheng et al, 2017;Sun et al, 2019;Angthong et al, 2020). The cultivated organisms recrute and enrich specific taxa from their environment (Bakke et al, 2015;Yan et al, 2016;Li et al, 2017;Xiong et al, 2019;Zhang et al, 2019). For multiple aquatic species, it has been reported that the larvae-associated microbiomes are more similar to the rearing water microbiomes as compared to those in the live or dry feed products (Mcintosh et al, 2008;Bakke et al, 2013;Giatsis et al, 2015).…”

Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

“…Environment [20], diet [21] and host genotype [22] have been demonstrated to play an important role in de ning the Atlantic salmon gut microbiota composition. However, up to now, only few studies have examined the association between disease severity and degree of dysbiosis in sh [11], [13], [14] and, to our knowledge, no study has checked for changes in the gut microbiota as a consequence of an external bacterial infection.…”