Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization.

Fernando Naya-Català,M Carla Piazzon,Gabriella Do Vale Pereira,Josep Alvar Calduch-Giner,Luis E C Conceição,Jaume Pérez-Sánchez,Ariadna Sitjà-Bobadilla,Ana Margarida Fernandes

doi:10.3389/fphys.2021.748265

Fernando Naya-Català, M Carla Piazzon + Show 6 more

Open Access

https://doi.org/10.3389/fphys.2021.748265

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Abstract

New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.

Highlights

Fish meal (FM) is the gold dietary protein in aquafeeds (Tacon and Metian, 2015; Ytrestøyl et al, 2015), but the global increase in aquaculture production needs to be supported by alternative feed ingredients, which very often, have a negative impact on growth, intestinal health, and immuno-competence of farmed marine fish (Conceição et al, 2012; Krogdahl et al, 2015; Estensoro et al, 2016; Aragão et al, 2020)
Concerning the individuals sampled for microbiota and gene expression analyses, the recorded body weight did not deviate from the expected values, with the trend being lowest in the body weight of fish fed with the Processed animal proteins (PAPs)-based diet
Fish production continues to be strongly dependent on FM (Ytrestøyl et al, 2015; Hua et al, 2019), but there is evidence that the use of a combination of plant proteins, poultry meal, and insect proteins is able to support optimal growth in a wide range of farmed marine fish, such as gilthead sea bream (Basto et al, 2021; Reis et al, 2021)

Summary

Introduction

Fish meal (FM) is the gold dietary protein in aquafeeds (Tacon and Metian, 2015; Ytrestøyl et al, 2015), but the global increase in aquaculture production needs to be supported by alternative feed ingredients, which very often, have a negative impact on growth, intestinal health, and immuno-competence of farmed marine fish (Conceição et al, 2012; Krogdahl et al, 2015; Estensoro et al, 2016; Aragão et al, 2020). Plant proteins have been considered as the most obvious FM alternative, but high levels of replacement can induce different signs of enteritis, including the shortening of mucosal folds, thickening of the lamina propia and submucosa, and infiltration of the distal intestine by inflammatory cells (Urán et al, 2009; Romarheim et al, 2013, Booman et al, 2018) These drawback effects are differentially exacerbated in each farmed fish species, but the supplementation of plant-based diets with fish protein hydrolysates or short-chain fatty acids (SCFAs) helps to mitigate most gut health detrimental effects in salmonid and non-salmonid fish (Estensoro et al, 2016; Piazzon et al, 2017; Egerton et al, 2020). Algae or algae-based products are currently used to replace or reduce the inclusion level of fish oil (FO) in aquafeeds, assuring the dietary supply of n-3 polyunsaturated fatty acids to meet the nutritional requirements of fish, as well as the healthy value of seafood products for human consumption (Maldonado-Othón et al, 2020; Pereira et al, 2020)

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