Abstract
Gut microbiota play key roles in host nutrition and metabolism. However, little is known about the relationship between host genetics, gut microbiota and metabolic profiles. Here, we used high-throughput sequencing and gas chromatography/mass spectrometry approaches to characterize the microbiota composition and the metabolite profiles in the gut of five cyprinid fish species with three different feeding habits raised under identical husbandry conditions. Our results showed that host species and feeding habits significantly affect not only gut microbiota composition but also metabolite profiles (ANOSIM, p ≤ 0.05). Mantel test demonstrated that host phylogeny, gut microbiota, and metabolite profiles were significantly related to each other (p ≤ 0.05). Additionally, the carps with the same feeding habits had more similarity in gut microbiota composition and metabolite profiles. Various metabolites were correlated positively with bacterial taxa involved in food degradation. Our results shed new light on the microbiome and metabolite profiles in the gut content of cyprinid fishes, and highlighted the correlations between host genotype, fish gut microbiome and putative functions, and gut metabolite profiles.
Highlights
Vertebrates harbor vast and complex microbial communities that colonize their gastrointestinal tracts (Walter et al, 2011)
Similarities of the bacterial communities and metabolite profiles between samples were compared by analysis of similarity (ANOSIM) and Non-metric Multidimensional Scaling (NMDS) based on Bray–Curtis (Singh et al, 2015)
There was a tendency for the bacterial profiles of fish to separate by feeding habits (ANOSIM, r = 0.60, p = 0.001)
Summary
Vertebrates harbor vast and complex microbial communities that colonize their gastrointestinal tracts (Walter et al, 2011). The composition of gut microbial communities is shaped by various internal and external factors, such as host genotype, diet, lifestyle, and surrounding environment (e.g., water temperature, salinity) (Nayak, 2010; Sullam et al, 2012). Previous studies of mammalian species revealed that their gut microbiota clustered according to diet rather than host phylogeny (Ley et al, 2008a; Muegge et al, 2011). Changes in the composition of gut microbiota may lead to shifts in its functions, which may influence host nutrition and environmental adaptability (Amato, 2013). Comparative analysis among various hosts and their microbiota revealed that both diet and host phylogeny have driven the evolution of gut microbiota (Ley et al, 2008a). Identifying shifts in gut microbiota composition and diversity over evolutionary timescales will be crucial to understanding how gut microbiota of cyprinid fishes is involved in evolution and environmental adaptation
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