Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus

Abstract

Wood is consistently found in high levels in the gastrointestinal tract of the Amazonian catfish Panaque nigrolineatus, which, depending on environmental conditions, can switch between xylivorous and detritivorous dietary strategies. This is highly unusual among primary wood consumers and provides a unique system to examine the effect of dietary change in a xylivorous system. In this study, microbiome and predictive metagenomic analyses were performed for P. nigrolineatus fed either wood alone or a less refractory mixed diet containing wood and plant nutrition. While diet had an impact on enteric bacterial community composition, there was a high degree of interindividual variability. Members of the Proteobacteria and Planctomycetes were ubiquitous and dominated most communities; Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia also contributed in a tissue and diet-specific manner. Although predictive metagenomics revealed functional differences between communities, the relative abundance of predicted lignocellulose-active enzymes remained similar across diets. The microbiomes from both diets appeared highly adapted for hemicellulose hydrolysis as the predicted metagenomes contained several classes of hemicellulases and lignin-modifying enzymes. Enteric communities from both diets appeared to lack the necessary cellobiohydrolases for efficient cellulose hydrolysis, suggesting that cellobiose is not the primary source of dietary carbon for the fish. Our findings suggest that the P. nigrolineatus gut environment selects for an enteric community based on function, rather than a vertically transferred symbiotic relationship. This functional selection strategy may provide an advantage to an organism that switches between dietary strategies to survive a highly variable environment.

Termite diet rather than geographical origin determines the microbiome composition and functional genetic structure of nests from South American and African representatives, as revealed by a multiomics approach

“…This group was also reported in R. santonensis gut (Yang et al, 2005) and gust from Coptotermes gestroi (Do et al, 2014), and have been appointed as active cellulose degraders (Xia et al, 2014), with abundance in wood-feeding termites (Tokuda et al, 2018;Hu et al, 2019). Gemmatales are Gram-negative chemoheterotrophic bacteria (Dedysh et al, 2020), which could act as an indicator of elevated phosphorus content in soil (Mason et al, 2021), and in a complex microbial community dedicated to the utilization of cellulose could be providing endocellulases and β-glucosidases activities (McDonald et al, 2019). The characterization of samples through biomarkers (LEfSe analysis, Fig.…”

“…Gemmatales are Gram-negative chemoheterotrophic bacteria (Dedysh et al, 2020), which could act as an indicator of elevated phosphorus content in soil (Mason et al, 2021), and in a complex microbial community dedicated to the utilization of cellulose could be providing endocellulases and β-glucosidases activities (McDonald et al, 2019).…”

The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests

“…This group was also reported in R. santonensis gut (Yang et al, 2005 ) and gust from Coptotermes gestroi (Do et al, 2014 ) and have been appointed as active cellulose degraders (Xia et al, 2014 ), with abundance in wood-feeding termites (Tokuda et al, 2018 ; Hu et al, 2019 ). Gemmatales are Gram-negative chemoheterotrophic bacteria (Dedysh et al, 2020 ), which could act as an indicator of elevated phosphorus content in soil (Mason et al, 2021 ), and in a complex microbial community dedicated to the utilization of cellulose could be providing endocellulases and β-glucosidases activities (McDonald et al, 2019 ). Another group of bacteria notably described in the literature is that of Rhizobiales , Gram-negative bacteria belonging to the Alphaproteobacterial class, and with many members capable of fixing nitrogen (Beeckmans and Xie, 2015 ) and associated with many plants, lichens, and mosses (Erlacher et al, 2015 ).…”

Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture

“…As is thoroughly acclaimed, healthy gut microbial communities in fish have an essential role in the establishment of normal gut function (Bird et al ., 2010; Liu et al ., 2016) including digestion of food, production of accessory digestive enzymes, development of microvasculature of the intestinal villi (Stappenbeck et al ., 2002), biological nitrogen fixation (McDonald et al ., 2019), production of secondary metabolites, and secretion of several antipathetic compounds including short-chain fatty acids (SCFAs), lysozyme, siderophores, bacteriocin as ribosomally synthesized antimicrobial peptides that render protection against colonization of opportunistic pathogens (Nayak, 2010; Li et al ., 2018; Mukherjee et al ., 2020); maneuvering this potential can profoundly indemnify host fitness.…”