Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

Abstract

BackgroundDiverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainbow trout could be associated with differential growth rates observed in fish breeding programs. If true, harnessing the functionality of this microbiota can improve the profitability of aquaculture. The first objective of this study was to test this hypothesis if gut microbiota is associated with fish growth rate (body weight). Four full-sibling families were stocked in the same tank and fed an identical diet. Two fast-growing and two slow-growing fish were selected from each family for 16S rRNA microbiota profiling.Microbiota diversity varies with different DNA extraction methods. The second objective of this study was to compare the effects of five commonly used DNA extraction methods on the microbiota profiling and to determine the most appropriate extraction method for this study. These methods were Promega-Maxwell, Phenol-chloroform, MO-BIO, Qiagen-Blood/Tissue, and Qiagen-Stool. Methods were compared according to DNA integrity, cost, feasibility and inter-sample variation based on non-metric multidimensional scaling ordination (nMDS) clusters.ResultsDifferences in DNA extraction methods resulted in significant variation in the identification of bacteria that compose the gut microbiota. Promega-Maxwell had the lowest inter-sample variation and was therefore used for the subsequent analyses. Beta diversity of the bacterial communities showed significant variation between breeding families but not between the fast- and slow-growing fish. However, an indicator analysis determined that cellulose, amylose degrading and amino acid fermenting bacteria (Clostridium, Leptotrichia, and Peptostreptococcus) are indicator taxa of the fast-growing fish. In contrary, pathogenic bacteria (Corynebacterium and Paeniclostridium) were identified as indicator taxa for the slow-growing fish.ConclusionDNA extraction methodology should be carefully considered for accurate profiling of the gut microbiota. Although the microbiota was not significantly different between the fast- and slow-growing fish groups, some bacterial taxa with functional implications were indicative of fish growth rate. Further studies are warranted to explore how bacteria are transmitted and potential usage of the indicator bacteria of fast-growing fish for development of probiotics that may improve fish health and growth.

Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout

“…Similarly, studies in stickleback fish identified association between gut microbial differences and host genetic divergence [24]. Besides, previous work from our lab group revealed significant variation in beta diversity of the bacterial communities of rainbow trout families showing variation in growth rate [25]. Together, these studies indicate a substantial impact of host selection or genetics in predicting the hostassociated microbial assemblages.…”

“…To extract DNA, fecal samples from 19 ARS-FY-H and 20 ARS-FY-L fish were subjected to DNA isolation using a Promega Maxwell DNA Isolation Kit (Promega Corporation, Madison, WI), as we previously described [25] with a minor modification where 20 µL of lysozyme was added in samples to facilitate cell wall lysis. Briefly, 200 mg of fecal sample was added to a microtube containing 160 µL of incubation buffer, 20 µL proteinase k solution, and 20 µL lysozyme.…”

The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution

“…Burkholderiaceae, Lachnospiraceae, Ruminococcaceae, and Paenibacillaceae were also enriched in A. digitifera fragments subjected to ALAN. It is worth noting that these microbial taxa are major taxonomic groups found in the human gut and in fecal microbiota [ 65 , 66 , 67 , 68 , 69 ], as well as in the fish gut microbiome [ 70 , 71 ]. The milkfish aquaculture zone and human settlements found in proximity to the Bolinao Marine Laboratory [ 72 ] are possible sources of these bacterial groups.…”

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

“…Similarly, studies in stickleback sh identi ed an association between gut microbial differences and host genetic divergence [24]. Previous work from our lab group revealed signi cant variation in beta diversity of the bacterial communities of rainbow trout families showing variation in growth rate [25]. Together, these studies indicate a substantial impact of host selection or genetics in predicting host-associated microbial assemblages.…”

“…To extract DNA, fecal samples from 19 high (ARS-FY-H) and 20 low (ARS-FY-L) genetic line sh were subjected to DNA isolation using a Promega Maxwell DNA Isolation Kit (Promega Corporation, Madison, WI), as we previously described [25] with a minor modi cation where 20 μL of lysozyme was added in samples to facilitate cell wall lysis. Brie y, 200 mg of fecal sample was added to a microtube containing 160 μL of incubation buffer, 20 μL proteinase k solution, and 20 μL lysozyme.…”