The development of the gut microbiota in rainbow trout (Oncorhynchus mykiss) is affected by first feeding and diet type

Abstract

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Archived at http://orgprints.org/24967 AbstractAn influence of the intestinal microbiota in connection to first-feeding of rainbow trout (Oncorhynchus mykiss) fry was demonstrated using Illumina HiSeq sequencing. The period from the end of yolk-sac feeding and until seven weeks post first-feeding was examined after administration of either a marine-or plant based diet with or without the probiont Pediococcus acidilactici. Before first feeding the main part of the sequence reads grouped to the genus Sediminibacterium probably originating from the surrounding water. The microbial abundance and diversity increased after first-feeding and the microbiota then changed towards Firmicutes phylum dominance for plant based fed fish and towards dominance of phylum Proteobacteria for the marine fed fish. After first-feeding, there were significantly higher abundances of Streptococcus, Leuconostoc and Weissella in fish fed the plant-based diet. The microbiota clustered separately according to the diet type, but only minor effects were seen from the probiont when using PCAanalysis. The constitutive transcription level of most examined immune genes increased during the ontogenic shift, but the results could not explain the differences in the composition of the A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT2 microbiota dependent on diet treatment after first-feeding. The results suggest that the intestine of rainbow trout is colonised at an early state, but is guided in new and different directions dependent on the diet type.

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

“…Further statistical analysis of the beta diversity in this study using PERMANOVA showed that multiple shifts in the gut microbial composition occurred across fish age, while ANOSIM supported these results with the detection of distinguishable separation between specific age groups (Table 2B). Ontogenetic and temporal changes in microbial beta diversity have been detected in other aquaculture fish species as well, such as rainbow trout [33], Atlantic cod [32], and coho salmon [31]. Similar microbiota shifts are commonly detected in other organisms too, including zebrafish [13, 30], humans [53–56], rodents [57, 58], and terrestrial mono-gastric livestock, such as pigs and chickens [59–60].…”

“…To date, only a few studies have explored the intestinal microbiota of aquaculture species from early larval stages through later developmental stages using molecular techniques. Yet, these studies have often been focused on marine species such as anadromous coho salmon Oncorhynchus kisutch [31] or marine Atlantic cod Gadus morhua [32], with only one such study evaluating the temporal development of the gut microbiota of a freshwater aquaculture species [33]. …”

Modulation of the intestinal microbiota and morphology of tilapia, Oreochromis niloticus, following the application of a multi-species probiotic

“…The introduction of high-throughput sequencing technologies has increased our understanding of microbial diversity and function in complex environments, including the gastro- 2011; Desai et al 2012;Wu et al 2012;Boutin et al 2013;Carda-Diéguez et al 2013;Wu et al 2013;Ingerslev et al 2014;Zarkasi et al 2014;Falcinelli et al 2015). At present, there is a paucity of information on the intestinal microbiome of tilapia using high-throughput sequencing; to the author's knowledge, this is the first study utilising high-throughput sequencing to assess the intestinal microbial communities in this fish species.…”

In Situ Prebiotics for Weaning Piglets: In Vitro Production and Fermentation of Potato Galacto-Rhamnogalacturonan

“…Fermentation samples were spun at 13,000 ϫ g for 10 min, and the DNA contained in the cell pellets was purified with a Maxwell LEV blood DNA purification kit (Promega Corporation, Madison, WI, USA) as described by Ingerslev et al (40).…”