Succession of embryonic and intestinal bacterial communities of Atlantic salmon

Host-associated microbiota undergoes continuous transition to achieve a stable community, and these modifications are immediately initiated from the birth of the host. In the present study, the succession of early life (eyed egg, embryo, and hatchling stages) and intestinal (the whole intestine at the early freshwater stages and the distal intestine at the late freshwater and seawater stages) bacterial communities of Atlantic salmon (Salmo salar; a prominent farmed fish) were studied using a 16S rRNA gene (V3 region) amplicon sequencing technique. Stage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities were relatively less diverse, but after hatching the diversity increased significantly. A marked transition of the intestinal communities also occurred during the development. The most abundant functional pathways associated with the different stages were not affected by the transition of the community composition A perceptible transition in the community composition occurred during the development of Atlantic salmon. The transition generally did not alter the core functions of the community. Hatching and transfer to seawater are the key events that affect the bacterial diversity and community composition. The contribution of host-derived factors and environment in shaping the bacterial communities need to be confirmed through further studies.

The presumptive functional pathways associated with the microbiota at different S5. Additional file 8: Table S5a lists the five most abundant KEGG modules and of the EE and EBH (Fig. 7, Additional file 9: Table S6a; p<0.01, R>0.85). The freshwater stages (20 wph) was significantly different from that of the fish at the late 2 6 2 freshwater stages (44 and 62 wph, Fig. 7, Additional file 9: Table S6c; p<0.01, 2 6 3 R>0.6). The seven pathways that were significantly abundant across stages were branched-2 6 6 chain amino acid transport system, peptides/nickel transport system, riboflavin 1 2 biosynthesis, multiple sugar transport system, pentose phosphate pathway, phosphate 2 6 8 transport system and glycolysis. The present study profiled the bacterial communities of Atlantic salmon to examine 2 7 2 the progressive transition of these fish communities during the early embryonic stages whereas Moraxella and Alcaligens were abundant on halibut eggs. In addition, 2 9 1 microbiota of cod larvae was highly distinct from those of their environment and live neutral assembly models have been proposed for zebrafish [19]. As zebrafish ages, the 3 0 1 assembly of the associated bacterial community is not decided according to chance  From the hatching stage onward, major mucosal organs, such as the gills, skin and 3 0 9 gut, become functionally active [24], and the specific phylotypes that colonize these 3 1 0 microenvironments might play key roles in the normal development of these organs 25-27, 23, 16]. In addition, at this stage, oxygen uptake changes from cutaneous to 3 1 2 pharyngeal [28], and this development could affect the community composition. These ontogenic changes might contribute to the HL-associated diverse bacterial  After the formation of the gut, i.e., 7 weeks after hatching, the bacterial community 3 1 7 associated with the whole intestine was assessed. The alpha diversity indices of the 3 1 8 intestinal microbiota at 7 wph (prior to first feeding) and the stages after feeding (8, suggest that feeding causes a phylum-level shift to Proteobacteria (at 8 wph) and (primarily reflecting the genus Weissella, at 12 wph). The distal intestine was clearly distinguishable at 20 wph; therefore, the bacterial 3 2 7 community associated with this intestinal region was analysed from this time point.

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The significant decrease in the alpha diversity index (20 vs. 44 wph) could reflect the In the present study, the phylum Firmicutes was significantly abundant at 20 wph.

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The genera Weissella, Laceyella* and Anaerofilum were the predominant contributors to the significant abundance of Firmicutes. Rainbow trout, also presents a high 3 3 6 abundance of Firmicutes, with OTUs belonging to Bacilli as the predominant type 3 3 7 [30]. This observation is similar to the findings in the present study. In contrast,  of the fish at the late freshwater stages. After the fish were in seawater, likely related to the specific needs of the associated bacterial communities or host. The fish were euthanized prior to sampling. The samples from the successive and Additional file 4: Table S1. Methods.

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A paired end, dual index protocol was adopted to amplify and prepare the 16S rRNA  reads with less than 10 sequences were discarded. OTUs were clustered at a 97% OTU tables were prepared and split into the 4 study groups (as described in the  analysis PCR, Polymerase chain reaction; PD Whole tree, phylogenetic diversity 19. Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K et al.

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Contribution of neutral processes to the assembly of gut microbial communities in the Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. ISME J. conserved responses to the gut microbiota. Proc Natl Acad Sci USA.  immune maturation depends on colonization with a host-specific microbiota. Cell. Metabolic reconstruction for metagenomic data and its application to the human