PT  - JOURNAL ARTICLE
AU  - Jep Lokesh
AU  - Viswanath Kiron
AU  - Detmer Sipkema
AU  - Jorge M.O. Fernandes
AU  - Truls Moum
TI  - Succession of embryonic and intestinal bacterial communities of Atlantic salmon
AID  - 10.1101/128066
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 128066
4099  - http://biorxiv.org/content/early/2017/04/17/128066.short
4100  - http://biorxiv.org/content/early/2017/04/17/128066.full
AB  - 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.16S rRNA16S ribosomal RNAEBHembryo before hatchingEEeyed egg stageFOTSForsøksdyrforvatningen tilsyns-og søknadssystemHLhatched larvaeHUMAnNHMP unified metabolic analysis networkKEGGKyoto encyclopedia of genes and genomesLEfSelinear discriminant analysis effect sizeNSTInearest sequenced taxon indexOTUoperational taxonomic unitPCoAprincipal coordinate analysisPCRPolymerase chain reactionPD Whole treephylogenetic diversity whole treePICRUStPhylotypic investigation of communities by reconstruction of unobserved statesQIIMEQuantitative insights into microbial ecologyV3 and V4 regionshypervariable regions 3 and 4wphweeks post hatch