Probiotic legacy effects on gut microbial assembly in tilapia larvae

Abstract

The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.

Environmental plasticity and colonisation history in the Atlantic salmon microbiome: A translocation experiment

“…For example, environmental stress or antibiotic treatment which disturbs the microbiome may allow resistant taxa to flourish in the absence of wider competition, delaying the restoration of the original complex community (Foster, Rinaman, & Cryan, ; Yassour et al, ). As observed in mammals, the microbial composition of fish is particularly dynamic during early development, as it is readily influenced by variation in the surrounding environment, host immunity and microbial seeding communities (Giatsis et al, ; Korpela et al, ; Lokesh, Kiron, Sipkema, Fernandes, & Moum, ; Stephens et al, ; Yan et al, ). This suggests that historical effects on microbiome structure due to environmental variation during early life may be particularly important (Gensollen, Iyer, Kasper, & Blumberg, ; Martínez et al, ; Sprockett et al, ).…”

Microbial interactions in the fish gut

“…The "core microbiota" observed here has not been previously reported as core in tilapia. However, many of the bacterial genera found here (Mycobacterium, Nocardia, Rhodococcus, Halomonas, and Ralstonia) were also encountered in our previous study (Giatsis et al, 2016a) suggesting that tilapia specificity for particular microbial taxa could be modulated by selective pressures within the host.…”

“…Giatsis C, Ramiro-Garcia J, Abernathy J, Verreth J, Smidt H, Sipkema D, Verdegem M. (2016a). Probiotic legacy on gut microbial assembly in fish larvae.…”

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

“…These efforts, however, remain relatively expensive on a per sample basis, and the richer but much more unstructured information content requires complex data modelling and analysis procedures 2 . Therefore targeted surveys for specific taxonomic marker genes, such as the 16S ribosomal RNA (rRNA) gene 3,4 , remain essential in many microbial ecological studies. These surveys rely on sequencing of short, PCR amplified, hypervariable subregions rather than of the full-length gene, mostly for reasons of throughput, sequence depth and cost-efficiency.…”