Biology subjects

Morkore, T.

Publications and source records attributed to Morkore, T..

4 recordsLinked to original sources

bioRxiv2025

Metatranscriptomic Insights into Microbial Dynamics Prior to Disease Onset in Atlantic Salmon Aquaculture

Poly(A)-selected RNA-seq datasets are routinely generated in aquaculture research, yet the microbial information contained in unmapped reads is seldom explored due to the low abundance of nonhost transcripts and concerns about contamination. In this study, we repurposed Atlantic salmon gill RNA-seq data to assess whether meaningful microbial signals can be recovered using a contamination-aware and compositionally appropriate framework. Unmapped reads were analyzed with a custom Kraken2 database composed exclusively of complete, circularized salmon-associated bacterial genomes together with all available Atlantic salmon assemblies and the human genome. Although microbial sequences represented only a small fraction of total reads, 21 genera were detectable across samples. Genus-level profiles, Jaccard-based ordination, and ANCOM-BC analyses consistently revealed clear differences between tanks, whereas no associations were observed for sex or survival status. Three species exhibited significant tank-specific effects, indicating that environmental factors contributed the strongest detectable structure in the data. The limited microbial diversity recovered here reflects the expected constraints of poly(A)-enriched libraries, yet the results demonstrate that unmapped reads from host-derived RNA-seq can still provide informative environmental signatures when analyzed with curated reference databases and compositional statistical approaches. This strategy offers a practical means to extract exploratory microbiome information from existing transcriptomic datasets.

microbiology↗

bioRxiv2024

Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon

Wild Atlantic salmon migrate to sea following completion of a developmental process known as parr - smolt transformation (PST), which establishes a seawater (SW) tolerant phenotype. Effective imitation of this aspect of anadromous life-history is a crucial aspect of commercial salmon production, with current industry practice being marred by significant losses during transition from the freshwater (FW) to SW phase of production. The natural photoperiodic control of PST can be mimicked by exposing farmed juvenile fish to a reduced duration photoperiod for at least 6 weeks before increasing the photoperiod in the last 1 - 2 months before SW transfer. While it is known that variations in this general protocol affect subsequent SW performance, there is no uniformly accepted industry standard; moreover, reliable prediction of SW performance from fish attributes in the FW phase remains a major challenge. Here we describe an experiment in which we took gill biopsies 1 week prior to SW transfer from 3000 individually tagged fish raised on 3 different photoperiod regimes during the FW phase. Biopsies were subjected to RNA profiling by Illumina sequencing, while individual fish growth and survival was monitored over 300 days in a SW cage environment, run as a common garden experiment. Using a random forest machine learning algorithm, we developed gene expression-based predictive models for initial survival and stunted growth in SW. Stunted growth phenotypes could not be predicted based on gill transcriptomes, but survival the first 40 days in SW could be predicted with moderate accuracy. While several previously identified marker genes contribute to this model, a surprisingly low weighting is ascribed to sodium potassium ATPase subunit genes, contradicting advocacy for their use as SW readiness markers. However, genes with photoperiod-history sensitive regulation were highly enriched among the genes with highest importance in the prediction model. This work opens new avenues for understanding and exploiting developmental changes in gill physiology during smolt development.

genomics↗

bioRxiv2024

Impact of three light smoltification regimes on performance and genetic parameters of traits in Atlantic salmon

2800 Atlantic salmon pre-smolts (50 g on average, the offspring of 53 sires and 100 dams) were individually tagged with PIT-tags and distributed among six circular 1200L tanks with approximately 450 fish per tank. Fish in duplicated tanks were put on three different light regimes, i.e. six weeks on either 8L:16D, 12L:12D or 24L:0D followed by six weeks on 24L:0D. One week prior to their transfer as 1+ smolt to a net cage in the sea in June 2021 their body weight, length, subjectively scored smolt status and fin damage were recorded. Recording of animal traits (body weight, wounds, fin damage, snout damage) were also performed in November 2021 and in April 2022. During the light regimes, fish on the two short day regimes had slower growth compared to fish on continuous light. However, after four (November 2021) and ten (April 2022) months in the sea the effect of light regime on fish size was not significantly different from zero (P>0.05). The fish on the 24L:0D regime showed increased mortality from day two after sea transfer with an accumulated recorded mortality of 8.9% during the two first months while it was only 1.0% and 0.7% for the 12L:12D and the 8L:16D fish, respectively. However, from the third until ten months in the sea recorded mortality was very similar for fish on the three light regimes. The effect of light regime on the recorded welfare traits (fin and snout damage and runts) was not significantly different from zero. For traits measured prior to seawater transfer the difference between fish that survived and those that died during the first two months in the sea were largest in the 24L:0D group indicating a positive effect of the short-day regimes also on the general smolt synchronization (i.e., group level uniformity). Moderate heritability estimates were found for the external smolt indicator traits condition factor, smolt status score and skin silveriness, as well as for snout damage, wounds, runts and body weight, but low estimates fin damage. For survival in the sea heritability on the liability scale was 0.09 after four months in the sea and 0.22 from five to ten months in the sea. The estimated genetic correlations between the same trait of the three different light regimes were moderate to high and thus unimportant genotype by light regime interaction. The genetic correlation of body in June 2021 with survival after two months in the sea was high (0.96), but not significantly different from zero with survival after four months in the sea and survival from five to ten months in the sea. Genetic correlations of survival with the other traits recorded in June 2021, November 2021 and April 2022 were low to medium in magnitude and not significantly different from zero. Therefore, for genetic improvement of survival in the seawater period direct selection for increased survival and growth during the first months is probably a better strategy than to perform indirect selection for smolt indicator traits.

genetics↗

bioRxiv2024

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on -MOS and {beta}-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their hitherto poorly characterized gut microbiomes. Our multi-omic analysis revealed that the investigated MDFs (two -mannans and an acetylated {beta}-galactoglucomannan), at a dose of 0.2%, had negligible effects on both host gene expression, and gut microbiome structure and function under studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of {beta}-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of {beta}-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline novel and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon. IMPORTANCEThis study focuses on the potential of MDFs to improve aquaculture production. Despite preliminary 16S rRNA amplicon data suggested that populations in the salmon gut microbiome could utilize structurally complex mannans, our findings indicates that endogenous microbes could not metabolize it, nor the host responds to its dietary inclusion, at least not under the trial conditions investigated in this study. We highlight that high-resolution and host-specific microbiome characterization can greatly improve trial design and selection of candidate MDFs for future nutritional interventions. Understanding the intricate interplay between host and its gut microbiome is paramount in studies seeking to leverage endogenous microbial communities to benefit the host. While each new condition, whether it is a disease onset or a nutritional stressor, has the potential to profoundly reshape the microbial diversity, composition and outputs, the functional microbiome information gained under healthy conditions represent a pivotal step towards designing more effective trials involving microbiome-reprogramming feed additives. Overall, we envisage that these results will lead to improved focus on coupling fundamental microbiome characterization to the design of next-generation feeds for salmon aquaculture.

microbiology↗