Source: UNIV OF MARYLAND submitted to NRP
INTEGRATED GENOMICS AND METAGENOMICS PREDICTIONS AND MODULATION OF THE GUT MICROBIOTA?MUSCLE AXIS TO IMPROVE FILLET YIELD IN RAINBOW TROUT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1029993
Grant No.
2023-67015-39742
Cumulative Award Amt.
$650,000.00
Proposal No.
2022-08051
Multistate No.
(N/A)
Project Start Date
Jun 1, 2023
Project End Date
May 31, 2027
Grant Year
2023
Program Code
[A1231]- Animal Health and Production and Animal Products: Improved Nutritional Performance, Growth, and Lactation of Animals
Recipient Organization
UNIV OF MARYLAND
(N/A)
COLLEGE PARK,MD 20742
Performing Department
(N/A)
Non Technical Summary
Muscle/fillet is the most valuable product of fish. Improving fillet yield and quality can enhance the efficiency of aquaculture production and customer satisfaction and have significant economic benefits.Classical breeding has limited success in improving fillet yield and requires several generations. The aquaculture industry is eager to adopt innovative genetic selection methods to increase the efficiency of genetic improvement, i.e., increasing the accuracy of breeding values and reducing generation intervals, consequently increasing genetic gain. Gut microbiota have recently shown a role in maintaining and regulating host physiology, including muscle gain and functions in mammals. However, host genetics' role on the gut microbiota-muscle axis remains to be discovered in Agri-animal species, including fish.A recent study in our laboratory showed that fillet yield genetic lines produced at USDA/ARS/NCCCWA are predictive of the gut microbiome composition in rainbow trout, indicating the presence of heritable fillet yield-associated microbiome components.In the proposed study, we will assess novel approaches to improve fillet yield in trout breeding programs at NCCCWA and one of the world's leading commercial producers of rainbow trout eggs. We will use host genotypes along with high-throughput gut microbiome/metagenomics data in microbiome genome-wide association studies to 1) identify gene variants associated with the microbiomeand detect heritable microbial groups associated with improved fillet yield that could be used as markers to develop improved fish for breeding purposes, 2) assess the feasibility of improving the genetic prediction accuracy and genotyping cost efficiency when the microbiome data and the genomic relationship information are integrated into genomics-metagenomics analyses.Additionally, we plan to assess the effects of modulating the gut microbial composition in favoring beneficial microbial flora to increase fillet yield via early-life fecal transplantation.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30308101080100%
Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
0810 - Finfish;

Field Of Science
1080 - Genetics;
Goals / Objectives
The ultimate goal of this project is to improve the muscle/fillet yield and quality traits of rainbow trout fish, thus improvingaquaculture production efficiency, converting fish feed to high-quality fish fillets. This research develops technologies that make animal protein production in the US more efficient, competitive, and environmentally cleaner.Our specific objectives are:1) Utilization of a 50K SNP "functional" chip to genotype fish representing high/low fillet yield genetic lines in addition to profiling their gut microbiome composition using 16S rRNA gene and shotgun metagenomics sequencing. Host genotyping data and microbiome profiles will be utilized in a microbiome GWAS (mGWAS) to identify genetic variants associated with individual taxa and/or the microbiome. Further, we will harness the microbiome high-throughput sequencing data to identify heritable microbial taxa and metagenomics genes/functions associated with the fillet yield/quality traits. Genotype-microbiome and microbiome-phenotype associations will be assessed in genetically selected lines for fillet yield in USDA/NCCCWA and a commercial breeding population from an industry partner. This objective will allow the utility of fecal samples to detect elite breeding candidates.2) Evaluation of improving the prediction accuracy and cost efficiency of fillet yield/quality traits when the joint action of the genomics and microbiota/metagenomics "hologenomics" data are integrated into the prediction model. Each data source's contribution to the fillet yield/qualitytraits will be evaluated by estimating a reduction in the prediction power when one data source is excluded from the prediction model. A five-fold cross-validation strategy will be used to evaluate the prediction performance. The outcome of this objective will allow the availability of prediction methods that use genomic information from the host (i.e., SNP chip) and the microbiome (e.g., microbiota/metagenomics) for the breeders to assess the future performance of fish better.3) Modulating the gut microbial composition to favor beneficial bacterial flora positively influences muscle mass. The gut microbiome composition in a low fillet yield genetic line eggs/larvae will be modulated by performing early-life fecal transplantation from high fillet yield genetic line donors. 16S rRNA gene sequencing will be used to assess the impact of fecal transplantation on modulating the microbiome community to enhance muscle growth and qualitytraits in rainbow trout. This objective will disclose possibilities for manipulating the microbiomein rainbow trout via early-life fecal transplantation.
Project Methods
In the project, we will assess novel approaches to improve fillet yield in trout breeding programs at NCCCWA and a commercial producer, one of the world's leading suppliers of rainbow trout eggs.Methods for each specific objectives are:1) Utilization of a 50K SNP "functional" chip to genotype fish representing high/low fillet yield genetic lines in addition to profiling their gut microbiome composition using 16S rRNA gene and shotgun metagenomics sequencing. Host genotyping data and microbiome profiles will be utilized in a microbiome GWAS (mGWAS) to identify genetic variants associated with individual taxa and/or the microbiome. Further, we will harness the microbiome high-throughput sequencing data to identify heritable microbial taxa and metagenomics genes/functions associated with the fillet yield/quality traits. Genotype-microbiome and microbiome-phenotype associations will be assessed in genetically selected lines for fillet yield in USDA/NCCCWA and a commercial breeding population from an industry partner. This objective will allow the utility of fecal samples to detect elite breeding candidates.Dr. Al-Tobasei, Middle Tennessee State University. He will help with the bioinformatics work of theSNP/mGWAS analyses.2) Evaluation of improving the prediction accuracy and cost efficiency of fillet yield/quality traits when the joint action of the genomics and microbiota/metagenomics "hologenomics" data are integrated into the prediction model. Each data source's contribution to the fillet yield/qualitytraits will be evaluated by estimating a reduction in the prediction power when one data source is excluded from the prediction model. A five-fold cross-validation strategy will be used to evaluate the prediction performance. The outcome of this objective will allow the availability of prediction methods that use genomic information from the host (i.e., SNP chip) and the microbiome (e.g., microbiota/metagenomics) for the breeders to assess the future performance of fish better.Drs. Daniela and Jeferson Lourenco, University of Georgia. will consult the GWAS and Genomicselection statistical analysis providing biostatistics expertise for this objective.3) Modulating the gut microbial composition to favor beneficial bacterial flora positively influences muscle mass. The gut microbiome composition in a low fillet yield genetic line eggs/larvae will be modulated by performing early-life fecal transplantation from high fillet yield genetic line donors. 16S rRNA gene sequencing will be used to assess the impact of fecal transplantation on modulating the microbiome community to enhance muscle growth and qualitytraits in rainbow trout. This objective will disclose possibilities for manipulating the microbiomein rainbow trout via early-life fecal transplantation.

Progress 06/01/24 to 05/31/25

Outputs
Target Audience:Aquaculture producers, breeders, and the scientific community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides opportunities for training one postdoctoral fellow, 2 PhD students, and several undergraduate students. How have the results been disseminated to communities of interest?Through scientific publications, conference presentations, and stakeholder communications. What do you plan to do during the next reporting period to accomplish the goals?The project will continue utilizing host genotyping data and microbiome profiles in microbiome GWAS (mGWAS) to identify genetic variants associated with specific microbial taxa and overall microbiome composition. Additionally, high-throughput microbiome sequencing will uncover heritable microbial taxa and metagenomic functions linked to fillet yield and quality traits. Genotype-microbiome and microbiome-phenotype associations will be examined in genetically selected fillet yield lines from USDA/NCCCWA and a commercial breeding population. The project aims to evaluate the impact of integrating genomic and microbiome (hologenomics) data on enhancing the accuracy and cost efficiency of fillet yield and quality trait predictions.

Impacts
What was accomplished under these goals? -A new study found that fecal microbiome analysis can uncover the hidden stress effects of stocking density on rainbow trout. The study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome. -The study assembled a comprehensive Rainbow Trout gut microbiome catalog from a domesticated farmed cohort (n = 118) using a hybrid assembly approach combining short and long reads with anaerobic culturing. 94 high-quality bacterial genomes were classified, identifying 21 species, 8 genera, 53 family-level classifications, and 9 potential novel species. Notably, 7 genomes exhibited >99% completeness. Metagenomic functional profiling revealed enrichment in short-chain fatty acid production, acetate-to-methane conversion, and nitrogen metabolism, highlighting key biochemical pathways in the anaerobic gut environment. These findings provide valuable insights into the microbiome's role in commercially relevant traits in aquaculture. - A study examinedthe interaction between host genetics and the gut microbiome in shaping fillet yield and quality in rainbow trout. Using a multi-omics approach, weidentified key genes (UBE3A, PDZK11, PEX5-L, SVC2C) linked to growth and muscle yield, along with Clostridium species correlated with high muscle yield. Genome-wide association analysis further pinpointed candidate genes for fatty acid profiles, muscle fiber traits, and fillet color. These findings highlight genetic and microbial biomarkers that canenhance selective breeding for improved fillet quality in aquaculture.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Ali, A., Gao, G., Al-Tobasei, R. et al. Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line. Sci Data 12, 345 (2025). https://doi.org/10.1038/s41597-025-04693-7
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Mohamed Salem, Rafet Al-Tobasei, Ali Ali, Liqi An, Ying Wang, Xuechen Bai, Ye Bi, Huaijun Zhou, Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution, GigaScience, Volume 13, 2024, giae092, https://doi.org/10.1093/gigascience/giae092
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Raymo, G., Januario, F., Ali, A. et al. Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout. anim microbiome 6, 57 (2024). https://doi.org/10.1186/s42523-024-00344-1
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Ahmed, R, Raymo, G, Ali A , Al-Tobasei R, Leeds T, Salem M Shotgun metagenomics reveals microbial taxa linked to fillet yield and quality traits in rainbow trout. Aquaculture America (March. 6-10, 2025), New Orleans, LA (International).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Raymo, G, Ahmed, R, Ali A, Al-Tobasei R, Leeds T, Salem M. Functional interrogation of the de-novo rainbow trout microbial genome atlas reveals longstanding symbiotic host-bacteria interrelationship. Aquaculture America (March. 6-10, 2025), New Orleans, LA (International).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Ahmed R, Raymo G, Ali A, Al-Tobasei R, Leeds T, Salem M. Multi-Omics Analysis Reveals Genetic and Microbial Biomarkers and Their Association with Growth Traits in Rainbow Trout. PAG- 32 Plant & Animal Genomes Conference (January 10-15, 2025), San Diego, California. (International).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Raymo G, Salem M. Functional Interrogation of the De-Novo Rainbow Trout Microbial Genome Atlas Reveals Longstanding Symbiotic Host-Bacteria Interrelationship. PAG- 32 Plant & Animal Genomes Conference (January 10-15, 2025), San Diego, California. (International).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Al-Tobasei, R, Salem M, Ali, A, An, L, Wang Y, Bai X, Bi Y, Zhou H. Comprehensive Epigenomic Mapping of Rainbow Trout Using ChromHMM: Insights into Regulatory Element Discovery and Evolutionary Adaptation. PAG- 32 Plant & Animal Genomes Conference (January 10-15, 2025), San Diego, California. (International).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Ali Ali, Salem M. Tracing 100 Million Years of Gene Evolution Following Whole Genome Duplication in Rainbow Trout. PAG- 32 Plant & Animal Genomes Conference (January 10-15, 2025), San Diego, California. (International).


Progress 06/01/23 to 05/31/24

Outputs
Target Audience:Aquaculture producers, breeders, and scientific community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides opportunities for training one postdoctoral fellow, 2 PhD students, and several undergraduate students. How have the results been disseminated to communities of interest?Some results have been published, and some have been presented at international conferences. What do you plan to do during the next reporting period to accomplish the goals?SNP genotyping the rest of the samples and completing the metagenomics analysis.

Impacts
What was accomplished under these goals? -A study demonstrated that modifying the gut microbial composition through early-life fecal transplantation from high-muscle-yield rainbow trout to low-muscle-yield recipients can accelerate somatic growth by modulating respiratory and mitochondrial efficiency. -Fish have been phenotyped for muscle growth and quality traits, and samples for DNA, RNA, and metagenomic work have been collected. -Putative SNPs associated with phenotypic traits have been identified in a subpopulation of the samples. The genotyping of the remaining samples is currently being processed. -The de novo assembly of the fish metagenome has been completed, and the identification of putative taxa associated with phenotypic traits is ongoing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Raymo G, Ali A, Ahmed RO, Salem M: Early-Life Fecal Transplantation from High Muscle Yield Rainbow Trout to Low Muscle Yield Recipients Accelerates Somatic Growth through Respiratory and Mitochondrial Efficiency Modulation. Microorganisms 2024, 12.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Salem M: Epigenomic Maps of the Rainbow Trout Reveal Epi-QTL Signatures of Genetic Selection and Epigenome Dynamics Correlating with Gene Expression and Genome Evolution. In International Plant and Animal Genome Conference (PAG); 1/16/2024; San Diego, CA. 2024
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Ahmed RO, Ali A, Leeds T, Salem M: RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout. BMC Genomics 2023, 24:579.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Ahmed RO, Ali A, Leeds T, Salem M: Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout. Microorganisms 2023, 11.