Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 17, 2025

The innovations of the "Omics Era" have ushered in significant advancements genetic improvement agriculturally important animal species through transforming genetics, genomics and breeding strategies. These were often coordinated, part, by support provided over 30 years 1993-2023 National Research Support Project 8 (NRSP8, Animal Genome Program, NAGRP) affiliate projects focused on enabling genomic discoveries livestock, poultry, aquaculture species. parallel advances demand strategic planning future research priorities. This paper, as an output from May 2023 Aquaculture Genomics, Genetics, Breeding Workshop, provides updated status resources for United States species, highlighting major achievements emerging Finfish shellfish genome omics enhance our understanding architecture heritability performance production traits. Workshop identified present aims genomics/omics to build this progress: (1) advancing reference assembly quality; (2) integrating multi-omics data analysis traits; (3) developing collection integration phenomics data; (4) creating pathways applying information across industries; (5) providing training, extension, outreach application phenome. focuses should emphasize collection, artificial intelligence, identifying causative relationships between genotypes phenotypes, establishing apply tools industries, expansion training programs next-generation workforce facilitate sciences into operations productivity, competitiveness, sustainability. collective vision with focus highlighted priorities is intended continued advancement genomics, genetics community industries. Critical challenges ahead include practical analytical frameworks beyond academic communities that require collaborative partnerships academia, government, industry. scope review encompasses use applications study aquatic animals cultivated human consumption settings throughout their life-cycle.

Язык: Английский

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Metagenomic approach for improved culture of whiteleg shrimp (Litopenaeus vannamei)

Academia Biology, Год журнала: 2025, Номер 3(1)

Опубликована: Фев. 20, 2025

The gut microbial community is essential for safeguarding the host against pathogens, modulating immune responses, and regulating metabolic activities. This review explores microbiota dynamics in Litopenaeus vannamei (whiteleg shrimp), focusing on methodologies used analysis factors influencing composition. Both traditional methods advanced molecular tools, such as 16S rRNA gene sequencing, have significantly expanded our understanding of diversity functions bacteria. Various environmental factors, dietary inputs, disease outbreaks, geographical variations play crucial roles shaping shrimp’s microbiome. Beneficial bacteria, Lactobacillus Bacillus subtilis, are found gut, contributing to improved digestion, enhanced immunity, homeostasis. On other hand, pathogenic bacteria like Vibrio parahaemolyticus, harveyi, Aeromonas hydrophila pose serious threats, causing diseases acute hepatopancreatic necrosis (AHPND) vibriosis, leading significant economic losses shrimp farming. Probiotics, particularly pond probiotics, shown promise alternatives antibiotics, exhibiting antibacterial properties promoting health. A comprehensive L. will aid developing sustainable aquaculture practices aimed at enhancing health, preventing disease, boosting productivity. consolidates current status metagenomics role health their responses critical pathogens affecting industry.

Язык: Английский

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Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture

mSystems, Год журнала: 2024, Номер 9(10)

Опубликована: Сен. 24, 2024

ABSTRACT Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT industries, our comprehension community composition functional potential floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate FAB shrimp systems, resulting reconstruction 520 metagenome-assembled genomes (MAGs) spanning both bacterial archaeal domains. Taxonomic analysis identified Pseudomonadota Bacteroidota as core members, with approximately 93% recovered MAGs unclassified at species level, indicating large uncharacterized phylogenetic diversity hidden community. Functional annotation these unveiled their complex carbohydrate-degrading involvement carbon, nitrogen, sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction ammonia, thiosulfate oxidation, sulfide oxidation pathways, suggesting community’s versatility for aerobic anaerobic Conversely, genes associated heterotrophic assimilatory reduction, sulfate were undetected. Members Rhodobacteraceae emerged most abundant metabolically versatile taxa this intriguing Our compendium is expected expand available genome collection from such underexplored environments. By elucidating structure metabolic capabilities, study provides valuable insights into key biogeochemical processes occurring aquacultures major contributors driving processes. IMPORTANCE Biofloc has sustainable approach, utilizing (bioflocs) improve health. However, specific within responsible benefits largely unknown. Compounding challenge, many resist laboratory cultivation, hindering taxonomic analyses. To address gaps, employed binning recover over 500 systems operating South Korea China. Through analyses, deciphered gene content diverse taxa, shedding light on roles like nitrogen Notably, findings underscore taxa-specific contributions microbes environments, particularly carbon degradation removal toxic substances nitrate, sulfide.

Язык: Английский

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Metagenomic profiling of rhizosphere microbiota: Unraveling the plant-soil dynamics

Physiological and Molecular Plant Pathology, Год журнала: 2024, Номер 133, С. 102381 - 102381

Опубликована: Авг. 20, 2024

Язык: Английский

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Rapid species-level metagenome profiling and containment estimation with sylph

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 8, 2024

Abstract Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k -mer statistics, enabling ANI-based taxa detection. On Critical Assessment Metagenome Interpretation II (CAMI2) Marine dataset, sylph was most accurate profiling method seven tested. For multisample profiling, took >10-fold less central processing unit time compared to Kraken2 used 30-fold memory. Sylph’s ANI provided an orthogonal signal abundance, allowing metagenome-wide association study Parkinson disease (PD) 289,232 genomes while confirming known butyrate–PD associations strain level. Sylph <1 min 16 GB random-access memory profile 85,205 prokaryotic 2,917,516 viral genomes, detecting more sequences in human gut RefSeq. offers precise, efficient with estimation low-coverage genomes.

Язык: Английский

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Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture

The Journal of Microbiology, Год журнала: 2024, Номер 62(11), С. 985 - 997

Опубликована: Ноя. 1, 2024

Язык: Английский

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Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics

Journal of Water and Health, Год журнала: 2025, Номер unknown

Опубликована: Фев. 21, 2025

ABSTRACT High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years those living with HIV AIDS. Treatment infectious diseases has also become increasingly difficult rapid rise antimicrobial resistance (AMR). Environmental surveillance wastewater can supplement gaps clinical as residents on a sewage system contribute to wastewater, providing simple, composite samples that improve understanding about both pathogens AMR community. This study evaluated effectiveness environmental shotgun metagenomics tool characterize broad range enteric pathogens, antibiotic genes, virulence factor genes (VFGs) from six neighborhoods Harare, Zimbabwe. Alpha beta diversity microbial community were similar between high-income low-income suburbs. Enteric high concern, including Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica, detected all samples. The top VFGs encoded for delivery, adherence, motility, functions important toxin secretion, colonization, immune modulation. findings provide foundation future studies explore public health monitoring diseases.

Язык: Английский

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Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system

Scientific Data, Год журнала: 2023, Номер 10(1)

Опубликована: Окт. 17, 2023

Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial of floc-associated bacterial (FAB) community pathogen control and animal health, earlier microbiota studies have primarily relied on metataxonomic approaches. Here, we employed shotgun sequencing eight biofloc metagenomes from commercial system. This resulted generation 106.6 Gbp, reconstruction 444 metagenome-assembled genomes (MAGs). Among recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), 214 medium-quality (≥50% ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae dominant members FAB community. The reported MAGs for elucidating diverse microorganisms their functional genes key processes such nitrification, denitrification, remineralization. study will contribute to scientific understanding phylogenetic diversity metabolic capabilities taxa environments.

Язык: Английский

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Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 20, 2023

Abstract Profiling metagenomes against databases allows for the detection and quantification of mi-crobes, even at low abundances where assembly is not possible. We introduce sylph ( https://github.com/bluenote-1577/sylph ), a metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph most accurate method on CAMI2 marine dataset, compared to Kraken2 multi-sample profiling, takes 10× less CPU time uses 30× memory. Sylph’s ANI provide an orthogonal signal abundance, metagenome-wide association study Parkinson’s disease (PD) 289,232 genomes while confirming known butyrate-PD associations strain level. < 1 minute 16 GB RAM profile 85,205 prokaryotic 2,917,521 viral genomes, detecting more sequences in human gut RefSeq. offers precise, efficient profiling with estimation low-coverage genomes.

Язык: Английский

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Understanding the role of microbes in health and disease of farmed aquatic organisms

Marine Life Science & Technology, Год журнала: 2024, Номер 6(4), С. 579 - 609

Опубликована: Сен. 19, 2024

Язык: Английский

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