ArticleMicrobiome2022
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss).
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed, 196 citations in OpenAlex.
- Trial
- Pathological response and metabolites' prognostic role in HER2-positive breast cancer treated with neoadjuvant pyrotinib, trastuzumab, nab-paclitaxel, and carboplatin: a single-arm phase II trial.Breast cancer research : BCR · 2025Trial
- Core, Resident, and Transient Members of the Trout Gut Microbiome: Dietary, Environmental, Stress and Pathogen/Antibiotic Modulation.Veterinary sciences · 2026Review
- Metabolomics Reveals Flavonoid Profiles and Metabolite-Based Chemotypes in Plum (Foods (Basel, Switzerland) · 2026Article
- Triphala Modulates the Membrane Vesicle Transcriptome of Enterococcus durans VIT3 to Influence Antibiotic Response and Probiotic Functions.Molecular biotechnology · 2026Article
- Article
- Gut Microbiome of Aquatic Organisms: Role in Immunity Formation and Effects on Aquaculture Productivity.Microorganisms · 2026Review
- Integrated UPLC-MS/MS profiling and network pharmacology-based analysis of the anti-hyperglycemic potential of Baihu Jia Renshen Decoction combined with Sanghuangporus vaninii extract in mice.Journal of molecular histology · 2026Article
- Prebiotics and probiotics in animal nutrition: implications for food safety, sustainability, and circular production systems.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Review
- Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.BMC genomics · 2026Article
- Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.Biology · 2026Review
- Comprehensive metabolomics and transcriptomics analysis to explore variations in components of Alpinia oxyphylla from four distinct areas.BMC plant biology · 2026Article
- HSP101-encoding NEO-TETRAPLOID RICE FERTILITY GENE 1 regulates tapetum development through interaction with SAPK2 in polyploid rice.Journal of integrative plant biology · 2026Article
- Omics technologies in aquafeed: unlocking the black box towards systems biology.Functional & integrative genomics · 2026Review
- Transcriptome, Proteome, and Metabolome Features in Diarrhea Challenge of Preweaning Piglets via Multi-Omics Integration Analyses.Animals : an open access journal from MDPI · 2026Article
- Metabolomic profiling reveals root exudation pattern as regulated by phosphorus and light in contrasting rice cultivars.BMC plant biology · 2026Article
- Genome and Secondary Metabolites Analysis ofJournal of fungi (Basel, Switzerland) · 2026Article
- The molecular mechanism of the α-linolenic acid metabolism pathway in rice in response to Cd stress.BMC plant biology · 2026Article
- Molecular mechanisms of peanut root responses to Cd stress regulated by ABC transporter and plant hormone signal transduction pathways.BMC plant biology · 2026Article
- Intestinal morphology and host‑ and system‑associated microbiome dynamics during short‑term fasting and refeeding of Atlantic salmon in recirculating aquaculture systems.Scientific reports · 2026Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnimal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism.
resultsOur findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites.
conclusionOur results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.