Potential Functions of the Gut Microbiome and Modulation Strategies for Improving Aquatic Animal Growth

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 11, 2024

ABSTRACT The increase in the body weight of animals, a pivotal indicator closely tied to production, is important aquaculture industry. Despite remarkable variability gut microbiomes, which are intricately associated with their hosts and affect overall performance, fitness, physiological outcomes, across individuals species, development practical application microbiota modulation remain underdeveloped. In this review, we systematically examine advancements focus on microbiomes aquatic animals different growth rates by literature search, summarizing existing knowledge regarding diversity, composition, significance microbiome individual growth. comparative analysis reveals substantial alterations that correspond changes rate species bias toward more carnivorous fish, shrimps sea cucumbers nonfish species. present review also discusses research as an emerging field great potential for advancing our understanding animal growth, screening candidate probiotics, facilitating strategies. Besides, gaps production farmed have been highlighted. We propose directions address challenges opportunities field, such priority effects establishment, especially early stage, host‐derived probiotics various animals. Finally, provide conceptual framework enhancing farming practices through intensified research.

Language: Английский

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Feed microbiome: confounding factor affecting fish gut microbiome studies

ISME Communications, Journal Year: 2022, Volume and Issue: 2(1)

Published: Feb. 2, 2022

There is an increasing interest in the impact of feed on fish gut microbiome. Most studies are based sequencing bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well dead bacteria. It has not been a common practice to include control, although it contains various nutritious ingredients that microorganisms can use before or after preparation. Thus, study designs using digesta proxy for intestinal microbiome raise concern composition might be biased by carry-over microbial DNA itself. Here we report analysis 15 feeds representative Atlantic salmon (Salmo salar) five independent case studies. This allowed us identify "feed microbiomes" were microbially diverse shared taxa with microbiomes. Digesta-specific microbiomes identified, though they mainly enriched few taxa, such Mycoplasma Ruminococcaceae. Overall, findings consistent model wherein profiles different degree influenced present itself through microbiome" effect.

Language: Английский

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Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Feb. 21, 2023

Abstract Gut microbiota (GM) plays many key functions and helps maintain the host’s health. Consequently, development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest different fields. In this study, we evaluated impact four culture media: Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation (FM), Carbohydrate Free Basal (CFBM) on preserving biodiversity metabolic activity human batch cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) LC-HR-MS/MS untargeted metabolomics supplemented GC–MS SCFA profiling. Before experiments, determined possibility pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce number variables ensure reproducibility tests. Results showed suitability pooling for study. Non-cultured MIX was characterized by higher α -diversity (Shannon effective count, Effective microbial richness) compared inocula individual donors. After 24 h cultivation, a significant effect media composition taxonomic metabolomic profiles observed. The SM GMM had highest count). core ASVs (125) shared non-cultured total SCFAs production observed SM. These results might contribute standardized protocols preventing methodological bias data.

Language: Английский

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You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches

Animal Microbiome, Journal Year: 2021, Volume and Issue: 3(1)

Published: Dec. 1, 2021

Animals evolved in a microbial world, and their gut symbionts have played role ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts bacteria, fewer examine the potentially adaptive functional contributions these microbes to dietary habits hosts. In this study, we examined predicted metabolic pathways bacteria more than 500 individual bats belonging 60 species compare enrichment functions across with distinct ecologies.We found that microbiome were differentially enriched different diets. Using machine-learning approach, also inferred could be used predict specialized host diets reasonable accuracy. We detected relationship both phylogeny diet respect repertoires. Because fill nutritional gaps for diets, considered discriminating niches as traits fit them comparative phylogenetic models evolution. Our results suggest some, but not all, may evolve toward optima thus visible forces natural selection operating on over evolutionary time.Our partially rely fulfill or augment critical pathways, including essential amino acid synthesis, fatty biosynthesis, generation cofactors vitamins proper nutrition. work adds growing body literature suggesting animal microbiomes are structured by combination processes sets stage future metagenomic characterization bat explore links bacterial metabolism

Language: Английский

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High carbohydrate to protein ratio promotes changes in intestinal microbiota and host metabolism in rainbow trout (Oncorhynchus mykiss) fed plant-based diet

Aquaculture, Journal Year: 2023, Volume and Issue: 578, P. 740049 - 740049

Published: Sept. 9, 2023

Language: Английский

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Structural differences in the gut microbiome of bats using terrestrial vs. aquatic feeding resources

BMC Microbiology, Journal Year: 2023, Volume and Issue: 23(1)

Published: April 1, 2023

Abstract Bat gut microbiomes are adapted to the specific diets of their hosts. Despite diet variation has been associated with differences in bat microbiome diversity, influence on microbial community assembly have not fully elucidated. In present study, we used available data characterize five selected species (i.e., Miniopterus schreibersii , Myotis capaccinii myotis pilosus and vivesi ), using network analysis. These contrasting habitat food preferences My. can be piscivorous and/or insectivorous; Mi. exclusively while is a marine predator) offer an invaluable opportunity test impact assembly. The results showed that most complex network, highest number nodes, least structured microbiome, lowest nodes its network. No common were observed networks species, possessing unique nodes. Only three presented core distribution local centrality measures was different networks. Taxa removal followed by measurement connectivity revealed had robust tolerance taxa removal. Prediction metabolic pathways PICRUSt2 significantly higher functional pathway’s richness compared other species. Most predicted (82%, total 435) shared between all but no or pathways. We concluded despite similar feeding habits, differ Other factors beyond may play major role assembly, host ecology, sociality overlap roosts likely providing additional predictors governing insectivorous bats.

Language: Английский

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Environmental RNA metabarcoding for ballast water microbial diversity: Minimizing false positives

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 955, P. 176902 - 176902

Published: Oct. 12, 2024

Language: Английский

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DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta

Environmental Microbiome, Journal Year: 2023, Volume and Issue: 18(1)

Published: Dec. 8, 2023

Abstract Background Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding provide no information on the most fundamental physiological state bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles maintaining health and functioning holobiont. However, coral holobiont contains both dead living bacteria. The former can be result feeding rapid swings from hyper- to hypoxic conditions tissue, presence antimicrobial compounds mucus, an abundance lytic bacteriophages. Results By combining propidium monoazide (PMA) treatment with high-throughput sequencing six species ( Acropora loripes , A. millepora kenti Platygyra daedalea Pocillopora acuta Porites lutea ) we were able obtain communities little noise non-viable microbial DNA. Metabarcoding 16S rRNA gene showed significantly higher community evenness (85%) diversity (31%) untreated compared PMA-treated tissue for only. While did not differ samples terms observed number ASVs, > 30% ASVs identified only, suggesting that they originated cell-free/non-viable Further, structure was different between P. indicating DNA microbes bias composition data low diversity. Conclusions Our study is highly relevant studies other host organisms as it delivers solution excluding community. These results novel insights into dynamic nature host-associated microbiomes underline importance applying versatile tools analysis or next-generation sets.

Language: Английский

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Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Dec. 19, 2023

Via 16S rRNA gene amplicon sequencing, this study explores whether the gut mucus microbiota of rainbow trout is affected by interaction a plant-protein-based diet and daily handling stressor (chasing with fishing net) across two genetic lines (A, B). Initial body weights fish from A B were 124.7 g 147.2 g, respectively. Fish fed 1.5% weight per day for 59 days either experimental diets, differing in their meal [fishmeal-based (F): 35%, plant-based (V): 7%] protein content (diet F: 47%, V: 73%). No diet- or stress-related effect on performance was observed at end trial. However, we found significantly increased ASVs intestinal F compared to V. significant differences Shannon diversity could be between treatments. The autochthonous V dominated representatives genera Mycoplasma, Cetobacterium, Ruminococcaceae, whereas Enterobacteriaceae Photobacterium associated F. bacteria both separated diet, but neither stress nor an interaction, as obtained via PERMANOVA. pairwise comparisons revealed that only stressed fish. Therefore, our findings indicate mucus-associated primarily modulated source, modulation mediated status

Language: Английский

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Rapid adaptation of the rainbow trout intestinal microbiota to the use of a high-starch 100% plant-based diet

FEMS Microbiology Letters, Journal Year: 2024, Volume and Issue: 371

Published: Jan. 1, 2024

Abstract Short-term adaptation of the microbiota could promote nutrient degradation and host health. While numerous studies are currently undertaking feeding trials using sustainable diets for aquaculture industry, extent to which adapts these novel is poorly described. The incorporation carbohydrates (CHO) within a 100% plant-based diet offer novel, cost-effective energy source that readily available, potentially replacing protein component in diets. In this study, we investigated short-term (3 weeks) effects high CHO, on mucosal digesta associated diversity composition, as well several metabolic parameters rainbow trout. We highlighted mucosa dominated by Mycoplasma (44.86%). did not have significant main phyla (Proteobacteria, Firmicutes, Actinobacteria), after 3 weeks, lower abundance Bacillus genus, higher abundances four lactic-acid bacteria were demonstrated digesta. addition, no post-prandial hyperglycemia was observed with carbohydrate intake. These results provide evidence rapid gut metabolism CHO combination plant ingredients

Language: Английский

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