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Zarantonello G, Cuenca A. Nanopore-Enabled Microbiome Analysis: Investigating Environmental and Host-Associated Samples in Rainbow Trout Aquaculture. Curr Protoc 2024; 4:e1069. [PMID: 38865207 DOI: 10.1002/cpz1.1069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Microbiome sequencing is at the forefront of health management development, and as such, it is becoming of great interest to monitor the microbiome in the aquaculture industry as well. Oxford Nanopore Technologies (ONT) platforms are gaining popularity to study microbial communities, enabling faster sequencing, extended read length, and therefore, improved taxonomic resolution. Despite this, there is a lack of clear guidelines to perform a metabarcoding study, especially when dealing with samples from non-mammalian species, such as aquaculture-related samples. In this article, we provide general guidelines for sampling, nucleic acid extraction, and ONT-based library preparation for both environmental (water, sediment) and host-associated (gill or skin mucus, skin, gut content, or gut mucosa) microbiome analysis. Our procedures focus specifically on rainbow trout (Oncorhynchus mykiss) reared in experimental facilities. However, these protocols can also be transferred to alternative types of samples, such as environmental DNA (eDNA) monitoring from alternative water sources, or to different fish species. The additional challenge posed by the low biomass and limited bacterial diversity inherent in fish-associated microbiomes is addressed through the implementation of troubleshooting solutions. Furthermore, we describe a bioinformatic pipeline starting from raw reads and leading to taxonomic abundance tables using currently available tools and software. Finally, we provide a set of specific guidelines and considerations related to the strategic planning of a microbiome study within the context of aquaculture. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Environmental sample collection Basic Protocol 2: Host-associated sample collection Alternate Protocol: Host-associated sample collection: Alternative sample types Basic Protocol 3: Sample pre-treatment and nucleic acid extraction Basic Protocol 4: Quality control and preparation for 16S rRNA gene sequencing Support Protocol 1: Assessment of inhibition by quantitative PCR Support Protocol 2: Bioinformatic analysis from raw files to taxonomic abundance tables.
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Affiliation(s)
- Giulia Zarantonello
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Argelia Cuenca
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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Watkins K, Hastie M, Ha M, Hepworth G, Warner R. Machine Vision Requires Fewer Repeat Measurements than Colorimeters for Precise Seafood Colour Measurement. Foods 2024; 13:1110. [PMID: 38611414 PMCID: PMC11011751 DOI: 10.3390/foods13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The colour of seafood flesh is often not homogenous, hence measurement of colour requires repeat measurements to obtain a representative average. The aim of this study was to determine the optimal number of repeat colour measurements required for three different devices [machine vision (digital image using camera, and computer processing); Nix Pro; Minolta CR400 colorimeter] when measuring three species of seafood (Atlantic salmon, Salmo salar, n = 8; rockling, Genypterus tigerinus, n = 8; banana prawns, Penaeus merguiensis, n = 105) for raw and cooked samples. Two methods of analysis for number of repeat measurements required were compared. Method 1 was based on minimising the standard error of the mean and Method 2 was based on minimising the difference in colour over repeat measurements. Across species, using Method 1, machine vision required an average of four repeat measurements, whereas Nix Pro and Minolta required 13 and 12, respectively. For Method 2, machine vision required an average of one repeat measurement compared to nine for Nix Pro and Minolta. Machine vision required fewer repeat measurements due to its lower residual variance: 0.51 compared to 3.2 and 2.5 for Nix Pro and Minolta, respectively. In conclusion, machine vision requires fewer repeat measurements than colorimeters to precisely measure the colour of salmon, prawns, and rockling.
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Affiliation(s)
- Kieren Watkins
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (K.W.); (M.H.); (M.H.)
| | - Melindee Hastie
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (K.W.); (M.H.); (M.H.)
| | - Minh Ha
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (K.W.); (M.H.); (M.H.)
| | - Graham Hepworth
- Statistical Consulting Centre, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Robyn Warner
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (K.W.); (M.H.); (M.H.)
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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; 11:2704. [PMID: 38004716 PMCID: PMC10673235 DOI: 10.3390/microorganisms11112704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.
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Affiliation(s)
- Ridwan O. Ahmed
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Tim Leeds
- United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV 25430, USA;
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
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Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å, Kortner TM. Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics. Anim Microbiome 2023; 5:47. [PMID: 37789427 PMCID: PMC10548677 DOI: 10.1186/s42523-023-00269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical composition of the gut microbiota and gut health status in Atlantic salmon and to explore possible modulatory effects of dietary prebiotics in one net-pen farm in open water. The fish with initial mean body weight of around 240 g were fed diets based on the same basal composition, either without (Ref diet) or with (Test diet) yeast cell wall based-prebiotics, during the marine production phase from December to September the following year. Sampling was conducted at three sampling time points: January, April, and September, with average water temperature of 3.9 ℃, 3.4 ℃ and 9.6 ℃, respectively. RESULTS As the fish progressed towards September, growth, brush border membrane enzyme activities, and the expression in the gut of most of the observed genes involved in immune (e.g., il8, cd4a, myd88, il1b, gilt, tgfb, cd8b and cd3), barrier (e.g., zo1, occludin, ecad, claudin25b and claudin15), and metabolism increased significantly. Lipid accumulation in pyloric enterocytes decreased remarkably, suggesting improvement of gut health condition. The growth of the fish did not differ between dietary treatments. Further, dietary prebiotics affected the gut health only marginally regardless of duration of administration. Regarding gut microbiota composition, a decrease in alpha diversity (Observed species, Pielou and Shannon) over time was observed, which was significantly associated with an increase in the relative abundance of genus Mycoplasma and decrease in 32 different taxa in genus level including lactic acid bacteria (LAB), such as Lactobacillus, Leuconostoc, and Lactococcus. This indicates that developmental stage of Atlantic salmon is a determinant for microbial composition. Multivariate association analysis revealed that the relative abundance of Mycoplasma was positively correlated with gut barrier gene expression, negatively correlated with plasma glucose levels, and that its relative abundance slightly increased by exposure to prebiotics. Furthermore, certain LAB (e.g., Leuconostoc), belonging to the core microbiota, showed a negative development with time, and significant associations with plasma nutrients levels (e.g., triglyceride and cholesterol) and gene expression related to gut immune and barrier function. CONCLUSIONS As Atlantic salmon grew older under large-scale, commercial farm settings, the Mycoplasma became more prominent with a concomitant decline in LAB. Mycoplasma abundance correlated positively with time and gut barrier genes, while LAB abundance negatively correlated to time. Dietary prebiotics affected gut health status only marginally.
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Affiliation(s)
- Jie Wang
- National Aquafeed Safety Assessment Center, Institute of Feed Research, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St, Beijing, China.
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway.
| | - Yanxian Li
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | | | - Olai Einen
- Cermaq Group AS, Dronning Eufemias gate 16, Oslo, 0191, Norway
| | - Jan Vidar Jakobsen
- Cargill Aqua Nutrition, Prof. Olav Hanssensvei 7A, Stavanger, 4021, Norway
| | - Åshild Krogdahl
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | - Trond M Kortner
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
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Histological and transcriptomic analysis of muscular atrophy associated with depleted flesh pigmentation in Atlantic salmon (Salmo salar) exposed to elevated seawater temperatures. Sci Rep 2023; 13:4218. [PMID: 36918611 PMCID: PMC10015013 DOI: 10.1038/s41598-023-31242-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Tasmania is experiencing increasing seawater temperatures during the summer period which often leads to thermal stress-induced starvation events in farmed Atlantic salmon, with consequent flesh pigment depletion. Our previous transcriptomic studies found a link between flesh pigmentation and the expression of genes regulating lipid metabolism accompanied by feeding behavior in the hindgut. However, the impact of prolonged exposure to elevated water temperature on muscle structural integrity and molecular mechanisms in muscle underlying pigment variation has not been elucidated to date. In this study, we investigated the effect of prolonged exposure to elevated water temperature on the farmed salmon flesh pigmentation and structural integrity, using muscle histological and transcriptomic analysis. On April 2019, after the end of the summer, two muscle regions of the fish fillet, front dorsal and back central (usually the most and least affected by depletion, respectively), were sampled from fifteen fish (weighing approximately 2 kg and belonging to the same commercial population split in two cages). The fish represented three flesh color intensity groups (n = 5 fish per group) categorized according to general level of pigmentation and presence of banding (i.e. difference in color between the two regions of interest) as follows: high red color-no banding (HN), high red color-banded (HB) and Pale fish. Histological analysis showed a distinction between the flesh color intensity phenotypes in both muscle regions. Muscle fibers in the HB fish were partly degraded, while they were atrophied and smaller in size in Pale fish compared to HN fish. In the Pale fish, interstitial spaces between muscle fibers were also enlarged. Transcriptomic analysis showed that in the front dorsal region of the HN fish, genes encoding collagens, calcium ion binding and metabolic processes were upregulated while genes related to lipid and fatty acid metabolism were downregulated when compared to HB fish. When comparing the back central region of the three phenotypes, actin alpha skeletal muscle and myosin genes were upregulated in the HN and HB fish, while tropomyosin genes were upregulated in the Pale fish. Also, genes encoding heat shock proteins were upregulated in the HN fish, while genes involving lipid metabolism and proteolysis were upregulated in the Pale fish. Starvation, likely caused by thermal stress during prolonged periods of elevated summer water temperatures, negatively affects energy metabolism to different extents, leading to localized or almost complete flesh color depletion in farmed Atlantic salmon. Based on our results, we conclude that thermal stress is responsible not only for flesh discoloration but also for loss of muscle integrity, which likely plays a key role in pigment depletion.
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Ringø E, Harikrishnan R, Soltani M, Ghosh K. The Effect of Gut Microbiota and Probiotics on Metabolism in Fish and Shrimp. Animals (Basel) 2022; 12:3016. [PMID: 36359140 PMCID: PMC9655696 DOI: 10.3390/ani12213016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/01/2022] [Accepted: 11/02/2022] [Indexed: 07/30/2023] Open
Abstract
The present paper presents an overview of the effects of gut microbiota and probiotics on lipid-, carbohydrate-, protein- and amino acid metabolism in fish and shrimp. In probiotic fish studies, the zebrafish (Danio rerio) model is the most frequently used, and probiotic administration reveals the effect on glucose homeostasis, anti-lipidemic effects and increasing short-chain fatty acids, and increased expressions of genes related to carbohydrate metabolism and innate immunity, along with down-regulation of oxidative stress-related genes. Further, improved length of the intestinal villi and expression of nutrient transporters in fish owing to probiotics exposure have been documented. The present review will present an appraisal of the effect of intestinal microbiota and probiotic administration on the metabolism of nutrients and metabolites related to stress and immunity in diverse fish- and shrimp species. Furthermore, to give the reader satisfactory information on the topics discussed, some information from endothermic animals is also presented.
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Affiliation(s)
- Einar Ringø
- Norwegian College of Fishery Science, Faculty of Bioscience, Fisheries and Economics, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Ramasamy Harikrishnan
- Department of Zoology, Pachaiyappa’s College for Men, University of Madras, Kanchipuram 631 501, Tamil Nadu, India
| | - Mehdi Soltani
- Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran 1419963111, Iran
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Burdwan 713 104, West Bengal, India
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Effects of Three Feed Additives on the Culturable Microbiota Composition and Histology of the Anterior and Posterior Intestines of Zebrafish (Danio rerio). Animals (Basel) 2022; 12:ani12182424. [PMID: 36139282 PMCID: PMC9495144 DOI: 10.3390/ani12182424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary This work is dedicated to the study of the effects of three feed additives that are promising for use in aquaculture on the culturable microbial community and the tissue structure (histology) of the intestines of laboratory zebrafish. The feed additives used in this research have different functional properties: (i) micronutrient chelated compounds, which eliminate mineral nutrition deficiencies; (ii) butyric acid, a postbiotic drug aimed at stimulating intestinal bacteria growth and improving immunity; and (iii) lycopene, a carotenoid and wide-spectrum antioxidant. All of the tested supplements resulted in changes in the intestinal microbial community in both the anterior and posterior intestines. The change in gut microbiota correlated with histological changes in the intestines. The results of the study showed that in most concentrations, the feed additives had a positive effect on certain groups of microorganisms. The method of microbiota research based on microorganism cultivation used in this work makes it possible to evaluate the effect of feed additives on the relative abundance of key representatives of the microbial community. Abstract In this study, the effect of three promising feed additives (chelated compounds of trace elements, butyric acid, lycopene) on changes in the culturable microbiota and histological parameters of two sections of the intestines of Danio rerio (zebrafish) was studied. The use of these feed additives can help to eliminate the deficiency of trace elements, modulate the composition of the microbiota due to the postbiotic properties of butyric acid, and reduce oxidative stress when using lycopene. Incorporation of the investigated supplements in the feed resulted in a significant change in the relative abundance of certain groups of microorganisms. The taxonomic diversity of cultured microorganisms did not differ in the anterior and posterior intestines, while there were differences in the relative abundance of these microorganisms. The most sensitive groups of microorganisms were the genera Bacillus and Serratia. A significant effect on the composition of the cultured microbiota was caused by lycopene (in all studied concentrations), leading to a significant increase in the relative abundance of Firmicutes in the anterior gut. Studies of the histological structure of the anterior and posterior guts have shown the relationship between the barrier and secretory functions of the gut and the composition of the microbiota while using butyric acid (1 and 2 g kg−1) and trace element chelated compounds (2 mg kg−1). This culture-dependent method of studying the microbiome makes it possible to assess changes in some representatives of the main groups of microorganisms (Firmicutes and Proteobacteria). Despite the incompleteness of the data obtained by the culture-dependent method, its application makes it possible to assess the bioactive properties of feed and feed additives and their impact on the microbiota involved in digestive processes.
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You Z, Deng J, Liu J, Fu J, Xiong H, Luo W, Xiong J. Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer ( Cervus albirostris). PeerJ 2022; 10:e13753. [PMID: 35873913 PMCID: PMC9302429 DOI: 10.7717/peerj.13753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/28/2022] [Indexed: 01/17/2023] Open
Abstract
The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer.
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Affiliation(s)
- Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jing Deng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jialin Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Junhua Fu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Huan Xiong
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Wei Luo
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jianli Xiong
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
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Romero J, Díaz O, Miranda CD, Rojas R. Red Cusk-Eel ( Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens. Microorganisms 2022; 10:microorganisms10010105. [PMID: 35056554 PMCID: PMC8779451 DOI: 10.3390/microorganisms10010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.
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Affiliation(s)
- Jaime Romero
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Macul, Santiago 783090, Chile;
- Correspondence: ; Tel.: +56-2-29781524
| | - Osmán Díaz
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Macul, Santiago 783090, Chile;
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile; (C.D.M.); (R.R.)
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Vo TTM, Nguyen TV, Amoroso G, Ventura T, Elizur A. Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar). BMC Genomics 2021; 22:545. [PMID: 34271869 PMCID: PMC8285899 DOI: 10.1186/s12864-021-07884-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3' mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3' mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes. RESULTS In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR. CONCLUSIONS Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3' mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1.
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Affiliation(s)
- Thu Thi Minh Vo
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.,School of Biotechnology, International University, Viet Nam National University, 700000, Ho Chi Minh City, Vietnam
| | - Tuan Viet Nguyen
- Centre for AgriBiosciences, AgriBio, Agriculture Victoria, Victoria, 3083, Bundoora, Australia
| | | | - Tomer Ventura
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.
| | - Abigail Elizur
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia.
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