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Molversmyr H, Øyås O, Rotnes F, Vik JO. Extracting functionally accurate context-specific models of Atlantic salmon metabolism. NPJ Syst Biol Appl 2023; 9:19. [PMID: 37244928 DOI: 10.1038/s41540-023-00280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/05/2023] [Indexed: 05/29/2023] Open
Abstract
Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular eukaryotes. Published CBMs are usually generic rather than context-specific, meaning that they do not capture differences in reaction activities, which, in turn, determine metabolic capabilities, between cell types, tissues, environments, or other conditions. Only a subset of a CBM's metabolic reactions and capabilities are likely to be active in any given context, and several methods have therefore been developed to extract context-specific models from generic CBMs through integration of omics data. We tested the ability of six model extraction methods (MEMs) to create functionally accurate context-specific models of Atlantic salmon using a generic CBM (SALARECON) and liver transcriptomics data from contexts differing in water salinity (life stage) and dietary lipids. Three MEMs (iMAT, INIT, and GIMME) outperformed the others in terms of functional accuracy, which we defined as the extracted models' ability to perform context-specific metabolic tasks inferred directly from the data, and one MEM (GIMME) was faster than the others. Context-specific versions of SALARECON consistently outperformed the generic version, showing that context-specific modeling better captures salmon metabolism. Thus, we demonstrate that results from human studies also hold for a non-mammalian animal and major livestock species.
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Affiliation(s)
- Håvard Molversmyr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ove Øyås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Filip Rotnes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jon Olav Vik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
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Agboola JO, Rocha SDC, Mensah DD, Hansen JØ, Øyås O, Lapeña D, Mydland LT, Arntzen MØ, Horn SJ, Øverland M. Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater. Anim Microbiome 2023; 5:21. [PMID: 37016467 PMCID: PMC10074822 DOI: 10.1186/s42523-023-00242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Yeasts are gaining attention as alternative ingredients in aquafeeds. However, the impact of yeast inclusion on modulation of intestinal microbiota of fish fed plant-based ingredients is limited. Thus, the present study investigates the effects of yeast and processing on composition, diversity and predicted metabolic capacity of gut microbiota of Atlantic salmon smolt fed soybean meal (SBM)-based diet. Two yeasts, Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA), were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h, followed by spray-drying (ACJ and AWA). In a 42-day feeding experiment, fish were fed one of six diets: a fishmeal (FM)-based diet, a challenging diet with 30% SBM and four other diets containing 30% SBM and 10% of each of the four yeast products (i.e., ICJ, ACJ, IWA and AWA). Microbial profiling of digesta samples was conducted using 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. RESULTS The microbial composition and predicted metabolic capacity of gut microbiota differed between fish fed FM diet and those fed SBM diet. The digesta of fish fed SBM diet was dominated by members of lactic acid bacteria, which was similar to microbial composition in the digesta of fish fed the inactivated yeasts (ICJ and IWA diets). Inclusion of autolyzed yeasts (ACJ and AWA diets) reduced the richness and diversity of gut microbiota in fish. The gut microbiota of fish fed ACJ diet was dominated by the genus Pediococcus and showed a predicted increase in mucin O-glycan degradation compared with the other diets. The gut microbiota of fish fed AWA diet was highly dominated by the family Bacillaceae. CONCLUSIONS The present study showed that dietary inclusion of FM and SBM differentially modulate the composition and predicted metabolic capacity of gut microbiota of fish. The inclusion of inactivated yeasts did not alter the modulation caused by SBM-based diet. Fish fed ACJ diet increased relative abundance of Pediococcus, and mucin O-glycan degradation pathway compared with the other diets.
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Affiliation(s)
- Jeleel O Agboola
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
| | - Sérgio D C Rocha
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Dominic D Mensah
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Jon Ø Hansen
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - David Lapeña
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Liv T Mydland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Margareth Øverland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
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Zakhartsev M, Rotnes F, Gulla M, Øyås O, van Dam JCJ, Suarez-Diez M, Grammes F, Hafþórsson RA, van Helvoirt W, Koehorst JJ, Schaap PJ, Jin Y, Mydland LT, Gjuvsland AB, Sandve SR, Martins dos Santos VAP, Vik JO. SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PLoS Comput Biol 2022; 18:e1010194. [PMID: 35687595 PMCID: PMC9223387 DOI: 10.1371/journal.pcbi.1010194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/23/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds. Atlantic salmon aquaculture generates billions of euros annually, but faces challenges of sustainability. Salmon are carnivores by nature, and fish oil and fish meal have become scarce resources in fish feed production. Novel, sustainable feedstuffs are being trialed hand in hand with studies of the genetics of growth and feed efficiency. This calls for a mathematical-biological framework to integrate data with understanding of the effects of novel feeds on salmon physiology and its interplay with genetics. We have developed the SALARECON model of the core salmon metabolic reaction network, linking its genome to metabolic fluxes and growth. Computational analyses show good agreement with observed growth, amino acid limitations, and feed efficiencies, illustrating the potential for in silico studies of potential feed mixtures. In particular, in silico screening of possible diets will enable more efficient animal experiments with improved knowledge gain. We have adopted best practices for test-driven development, virtual experiments to assay metabolic capabilities, revision control, and FAIR data and model management. This facilitates fast, collaborative, reliable development of the model for future applications in sustainable production biology.
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Affiliation(s)
- Maksim Zakhartsev
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Filip Rotnes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Marie Gulla
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ove Øyås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jesse C. J. van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Fabian Grammes
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Wout van Helvoirt
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Yang Jin
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Liv Torunn Mydland
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Arne B. Gjuvsland
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Simen R. Sandve
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Jon Olav Vik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
- * E-mail:
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Agboola JO, Mensah DD, Hansen JØ, Lapeña D, Mydland LT, Arntzen MØ, Horn SJ, Øyås O, Press CM, Øverland M. Effects of Yeast Species and Processing on Intestinal Health and Transcriptomic Profiles of Atlantic Salmon ( Salmo salar) Fed Soybean Meal-Based Diets in Seawater. Int J Mol Sci 2022; 23:1675. [PMID: 35163597 PMCID: PMC8836103 DOI: 10.3390/ijms23031675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/26/2022] Open
Abstract
The objective of the current study was to examine the effects of yeasts on intestinal health and transcriptomic profiles from the distal intestine and spleen tissue of Atlantic salmon fed SBM-based diets in seawater. Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA) yeasts were heat-inactivated with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h (ACJ and AWA), followed by spray-drying. Six diets were formulated, one based on fishmeal (FM), a challenging diet with 30% soybean meal (SBM) and four other diets containing 30% SBM and 10% of each of the four yeast fractions (i.e., ICJ, ACJ, IWA and AWA). The inclusion of CJ yeasts reduced the loss of enterocyte supranuclear vacuolization and reduced the population of CD8α labeled cells present in the lamina propria of fish fed the SBM diet. The CJ yeasts controlled the inflammatory responses of fish fed SBM through up-regulation of pathways related to wound healing and taurine metabolism. The WA yeasts dampened the inflammatory profile of fish fed SBM through down-regulation of pathways related to toll-like receptor signaling, C-lectin receptor, cytokine receptor and signal transduction. This study suggests that the yeast species, Cyberlindnera jadinii and Wickerhamomyces anomalus are novel high-quality protein sources with health-beneficial effects in terms of reducing inflammation associated with feeding plant-based diets to Atlantic salmon.
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Affiliation(s)
- Jeleel O. Agboola
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
| | - Dominic D. Mensah
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
| | - Jon Ø. Hansen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
| | - David Lapeña
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.L.); (M.Ø.A.); (S.J.H.)
| | - Liv T. Mydland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
| | - Magnus Ø. Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.L.); (M.Ø.A.); (S.J.H.)
| | - Svein J. Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.L.); (M.Ø.A.); (S.J.H.)
| | - Ove Øyås
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.L.); (M.Ø.A.); (S.J.H.)
| | - Charles McL. Press
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway;
| | - Margareth Øverland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; (D.D.M.); (J.Ø.H.); (L.T.M.); (O.Ø.)
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Weththasinghe P, Rocha SDC, Øyås O, Lagos L, Hansen JØ, Mydland LT, Øverland M. Modulation of Atlantic salmon (Salmo salar) gut microbiota composition and predicted metabolic capacity by feeding diets with processed black soldier fly (Hermetia illucens) larvae meals and fractions. Anim Microbiome 2022; 4:9. [PMID: 35033208 PMCID: PMC8760679 DOI: 10.1186/s42523-021-00161-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Black soldier fly (Hermetia illucens) is a promising insect species to use as a novel ingredient in fish feeds. Black soldier fly larvae consists of three major fractions, namely protein, lipid, and exoskeleton. These fractions contain bioactive compounds that can modulate the gut microbiota in fish such as antimicrobial peptides, lauric acid, and chitin. However, it is not certain how, or which fractions of black solider fly would affect gut microbiota in fish. In the present study, black soldier fly larvae were processed into three different meals (full-fat, defatted and de-chitinized) and two fractions (oil and exoskeleton), and included in diets for Atlantic salmon (Salmo salar). Atlantic salmon pre-smolts were fed with these diets in comparison with a commercial-like control diet for eight weeks to investigate the effects of insect meals and fractions on the composition and predicted metabolic capacity of gut microbiota. The gut microbiota was profiled by 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. RESULTS The inclusion of insect meals and fractions decreased abundance of Proteobacteria and increased abundance of Firmicutes in salmon gut. The diets that contained insect chitin, i.e., insect meals or exoskeleton diets, increased abundance of chitinolytic bacteria including lactic acid bacteria and Actinomyces in salmon gut, with fish fed full-fat meal diet showing the highest abundances. The diets that contained insect lipids, i.e., insect meals and oil diets enriched Bacillaceae in fish gut. The fish fed diets containing full-fat insect meal had a unique gut microbiota composition dominated by beneficial lactic acid bacteria and Actinomyces, and showed a predicted increase in mucin degradation compared to the other diets. CONCLUSIONS The present results showed that the dietary inclusion of insect meals and fractions can differently modulate the composition and predicted metabolic capacity of gut microbiota in Atlantic salmon pre-smolts. The use of full-fat black soldier fly larvae meal in diets for salmon is more favorable for beneficial modulation of gut microbiota than larvae processed by separation of lipid or exoskeleton fractions.
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Affiliation(s)
- Pabodha Weththasinghe
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Sérgio D. C. Rocha
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Ove Øyås
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Leidy Lagos
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Jon Ø. Hansen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Liv T. Mydland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Margareth Øverland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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Morales-Lange B, Agboola JO, Hansen JØ, Lagos L, Øyås O, Mercado L, Mydland LT, Øverland M. The Spleen as a Target to Characterize Immunomodulatory Effects of Down-Stream Processed Cyberlindnera jadinii Yeasts in Atlantic Salmon Exposed to a Dietary Soybean Meal Challenge. Front Immunol 2021; 12:708747. [PMID: 34489959 PMCID: PMC8417602 DOI: 10.3389/fimmu.2021.708747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Aquaculture feeds have changed dramatically from being largely based on fishmeal (FM) towards increased use of plant protein sources, which could impact the fish's immune response. In order to characterize immunomodulatory properties of novel functional ingredients, this study used four diets, one based on FM, a challenging diet with 40% soybean meal (SBM), and two diets containing 40% SBM with 5% of Cyberlindnera jadinii yeast exposed to different down-stream processing conditions: heat-inactivated (ICJ) or autolysation (ACJ). The immunomodulatory effects of the diets were analyzed in the spleen of Atlantic salmon after 37 days of feeding, using a transcriptomic evaluation by RNA sequencing (RNA-seq) and the detection of specific immunological markers at the protein level through indirect Enzyme-linked Immunosorbent Assay (indirect ELISA). The results showed that SBM (compared to FM) induced a down-regulation of pathways related to ion binding and transport, along with an increase at the protein level of pro-inflammatory cytokines such as tumor necrosis factor alpha (TNFα) and interferon gamma (IFNγ). On the other hand, while ICJ (compared to FM-group) maintain the inflammatory response associated with SBM, with higher levels of TNFα and IFNγ, and with an upregulation of creatine kinase activity and phosphagen metabolic process, the inclusion of ACJ was able to modulate the response of Atlantic salmon compared to fish fed the SBM-diet by the activation of biological pathways related to endocytosis, Pattern recognition receptor (PPRs)-signal transduction and transporter activity. In addition, ACJ was also able to control the pro-inflammatory profile of SBM, increasing Interleukin 10 (IL-10) levels and decreasing TNFα production, triggering an immune response similar to that of fish fed an FM-based diet. Finally, we suggest that the spleen is a good candidate to characterize the immunomodulatory effects of functional ingredients in Atlantic salmon. Moreover, the inclusion of ACJ in fish diets, with the ability to control inflammatory processes, could be considered in the formulation of sustainable salmon feed.
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Affiliation(s)
- Byron Morales-Lange
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jeleel Opeyemi Agboola
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jon Øvrum Hansen
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Leidy Lagos
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ove Øyås
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Liv Torunn Mydland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Margareth Øverland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, Michetti P, Mueller C, Geuking M, Pittet VEH, Maillard MH, Rogler G, Wiest R, Stelling J, Macpherson AJ. Publisher Correction: Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019; 25:701. [PMID: 30846883 DOI: 10.1038/s41591-019-0411-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Owing to an error during typesetting, a number of references were deleted from the Methods reference list. This altered all of the references in the Methods section and some of the references in Extended Data Fig. 5, making them inaccurate. References 121-134 were added back into the Methods reference list, and the references in the Methods section and in Extended Data Fig. 5 were renumbered accordingly. The error has been corrected in the PDF and HTML versions of this article.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Francisco Damian Bravo
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yannick Franc
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Fournier
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre Michetti
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Christoph Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Markus Geuking
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Valerie E H Pittet
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Michel H Maillard
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Reiner Wiest
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland. .,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.
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Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, Michetti P, Mueller C, Geuking M, Pittet VEH, Maillard MH, Rogler G, Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019; 25:323-336. [PMID: 30664783 DOI: 10.1038/s41591-018-0308-z] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD) can be broadly divided into Crohn's disease (CD) and ulcerative colitis (UC) from their clinical phenotypes. Over 150 host susceptibility genes have been described, although most overlap between CD, UC and their subtypes, and they do not adequately account for the overall incidence or the highly variable severity of disease. Replicating key findings between two long-term IBD cohorts, we have defined distinct networks of taxa associations within intestinal biopsies of CD and UC patients. Disturbances in an association network containing taxa of the Lachnospiraceae and Ruminococcaceae families, typically producing short chain fatty acids, characterize frequently relapsing disease and poor responses to treatment with anti-TNF-α therapeutic antibodies. Alterations of taxa within this network also characterize risk of later disease recurrence of patients in remission after the active inflamed segment of CD has been surgically removed.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Francisco Damian Bravo
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yannick Franc
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Fournier
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre Michetti
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Christoph Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Markus Geuking
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Valerie E H Pittet
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Michel H Maillard
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Reiner Wiest
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland. .,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.
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