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Williams MB, Green GBH, Palmer JW, Fay CX, Chehade SB, Lawrence AL, Barry RJ, Powell ML, Harris ML, Watts SA. Replacement of Dietary Fish Protein with Bacterial Protein Results in Decreased Adiposity Coupled with Liver Gene Expression Changes in Female Danio rerio. Curr Dev Nutr 2024; 8:102057. [PMID: 38234580 PMCID: PMC10792695 DOI: 10.1016/j.cdnut.2023.102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
Background Effective use of Danio rerio as a preclinical model requires standardization of macronutrient sources to achieve scientific reproducibility across studies and labs. Objective Our objective was to evaluate a bacterial-based single-cell protein (SCP) for the production of open-source standardized diets with defined health characteristics for the zebrafish research community. Methods We completed a 16-wk feeding trial using juvenile D. rerio 31 d postfertilization (10 tanks per diet and 14 D. rerio per tank) with formulated diets containing either a typical fish protein ingredient [standard reference (SR) diet] or a novel bacterial SCP source [bacterial protein (BP) diet]. At the end of the feeding trial, growth metrics, body composition, reproductive success, and bulk transcriptomics of the liver (RNAseq on female D. rerio with confirmatory rtPCR) were performed for each diet treatment. Results D. rerio fed the BP diet had body weight gains equivalent to the D. rerio fed fish protein, and females had significantly lower total carcass lipid, indicating reduced adiposity. Reproductive success was similar between treatments, suggesting normal physiological function. Genes differentially expressed in female D. rerio fed the BP diet compared with females fed the SR diet were overrepresented in the gene ontologies of metabolism, biosynthesis of cholesterol precursors and products, and protein unfolding responses. Conclusion Protein source substantially affected body growth metrics and composition as well as gene expression. These data support the development of an open-source diet utilizing an ingredient that correlates with improved health profiles and reduced variability in notable outcomes.
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Affiliation(s)
- Michael B Williams
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - George BH Green
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Joseph W Palmer
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christian X Fay
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sophie B Chehade
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Addison L Lawrence
- Agriculture and Lifesciences, Texas A&M University, College Station, TX, United States
| | - Robert J Barry
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mickie L Powell
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Melissa L Harris
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
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Williams M, Green GBH, Palmer JW, Fay CX, Chehade SB, Lawrence AL, Barry RJ, Powell ML, Harris ML, Watts SA. Replacement of Dietary Fish Protein With Bacterial Single Cell Protein Results in Decreased Adiposity Coupled With Liver Expression Changes in Female Danio Rerio. RESEARCH SQUARE 2023:rs.3.rs-3044822. [PMID: 37398488 PMCID: PMC10312982 DOI: 10.21203/rs.3.rs-3044822/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Effective use of Danio rerio as a preclinical model requires standardization of macronutrient sources to achieve scientific reproducibility across studies and labs. Our objective was to evaluate single cell protein (SCP) for production of open-source standardized diets with defined heath characteristics for the zebrafish research community. We completed a 16-week feeding trial using juvenile D. rerio 31 days post-fertilization (dpf) (10 tanks per diet, 14 D. rerio per tank) with formulated diets containing either a typical fish protein ingredient or a novel bacterial SCP source. At the end of the feeding trial, growth metrics, body composition, reproductive success, and bulk transcriptomics of the liver (RNAseq on female D. rerio only with confirmatory rtPCR) were performed for each diet treatment. Results D. rerio fed the SCP containing diet had body weight gains equivalent to the D. rerio fed fish protein, and females had significantly lower total carcass lipid, indicating reduced adiposity. Reproductive success was similar between treatments. Genes differentially expressed in female D. rerio provided the bacterial SCP compared to females given fish protein were overrepresented in the gene ontologies of metabolism, biosynthesis of cholesterol precursors and products, and protein unfolding responses. Conclusion These data support the development of an open-source diet utilizing an ingredient that correlates with improved health profiles and reduced variability in notable outcomes.
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Effect of Feeding Insoluble Fiber on the Microbiota and Metabolites of the Caecum and Feces of Rabbits Recovering from Epizootic Rabbit Enteropathy Relative to Non-Infected Rabbits. Pathogens 2022; 11:pathogens11050571. [PMID: 35631092 PMCID: PMC9146049 DOI: 10.3390/pathogens11050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
This study aimed to investigate the effect of feeding insoluble fiber on the microbiota and metabolites of the caecum and feces of rabbits recovering from epizootic rabbit enteropathy relative to non-infected rabbits. Rabbits that had either recovered from epizootic rabbit enteropathy or ones that had never had epizootic rabbit enteropathy were fed on a diet of 32% or 36% neutral detergent fiber until they were 70 days of age. At this point, the short-chain fatty acid and ammonia levels were measured in caecotroph and fecal samples and compared using 2 × 2 ANOVA. The microbial composition of the samples was also analyzed using next-generation sequencing and compared by PERMANOVA. Caecotrophic samples from previously affected rabbits on lower fiber diets had higher short-chain fatty acid contents and higher species diversity index values for some indices (p < 0.05), although the fecal samples showed lower species diversity levels (p < 0.05). In addition, the PERMANOVA analyses demonstrated that differences were detected in the microbial composition of both fecal and caecotrophic samples, depending on the disease status at the outset of the experiment (p < 0.05). The results of this work show that, although there is some potential in the use of high-fiber diets for the treatment of rabbits that have had epizootic rabbit enteropathy, they are not able to produce the same digestive tract properties as those seen in rabbits that have never had the condition. This is true even after the rabbits have recovered from epizootic rabbit enteropathy.
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Oczkowicz M, Pawlina-Tyszko K, Świątkiewicz M, Szmatoła T. Feeding pigs with coconut oil affects their adipose miRNA profile. Mol Biol Rep 2022; 49:6919-6929. [DOI: 10.1007/s11033-022-07303-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
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Oczkowicz M, Szmatoła T, Świątkiewicz M, Koseniuk A, Smołucha G, Witarski W, Wierzbicka A. 3'quant mRNA-Seq of Porcine Liver Reveals Alterations in UPR, Acute Phase Response, and Cholesterol and Bile Acid Metabolism in Response to Different Dietary Fats. Genes (Basel) 2020; 11:genes11091087. [PMID: 32961898 PMCID: PMC7565913 DOI: 10.3390/genes11091087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022] Open
Abstract
Animal fats are considered to be unhealthy, in contrast to vegetable fats, which are rich in unsaturated fatty acids. However, the use of some fats, such as coconut oil, is still controversial. In our experiment, we divided experimental animals (domestic pigs) into three groups differing only in the type of fat used in the diet: group R: rapeseed oil (n = 5); group B: beef tallow (n = 5); group C: coconut oil (n = 6). After transcriptomic analysis of liver samples, we identified 188, 93, and 53 DEGs (differentially expressed genes) in R vs. B, R vs. C, and B vs. C comparisons, respectively. Next, we performed a functional analysis of identified DEGs with String and IPA software. We observed the enrichment of genes engaged in the unfolded protein response (UPR) and the acute phase response among genes upregulated in B compared to R. In contrast, cholesterol biosynthesis and cholesterol efflux enrichments were observed among genes downregulated in B when compared to R. Moreover, activation of the UPR and inhibition of the sirtuin signaling pathway were noted in C when compared to R. The most striking difference in liver transcriptomic response between C and B was the activation of the acute phase response and inhibition of bile acid synthesis in the latest group. Our results suggest that excessive consumption of animal fats leads to the activation of a cascade of mutually propelling processes harmful to the liver: inflammation, UPR, and imbalances in the biosynthesis of cholesterol and bile acids via altered organelle membrane composition. Nevertheless, these studies should be extended with analysis at the level of proteins and their function.
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Affiliation(s)
- Maria Oczkowicz
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
- Correspondence: ; Tel.: +48666081109
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
- Centre of Experimental and Innovative Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland
| | - Małgorzata Świątkiewicz
- Department of Animal Nutrition and Feed Science, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland;
| | - Anna Koseniuk
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
| | - Grzegorz Smołucha
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
| | - Wojciech Witarski
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
| | - Alicja Wierzbicka
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul Krakowska 1, 32-083 Balice, Poland; (T.S.); (A.K.); (G.S.); (W.W.); (A.W.)
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Source of Dietary Fat in Pig Diet Affects Adipose Expression of Genes Related to Cancer, Cardiovascular, and Neurodegenerative Diseases. Genes (Basel) 2019; 10:genes10120948. [PMID: 31756991 PMCID: PMC6947373 DOI: 10.3390/genes10120948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 01/06/2023] Open
Abstract
It has been known for many years that excessive consumption of saturated fats has proatherogenic properties, contrary to unsaturated fats. However, the molecular mechanism covering these effects is not fully understood. In this paper, we aimed to identify differentially expressed genes (DEGs) using RNA-sequencing, following feeding pigs with different sources of fat. After comparison of adipose samples from three dietary groups (rapeseed oil (n = 6), beef tallow (n = 5), coconut oil (n = 5)), we identified 29 DEGs (adjusted p-value < 0.05, fold change > 1.3) between beef tallow and rapeseed oil and 2 genes between coconut oil and rapeseed oil groups. No differentially expressed genes were observed between coconut oil and beef tallow groups. Almost all 29 DEGs between rapeseed oil and beef tallow groups are connected to neurodegenerative, cardiovascular diseases, or cancer (e.g., PLAU, CYBB, NCF2, ZNF217, CHAC1, CTCFL). Functional analysis of these genes revealed that they are associated with fluid shear stress response, complement and coagulation cascade, ROS signaling, neurogenesis, and regulation of protein binding and protein catabolic processes. Furthermore, gene set enrichment analysis (GSEA) of the whole datasets from all three comparisons suggests that both beef tallow and coconut oil may trigger changes in the expression level of genes crucial in the pathogenesis of civilization diseases.
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Skugor A, Kjos NP, Sundaram AYM, Mydland LT, Ånestad R, Tauson AH, Øverland M. Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs. PLoS One 2019; 14:e0220441. [PMID: 31390356 PMCID: PMC6685631 DOI: 10.1371/journal.pone.0220441] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
This study was performed to investigate the effects of dietary inclusion of 20% rapeseed meal (RSM) as an alternative to soybean meal (SBM) in a three-month feeding experiment with growing finishing pigs. Dietary alteration affected growth performance, several carcass traits and transcriptional responses in the skeletal muscle, but did not affect measured meat quality traits. In general, pigs fed the RSM test diet exhibited reduced growth performance compared to pigs on SBM control diet. Significant transcriptional changes in the skeletal muscle of growing pigs fed RSM diet were likely the consequence of an increased amount of fiber and higher polyunsaturated fatty acids, and presence of bioactive phytochemicals, such as glucosinolates. RNAseq pipeline using Tophat2-Cuffdiff identified 57 upregulated and 63 downregulated genes in RSM compared to SBM pigs. Significantly enriched among downregulated pathways was p53-mediated signalling involved in cellular proliferation, while activation of negative growth regulators (IER5, KLF10, BTG2, KLF11, RETREG1, PRUNE2) in RSM fed pigs provided further evidence for reduced proliferation and increased cellular death, in accordance with the observed reduction in performance traits. Upregulation of well-known metabolic controllers (PDK4, UCP3, ESRRG and ESRRB), involved in energy homeostasis (glucose and lipid metabolism, and mitochondrial function), suggested less available energy and nutrients in RSM pigs. Furthermore, several genes supported more pronounced proteolysis (ABTB1, OTUD1, PADI2, SPP1) and reduced protein synthesis (THBS1, HSF4, AP1S2) in RSM muscle tissue. In parallel, higher levels of NR4A3, PDK4 and FGF21, and a drop in adropin, ELOVL6 and CIDEC/FSP27 indicated increased lipolysis and fatty acid oxidation, reflective of lower dressing percentage. Finally, pigs exposed to RSM showed greater expression level of genes responsive to oxidative stress, indicated by upregulation of GPX1, GPX2, and TXNIP.
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Affiliation(s)
- Adrijana Skugor
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Nils Petter Kjos
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | | | - Liv Torunn Mydland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Ragnhild Ånestad
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Anne-Helene Tauson
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Margareth Øverland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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