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Weston BR, Thiele I. A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models. Metab Eng 2023; 76:167-178. [PMID: 36724839 DOI: 10.1016/j.ymben.2023.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/13/2022] [Accepted: 01/25/2023] [Indexed: 01/30/2023]
Abstract
The optimization of animal feeds and cell culture media are problems of interest to a wide range of industries and scientific disciplines. Both problems are dictated by the properties of an organism's metabolism. However, due to the tremendous complexity of metabolic systems, it can be difficult to predict how metabolism will respond to changes in nutrient availability. A common tool used to capture the complexity of metabolism in a computational framework is a genome-scale metabolic model (GEM). GEMs are useful for predicting the fluxes of reactions within an organism's metabolism. To optimize feed or media, in silico experiments can be performed with GEMs by systematically varying nutritional constraints and predicting metabolic activity. In this way, the influence of various nutritional changes on metabolic outcomes can be evaluated. However, this methodology does not guarantee an optimal solution. Here, we develop a nutrition algorithm that utilizes linear programming to search the entire flux solution space of possible dietary intervention strategies to identify the most efficient changes to nutrition for a desirable metabolic outcome. We illustrate the utility of the nutrition algorithm on GEMs of Atlantic salmon (Salmo salar) and Chinese hamster ovary (CHO) cell metabolism and find that the nutrition algorithm makes predictions that not only align with experimental findings but reveal new insights into promising feeding strategies. We show that the nutrition algorithm is highly versatile and customizable to meet the user's needs. For instance, we demonstrate that the nutrition algorithm can be used to predict feed/media compositions that maximize profit margins. While the nutrition algorithm can be used to define an optimal feed/medium ab initio, it can also identify minimal changes to be made to an existing feed/medium to drive the largest metabolic shift. Moreover, the nutrition algorithm can target multiple metabolic pathways simultaneously with only a marginal increase in computational expense. While the nutrition algorithm has its limitations, we believe that this tool can be leveraged in a broad range of biotechnological applications to enhance the feed/medium optimization process.
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Affiliation(s)
- Bronson R Weston
- School of Medicine, University of Galway, Galway, H91 TK33, Ireland; Ryan Institute, University of Galway, Galway, H91 TK33, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, H91 TK33, Ireland; Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Discipline of Microbiology, University of Galway, Galway, H91 TK33, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland, Cork, T12 K8AF, Ireland.
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Darabighane B, Aghjehgheshlagh FM, Mahdavi A, Navidshad B, Bernard JK. Replacing alfalfa hay with dry corn gluten feed alters eating behavior, nutrient digestibility, and performance of lactating dairy cows. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1830722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Babak Darabighane
- Department of Animal Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | | | - Ali Mahdavi
- Faculty of Veterinary Medicine, Semnan University, Semnan, Iran
| | - Bahman Navidshad
- Department of Animal Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - John K. Bernard
- Department of Animal and Dairy Science, University of Georgia, Tifton, GA, USA
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Darabighane B, Mirzaei Aghjehgheshlagh F, Mahdavi A, Navidshad B, Bernard JK. Effects of inclusion of corn gluten feed in dairy rations on dry matter intake, milk yield, milk components, and ruminal fermentation parameters: a meta-analysis. Trop Anim Health Prod 2020; 52:2359-2369. [PMID: 32170651 DOI: 10.1007/s11250-020-02261-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/03/2020] [Indexed: 11/25/2022]
Abstract
Corn gluten feed (CGF) is a co-product of wet milling that can replace energy or fiber ingredients in dairy cow rations. The present meta-analysis examines how inclusion of CGF can affect dry matter intake (DMI), milk yield (MY), milk components, and ruminal fermentation parameters. A literature search was conducted to identify papers published from 1990 to 2018. Effect size for all parameters was calculated as standardized mean difference with a 95% confidence interval. Heterogeneity was determined using Q test and I2 statistic, while meta-regression was used to examine factors influencing heterogeneity. Results indicate that feeding CGF increased the effect size for DMI and MY. No differences were observed for effect size for percentage milk fat or protein; however, increases were observed in the effect size for milk fat yield, milk protein yield, milk lactose percentage, and milk lactose yield. Ruminal fermentation parameters revealed a decrease in the effect size for pH and acetate and an increase for propionate. No differences were observed in the effect size for total VFA or butyrate. The Q test demonstrated heterogeneity (P < 0.1) for MY, MFP, and pH. The results indicate differences in forage intake between groups receiving CGF and control as an important factor contributing to heterogeneity for DMI, MFP, and pH. It can be concluded from this meta-analysis that in addition to increased DMI, inclusion of CGF in cow diets increases MY and improves milk components. Furthermore, inclusion of CGF in the diet lowers ruminal pH while decreasing acetate and increasing propionate contents.
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Affiliation(s)
- Babak Darabighane
- Department of Animal Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | | | - Ali Mahdavi
- Faculty of Veterinary Medicine, Semnan University, Semnan, Iran
| | - Bahman Navidshad
- Department of Animal Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - John K Bernard
- Department of Animal and Dairy Science, University of Georgia, Tifton, GA, 31793, USA
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RIBEIRO KDO, GARCIA MC, OLIVEIRA AR, SOARES JÚNIOR MS, CALIRI M. Characterization and proposal of potential use in foods of coproducts from waxy maize wet milling. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.26817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Weiss WP. Effects of feeding diets composed of corn silage and a corn milling product with and without supplemental lysine and methionine to dairy cows. J Dairy Sci 2019; 102:2075-2084. [PMID: 30612798 DOI: 10.3168/jds.2018-15535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/08/2018] [Indexed: 11/19/2022]
Abstract
Formulating diets with high inclusion rates of a feed that provides necessary nutrients at lower-than-market prices for those nutrients should increase income over feed costs if the feed is not detrimental to yields of milk and milk components. The objective of this study was to determine whether cows fed a diet composed of approximately 53% corn silage, 44% corn milling product (68% dry matter, 21% crude protein, 37% neutral detergent fiber, and 9% starch) and 3% minerals (CMP) would have similar productivity as cows fed a control diet of predominantly corn silage, alfalfa silage, corn grain, and soybean meal. Based on the National Research Council (2001) dairy model, the CMP diet was inadequate in metabolizable methionine and extremely low in metabolizable lysine. A third treatment (CMP+AA) was the same as the CMP diet but was supplemented with rumen-protected lysine and methionine. Twenty-one Holstein cows were used in a replicated Latin square (28-d periods) design to evaluate production responses to the 3 diets. Diets were formulated to contain the same concentration of net energy for lactation and metabolizable protein (MP) based on the National Research Council model, but diets with CMP contained more neutral detergent fiber (38.3 vs. 31.4%) and less starch (21.6 vs. 30.5%) than the control diet. Lysine as a percent of MP was 6.5, 6.0, and 6.8 for the control, CMP, and CMP+AA diets, respectively, and methionine was 1.8, 1.8, and 2.3% of MP, respectively. Dry matter intake was not affected by diet (24.3 kg/d), but milk yield was lower for cows fed either CMP diet than for those fed control (36.0 vs 38.1 kg/d). Milk fat concentrations were normal and not affected by diet (3.7%). Milk protein concentration was greater for cows fed CMP+AA than for cows fed the other 2 treatments (3.19 vs. 3.11%); however, milk protein yield was greatest for cows fed the conventional diet. The concentration of methionine in plasma was significantly greater for cows fed CMP+AA than for cows fed the other diets. Plasma lysine concentrations were greater for cows fed the conventional diet than for those fed the other 2 diets. Plasma concentrations of several essential AA were lower for cows fed either CMP diet. Based on calculated energy balance, diets contained similar concentrations of net energy for lactation, but cows fed CMP diets partitioned more energy toward body energy reserves than did control cows, perhaps because supply of specific AA limited milk synthesis.
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Affiliation(s)
- W P Weiss
- Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster 44691.
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Malumba P, Boudry C, Roiseux O, Bindelle J, Beckers Y, Béra F. Chemical characterisation and in vitro assessment of the nutritive value of co-products yield from the corn wet-milling process. Food Chem 2015; 166:143-149. [DOI: 10.1016/j.foodchem.2014.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/21/2014] [Accepted: 06/01/2014] [Indexed: 10/25/2022]
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Miller-Cushon E, Montoro C, Ipharraguerre I, Bach A. Dietary preference in dairy calves for feed ingredients high in energy and protein. J Dairy Sci 2014; 97:1634-44. [DOI: 10.3168/jds.2013-7199] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 12/01/2013] [Indexed: 11/19/2022]
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Phesatcha K, Wanapat M. Performance of lactating dairy cows fed a diet based on treated rice straw and supplemented with pelleted sweet potato vines. Trop Anim Health Prod 2012; 45:533-8. [PMID: 22961296 DOI: 10.1007/s11250-012-0255-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
Abstract
The purpose of this study was to evaluate the effects of sweet potato vine pellet (SWEPP) in concentrate diets on nutrient digestibility and rumen ecology in lactating dairy cows fed on urea-treated rice straw. Three multiparous Holstein crossbred cows in mid-lactation were randomly assigned according to a 3 × 3 Latin square design, and the treatments were as follows: T1 = control (no supplementation), T2 = supplementation of sweet potato vine pellet with 50 g/kg urea (SWEPP I) at 300 g/head/day, and T3 = supplementation of sweet potato pellet with 100 g/kg urea (SWEPP II) at 300 g/head/day, in concentrate diets, respectively. The result revealed that supplementation of SWEPP did not affect feed intake, ruminal pH, and blood urea nitrogen (P > 0.05). However, apparent digestibilities of organic matter, crude protein, and neutral detergent fiber were higher in SWEPP II than those in others. Furthermore, ruminal ammonia nitrogen (NH(3)-N) and milk yield were significantly higher (P < 0.05) in animals fed with SWEPP II than those fed with SWEPP I and control, respectively. In addition, there were no differences in purine derivatives and microbial nitrogen supply among all the treatments. Based on this study, it could be concluded that SWEPP is a good source of supplement which resulted in significant improvement in apparent digestibility, rumen fermentation, and milk yield in lactating dairy cows fed on urea-treated rice straw.
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Affiliation(s)
- Kampanat Phesatcha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
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Sullivan M, Grigsby K, Bradford B. Effects of wet corn gluten feed on ruminal pH and productivity of lactating dairy cattle fed diets with sufficient physically effective fiber. J Dairy Sci 2012; 95:5213-5220. [DOI: 10.3168/jds.2012-5320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022]
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Rezac D, Grigsby K, Bello N, Bradford B. Effects of varying rates of tallgrass prairie hay and wet corn gluten feed on productivity of lactating dairy cows. J Dairy Sci 2012; 95:842-9. [DOI: 10.3168/jds.2011-4752] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/20/2011] [Indexed: 11/19/2022]
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Mullins C, Grigsby K, Anderson D, Titgemeyer E, Bradford B. Effects of feeding increasing levels of wet corn gluten feed on production and ruminal fermentation in lactating dairy cows. J Dairy Sci 2010; 93:5329-37. [DOI: 10.3168/jds.2010-3310] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022]
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Effects of treating rice straw with urea or urea and calcium hydroxide upon intake, digestibility, rumen fermentation and milk yield of dairy cows. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.05.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mullins C, Grigsby K, Bradford B. Effects of alfalfa hay inclusion rate on productivity of lactating dairy cattle fed wet corn gluten feed-based diets. J Dairy Sci 2009; 92:3510-6. [DOI: 10.3168/jds.2008-1873] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kononoff PJ, Ivan SK, Matzke W, Grant RJ, Stock RA, Klopfenstein TJ. Milk Production of Dairy Cows Fed Wet Corn Gluten Feed During the Dry Period and Lactation. J Dairy Sci 2006; 89:2608-17. [PMID: 16772581 DOI: 10.3168/jds.s0022-0302(06)72338-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An experiment was conducted with 36 primiparous and 40 multiparous Holstein cows to examine the effects of feeding wet corn gluten feed (WCGF) on 305-d milk production, dry matter (DM) intake, body condition score (BCS), and health. The experimental treatments included: 1) control--WCGF not fed (n = 27); 2) WCGF-L-cows received diets containing WCGF (38% DM basis) during lactation (n = 23); and 3) WCGF-DL--cows received diets containing WCGF (38% DM basis) during the dry period and lactation (n = 26). During the dry period, cows consuming WCGF were observed to have a significant gain in BCS (0.07 +/- 0.06) compared with a loss in BCS in cows fed the control diet (control = -0.11 +/- 0.06 and WCGF-L = -0.04 +/- 0.06). During lactation, there were no differences by treatment on BCS. Cows consuming WCGF during lactation consumed more feed compared with the control: 25.4, 23.8, and 21.2 +/- 0.76 kg/d for WCGF-L, WCGF-DL, and the control, respectively. Milk production was higher for cows consuming WCGF: 35.0, 34.7, and 31.1 +/- 2.1 kg/d for WCGF-L, WCGF-DL, and the control, respectively. No differences were found in either DM intake or actual milk yield between the WCGF-L and WCGF-DL treatments, indicating that prepartum diets did not influence lactational performance. The WCGF diets resulted in significant reductions in the concentration of milk fat (3.94, 3.74, and 4.15 +/- 0.08% for WCGF-L, WCGF-DL, and the control, respectively), but because total milk yield was increased, there were no differences in total milk fat yield. In addition, 3.5% of fat-corrected milk tended to be affected by diet: 38.9, 36.3, and 34.7 +/- 1.93 kg/d for WCGF-L, WCGF-DL, and the control, respectively. The increasing effect of DM intake and milk yield in cows consuming WCGF resulted in a similar efficiency of 3.5% fat-corrected milk production for all treatments, averaging 1.5 +/- 0.09. Total protein yields were significantly higher for cows consuming WCGF diets during lactation: 1.15, 1.10, 1.00 +/- 0.06 kg/d for WCGF-L, WCGF-DL, and the control, respectively. These results indicate that diets may be formulated to contain as much as 37.5% WCGF (DM basis).
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Affiliation(s)
- P J Kononoff
- Department of Animal Science, University of Nebraska, Lincoln 68583-0908, USA.
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