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El Jeni R, Villot C, Koyun OY, Osorio-Doblado A, Baloyi JJ, Lourenco JM, Steele M, Callaway TR. Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust". J Dairy Sci 2024; 107:1832-1856. [PMID: 37949397 DOI: 10.3168/jds.2023-23831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.
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Affiliation(s)
- R El Jeni
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - C Villot
- Lallemand SAS, Blagnac, France, 31069
| | - O Y Koyun
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - A Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - J J Baloyi
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - M Steele
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602.
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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] [Received: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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Congiu M, Lourenco J, Cesarani A, Lamichhane U, Macciotta NPP, Dimauro C. Predicting feed efficiency of Angus steers using the gastrointestinal microbiome. Animal 2024; 18:101102. [PMID: 38430665 DOI: 10.1016/j.animal.2024.101102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.
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Affiliation(s)
- M Congiu
- Dipartimento di Agraria, University of Sassari, Sassari 07100, Italy; Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USA
| | - J Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USA
| | - A Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari 07100, Italy; Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USA.
| | - U Lamichhane
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USA
| | - N P P Macciotta
- Dipartimento di Agraria, University of Sassari, Sassari 07100, Italy
| | - C Dimauro
- Dipartimento di Agraria, University of Sassari, Sassari 07100, Italy
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Ahvenjärvi S, Bayat AR, Toivanen M, Mäntysaari P, Tapio I. The effects of residual energy intake on nutrient use, methane emissions and microbial composition in dairy cows. Sci Rep 2024; 14:613. [PMID: 38182709 PMCID: PMC10770142 DOI: 10.1038/s41598-024-51300-7] [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] [Received: 09/01/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
For sustainable food production selection and breeding of feed efficient animals is crucial. The objective of this study was to evaluate whether multiparous dairy cows, ranked during their first lactation based on residual energy intake (REI) as efficient (low; L-REI) or inefficient (high; H-REI), differ in terms of nutrient use efficiency, methane emissions, rumen fermentation, and gut microbiota composition. Six L-REI and 6 H-REI cows were offered two diets with either a low or high proportion of concentrates (30 vs. 50% of DM) on two consecutive periods of 21 d. Gas exchanges, milk yield, feces and urine excretions were measured in open-circuit respiratory chambers. The results indicated that L-REI cows had higher methane yields (22.6 vs. 20.4 g/kg DM intake) and derived more energy (energy balance - 36.6 vs. - 16.9 MJ/d) and protein (N balance - 6.6 vs. 18.8 g/d) from the tissues to support similar milk yields compared to H-REI cows. Nutrient intake and digestibility were not affected by REI, and there were no interactions between REI and diet. Milk yield, milk production efficiency, and milk composition were not affected by REI except for milk urea concentration that was higher for L-REI cows (14.1 vs. 10.8 mg/100 ml). The rumen and fecal microbiota community structure and function were associated with both the diet and REI, but the diet effect was more pronounced. The current study identified several physiological mechanisms underlying the differences between high and low REI cows, but further studies are needed to distinguish the quantitative role of each mechanism.
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Affiliation(s)
- Seppo Ahvenjärvi
- Natural Resources Institute Finland (Luke), Production Systems, 31600, Jokioinen, Finland.
| | - Ali-Reza Bayat
- Natural Resources Institute Finland (Luke), Production Systems, 31600, Jokioinen, Finland
| | - Maria Toivanen
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Päivi Mäntysaari
- Natural Resources Institute Finland (Luke), Production Systems, 31600, Jokioinen, Finland
| | - Ilma Tapio
- Natural Resources Institute Finland (Luke), Production Systems, 31600, Jokioinen, Finland.
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Conteville LC, da Silva JV, Andrade BGN, Cardoso TF, Bruscadin JJ, de Oliveira PSN, Mourão GB, Coutinho LL, Palhares JCP, Berndt A, de Medeiros SR, Regitano LCDA. Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle. Front Microbiol 2023; 14:1282851. [PMID: 38163076 PMCID: PMC10754987 DOI: 10.3389/fmicb.2023.1282851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Background Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. Results The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Conclusion Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.
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Affiliation(s)
| | - Juliana Virginio da Silva
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | | | | | - Jennifer Jessica Bruscadin
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Priscila Silva Neubern de Oliveira
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
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6
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Edmunds CE, Welch CB, Lourenco JM, Callaway TR, Pringle TD, Dove CR. The Effects of Dietary Manganese and Selenium on Growth and the Fecal Microbiota of Nursery Piglets. Vet Sci 2023; 10:650. [PMID: 37999473 PMCID: PMC10675067 DOI: 10.3390/vetsci10110650] [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: 09/26/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
The objective of this study was to determine the impact of varying dietary manganese and selenium concentrations, antioxidant cofactors, on the growth performance and fecal microbial populations of nursery pigs. The piglets (N = 120) were blocked by weight (5.22 ± 0.7 kg) and sex. The pens (n = 5/treatment) within a block were randomly assigned to diets in a 2 × 3 factorial design to examine the effects of Se (0.1 and 0.3 mg/kg added Se) and Mn (0, 12, and 24 mg/kg added Mn) and were fed in three phases (P1 = d 1-7, P2 = d 8-21, P3 = d 22-35). The pigs and orts were weighed weekly. Fecal samples were collected d 0 and 35 for 16S rRNA bacterial gene sequencing and VFA analysis. The data were analyzed as factorial via GLM in SAS. There was a linear response (p < 0.05) in overall ADG across dietary Mn. Supplementing 24 mg/kg Mn tended to decrease (p < 0.10) the relative abundance of many bacteria possessing pathogenic traits relative to Mn controls. Meanwhile, increasing Mn concentration tended to foster the growth of bacteria correlated with gut health and improved growth (p < 0.10). The data from this study provide preliminary evidence on the positive effects of manganese on growth and gut health of nursery pigs.
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Affiliation(s)
- Clint E. Edmunds
- School of Sciences, Clayton State University, Morrow, GA 30260, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Christina B. Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Jeferson M. Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - T. Dean Pringle
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, USA;
| | - C. Robert Dove
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
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Fagan MM, Welch CB, Scheulin KM, Sneed SE, Jeon JH, Golan ME, Cheek SR, Barany DA, Oeltzschner G, Callaway TR, Zhao Q, Park HJ, Lourenco JM, Duberstein KJ, West FD. Fecal microbial transplantation limits neural injury severity and functional deficits in a pediatric piglet traumatic brain injury model. Front Neurosci 2023; 17:1249539. [PMID: 37841685 PMCID: PMC10568032 DOI: 10.3389/fnins.2023.1249539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Pediatric traumatic brain injury (TBI) is a leading cause of death and disability in children. Due to bidirectional communication between the brain and gut microbial population, introduction of key gut bacteria may mitigate critical TBI-induced secondary injury cascades, thus lessening neural damage and improving functional outcomes. The objective of this study was to determine the efficacy of a daily fecal microbial transplant (FMT) to alleviate neural injury severity, prevent gut dysbiosis, and improve functional recovery post TBI in a translational pediatric piglet model. Male piglets at 4-weeks of age were randomly assigned to Sham + saline, TBI + saline, or TBI + FMT treatment groups. A moderate/severe TBI was induced by controlled cortical impact and Sham pigs underwent craniectomy surgery only. FMT or saline were administered by oral gavage daily for 7 days. MRI was performed 1 day (1D) and 7 days (7D) post TBI. Fecal and cecal samples were collected for 16S rRNA gene sequencing. Ipsilateral brain and ileum tissue samples were collected for histological assessment. Gait and behavior testing were conducted at multiple timepoints. MRI showed that FMT treated animals demonstrated decreased lesion volume and hemorrhage volume at 7D post TBI as compared to 1D post TBI. Histological analysis revealed improved neuron and oligodendrocyte survival and restored ileum tissue morphology at 7D post TBI in FMT treated animals. Microbiome analysis indicated decreased dysbiosis in FMT treated animals with an increase in multiple probiotic Lactobacilli species, associated with anti-inflammatory therapeutic effects, in the cecum of the FMT treated animals, while non-treated TBI animals showed an increase in pathogenic bacteria, associated with inflammation and disease such in feces. FMT mediated enhanced cellular and tissue recovery resulted in improved motor function including stride and step length and voluntary motor activity in FMT treated animals. Here we report for the first time in a highly translatable pediatric piglet TBI model, the potential of FMT treatment to significantly limit cellular and tissue damage leading to improved functional outcomes following a TBI.
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Affiliation(s)
- Madison M. Fagan
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Christina B. Welch
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Kelly M. Scheulin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Sydney E. Sneed
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Julie H. Jeon
- Department of Nutritional Sciences, College of Family and Consumer Sciences, University of Georgia, Athens, GA, United States
| | - Morgane E. Golan
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Savannah R. Cheek
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Deborah A. Barany
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Department of Kinesiology, College of Education, University of Georgia, Athens, GA, United States
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Todd R. Callaway
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Qun Zhao
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Department of Physics and Astronomy, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, United States
| | - Hea Jin Park
- Department of Nutritional Sciences, College of Family and Consumer Sciences, University of Georgia, Athens, GA, United States
| | - Jeferson M. Lourenco
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Kylee J. Duberstein
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Franklin D. West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
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Freetly HC, Lindholm-Perry AK. Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet. J Anim Sci 2023; 101:skad292. [PMID: 37666002 PMCID: PMC10552577 DOI: 10.1093/jas/skad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
Most of the research addressing feed efficiency and the microbiota has been conducted in cattle fed grain diets, although cattle evolved to consume forage diets. Our hypothesis was that the bacteria in the rumen and cecum differed in cattle that have a common feed intake but had different ^average daily body weight gains (ADG) on a forage diet. Heifers (n = 134) were 606 ± 1 d of age and weighed 476 ± 3 kg at the start of the 84-d feeding study. Heifers were offered ad libitum access to a totally mixed ration that consisted of 86% ground brome hay, 10% wet distillers grains with solubles, and 4% mineral supplement as dry matter. Feed intake and body weight gain were measured, and gain was calculated. Heifers with the least (n = 8) and greatest (n = 8) ADG within 0.32 SD of the mean daily dry matter intake were selected for sampling. Digesta samples from the rumen and cecum were collected, and subsequent 16S analysis was conducted to identify Amplicon Sequence Variants. There were no differences in Alpha and Beta diversity between ADG classification within sample sites (P > 0.05). Both sample sites contained calculated balances of sister clades using phylogenetic isometric log ratio transferred data that differed across ADG classification. These findings suggest that bacteria did not differ at the community level, but there was structural difference at the clade level.
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Affiliation(s)
- Harvey C Freetly
- Nutrition, Growth & Physiology Research Unit, USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - Amanda K Lindholm-Perry
- Nutrition, Growth & Physiology Research Unit, USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
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9
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Lee S, Jung S, Lourenco J, Pringle D, Ahn J. Resampling-based inferences for compositional regression with application to beef cattle microbiomes. Stat Methods Med Res 2023; 32:151-164. [PMID: 36267026 DOI: 10.1177/09622802221133550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Gut microbiomes are increasingly found to be associated with many health-related characteristics of humans as well as animals. Regression with compositional microbiomes covariates is commonly used to identify important bacterial taxa that are related to various phenotype responses. Often the dimension of microbiome taxa easily exceeds the number of available samples, which creates a serious challenge in the estimation and inference of the model. The sparse log-contrast regression method is useful for such cases as it can yield a model estimate that depends on only a small number of taxa. However, a formal statistical inference procedure for individual regression coefficients has not been properly established yet. We propose a new estimation and inference procedure for linear regression models with extremely low-sample-sized compositional predictors. Under the compositional log-contrast regression framework, the proposed approach consists of two steps. The first step is to screen relevant predictors by fitting a log-contrast model with a sparse penalty. The screened-in variables are used as predictors in the non-sparse log-contrast model in the second step, where each of the regression coefficients is tested using nonparametric, resampling-based methods such as permutation and bootstrap. The performances of the proposed methods are evaluated by a simulation study, which shows they outperform traditional approaches based on normal assumptions or large sample asymptotics. Application to steer microbiome data successfully identifies key bacterial taxa that are related to important cattle quality measures.
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Affiliation(s)
- Sujin Lee
- Department of Statistics, 26725Seoul National University, Seoul, Republic of Korea
| | - Sungkyu Jung
- Department of Statistics, 26725Seoul National University, Seoul, Republic of Korea
| | - Jeferson Lourenco
- Department of Animal and Dairy Science, 1355University of Georgia, Athens, GA, USA
| | - Dean Pringle
- Department of Animal and Dairy Science, 1355University of Georgia, Athens, GA, USA
| | - Jeongyoun Ahn
- Department of Industrial and Systems Engineering, 34968KAIST, Daejeon, Republic of Korea
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10
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Fuerniss LK, Kreikemeier KK, Reed LD, Cravey MD, Johnson BJ. Cecal microbiota of feedlot cattle fed a four-species Bacillus supplement. J Anim Sci 2022; 100:skac258. [PMID: 35953238 PMCID: PMC9576023 DOI: 10.1093/jas/skac258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
As commercial fed cattle consume large amounts of concentrate feedstuffs, hindgut health can be challenged. The objective of this study was to evaluate the effects of a commercially available Bacillus feed additive on cattle health outcomes and cecal microbiota of fed cattle at the time of harvest. Commercial cattle from a single feedlot were identified for characterization of cecal microbial communities using 16S ribosomal ribonucleic acid gene sequencing. All cattle were fed a common corn-based finishing diet. Control cattle (CON) were administered no treatment while treated cattle (TRT) were supplemented daily with 0.050 g of MicroSaf 4C 40 (2 billion colony forming units of Bacillus spp.; Phileo by Lesaffre, Milwaukee, WI). Immediately after harvest and evisceration, the cecal contents of cattle were sampled. After DNA extraction, amplification, and sequencing, reads from CON samples (N = 12) and TRT samples (N = 12) were assigned taxonomy using the SILVA 138 database. Total morbidity, first treatment of atypical interstitial pneumonia, and early shipments for harvest were decreased among TRT cattle compared to CON cattle (P ≤ 0.021). On average, cecal microbiota from TRT cattle had greater alpha diversity than microbiota from CON cattle as measured by Shannon diversity, Pielou's evenness, and feature richness (P < 0.010). Additionally, TRT microbial communities were different (P = 0.001) and less variable (P < 0.001) than CON microbial communities when evaluated by unweighted UniFrac distances. By relative abundance across all samples, the most prevalent phyla were Firmicutes (55.40%, SD = 15.97) and Bacteroidetes (28.17%, SD = 17.74) followed by Proteobacteria (6.75%, SD = 10.98), Spirochaetes (4.54%, SD = 4.85), and Euryarchaeota (1.77%, SD = 3.00). Spirochaetes relative abundance in TRT communities was greater than that in CON communities and was differentially abundant between treatments by ANCOM testing (W = 11); Monoglobaceae was the only family-level taxon identified as differentially abundant (W = 59; greater mean relative abundance in TRT group by 2.12 percentage points). Half (N = 6) of the CON samples clustered away from all other samples based on principal coordinates and represented cecal dysbiosis among CON cattle. The results of this study indicated that administering a four-species blend of Bacillus positively supported the cecal microbial communities of finishing cattle. Further research is needed to explore potential mechanisms of action of Bacillus DFM products in feedlot cattle.
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Affiliation(s)
- Luke K Fuerniss
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | | | - Lynn D Reed
- Phileo by Lesaffre, Milwaukee, WI 52404, USA
| | | | - Bradley J Johnson
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
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11
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Williamson JR, Callaway TR, Lourenco JM, Ryman VE. Characterization of rumen, fecal, and milk microbiota in lactating dairy cows. Front Microbiol 2022; 13:984119. [PMID: 36225385 PMCID: PMC9549371 DOI: 10.3389/fmicb.2022.984119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p < 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p < 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p < 0.001). While diversity indices were not linked (p > 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.
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12
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Bao W, Yu J, He Y, Liu M, Yang X. The diversity analysis and gene function prediction of intestinal bacteria in three equine species. Front Microbiol 2022; 13:973828. [PMID: 36160217 PMCID: PMC9490377 DOI: 10.3389/fmicb.2022.973828] [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: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) was significantly different (P < 0.05) between the same species in the two wildlife parks, but neither the intestinal bacterial diversity index (Shannon) nor the community composition were significantly different (P > 0.05). The bacterial abundance index (Chao1) was significantly higher in MA than SP (P < 0.05) and highly significantly higher than PZ (P < 0.01); the bacterial diversity index (Shannon) was higher in MA than PZ, but there was no significant difference, but both MA and PZ were significantly higher than SP (P < 0.05). Moreover, the intestinal bacterial community composition was significantly different among the three equine species (P = 0.001). The dominant bacterial phyla for SP, MA, and PZ were Firmicutes and Bacteroidota; among them, the bacterial family with the highest relative abundance was Lachnospiraceae and the bacterial genus was Rikenellaceae_RC9_gut_group. Analysis of the metabolic gene functions of intestinal bacteria revealed that the highest relative abundance at Pathway level 2 was for global and overview maps; at Pathway level 3, the highest relative abundance was for biosynthesis of secondary metabolites. In sum, the intestinal bacterial community composition and diversity of the above three equine species differed significantly, but their metabolic gene functions were similar. Moreover, the results of this manuscript fill the gap in the study of intestinal bacterial diversity in SP, MA, and PZ. It also provides a reference for the study of the dominant bacteria in the intestinal microorganisms of these three equine species and the discovery of novel functional genes.
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13
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Seidel DS, Walker JW, Musser JM, Lourenco JM, Welch CB, Whitney TR, Callaway TR. Impact of concentrations of camphor on the in vitro mixed ruminal microorganism fermentation from goats selected for consumption of low and high levels of Juniperus spp.-2. Transl Anim Sci 2022; 6:txac098. [PMID: 35959416 PMCID: PMC9360777 DOI: 10.1093/tas/txac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
The microbial population in the gastrointestinal tract of ruminant animals aids in the utilization of forages with high levels of secondary plant compounds. Two divergent bloodlines of meat goats have been selected by screening fecal samples with near-infrared reflectance spectroscopy to assess the goat’s consumption of high or low levels of Juniperus sp. leaves containing several monoterpenes, including camphor. The mechanism by which these goats can consume greater concentrations of Juniperus spp. leaves than their counterparts is unclear, and therefore, this study was designed to determine if differences existed between the ruminal microbial populations of the low and high juniper-consuming bloodlines (LJC vs. HJC) by analyzing their ruminal microbiota and fermentation end products. In the present study, concentrations (0.00, 0.5, 0.99, 1.97, or 5.91 mM) of camphor were added to mixed ruminal microorganism fermentation. Five LJC and five HJC goats were fed a juniper-free diet (n = 10), and five LJC and five HJC goats (n = 10) were fed a diet that contained 30% fresh Juniperus ashei leaves for 21 d prior to ruminal fluid collection. In vitro fermentations used LJC and HJC, ruminal fluid inoculum added (33% v/v) to anoxic media in sealed Balch tubes. Camphor increased (P < 0.05) total short-chain fatty acid (SCFA) concentrations for all but one experimental group. Between the main dietary and bloodline goat effects, the diet was significant for all SCFA results except butyrate. In contrast, bloodline was only significant for acetate and butyrate molar proportions. Rumen fluid from juniper-free-fed goats exhibited greater concentrations of Ruminococcaceae, whereas juniper-fed goats contained more Coriobacteriaceae. Results demonstrated that mixed ruminal microorganisms fermentations from HJC goats did not produce greater concentrations of SCFAs or have the ability to degrade camphor at a higher rate than did that from LJC goats. Results suggest that camphor tolerance from J. ashei, was related to hepatic catabolic mechanisms instead of ruminal microbial degradation; however, further in vivo work is warranted.
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Affiliation(s)
- Darren S Seidel
- Department of Animal and Dairy Science, University of Georgia , Athens, GA 30602 , USA
| | - John W Walker
- Texas A&M AgriLife Research , San Angelo, TX 76901 , USA
| | - Jeffrey M Musser
- Department of Animal and Dairy Science, University of Georgia , Athens, GA 30602 , USA
| | - Jeferson M Lourenco
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University , College Station, TX 77843 , USA
| | - Christina B Welch
- Department of Animal and Dairy Science, University of Georgia , Athens, GA 30602 , USA
| | | | - Todd R Callaway
- Department of Animal and Dairy Science, University of Georgia , Athens, GA 30602 , USA
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14
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Lourenco JM, Welch CB, Krause TR, Wieczorek MA, Fluharty FL, Rothrock MJ, Pringle TD, Callaway TR. Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase. Microorganisms 2022; 10:microorganisms10061128. [PMID: 35744646 PMCID: PMC9227454 DOI: 10.3390/microorganisms10061128] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/12/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle.
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Affiliation(s)
- Jeferson M. Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
- Correspondence:
| | - Christina B. Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
| | - Taylor R. Krause
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
| | - Michael A. Wieczorek
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
| | - Francis L. Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
| | - Michael J. Rothrock
- Egg Safety and Quality Research Unit, Richard B. Russell Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA;
| | - T. Dean Pringle
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (T.R.K.); (M.A.W.); (F.L.F.); (T.D.P.); (T.R.C.)
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15
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Lourenco JM, Welch CB. Using microbiome information to understand and improve animal performance. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2077147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Liu Y, Liu C, Wu H, Meng Q, Zhou Z. Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers. Front Microbiol 2022; 13:862151. [PMID: 35531283 PMCID: PMC9069012 DOI: 10.3389/fmicb.2022.862151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
The gastrointestinal tract (GIT) contains complex microbial communities and plays an essential role in the overall health of the host. Previous studies of beef cattle feed efficiency have primarily concentrated on the ruminal microbiota because it plays a key role in energy production and nutrient supply in the host. Although the small intestine is the important site of post-ruminal digestion and absorption of nutrients, only a few studies have explored the relationship between the microbial populations in the small intestine and feed efficiency. Moreover, variations in GIT metabolites contribute to differences in feed efficiency. The objective of this study was to investigate relationships among bacterial populations of duodenum, jejunum, ileum; microbial metabolites; and RFI phenotype of beef cattle. We carried out by using Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC–MS). In the duodenum, the relative abundances of Firmicutes ( p < 0.01), Lachnospiraceae, Ruminococcaceae, Family_XIII, Christensenellaceae, Christensenellaceae_R-7_group ( p < 0.05), and Lachnospiraceae_NK3A20_group ( p < 0.05) were higher in the low residual feed intake (LRFI) group compared with the high residual feed intake (HRFI) group, whereas the HRFI group had higher abundances of Proteobacteria and Acinetobacter ( p < 0.01). In the jejunum, the relative abundances of Lachnospiraceae and Lachnospiraceae_NK3A20_group were higher in the LRFI group ( p < 0.05). In the ileum, the relative abundances of Ruminococcaceae ( p < 0.01), Christensenellaceae, Christensenellaceae_R-7_group, and Ruminococcus_2 were also higher in the LRFI group ( p < 0.05). Moreover, the genera Lachnospiraceae_NK3A20_group, Christensenellaceae_R-7_group, and Ruminococcus_2 were negatively associated with RFI, while the genus Acinetobacter was positively associated with RFI. The metabolomics analysis revealed that the LRFI group significantly improved protein digestion and absorption, as well as glycerophospholipid metabolism in the duodenum, jejunum, ileum. The correlation between intestinal microorganisms and metabolites revealed that some microorganisms play an important role in amino acid metabolism, glycerophospholipid metabolism, nutrient digestion and absorption, and antioxidant enhancement. The present study provides a better understanding of the small intestinal microbiota and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chang Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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17
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Qin X, Zhang D, Qiu X, Zhao K, Zhang S, Liu C, Lu L, Cui Y, Shi C, Chen Z, Hao R, Li Y, Yang S, Wang L, Wang H, Cao B, Su H. 2-Hydroxy-4-(Methylthio) Butanoic Acid Isopropyl Ester Supplementation Altered Ruminal and Cecal Bacterial Composition and Improved Growth Performance of Finishing Beef Cattle. Front Nutr 2022; 9:833881. [PMID: 35600827 PMCID: PMC9116427 DOI: 10.3389/fnut.2022.833881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/24/2022] [Indexed: 01/05/2023] Open
Abstract
The objective of this study was to evaluate the effects of isopropyl ester of 2-hydroxy-4-(methylthio)-butyrate acid (HMBi) on ruminal and cecal fermentation, microbial composition, nutrient digestibility, plasma biochemical parameters, and growth performance in finishing beef cattle. The experiment was conducted for 120 days by a complete randomized block design. Sixty 24-month-old Angus steers (723.9 ± 11.6 kg) were randomly assigned to one of the flowing three treatments: basal diet (the concentrate: 7.6 kg/head·d-1, the rice straw: ad libitum) supplemented with 0 g/d MetaSmart® (H0), a basal diet supplemented with 15 g/d of MetaSmart® (H15), and a basal diet supplemented with 30 g/d of MetaSmart® (H30). Results showed that the average daily gain (ADG) increased linearly (P = 0.004) and the feed conversion ratio (FCR) decreased linearly (P < 0.01) with the increasing HMBi supplementation. Blood urea nitrogen (BUN) concentration significantly decreased in the H30 group (P < 0.05) compared with H0 or H15. The ruminal pH value tended to increase linearly (P = 0.086) on day 56 with the increased HMBi supplementation. The concentrations of ammonia-nitrogen (NH3-N), propionate, isobutyrate, butyrate, isovalerate, valerate, and total volatile fatty acid (VFA) were linearly decreased in the cecum (P < 0.05). The results of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that the abundance of most pathways with a significant difference was higher in the rumen and lower in the cecum in the H30 group compared to the H0 group, and those pathways were mainly related to the metabolism of amino acids, carbohydrates, and lipids. Correlation analysis showed that ADG was positively associated with the ratio of firmicutes/bacteroidetes both in the rumen and cecum. Additionally, the abundance of Lachnospiraceae, Saccharofermentans, Lachnospiraceae_XPB1014_group, and Ruminococcus_1 was positively correlated with ADG and negatively correlated with FCR and BUN in the rumen. In the cecum, ADG was positively correlated with the abundances of Peptostreptococcaceae, Romboutsia, Ruminococcaceae_UCG-013, and Paeniclostridium, and negatively correlated with the abundances of Bacteroidaceae and Bacteroides. Overall, these results indicated that dietary supplementation of HMBi can improve the growth performance and the feed efficiency of finishing beef cattle by potentially changing bacterial community and fermentation patterns of rumen and cecum.
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Affiliation(s)
- Xiaoli Qin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Depeng Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinjun Qiu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Zhao
- Faculty of Engineering and Applied Science, University of Regina, Regina, SK, Canada
| | - Siyu Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunlan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lianqiang Lu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yafang Cui
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changxiao Shi
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhiming Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Rikang Hao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yingqi Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shunran Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lina Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huili Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Binghai Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huawei Su
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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18
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Liu Y, Wu H, Chen W, Liu C, Meng Q, Zhou Z. Rumen Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers. Front Vet Sci 2022; 9:812861. [PMID: 35400092 PMCID: PMC8993041 DOI: 10.3389/fvets.2022.812861] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
Feed cost is the greatest expense during cattle production; therefore, reducing it is critical to increasing producer profits. In ruminants, the microbial population is important to nutrient digestion and absorption in the rumen. The objective of this study was to investigate the relationships among rumen bacteria, rumen metabolites, and the residual feed intake (RFI) phenotype of beef cattle. Twelve Angus heifers were selected to be sampled and divided into high RFI (HRFI; n = 6) group and low RFI (LRFI; n = 6) group according to their RFI classification determined during the feedlot-finishing period. After the ruminal liquid samples were collected at slaughter, Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC-MS) were performed to determine their bacterial composition and metabolites, respectively. At the phylum level, the relative abundance of Proteobacteria was higher in the LRFI group than in the HRFI group (P < 0.01). At the family level, the relative abundances of Rikenellaceae (P < 0.01), Ruminococcaceae, Bacteroidales_S24-7_group, and Lachnospiraceae (P < 0.05) were significantly higher in the LRFI group. At the genus level, the relative abundances of Rikenellaceae_RC9_gut_group and Ruminiclostridium_1 were higher in the LRFI group (P < 0.01), as were the relative abundances of norank_f__Bacteroidales_S24-7_group, Lachnospiraceae_ND3007_group, and Lachnospiraceae_NK3A20_group (P < 0.05). Moreover, the genera Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Christensenellaceae_R-7_group, Ruminococcaceae_UCG-010, Lachnospiraceae_ND3007_group, Ruminiclostridium_1, and Lachnospiraceae_NK3A20_group were negatively associated with the RFI; both foundational and key species are associated with feed efficiency phenotype. In addition, rumen metabolomics analysis revealed that the RFI was associated with significantly altered concentrations of rumen metabolites involved in protein digestion and absorption, Linoleic acid metabolism, Lysine degradation, and Fatty acid degradation. Correlation analysis revealed the potential relationships between the significantly differential ruminal metabolites and the genera ruminal bacteria. The present study provides a better understanding of rumen bacteria and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wanbao Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chang Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Chida S, Sakamoto M, Takino T, Kawamoto S, Hagiwara K. Changes in immune system and intestinal bacteria of cows during the transition period. Vet Anim Sci 2021; 14:100222. [PMID: 34917853 PMCID: PMC8666551 DOI: 10.1016/j.vas.2021.100222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Transitional high-energy diets reduce peripheral blood lymphocytes in dairy cows. High-energy diets upregulate IL-1β and IL-2 and downregulate IL-10 expression. Functional lactobacillus plantarum LP1 restores normal levels of lymphocytes subset. Lactobacillus plantarum LP1-added diets reduce inflammatory cytokine expression. LP1 mitigates immune response imbalances caused by transitional high energy diets.
High-yield dairy cows need high energy feed during periods of increased milk production. The transitional feeding to high energy feed increases the risk of developing a variety of metabolic disorders. Here, five Holstein cows were fed a four-stage feeding protocol (3 weeks for each stage) ranging from 54.9 to 73.7% total digestive nutrients (TDN). The purpose of the study was to investigate the effect of lactic acid bacteria on high-energy-fed cows associated with transitional feeding, and to evaluate the effects of probiotics on intestinal bacterial changes and inflammatory responses. Three feed transition periods were established for five cows, and Lactobacillus plantarum RGU-LP1 (LP1) was fed as a probiotic during the high-energy feeding period. The number of lymphocyte subsets such as CD3-, CD4-, and CD8 positive cells decreased in response to the high energy feed. Lipopolysaccharide (LPS)-induced cytokine (IL-1β and IL-2) gene expression in peripheral blood mononuclear cells (PBMCs) was shown to increase in those animals receiving the high energy feed. However, supplementation with LP1 resulted in an increase in the number of lymphocyte subsets and the expression of IL-1β and IL-2 were returned to the level at low energy diet. These results suggest that high energy diets induce inflammatory cytokine responses following LPS stimulation, and that the addition of LP1 mitigates these results by regulating the LPS-induced inflammatory reaction. Therefore, the functional lactic acid bacteria LP1 is expected to regulate inflammation resulting from high energy feeding, and this probiotic could be applied to support inflammatory regulation in high-yield dairy cows.
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Key Words
- Anti-inflammatories
- CD, cluster of differentiation
- Dairy cows
- EDTA, ethylenediaminetetraacetic acid
- GAPDH, Glyceraldehyde 3-phosphate dehydrogenase
- High-energy feed
- IL, Interleukin
- LPS, Lipopolysaccharide
- Lactobacillus plantarum
- PBMC, peripheral blood mononuclear cell
- Probiotics
- TDN, Total-Digestible-Nutrients
- TGF, Transforming Growth Factor
- TMR, Total-Mixed-Ration
- TNF, Tumor Necrosis Factor
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Affiliation(s)
- S Chida
- School of veterinary Medicene, Rakuno Gakuen University, 582 Bunkyodai Ebetsu, Hokkaido, 069-8501 Japan
| | - M Sakamoto
- School of veterinary Medicene, Rakuno Gakuen University, 582 Bunkyodai Ebetsu, Hokkaido, 069-8501 Japan
| | - T Takino
- School of veterinary Medicene, Rakuno Gakuen University, 582 Bunkyodai Ebetsu, Hokkaido, 069-8501 Japan.,Scientific Feed Laboratory co., ltd., R & D center, Sakura city, Chiba, 285-0043 Japan
| | - S Kawamoto
- School of veterinary Medicene, Rakuno Gakuen University, 582 Bunkyodai Ebetsu, Hokkaido, 069-8501 Japan
| | - K Hagiwara
- School of veterinary Medicene, Rakuno Gakuen University, 582 Bunkyodai Ebetsu, Hokkaido, 069-8501 Japan
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20
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Microbiome Clusters Disclose Physiologic Variances in Dairy Cows Challenged by Calving and Lipopolysaccharides. mSystems 2021; 6:e0085621. [PMID: 34665011 PMCID: PMC8525563 DOI: 10.1128/msystems.00856-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dairy cows respond individually to stressful situations, even under similar feeding and housing conditions. The phenotypic responsiveness might trace back to their microbiome and its interactions with the host. This long-term study investigated the effects of calving, lipopolysaccharide (LPS)-induced inflammation, and l-carnitine supplementation on fecal bacteria and metabolites, dairy cow milk production, health, energy metabolism, and blood metabolites. Fifty-four multiparous Holstein dairy cows were examined over a defined period of life (168 days). The obtained data allowed a holistic analysis combining microbiome data such as 16S rRNA amplicon sequencing and fecal targeted metabolome (188 metabolites) with host parameters. The conducted analyses allowed the definition of three enterotype-like microbiome clusters in dairy cows which could be linked to the community diversity and dynamics over time. The microbiome clusters were discovered to be treatment independent, governed by Bifidobacterium (C-Bifi), unclassified (uncl.) Clostridiales (C-Clos), and unclassified Spirochaetaceae (C-Spiro). Animals between the clusters varied significantly in terms of illnesses, body weight, microbiome composition, and milk and blood parameters. C-Bifi animals were healthier and leaner with a less diverse but dynamic microbiome. C-Spiro animals were heavier, but the diversity of the static microbiome was higher. This pioneering study uncovered microbiome clusters in dairy cows, each contributing differently to animal health and productive performance and with a crucial role of Bifidobacterium. IMPORTANCE The health of dairy cows has to be carefully considered for sustainable and efficient animal production. The microbiome of animals plays an important role in the host's nutrient supply and regulation of immune functions. We show that a certain composition of the fecal microbiome, called microbiome clusters, can be linked to an animal's health at challenging life events such as calving and inflammation. Cows with a specific set of bacteria have coped better under these stressors than have others. This novel information has great potential for implementing microbiome clusters as a trait for sustainable breeding strategies.
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21
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Welch CB, Lourenco JM, Krause TR, Seidel DS, Fluharty FL, Pringle TD, Callaway TR. Evaluation of the Fecal Bacterial Communities of Angus Steers With Divergent Feed Efficiencies Across the Lifespan From Weaning to Slaughter. Front Vet Sci 2021; 8:597405. [PMID: 34268344 PMCID: PMC8275654 DOI: 10.3389/fvets.2021.597405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P < 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R2 = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P < 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P < 0.001). The acetate:propionate ratio decreased linearly (P < 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.
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Affiliation(s)
- Christina B Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Jeferson M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Taylor R Krause
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Darren S Seidel
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Francis L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - T Dean Pringle
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Todd R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
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22
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Effects of feeding level on efficiency of high and low residual feed intake beef steers. J Anim Sci 2020; 98:5918960. [DOI: 10.1093/jas/skaa317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 11/14/2022] Open
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23
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Krause TR, Lourenco JM, Welch CB, Rothrock MJ, Callaway TR, Pringle TD. The relationship between the rumen microbiome and carcass merit in Angus steers. J Anim Sci 2020; 98:skaa287. [PMID: 32877916 PMCID: PMC7526868 DOI: 10.1093/jas/skaa287] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and carcass data were collected. Ruminal microbial deoxyribonucleic acid (DNA) extraction and 16S ribosomal ribonucleic acid (rRNA) gene sequencing were performed to determine microbial relative abundances, to estimate microbial diversity, and to predict microbial metabolic pathways. A variety of correlation analyses and one-way ANOVA were performed to investigate the relationships between the rumen microbiome and carcass traits. Marbling score (P = 0.001) and longissimus lipid content (P = 0.009) were positively correlated to Chao1 Richness Index, suggesting that increased intramuscular fat was associated with increased numbers of ruminal microbial species. The phyla Tenericutes and TM7 were negatively correlated (P ≤ 0.05) to marbling score and longissimus lipid content, indicating that lower abundances of these phyla may be associated with improvements in intramuscular fat content. Greater abundance of the bacterial family S24-7 was positively correlated (P = 0.002) to marbling score. Analysis by marbling classification revealed further linkages to microbial richness (P ≤ 0.063), diversity (P = 0.044), and S24-7 (P < 0.001) populations. Computational prediction of the microbial metabolic pathways revealed no differences (P ≥ 0.05) in metabolic pathway expression in rumen microbes between steers in the high- and low-marbling classes. Several phyla, families, and genera were positively correlated (P ≤ 0.05) to both rib fat thickness and yield grade. Collectively, our results suggest that microbial composition is associated to differing performance in carcass adipose traits. Overall, most of the bacterial taxa correlated to the intramuscular and subcutaneous fat depots did not overlap, suggesting the microbial population end products likely impacted adipose accumulation largely via separate adipogenic pathways of the host animal.
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Affiliation(s)
- Taylor R Krause
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | | | - Christina B Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, Richard B. Russell Research Center, Agricultural Research Service, USDA, Athens, GA
| | - Todd R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | - T Dean Pringle
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
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