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Hu Q, Luo J, Cheng F, Wang P, Gong P, Lv X, Wang X, Yang M, Wei P. Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats. Appl Microbiol Biotechnol 2024; 108:356. [PMID: 38822843 DOI: 10.1007/s00253-024-13200-8] [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: 12/29/2023] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.
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Affiliation(s)
- Qingyong Hu
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Jun Luo
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China.
| | - Fei Cheng
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Ping Wang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Husbandry Science, Urumqi Xinjiang, 830000, People's Republic of China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Husbandry Science, Urumqi Xinjiang, 830000, People's Republic of China
| | - Xinpei Wang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Min Yang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Pengbo Wei
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
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Zhang H, Wang Y, Hu L, Cong J, Xu Z, Chen X, Rao S, Li M, Shen Z, Mauck J, Loor JJ, Yang Z, Mao Y. Potential Role of Lauric Acid in Milk Fat Synthesis in Chinese Holstein Cows Based on Integrated Analysis of Ruminal Microbiome and Metabolome. Animals (Basel) 2024; 14:1493. [PMID: 38791709 PMCID: PMC11117337 DOI: 10.3390/ani14101493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The composition and metabolic profile of the ruminal microbiome have an impact on milk composition. To unravel the ruminal microbiome and metabolome affecting milk fat synthesis in dairy cows, 16S rRNA and internal transcribed spacer (ITS) gene sequencing, as well as ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) methods were used to investigate the significant differences in ruminal bacterial and fungal communities as well as metabolome among Chinese Holstein cows with contrasting milk fat contents under the same diet (H-MF 5.82 ± 0.41% vs. L-MF 3.60 ± 0.12%). Another objective was to culture bovine mammary epithelial cells (BMECs) to assess the effect of metabolites on lipid metabolism. Results showed that the acetate-to-propionate ratio and xylanase activity in ruminal fluid were both higher in H-MF. Microbiome sequencing identified 10 types of bacteria and four types of fungi differently abundant at the genus level. Metabolomics analysis indicated 11 different ruminal metabolites between the two groups, the majority of which were lipids and organic acids. Among these, lauric acid (LA) was enriched in fatty acid biosynthesis with its concentration in milk fat of H-MF cows being greater (217 vs. 156 mg per 100 g milk), thus, it was selected for an in vitro study with BMECs. Exogenous LA led to a marked increase in intracellular triglyceride (TG) content and lipid droplet formation, and it upregulated the mRNA abundance of fatty acid uptake and activation (CD36 and ACSL1), TG synthesis (DGAT1, DGAT2 and GPAM), and transcriptional regulation (SREBP1) genes. Taken together, the greater relative abundance of xylan-fermenting bacteria and fungi, and lower abundance of bacteria suppressing short-chain fatty acid-producing bacteria or participating in fatty acid hydrogenation altered lipids and organic acids in the rumen of dairy cows. In BMECs, LA altered the expression of genes involved in lipid metabolism in mammary cells, ultimately promoting milk fat synthesis. Thus, it appears that this fatty acid plays a key role in milk fat synthesis.
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Affiliation(s)
- Huimin Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yi Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - Liping Hu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - Jiahe Cong
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - Zhengzhong Xu
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiang Chen
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Shengqi Rao
- Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - Ziliang Shen
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - John Mauck
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Juan J. Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Z.)
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Wang B, Ormston S, Płatosz N, Parker JK, Qin N, Humphries DJ, Pétursdóttir ÁH, Halmemies-Beauchet-Filleau A, Juniper DT, Stergiadis S. Effect of dietary protein source and Saccharina latissima on nutritional and safety characteristics of milk. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38661233 DOI: 10.1002/jsfa.13556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 04/11/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Wheat distillers' grains (WDG) and seaweeds are recommended as alternative protein sources and enteric methane mitigators in dairy cow diets, respectively, but little is known about their impact on milk quality and safety. In the present study, 16 cows in four 4 × 4 Latin squares were fed isonitrogenous diets (50:50 forage:concentrate ratio), with rapeseed meal (RSM)-based or WDG-based concentrate (230 and 205 g kg-1 dry matter) and supplemented with or without Saccharina latissima. RESULTS Replacement of RSM with WDG enhanced milk nutritional profile by decreasing milk atherogenicity (P = 0.002) and thrombogenicity (P = 0.019) indices and the concentrations of the nutritionally undesirable saturated fatty acids - specifically, lauric (P = 0.045), myristic (P = 0.022) and palmitic (P = 0.007) acids. It also increased milk concentrations of the nutritionally beneficial vaccenic (P < 0.001), oleic (P = 0.030), linoleic (P < 0.001), rumenic (P < 0.001) and α-linolenic (P = 0.012) acids, and total monounsaturated (P = 0.044), polyunsaturated (P < 0.001) and n-6 (P < 0.001) fatty acids. Feeding Saccharina latissima at 35.7 g per cow per day did not affect the nutritionally relevant milk fatty acids or pose any risk on milk safety, as bromoform concentrations in milk were negligible and unaffected by the dietary treatments. However, it slightly reduced milk concentrations of pantothenate. CONCLUSION Feeding WDG to dairy cows improved milk fatty acid profiles, by increasing the concentrations of nutritionally beneficial fatty acids and reducing the concentration of nutritionally undesirable saturated fatty acids, while feeding seaweed slightly reduced pantothenate concentrations. However, when considering the current average milk intakes in the population, the milk compositional differences between treatments in this study appear relatively small to have an effect on human health. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Bing Wang
- College of Animal Science and Technology, State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing, PR China
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
| | - Sabrina Ormston
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
| | - Natalia Płatosz
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
- Polish Academy of Sciences, Institute of Animal Reproduction and Food Research, Olsztyn, Poland
| | - Jane K Parker
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Nanbing Qin
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
| | - David J Humphries
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
| | | | | | - Darren T Juniper
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
| | - Sokratis Stergiadis
- School of Agriculture, Policy and Development, Department of Animal Sciences, University of Reading, Reading, UK
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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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Fusco V, Chieffi D, Fanelli F, Montemurro M, Rizzello CG, Franz CMAP. The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential. Front Microbiol 2023; 14:1289937. [PMID: 38169702 PMCID: PMC10758620 DOI: 10.3389/fmicb.2023.1289937] [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: 09/06/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.
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Affiliation(s)
- Vincenzina Fusco
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Daniele Chieffi
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Marco Montemurro
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
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Martínez-Álvaro M, Mattock J, Auffret M, Weng Z, Duthie CA, Dewhurst RJ, Cleveland MA, Watson M, Roehe R. Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions. MICROBIOME 2022; 10:166. [PMID: 36199148 PMCID: PMC9533493 DOI: 10.1186/s40168-022-01352-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/13/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome function provides a permanent and accumulative solution, which may have also favourable consequences in other traits of interest (e.g. methane emissions). Possibly due to a lack of data, this strategy has never been explored. RESULTS This study provides a comprehensive identification of ruminal microbial mechanisms under host genomic influence that directly or indirectly affect the content of unsaturated fatty acids in beef associated with human dietary health benefits C18:3n-3, C20:5n-3, C22:5n-3, C22:6n-3 or cis-9, trans-11 C18:2 and trans-11 C18:1 in relation to hypercholesterolemic saturated fatty acids C12:0, C14:0 and C16:0, referred to as N3 and CLA indices. We first identified that ~27.6% (1002/3633) of the functional core additive log-ratio transformed microbial gene abundances (alr-MG) in the rumen were at least moderately host-genomically influenced (HGFC). Of these, 372 alr-MG were host-genomically correlated with the N3 index (n=290), CLA index (n=66) or with both (n=16), indicating that the HGFC influence on beef fatty acid composition is much more complex than the direct regulation of microbial lipolysis and biohydrogenation of dietary lipids and that N3 index variation is more strongly subjected to variations in the HGFC than CLA. Of these 372 alr-MG, 110 were correlated with the N3 and/or CLA index in the same direction, suggesting the opportunity for enhancement of both indices simultaneously through a microbiome-driven breeding strategy. These microbial genes were involved in microbial protein synthesis (aroF and serA), carbohydrate metabolism and transport (galT, msmX), lipopolysaccharide biosynthesis (kdsA, lpxD, lpxB), or flagellar synthesis (flgB, fliN) in certain genera within the Proteobacteria phyla (e.g. Serratia, Aeromonas). A microbiome-driven breeding strategy based on these microbial mechanisms as sole information criteria resulted in a positive selection response for both indices (1.36±0.24 and 0.79±0.21 sd of N3 and CLA indices, at 2.06 selection intensity). When evaluating the impact of our microbiome-driven breeding strategy to increase N3 and CLA indices on the environmental trait methane emissions (g/kg of dry matter intake), we obtained a correlated mitigation response of -0.41±0.12 sd. CONCLUSION This research provides insight on the possibility of using the ruminal functional microbiome as information for host genomic selection, which could simultaneously improve several microbiome-driven traits of interest, in this study exemplified with meat quality traits and methane emissions. Video Abstract.
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Affiliation(s)
| | - Jennifer Mattock
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | | | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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Popova M, Ferlay A, Bougouin A, Eugène M, Martin C, Morgavi DP. Associating changes in the bacterial community of rumen and faeces and milk fatty acid profiles in dairy cows fed high-starch or starch and oil-supplemented diets. J DAIRY RES 2022; 89:1-10. [PMID: 36039952 DOI: 10.1017/s0022029922000498] [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: 11/05/2022]
Abstract
The experiment reported in this research paper aimed to evaluate the effects of high-starch or starch and oil-supplemented diets on rumen and faecal bacteria, and explore links between the structure of bacterial communities and milk fatty acid (FA) profiles. We used four Holstein dairy cows in a 4 × 4 Latin square design. Cows were fed a diet rich in cereals (high-starch diet with 23% starch content on dry matter (DM) basis), a diet supplemented with saturated FA from Ca salts of palm oil + 18% DM starch, a diet with high content of monounsaturated FA (from extruded rapeseeds) + 18% DM starch or a diet rich in polyunsaturated FA (from extruded sunflower seeds) + 17% DM starch. At the end of each experimental period, cows were sampled for rumen and faecal contents, which were used for DNA extraction and amplicon sequencing. Partial least squares (PLS) regression analysis highlighted diet-related changes in both rumen and faecal bacterial structures. Sparse PLS discriminant analysis was further employed to identify biologically relevant operational taxonomical units (OTUs) driving these differences. Our results show that Butyrivibrio discriminated the high-starch diet and linked positively with higher concentrations of milk odd- and branched-chain FA. YS2-related OTUs were key taxa distinguishing diets supplemented with Ca salts of palm oil or sunflower seeds and correlated positively with linoleic acid in milk. Similarly, diets modulated faecal bacterial composition. However, correlations between changes in faecal and rumen bacteria were poor. With this work, we demonstrated that high-starch or lipid-supplemented diets affect rumen and faecal bacterial community structure, and these changes could have a knock-on effect on milk FA profiles.
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Affiliation(s)
- Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Anne Ferlay
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Adeline Bougouin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Maguy Eugène
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Cécile Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
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Organic Farm Bedded Pack System Microbiomes: A Case Study with Comparisons to Similar and Different Bedded Packs. DAIRY 2022. [DOI: 10.3390/dairy3030042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Animal housing and bedding materials influence cow and farm worker exposure to microbial pathogens, biocontrol agents, and/or allergens. This case study represents an effort to characterize the bacterial and fungal community of bedding systems using an amplicon sequencing approach supplemented with the ecological assessment of cultured Trichocomaceae isolates (focusing on Penicillium and Aspergillus species) and yeasts (Saccharomycetales). Bedding from five certified organic dairy farms in northern Vermont USA were sampled monthly between October 2015 and May 2016. Additional herd level samples from bulk tank milk and two bedding types were collected from two farms to collect fungal isolates for culturing and ecology. Most of the microorganisms in cattle bedding were microbial decomposers (saprophytes) or coprophiles, on account of the bedding being composed of dead plant matter, cattle feces, and urine. Composition of bacterial and fungal communities exhibited distinct patterns of ecological succession measured through time and by bedding depth. Community composition patterns were related to management practices and choice of bedding material. Aspergillus and Penicillium species exhibited niche differentiation expressed as differential substrate requirements; however, they generally exhibited traits of early colonizers of bedding substrates, typically rich in carbon and low in nitrogen. Pichia kudriavzevii was the most prevalent species cultured from milk and bedding. P. kudriavzevii produced protease and its abundance directly related to temperature. The choice of bedding and its management represent a potential opportunity to curate the microbial community of the housing environment.
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Taylor EN, Han J, Fan C, Beckmann M, Hewinson G, Rooke D, Koets AP, Mur LAJ. Defining Fatty Acid Changes Linked to Rumen Development, Weaning and Growth in Holstein-Friesian Heifers. Metabolites 2022; 12:metabo12050374. [PMID: 35629878 PMCID: PMC9143779 DOI: 10.3390/metabo12050374] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
After birth, as effectively monogastric animals, calves undergo substantial physiological changes to become ruminants by 3 months of age and reach sexual maturity at approximately 15 months of age. Herein, we assess longitudinal metabolomic changes in Holstein-Friesian (HF) heifers from birth until sexual maturity during this developmental process. Sera from 20 healthy, HF heifers were sampled biweekly from 2 weeks of age until 13 months of age and then monthly until 19 months of age. Sera were assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer for high-throughput, sensitive, non-targeted metabolite fingerprinting. Partial least squares discriminant analysis (PLS-DA) and unsupervised hierarchical clustering analysis (HCA) of the derived metabolomes indicated changes detectable in heifers’ sera over time. Time series analyses identified 30 metabolites that could be related to rumen development and weaning at ~3 months of age. Further time series analysis identified 40 metabolites that could be correlated with growth. These findings highlight the role of acetic acid and 3-phenylpropionate (3-PP) in rumen development and growth, suggest that weaning induces elevated levels of fatty acyls in response to a post-weaning stress-induced innate immune response and demonstrate the utilization of fatty acyls in growth. The identified metabolites offer serum metabolites which could inform the nutrition and healthy development of heifers.
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Affiliation(s)
- Emma N. Taylor
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, UK; (E.N.T.); (M.B.); (G.H.)
| | - Jiwan Han
- College of Software, Shanxi Agricultural University, Taigu District, Jinzhong 030810, China; (J.H.); (C.F.)
| | - Congying Fan
- College of Software, Shanxi Agricultural University, Taigu District, Jinzhong 030810, China; (J.H.); (C.F.)
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, UK; (E.N.T.); (M.B.); (G.H.)
| | - Glyn Hewinson
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, UK; (E.N.T.); (M.B.); (G.H.)
- Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | | | - Ad P. Koets
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands
- Population Health Systems, Faculty of Veterinary Medicine, Utrecht University, 3584 CS Utrecht, The Netherlands
- Correspondence: (A.P.K.); (L.A.J.M.)
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, UK; (E.N.T.); (M.B.); (G.H.)
- College of Software, Shanxi Agricultural University, Taigu District, Jinzhong 030810, China; (J.H.); (C.F.)
- Correspondence: (A.P.K.); (L.A.J.M.)
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10
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Zhu Y, Bu D, Ma L. Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research. Metabolites 2022; 12:metabo12030225. [PMID: 35323668 PMCID: PMC8955540 DOI: 10.3390/metabo12030225] [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: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.
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Affiliation(s)
- Yingkun Zhu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- School of Agriculture & Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Joint Laboratory on Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR), and World Agroforestry Center (ICRAF), Beijing 100193, China
- Correspondence: (D.B.); (L.M.)
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.B.); (L.M.)
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11
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Davis H, Magistrali A, Butler G, Stergiadis S. Nutritional Benefits from Fatty Acids in Organic and Grass-Fed Beef. Foods 2022; 11:foods11050646. [PMID: 35267281 PMCID: PMC8909876 DOI: 10.3390/foods11050646] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Livestock production is under increasing scrutiny as a component of the food supply chain with a large impact on greenhouse gas emissions. Amidst growing calls to reduce industrial ruminant production, there is room to consider differences in meat quality and nutritional benefits of organic and/or pasture-based management systems. Access to forage, whether fresh or conserved, is a key influencing factor for meat fatty acid profile, and there is increasing evidence that pasture access is particularly beneficial for meat’s nutritional quality. These composition differences ultimately impact nutrient supply to consumers of conventional, organic and grass-fed meat. For this review, predicted fatty acid supply from three consumption scenarios were modelled: i. average UK population National Diet and Nutrition Survey (NDNS) (<128 g/week) red meat consumption, ii. red meat consumption suggested by the UK National Health Service (NHS) (<490 g/week) and iii. red meat consumption suggested by the Eat Lancet Report (<98 g/week). The results indicate average consumers would receive more of the beneficial fatty acids for human health (especially the essential omega-3, alpha-linolenic acid) from pasture-fed beef, produced either organically or conventionally.
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Affiliation(s)
- Hannah Davis
- School of Natural and Environmental Science, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK; (A.M.); (G.B.)
- Correspondence: (H.D.); (S.S.)
| | - Amelia Magistrali
- School of Natural and Environmental Science, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK; (A.M.); (G.B.)
| | - Gillian Butler
- School of Natural and Environmental Science, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK; (A.M.); (G.B.)
| | - Sokratis Stergiadis
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
- Correspondence: (H.D.); (S.S.)
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12
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Samková E, Čítek J, Brzáková M, Hanuš O, Večerek L, Jozová E, Hoštičková I, Trávníček J, Hasoňová L, Rost M, Hálová K, Špička J. Associations among Farm, Breed, Lactation Stage and Parity, Gene Polymorphisms and the Fatty Acid Profile of Milk from Holstein, Simmental and Their Crosses. Animals (Basel) 2021; 11:ani11113284. [PMID: 34828016 PMCID: PMC8614357 DOI: 10.3390/ani11113284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to analyze the factors affecting the fatty acid (FA) profile in cow's milk. The effects of a farm, lactation parity and stage, breed and polymorphisms in the AGPAT6, DGAT1, LEP, FASN and SCD1 genes were evaluated. A total of 196 Holstein cows, 226 Simmental cows and seven crosses were sampled 751 times. The cows were kept at five farms and were in the first up to the sixth lactation, and 49 individual FAs and 11 groups were analyzed. The farm significantly affected the proportion of all FAs except for C16:1n-7c and isoC14:0. Additionally, the lactation stage was significant for most FAs, and the opposite was true for lactation parity. The effect of the breed was negligible. For the gene polymorphisms, the SCD1 TT genotype exceeded the CC in C10:0, C12:0, C14:0, C16:1n-7c and C18:2, and the opposite was true for C10:1, C12:1, C14:1n-5c, isoC17:0, C16:1 and C18:1, i.e., the TT genotype was higher for saturated FAs, and the CT genotype was higher for monounsaturated FAs. The results hint at the intermediary heredity of the SCD1 gene. The FASN gene was strongly associated with four FAs and branched-chain FAs, and genotype AG was better than GG. LEP was significant for five individual FAs and branched-chain FAs. The differences in FA composition among genotypes were rather small, which could lead to overestimation of the effect and needs to be considered in the next research.
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Affiliation(s)
- Eva Samková
- Department of Food Biotechnologies and Agricultural Products Quality, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (L.H.); (K.H.)
- Correspondence: ; Tel.: +420-387-772-618
| | - Jindřich Čítek
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.Č.); (L.V.); (E.J.); (I.H.); (M.R.)
| | - Michaela Brzáková
- Institute of Animal Science, Přátelství 815, 104 00 Praha-Uhříněves, Czech Republic;
| | - Oto Hanuš
- Dairy Research Institute, s.r.o., Ke Dvoru 12a, 160 00 Prague, Czech Republic;
| | - Libor Večerek
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.Č.); (L.V.); (E.J.); (I.H.); (M.R.)
| | - Eva Jozová
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.Č.); (L.V.); (E.J.); (I.H.); (M.R.)
| | - Irena Hoštičková
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.Č.); (L.V.); (E.J.); (I.H.); (M.R.)
| | - Jan Trávníček
- Department of Animal Science, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
| | - Lucie Hasoňová
- Department of Food Biotechnologies and Agricultural Products Quality, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (L.H.); (K.H.)
| | - Michael Rost
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (J.Č.); (L.V.); (E.J.); (I.H.); (M.R.)
| | - Karolína Hálová
- Department of Food Biotechnologies and Agricultural Products Quality, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (L.H.); (K.H.)
| | - Jiří Špička
- Department of Applied Chemistry, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
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