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Fregulia P, Campos MM, Dhakal R, Dias RJP, Neves ALA. Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175263. [PMID: 39102957 DOI: 10.1016/j.scitotenv.2024.175263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.
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Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Mariana Magalhães Campos
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Brazil
| | - Rajan Dhakal
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
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Abebe BK, Wang J, Guo J, Wang H, Li A, Zan L. A review of emerging technologies, nutritional practices, and management strategies to improve intramuscular fat composition in beef cattle. Anim Biotechnol 2024; 35:2388704. [PMID: 39133095 DOI: 10.1080/10495398.2024.2388704] [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: 11/21/2023] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
The flavour, tenderness and juiciness of the beef are all impacted by the composition of the intramuscular fat (IMF), which is a key determinant of beef quality. Thus, enhancing the IMF composition of beef cattle has become a major area of research. Consequently, the aim of this paper was to provide insight and synthesis into the emerging technologies, nutritional practices and management strategies to improve IMF composition in beef cattle. This review paper examined the current knowledge of management techniques and nutritional approaches relevant to cattle farming in the beef industry. It includes a thorough investigation of animal handling, weaning age, castration, breed selection, sex determination, environmental factors, grazing methods, slaughter weight and age. Additionally, it rigorously explored dietary energy levels and optimization of fatty acid profiles, as well as the use of feed additives and hormone implant techniques with their associated regulations. The paper also delved into emerging technologies that are shaping future beef production, such as genomic selection methods, genome editing techniques, epigenomic analyses, microbiome manipulation strategies, transcriptomic profiling approaches and metabolomics analyses. In conclusion, a holistic approach combining genomic, nutritional and management strategies is imperative for achieving targeted IMF content and ensuring high-quality beef production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Department of Animal Science, Werabe University, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Keogh K, Kenny DA, Alexandre PA, Waters SM, McGovern E, McGee M, Reverter A. Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency. Anim Microbiome 2024; 6:52. [PMID: 39304935 DOI: 10.1186/s42523-024-00337-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 08/24/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis. RESULTS Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG. CONCLUSIONS Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.
| | - David A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Pamela A Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Sinead M Waters
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Emily McGovern
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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Li Z, Xu J, Zhang F, Wang L, Yue Y, Wang L, Chen J, Ma H, Feng J, Min Y. Dietary starch structure modulates nitrogen metabolism in laying hens via modifying glucose release rate. Int J Biol Macromol 2024; 279:135554. [PMID: 39270891 DOI: 10.1016/j.ijbiomac.2024.135554] [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: 04/09/2024] [Revised: 09/03/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024]
Abstract
The objective of this study was to investigate the effects of starch structure (Amylopectin/Amylose, AP/AM) in a low-protein diet on production performance, nitrogen utilization efficiency, and cecal flora in laying hens. Four hundred eighty 45-wk-age Hy-Line Gray laying hens were randomly allocated to five dietary groups and subjected to a 12-wk feeding trial. The AP/AM ratios of the five experiment diets were 1.0, 1.5, 2.0, 3.0, and 4.0. The results indicated that compared to other groups, laying hens fed with AP/AM 4.0 diets showed significantly improved average egg weight and feed conversion ratio (P < 0.05). Furthermore, as the AP/AM ratio increased, there was a significant linear enhancement in intestinal amino acids apparent digestibility, apparent metabolizable energy, and villus area (P < 0.05). Compared to the high AP groups, high-AM diets significantly increased eggshell thickness, crude protein digestibility, and reduced energy supply from amino acid oxidation in ileum (P < 0.05). Additionally, moderate-AM diets enriched with short-chain fatty acid-producing bacteria in the cecum, such as Lactobacillus, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group, which are associated with the promoting nitrogen utilization. These findings may offer useful information on optimizing starch structure for the design of food products and relevant therapies due to the potential effects on nutrient metabolism and gut homeostasis.
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Affiliation(s)
- Zhuorui Li
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingya Xu
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengdong Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Leiqing Wang
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yanrui Yue
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lijun Wang
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jian Chen
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Ma
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jia Feng
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yuna Min
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Zhang W, Lan F, Zhou Q, Gu S, Li X, Wen C, Yang N, Sun C. Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens. J Anim Sci Biotechnol 2024; 15:123. [PMID: 39245742 PMCID: PMC11382517 DOI: 10.1186/s40104-024-01076-7] [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: 04/03/2024] [Accepted: 07/14/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Feed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear. METHODS In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency. RESULTS The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency. CONCLUSIONS This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.
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Affiliation(s)
- Wenxin Zhang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Qianqian Zhou
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
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6
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Lima J, Martínez-Álvaro M, Mattock J, Auffret MD, Duthie CA, Cleveland MA, Dewhurst RJ, Watson M, Roehe R. Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle. Sci Rep 2024; 14:20772. [PMID: 39237607 PMCID: PMC11377694 DOI: 10.1038/s41598-024-70770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024] Open
Abstract
The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal stability of rumen microbiomes considering taxonomic and functional aspects across the 7-month growing-finishing phase spanning 6 timepoints. We identified a temporally stable core microbiome, encompassing 515 microbial genera (e.g., Methanobacterium) and 417 microbial KEGG genes (e.g., K00856-adenosine kinase). The temporally stable core microbiome profiles collected from all timepoints were strongly associated with production traits with substantial economic and environmental impact (e.g., average daily gain, daily feed intake, and methane emissions); 515 microbial genera explained 45-83%, and 417 microbial genes explained 44-83% of their phenotypic variation. Microbiome profiles influenced by the bovine genome explained 54-87% of the genetic variation of bovine traits. Overall, our results provide evidence that the temporally stable core microbiome identified can accurately predict host performance traits at phenotypic and genetic level based on a single timepoint sample taken as early as 7 months prior to slaughter.
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Affiliation(s)
- Joana Lima
- Scotland's Rural College, Edinburgh, UK.
| | | | - 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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Guo J, Zhang Z, Guan LL, Yoon I, Plaizier JC, Khafipour E. Postbiotics from Saccharomyces cerevisiae fermentation stabilize microbiota in rumen liquid digesta during grain-based subacute ruminal acidosis (SARA) in lactating dairy cows. J Anim Sci Biotechnol 2024; 15:101. [PMID: 39085941 PMCID: PMC11293205 DOI: 10.1186/s40104-024-01056-x] [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: 02/05/2024] [Accepted: 05/28/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Subacute ruminal acidosis (SARA) is a common metabolic disorder of high yielding dairy cows, and it is associated with dysbiosis of the rumen and gut microbiome and host inflammation. This study evaluated the impact of two postbiotics from Saccharomyces cerevisiae fermentation products (SCFP) on rumen liquid associated microbiota of lactating dairy cows subjected to repeated grain-based SARA challenges. A total of 32 rumen cannulated cows were randomly assigned to 4 treatments from 4 weeks before until 12 weeks after parturition. Treatment groups included a Control diet or diets supplemented with postbiotics (SCFPa, 14 g/d Original XPC; SCFPb-1X, 19 g/d NutriTek; SCFPb-2X, 38 g/d NutriTek, Diamond V, Cedar Rapids, IA, USA). Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% DM of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. Total DNA from rumen liquid samples was subjected to V3-V4 16S rRNA gene amplicon sequencing. Characteristics of rumen microbiota were compared among treatments and SARA stages. RESULTS Both SARA challenges reduced the diversity and richness of rumen liquid microbiota, altered the overall composition (β-diversity), and its predicted functionality including carbohydrates and amino acids metabolic pathways. The SARA challenges also reduced the number of significant associations among different taxa, number of hub taxa and their composition in the microbial co-occurrence networks. Supplementation with SCFP postbiotics, in particular SCFPb-2X, enhanced the robustness of the rumen microbiota. The SCFP supplemented cows had less fluctuation in relative abundances of community members when exposed to SARA challenges. The SCFP supplementation promoted the populations of lactate utilizing and fibrolytic bacteria, including members of Ruminococcaceae and Lachnospiraceae, and also increased the numbers of hub taxa during non-SARA and SARA stages. Supplementation with SCFPb-2X prevented the fluctuations in the abundances of hub taxa that were positively correlated with the acetate concentration, and α- and β-diversity metrics in rumen liquid digesta. CONCLUSIONS Induction of SARA challenges reduced microbiota richness and diversity and caused fluctuations in major bacterial phyla in rumen liquid microbiota in lactating dairy cows. Supplementation of SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.
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Affiliation(s)
- Junfei Guo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Zhengxiao Zhang
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Present Address: College of Food and Biological Engineering, Jimei University, Xiamen, Fujian, 361021, China
| | - Le Luo Guan
- Department of Agriculture, Food and Nutrition Department, University of Alberta, Edmonton, AB, T6G 2R3, Canada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilkyu Yoon
- Diamond V, Cedar Rapids, IA, 52404, United States
| | - Jan C Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
- Present Address: Cargill Animal Nutrition, 15407 McGinty Road West, Wayzata, MN, 55391, USA.
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Sarmikasoglou E, Sumadong P, Roesch LFW, Halima S, Arriola K, Yuting Z, Jeong KCC, Vyas D, Hikita C, Watanabe T, Faciola A. Effects of cashew nut shell extract and monensin on in vitro ruminal fermentation, methane production, and ruminal bacterial community. J Dairy Sci 2024; 107:840-856. [PMID: 37730175 DOI: 10.3168/jds.2023-23669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
The objective of this study was to evaluate the effects of cashew nut shell extract (CNSE) and monensin on ruminal in vitro fermentation, CH4 production, and ruminal bacterial community structure. Treatments were as follows: control (CON, basal diet without additives); 2.5 μM monensin (MON); 0.1 mg CNSE granule/g DM (CNSE100); and 0.2 mg CNSE granule/g DM (CNSE200). Each treatment was incubated with 52 mL of buffered ruminal content and 500 mg of total mixed ration for 24 h using serum vials. The experiment was performed as a complete randomized block design with 3 runs. Run was used as a blocking factor. Each treatment had 5 replicates, in which 2 were used to determine nutrient degradability, and 3 were used to determine pH, NH3-N, volatile fatty acids, lactate, total gas, CH4 production, and bacterial community composition. Treatment responses for all data, excluding bacterial abundance, were analyzed with the GLIMMIX procedure of SAS v9.4. Treatment responses for bacterial community structure were analyzed with a PERMANOVA test run with the R package vegan. Orthogonal contrasts were used to test the effects of (1) additive inclusion (ADD: CON vs. MON, CNSE100, and CNSE200); (2) additive type (MCN: MON vs. CNSE100 and CNSE200); and (3) CNSE dose (DOS: CNSE100 vs. CNSE200). We observed that pH, acetate, and acetate:propionate ratio in the CNSE100 treatment were lower compared with CNSE200, and propionate in the CNSE100 treatment was greater compared with CNSE200. Compared with MON, CNSE treatments tended to decrease total lactate concentration. Total gas production of CON was greater by 2.63% compared with all treatments, and total CH4 production was reduced by 10.64% in both CNSE treatments compared with MON. Also, compared with MON, in vitro dry matter degradabilities in CNSE treatments were lower. No effects were observed for NH3-N or in vitro neutral detergent fiber degradability. Finally, the relative abundances of Prevotella, Treponema, and Schwartzia were lower, whereas the relative abundances of Butyrivibrio and Succinivibrio were greater in all treatments compared with CON. Overall, the inclusion of CNSE decreased CH4 production compared with MON, making CNSE a possible CH4 mitigation additive in dairy cattle diets.
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Affiliation(s)
- E Sarmikasoglou
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - P Sumadong
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611; Department of Animal Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - L F W Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603
| | - S Halima
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - K Arriola
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Z Yuting
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - K C C Jeong
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - D Vyas
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - C Hikita
- SDS Biotech K.K., Tokyo, Japan 101-0022
| | | | - A Faciola
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611.
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9
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Sadek A, Taminiau B, Daube G, Sapountzis P, Chaucheyras-Durand F, Castex M, Coucheney F, Drider D. Impact of Dietary Regime and Seasonality on Hindgut's Mycobiota Diversity in Dairy Cows. Microorganisms 2023; 12:84. [PMID: 38257911 PMCID: PMC10820462 DOI: 10.3390/microorganisms12010084] [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: 11/23/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3-5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.
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Affiliation(s)
- Ali Sadek
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Bernard Taminiau
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Panagiotis Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Françoise Coucheney
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
| | - Djamel Drider
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
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10
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Sun Y, Hao Y, Zhang Q, Liu X, Wang L, Li J, Li M, Li D. Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167079. [PMID: 37714349 DOI: 10.1016/j.scitotenv.2023.167079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.
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Affiliation(s)
- Yanfeng Sun
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China
| | - Yaotong Hao
- Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China
| | - Qian Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xu Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Limin Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Juyong Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mo Li
- College of Life Sciences, Cangzhou Normal University, Cangzhou 061001, China.
| | - Dongming Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China.
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11
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Linde DA, Schokker D, du Toit CJL, Ramkilawon GD, van Marle-Köster E. The Effect of a Bacillus Probiotic and Essential Oils Compared to an Ionophore on the Rumen Microbiome Composition of Feedlot Cattle. Animals (Basel) 2023; 13:2927. [PMID: 37760327 PMCID: PMC10525249 DOI: 10.3390/ani13182927] [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: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The rising concern of antibiotic growth promoter use in livestock has necessitated the investigation into alternative feed additives. The effect of a probiotic and essential oils to an ionophore on the rumen microbiome composition of Bonsmara bulls raised under feedlot conditions was compared. Forty-eight Bonsmara weaners were allocated to four groups: a group with basal diet (CON) and three groups supplemented with monensin (MON), probiotic (PRO), and essential oils (EO). During the 120 days feeding period, rumen content was collected from four animals per group within each phase via a stomach tube for 16S rRNA and internal transcribed spacer (ITS) sequencing as well as volatile fatty acid analysis. In the starter phase, MON had a significantly lower acetate to propionate ratio and a higher Succinivibrionaceae abundance. The abundance of Lachnospiraceae was significantly higher in EO compared to MON. In the finisher phase, PRO had a significantly higher bacterial diversity. The alpha diversity did not differ between the fungal populations of the groups. The abundance of Proteobacteria was the lowest in PRO compared to the other groups. Limited variation was observed between the rumen microbiome composition of monensin compared to the other treatment groups, indicating that these alternatives can be considered.
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Affiliation(s)
- Dina A. Linde
- Department of Animal Science, University of Pretoria, Pretoria 0043, South Africa
| | - Dirkjan Schokker
- Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA Lelystad, The Netherlands
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12
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Li Y, Li X, Nie C, Wu Y, Luo R, Chen C, Niu J, Zhang W. Effects of two strains of Lactobacillus isolated from the feces of calves after fecal microbiota transplantation on growth performance, immune capacity, and intestinal barrier function of weaned calves. Front Microbiol 2023; 14:1249628. [PMID: 37727287 PMCID: PMC10505964 DOI: 10.3389/fmicb.2023.1249628] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Weaning stress seriously affects the welfare of calves and causes huge economic losses to the cattle breeding industry. Probiotics play an important role in improving animal growth performance, enhancing immune function, and improving gut microbiota. The newly isolated strains of Lactobacillus reuteri L81 and Lactobacillus johnsonii L29 have shown potential as probiotics. Here, we studied the probiotic properties of these two strains on weaned calves. Methods Forty calves were randomly assigned to four groups before weaning, with 10 calves in each group, control group (Ctrl group), L. reuteri L81 supplementation group (2 g per day per calf), L. johnsonii L29 supplementation group (2 g per day per calf), L. reuteri L81 and L. johnsonii L29 composite group (2 g per day per calf), and the effects of Lactobacillus reuteri L81 and Lactobacillus johnsonii L29 supplementation on growth performance, immune status, antioxidant capacity, and intestinal barrier function of weaned calves were evaluated. Results The results showed that probiotics supplementation increased the average daily weight gain of calves after weaning, reduced weaning diarrhea index (p < 0.05), and increased serum IgA, IgM, and IgG levels (p < 0.05). L. reuteri L81 supplementation significantly decreased IL-6, increased IL-10 and superoxide dismutase (SOD) levels at 21 d after weaning (p < 0.05). Moreover, probiotics supplementation significantly decreased serum endotoxin (ET), diamine oxidase (DAO), and D-lactic acid (D-LA) levels at different time points (p < 0.05). In addition, supplementation with L. reuteri L81 significantly reduced the crypt depth and increased the ratio of villus height to crypt depth (p < 0.05) in the ileum, increased gene expression of tight junction protein ZO-1, Claudin-1 and Occludin in jejunum and ileum mucosa, reduced the gene expression of INF- γ in ileum mucosa and IL-8 in jejunum mucosa, and increased the abundance of beneficial bacteria, including Bifidobacterium, Lactobacillus, Oscillospira, etc. Discussion verall, these results showed that the two strains isolated from cattle feces after low concentration fecal microbiota transplantation improved the growth performance, immune performance, antioxidant capacity, and intestinal barrier function of weaned calves, indicating their potential as supplements to alleviate weaning diarrhea in calves.
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Affiliation(s)
- Yuanyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xin Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Cunxi Nie
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yanyan Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Ruiqing Luo
- Xinjiang Tianshan Junken Animal Husbandry Co., Ltd.,Shihezi, China
| | - Cheng Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Junli Niu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Wenju Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
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13
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Vigors S, Flores-Villalva S, Meade KG. The impact of vitamin D3 supplementation on the faecal and oral microbiome of dairy calves indoors or at pasture. Sci Rep 2023; 13:9111. [PMID: 37277407 DOI: 10.1038/s41598-023-34840-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Vitamin D (VitD) is emerging as an immune regulator in addition to its established role in metabolism and mineral homeostasis. This study sought to determine if in vivo VitD modulated the oral and faecal microbiome in Holstein-Friesian dairy calves. The experimental model consisted of two control groups (Ctl-In, Ctl-Out) which were fed with a diet containing 6000 IU/Kg of VitD3 in milk replacer and 2000 IU/Kg in feed, and two treatment groups (VitD-In, VitD-Out) with 10,000 IU/Kg of VitD3 in milk replacer and 4000 IU/Kg in feed. One control and one treatment group were moved outdoors post-weaning at approximately 10 weeks of age. Saliva and faecal samples were collected after 7 months of supplementation and analysis of the microbiome was performed using 16S rRNA sequencing. Bray-Curtis dissimilarity analysis identified that both sampling site (oral vs. faecal) and housing (indoor vs. outdoor) had significant influences on the composition of the microbiome. The calves housed outdoors had greater microbial diversity in the faecal samples based on Observed, Chao1, Shannon, Simpson and Fisher measures in comparison to calves housed indoors (P < 0.05). A significant interaction between housing and treatment was observed for the genera Oscillospira, Ruminococcus, CF231 and Paludibacter in faecal samples. The genera Oscillospira and Dorea were increased while Clostridium and Blautia were decreased following VitD supplementation in the faecal samples (P < 0.05). An interaction between VitD supplementation and housing was detected in the abundance of the genera Actinobacillus and Streptococcus in the oral samples. VitD supplementation increased the genera Oscillospira, Helcococcus and reduced the genera Actinobacillus, Ruminococcus, Moraxella, Clostridium, Prevotella, Succinivibrio and Parvimonas. These preliminary data suggest that VitD supplementation alters both the oral and faecal microbiome. Further research will now be conducted to establish the significance of microbial alterations for animal health and performance.
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Affiliation(s)
- S Vigors
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- Institute of Food and Health, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Flores-Villalva
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- CENID Fisiología, INIFAP, Querétaro, México
| | - K G Meade
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
- Institute of Food and Health, University College Dublin, Belfield, Dublin 4, Ireland.
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14
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Payen C, Kerouanton A, Novoa J, Pazos F, Benito C, Denis M, Guyard M, Moreno FJ, Chemaly M. Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach. Microorganisms 2023; 11:1464. [PMID: 37374967 DOI: 10.3390/microorganisms11061464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on the gastrointestinal microbiota of poultry, pigs and ruminants and their consequences on host physiology. To this end, 65, 32 and 4 controlled trials or systematic reviews were selected from PubMed for poultry, pigs and ruminants, respectively. Microorganisms and their derivatives were the most studied modulator family in poultry, while in pigs, the micronutrient family was the most investigated. With only four controlled trials selected for ruminants, it was difficult to conclude on the modulators of interest for this species. For some modulators, most studies showed a beneficial effect on both the phenotype and the microbiota. This was the case for probiotics and plants in poultry and minerals and probiotics in pigs. These modulators seem to be a good way for improving animal performance.
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Affiliation(s)
- Cyrielle Payen
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, 22440 Ploufragan, France
| | - Annaëlle Kerouanton
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, 22440 Ploufragan, France
| | - Jorge Novoa
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Florencio Pazos
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Carlos Benito
- Instituto de Gestión de la Innovación y del Conocimiento, INGENIO (CSIC and U. Politécnica de Valencia), Edificio 8E, Cam. de Vera, 46022 Valencia, Spain
| | - Martine Denis
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, 22440 Ploufragan, France
| | - Muriel Guyard
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, 22440 Ploufragan, France
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM + CSIC), Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Marianne Chemaly
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, 22440 Ploufragan, France
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15
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Li Y, Gao J, Xue Y, Sun R, Sun X, Sun Z, Liu S, Tan Z, Zhu W, Cheng Y. Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep. BMC Microbiol 2023; 23:70. [PMID: 36922757 PMCID: PMC10015938 DOI: 10.1186/s12866-023-02814-z] [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: 11/30/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The nutrient availability of roughages could affect the dietary utilization efficiency of ruminants even in isocaloric and isonitrogenous diets. Here, we analyzed the bacterial composition and their metabolic pathways in the gastrointestinal tracts (GITs) of Hu sheep fed with wheat straw (WS) instead of alfalfa (AL) in isocaloric and isonitrogenous diets, trying to explore the reasons from the perspective of GITs bacterial network structure changes. RESULTS We employed 16S rRNA gene sequencing in combination with the Kruskal-Wallis test, Spearman correlation analysis, and other statistical methods to describe the microbiota composition in the GITs of Hu sheep. The results showed after the roughage was replaced from AL to WS, the most positive response occurred in the rumen microbiota, resulting in a more obvious microbiological and functional redundancy phenomenon. Whereas extended biogeographic studies of the GITs bacterial community found opposite results for the hindgut microbiota and metabolism networks compared to the forestomach. The abundance of fiber-degrading bacteria such as Prevotella, Oscillospiraceae NK4A214 group, and Treponema was significantly increased in GITs, but low-efficiency crude fiber degradation inhibited energy use efficiency, the pentose phosphate pathway, gluconeogenesis, and volatile acid synthesis. In addition, dietary shifting from AL to WS decreased the abundance of beneficial bacteria such as the Lachnospiraceae NK3A20 group and Alistipes, thereby enhancing the underlying inflammatory response. CONCLUSIONS These findings suggest that feeding untreated WS affected the structure and function of the bacterial network in the GITs due to limited total digestible nutrients, and in particular increases the complexity of the rumen bacterial network, and limit the abundance of bacteria involved in the crude fiber degradation in the hindgut.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Gao
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihan Xue
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruolin Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, 860000, China
| | - Zhankun Tan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, 860000, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
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Microbial Populations in Ruminal Liquid Samples from Beefmaster Steers at Both Extremes of RFI Values. Microorganisms 2023; 11:microorganisms11030663. [PMID: 36985235 PMCID: PMC10055678 DOI: 10.3390/microorganisms11030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster steers (n = 10) at both extremes of residual feed intake (RFI) values (5 with the lowest and 5 with the highest RFI) from two consecutive days. Samples were processed using two different DNA extraction methods. The V3 and V4 regions of the 16S rRNA gene were amplified using PCR and sequenced with a MiSeq instrument (Illumina). We analyzed 1.6 million 16S sequences from all 40 samples (10 steers, 2 time points, and 2 extraction methods). The abundance of most microbes was significantly different between DNA extraction methods but not between high-efficiency (LRFI) and low-efficiency (HRFI) animals. Exceptions include the genus Succiniclasticum (lower in LRFI, p = 0.0011), and others. Diversity measures and functional predictions were also mostly affected by DNA extraction methods, but some pathways showed significant differences between RFI levels (e.g., methylglyoxal degradation, higher in LRFI, p = 0.006). The results suggest that the abundance of some ruminal microbes is associated with feed efficiency and serves as a cautionary tale for the interpretation of results obtained with a single DNA extraction method.
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Yu Z, Cao M, Peng J, Wu D, Li S, Wu C, Qing L, Zhang A, Wang W, Huang M, Zhao J. Lacticaseibacillus casei T1 attenuates Helicobacter pylori-induced inflammation and gut microbiota disorders in mice. BMC Microbiol 2023; 23:39. [PMID: 36765272 PMCID: PMC9921057 DOI: 10.1186/s12866-023-02782-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
Probiotics are defined as live microbial food elements that are beneficial to human health. Lacticaseibacillus casei T1 was considered to have potential as a bioactive ingredient in functional foods, which was isolated from kurut. Previous research by our group proved that L. casei T1 could prevent inflammatory responses caused by Helicobacter pylori. This study aimed to investigate whether treatment with L. casei T1 resulted in a suppressive effect on H. pylori-induced oxidative stress and inflammatory responses. The results showed that treatment with L. casei T1 could relieve H. pylori-induced overexpression of inflammatory cytokines in GES-1 cells. Experiments in animals suggested that taking long-term L. casei T1 could reduce oxidative stress and inflammatory cytokines and improve H. pylori-induced gastric mucosal damage. Furthermore, taking L. casei T1 could increase the relative abundance of beneficial intestinal bacterium (Lachnospiraceae and Odoribacter) of H. pylori-infected mice and help in maintaining the balance of intestinal microflora.Collectively, L. casei T1 had certain degrees of therapeutic effect against H. pylori. In the future, it combined with antibiotics for H. pylori eradication deserves further study.
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Affiliation(s)
- Zhihao Yu
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Mei Cao
- grid.54549.390000 0004 0369 4060Core Laboratory, School of Medicine, Sichuan Provincial People’s Hospital Affiliated to University of Electronic Science and Technology of China, Chengdu, 610072 People’s Republic of China
| | - Jingshan Peng
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Daoyan Wu
- grid.413458.f0000 0000 9330 9891Department of Microbiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025 People’s Republic of China
| | - Shu Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Chengmeng Wu
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Liting Qing
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Andong Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Wenjie Wang
- grid.13291.380000 0001 0807 1581Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064 People’s Republic of China
| | - Min Huang
- Irradiation Preservation Technology Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy, Chengdu, 610101 People’s Republic of China
| | - Jian Zhao
- Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064, People's Republic of China.
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18
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Kim M. - Invited Review - Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition. Anim Biosci 2023; 36:364-373. [PMID: 36701925 PMCID: PMC9899581 DOI: 10.5713/ab.22.0382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.
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Affiliation(s)
- Minseok Kim
- Division of Animal Science, Chonnam National University, Gwangju 61186,
Korea,Corresponding Author: Minseok Kim, Tel: +82-62-530-2128, Fax: +82-62-530-2129, E-mail:
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Barekatain R, Chrystal PV, Nowland T, Moss AF, Howarth GS, Hao Van TT, Moore RJ. Negative consequences of reduced protein diets supplemented with synthetic amino acids for performance, intestinal barrier function, and caecal microbiota composition of broiler chickens. ANIMAL NUTRITION 2023. [DOI: 10.1016/j.aninu.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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20
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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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Li Z, Shi J, Lei Y, Wu J, Zhang R, Zhang X, Jia L, Wang Y, Ma Y, He P, Ma Y, Cheng Q, Zhang Z, Zhang K, Lei Z. Castration alters the cecal microbiota and inhibits growth in Holstein cattle. J Anim Sci 2022; 100:skac367. [PMID: 36326798 PMCID: PMC9733532 DOI: 10.1093/jas/skac367] [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: 08/06/2022] [Accepted: 11/03/2022] [Indexed: 11/05/2022] Open
Abstract
To determine the effects of castration on growth performance, serum hormone levels, cecal microbiota composition, and metabolites in cattle. A total of 18 Holstein bulls and steers were divided into bull and steer groups and randomly assigned to 3 pens (3 cattle per pen, and each cattle were separated by a fence) to determine the average daily gain (ADG), daily dry matter intake (DMI), and feed efficiency (G/F). After the finishing trial, six cattle per group were randomly slaughtered. Serum was collected to measure the hormone concentration, and the cecal content was collected to measure the pH, short-chain fatty acids, and digestive enzyme activities. Metagenome sequencing and untargeted metabolomics were used to investigate the microbiota composition, functional profiles, and differential metabolites of the cecal contents. We found that castration significantly decreased ADG, DMI, and G/F in cattle (P < 0.05). The serum testosterone, thyroxine, growth hormone (P < 0.05), and triiodothyronine (P < 0.01) concentrations significantly decreased in the steer group when compared to those of the bull group. The activities of cellulase, xylanase, pectinase, and β-glucosidase (P < 0.05) significantly decreased in the steer group, whereas the activities of lipase and α-amylase significantly increased. Moreover, castration significantly decreased the relative abundance of Ruminococcaceae_bacterium, Treponema_porcinum, Oscillibacter_sp. (P < 0.05), and Alistipes_senegalensis (P < 0.01), whereas the relative abundance of Phocaeicola_plebeius (P < 0.05) was significantly increased. Also, the relative abundance of Phocaeicola_plebeius was negatively correlated with testosterone levels, and the function of the cecal microbiota was enriched in the GH29 and GH97 families in the steer group. Metabolomic analysis indicated that castration increased the levels of L-valine, L-phenylalanine, L-aspartic acid, L-isoleucine, L-lysine, methionine, L-glutamic acid, and L-leucine, while decreasing the levels of α-ketoglutaric acid through the 2-oxocarboxylic acid metabolism pathway. In addition, α-ketoglutaric acid was negatively correlated with Oscillibacter_sp. (P < 0.01). Overall, castration can inhibit cattle growth by altering the composition of the cecal microbiota. Therefore, this study provides a theoretical and practical basis for improving the growth performance of steers.
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Affiliation(s)
- Zemin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yu Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jianping Wu
- Institute of Rural Development, Northwest Normal University, Lanzhou, China
| | - Rui Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiao Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Li Jia
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ying Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yue Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengjia He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yannan Ma
- Institute of Rural Development, Northwest Normal University, Lanzhou, China
| | - Qiang Cheng
- Jingchuan Xukang Food Co., Ltd, Pingliang, China
| | - Zhao Zhang
- Gansu Huarui Agriculture Co., Ltd, Zhangye, China
| | - Ke Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhaomin Lei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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22
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Yuan B, Ma Y, Ren J, Ding G, Zhou N, Liang J, Sun Y. Risk assessment of three sheep stocking modes via identification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116270. [PMID: 36261965 DOI: 10.1016/j.jenvman.2022.116270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/15/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
In order to protect the prairie ecological environment, intensive farming has become a prevalent method of sheep stocking. However, the link between captivity stocking mode and ecological risk of sheep feces is still poorly understood. In this study, metagenomics was used to identify the environmental risk of sheep feces among three stocking modes. Our results showed that captivity mode (C) elevated antibiotic resistance in feces, with the abundance of antibiotic resistance genes (ARGs) (5.381 copies/cell) higher than that of half-pen stocking (Fh) (1.093 copies/cell) and grazing mode (Fr) (0.315 copies/cell) (Duncan's test, P < 0.05). Virulence factor genes (VFGs) analysis showed offensive virulence factors had the highest abundance in captivity feces (C: 3.826 copies/cell, Fh: 0.342 copies/cell, Fr: 0.163 copies/cell) (Duncan's test, P < 0.05). 15 metagenome-assembled genomes (MAGs) were identified as potential pathogenic antibiotic resistant bacteria (PARB) and revealed that Escherichia, Klebsiella may be the main host of ARGs and VFGs in sheep feces. Furthermore, the minimal inhibition concentrations (MIC) of tetracycline of E. coli in the captivity feces was 8.6 times and 4.7 times than that of grazing and half-pen stocking samples, respectively. The Non-metric multidimensional scaling (NMDS) revealed that high stocking density leads to feces causing increased harm to the environment. Although feces from sheep raised in captivity and half-pen stocking modes are easier to collect, they are more harmful to the environment and aerobic composting should be done before their application to farmland. This work provides a guideline for better control of the environmental risk of sheep feces from different stocking modes.
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Affiliation(s)
- Bo Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yanwen Ma
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingyao Ren
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guochun Ding
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ningcong Zhou
- Ulanqab Animal Husbandry Station of Inner Mongolia Autonomous Region, Inner Mongolia, 012000, China
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China.
| | - Ying Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
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Daugaliyeva A, Daugaliyeva S, Ashanin A, Beltramo C, Mamyrova L, Yessembekova Z, Peletto S. Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111911. [PMID: 36431046 PMCID: PMC9695961 DOI: 10.3390/life12111911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
In this study, we analyzed the microbial composition of the rumen contents of cattle from Kazakhstan. Specifically, samples of the liquid and solid fractions of the rumen were collected to determine the quantitative and qualitative composition of methanogenic archaea. Cattle were six steers receiving hay-concentrate feeding. Methane emission was determined by repeated measurements for each animal. Rumen samples were then taken from fistulas and analyzed using 16S metabarcoding via Next-Generation Sequencing (NGS). The difference between the rumen fractions was investigated, resulting in differential distribution of the families Streptococccaceae, Lactobacillaceae, Desulfobulbaceae, and Succinivibrionaceae, which were more abundant in the liquid fraction, while Thalassospiraceae showed a higher presence in the solid fraction. These differences can be explained by the fact that fibrolytic bacteria are associated with the solid fraction compared to the liquid. A relationship between methane emission and methanogenic microbiota was also observed. Steers producing more methane showed microbiota richer in methanogens; specifically, most Mathanobacteriaceae resided in the liquid fraction and solid fraction of animals 1 and 6, respectively. The same animals carried most of the Methanobrevibacter and Methanosphaera genera. On the contrary, animals 2, 3, and 5 hosted a lower amount of methanogens, which also agreed with the data on methane emissions. In conclusion, this study demonstrated a relationship between methane emission and the content of methanogenic archaea in different rumen fractions collected from cattle in Kazakhstan. As a result of the studies, it was found that the solid fraction of the rumen contained more genera of methanogens than the liquid fraction of the rumen. These results prove that taking rumen contents through a fistula is more useful than taking it through a probe. The presented data may be of interest to scientists from all over the world engaged in similar research in a comparative aspect.
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Affiliation(s)
- Aida Daugaliyeva
- LLP ‘Kazakh Research Institute for Livestock and Fodder Production’, St. Zhandosova 51, Almaty 050035, Kazakhstan
| | - Saule Daugaliyeva
- LLP ‘Scientific Production Center of Microbiology and Virology’, Bogenbay Batyr Str. 105, Almaty 050010, Kazakhstan
- Correspondence:
| | - Alexander Ashanin
- LLP ‘Kazakh Research Institute for Livestock and Fodder Production’, St. Zhandosova 51, Almaty 050035, Kazakhstan
| | - Chiara Beltramo
- Istituto Zooprofilattico Sperimentale del Piemonte, Ligura e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
| | - Latipa Mamyrova
- LLP ‘Kazakh Research Institute for Livestock and Fodder Production’, St. Zhandosova 51, Almaty 050035, Kazakhstan
| | - Zinagul Yessembekova
- LLP ‘Kazakh Research Institute for Livestock and Fodder Production’, St. Zhandosova 51, Almaty 050035, Kazakhstan
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Ligura e Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy
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Choi S, Cha J, Song M, Son J, Park MR, Lim YJ, Kim TH, Lee KT, Park W. Analysis of 16S rRNA gene sequencing data for the taxonomic characterization of the vaginal and the fecal microbial communities in Hanwoo. Anim Biosci 2022; 35:1808-1816. [PMID: 36108700 PMCID: PMC9659453 DOI: 10.5713/ab.22.0040] [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: 01/25/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome. METHODS A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples. RESULTS The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome. CONCLUSION There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.
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Affiliation(s)
- Soyoung Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Jihye Cha
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Minji Song
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - JuHwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Mi-Rim Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Yeong-jo Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365,
Korea,Corresponding Author: Woncheoul Park, Tel: +82-63-238-7317, E-mail:
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25
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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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Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis. Sci Rep 2022; 12:16410. [PMID: 36180559 PMCID: PMC9525287 DOI: 10.1038/s41598-022-20732-4] [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: 11/11/2021] [Accepted: 09/19/2022] [Indexed: 11/08/2022] Open
Abstract
Methane (CH4) is an important greenhouse gas (GHG). Enteric methane emissions from farmed ruminant livestock account for approximately 15% of global GHG emissions, with approximately 44% of livestock emissions in the form of methane. The purpose of the research is to study the influence of feeding types and regional characteristics of Kazakhstan on the microbiota of feces and the number of methane-forming archaea of beef and meat-and-dairy cattle productivity. For this purpose, fecal samples were taken rectally from 37 cattle heads from four regions of Kazakhstan (Western, Southern, Northern and Southeast). The taxonomic composition of the community in all samples was determined by 16S metabarcoding; additionally alpha and beta diversities were calculated. The dominant phyla were: Firmicutes (57.30%), Bacteroidetes (17.00%), Verrucomicrobia (6.88%), Euryarchaeota (6.49%), Actinobacteria (4.77%) and Patescibacteria (3.38%). Significant differences with regard to methanogens bacteria were found: Euryarchaeota were less present in animals from Western Kazakhstan (2.40%), while Methanobacteriales and Methanobrevibacter were prevalent in Southeast, and less abundant in Western region. Western Kazakhstan differs from the other regions likely because animals are mainly grazed in the pasture. Thus, grazing animals has an impact on their microbiota thus leading to a decrease in methane emissions.
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Na SW, Guan LL. Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 10:41-53. [PMID: 35647325 PMCID: PMC9117530 DOI: 10.1016/j.aninu.2022.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/23/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Feed efficiency is one of the economically important traits for the cattle industry that affects profit (feed costs) and the environment (production of manure and methane). Due to that feed efficiency is driven by multi-factors, mechanisms contributing to the animal to animal variation in this trait have not been well defined, limiting the development of precision feeding strategies to improve the herd production efficiency. Rumen microbial fermentation and volatile fatty acids (VFA) production have been recently reported to be associated with cattle feed efficiency, however the roles of rumen epithelial function in feed efficiency are less studied although the rumen epithelium has an important function in VFA absorption and metabolism which can affect host feed efficiency. Rumen epithelium is colonized with a diverse microbial population, termed epimural microbiota, which has proposed functions in tissue development, barrier and inflammation, urea transport, and oxygen scavenging, suggesting that they can affect rumen epithelial functions and subsequently cattle feed efficiency. Especially, prospective functions of epimural microbiota, enhanced rumen immunity and increased rumen epithelial thickness, might contribute to less nutritional requirement for tissue recuperation. Thus, the understanding of the functions of rumen epithelium, epimural microbiota, and rumen epithelial host-microbe interactions is essential to identify their roles in contributing to feed efficiency. In this review, we will focus on to date research findings on the structure of rumen epithelium, epimural microbiota, and epithelial host-microbe interactions together with their functions and how these are associated with feed efficiency, aiming to provide insights on future directions to study rumen epithelial host-microbe interactions and improve the rumen functions in cattle.
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Affiliation(s)
- Sang Weon Na
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Le Luo Guan
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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28
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Mansilla FI, Ficoseco CA, Miranda MH, Puglisi E, Nader-Macías MEF, Vignolo GM, Fontana CA. Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle. Sci Rep 2022; 12:12957. [PMID: 35902668 PMCID: PMC9334624 DOI: 10.1038/s41598-022-16786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72-98%) and Actinobacteria (0.8-27%) phyla, while a lower abundance of Bacteroidetes (0.08-4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.
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Affiliation(s)
| | | | | | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | | | | | - Cecilia Alejandra Fontana
- Instituto Nacional de Tecnología Agropecuaria INTA EEA-Famaillá, Tucumán, Argentina.
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy.
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29
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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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Ma Y, Deng X, Yang X, Wang J, Li T, Hua G, Han D, Da L, Li R, Rong W, Deng X. Characteristics of Bacterial Microbiota in Different Intestinal Segments of Aohan Fine-Wool Sheep. Front Microbiol 2022; 13:874536. [PMID: 35572716 PMCID: PMC9097873 DOI: 10.3389/fmicb.2022.874536] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial community performs vital functions in the intestinal system of animals. Modulation of the gut microbiota structure can indirectly or directly affect gut health and host metabolism. Aohan fine-wool sheep grow in semi-desert grasslands in China and show excellent stress tolerance. In this study, we amplified 16S rRNA gene to investigate the dynamic distribution and adaptability of the gut microbiome in the duodenum, jejunum, ileum, cecum, colon, and rectum of seven Aohan fine-wool sheep at 12 months. The results showed that the microbial composition and diversity of the ileum and the large intestine (collectively termed the hindgut) were close together, and the genetic distance and functional projections between them were similar. Meanwhile, the diversity index results revealed that the bacterial richness and diversity of the hindgut were significantly higher than those of the foregut. We found that from the foregut to the hindgut, the dominant bacteria changed from Proteobacteria to Bacteroidetes. In LEfSe analysis, Succiniclasticum was found to be significantly abundant bacteria in the foregut and was involved in succinic acid metabolism. Ruminococcaceae and Caldicoprobacteraceae were significantly abundant in hindgut, which can degrade cellulose polysaccharides in the large intestine and produce beneficial metabolites. Moreover, Coriobacteriaceae and Eggthellaceae are involved in flavonoid metabolism and polyphenol production. Interestingly, these unique bacteria have not been reported in Mongolian sheep or other sheep breeds. Collectively, the gut microbiota of Aohan fine-wool sheep is one of the keys to adapting to the semi-desert grassland environment. Our results provide new insights into the role of gut microbiota in improving stress tolerance and gut health in sheep.
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Affiliation(s)
- Yuhao Ma
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Xiaotian Deng
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Xue Yang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Jiankui Wang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Tun Li
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Guoying Hua
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Deping Han
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Lai Da
- Inner Mongolia Academy of Agriculture and Animal Husbandry, Hohhot, China
| | - Rui Li
- Inner Mongolia Grassland Jinfeng Animal Husbandry Co., Ltd., Chifeng, China
| | - Weiheng Rong
- Inner Mongolia Academy of Agriculture and Animal Husbandry, Hohhot, China
| | - Xuemei Deng
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
- *Correspondence: Xuemei Deng,
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Translational multi-omics microbiome research for strategies to improve cattle production and health. Emerg Top Life Sci 2022; 6:201-213. [PMID: 35311904 DOI: 10.1042/etls20210257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/27/2022]
Abstract
Cattle microbiome plays a vital role in cattle growth and performance and affects many economically important traits such as feed efficiency, milk/meat yield and quality, methane emission, immunity and health. To date, most cattle microbiome research has focused on metataxonomic and metagenomic characterization to reveal who are there and what they may do, preventing the determination of the active functional dynamics in vivo and their causal relationships with the traits. Therefore, there is an urgent need to combine other advanced omics approaches to improve microbiome analysis to determine their mode of actions and host-microbiome interactions in vivo. This review will critically discuss the current multi-omics microbiome research in beef and dairy cattle, aiming to provide insights on how the information generated can be applied to future strategies to improve production efficiency, health and welfare, and environment-friendliness in cattle production through microbiome manipulations.
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Stockler RM, Hallowell H, Higgins KV, Groover ES, Hiltbold EM, Newcomer B, Walz PH. Characterization and Comparison of the Rumen Luminal and Epithelial Microbiome Profiles Using Metagenomic Sequencing Technique. Front Vet Sci 2022; 9:799063. [PMID: 35280141 PMCID: PMC8907629 DOI: 10.3389/fvets.2022.799063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Bacterial dysbiosis as a result of nutritional, bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health of cattle. The purpose of this project was to characterize the commensal microbiota present in two locations of the rumen concomitantly in vivo with the animals undergoing habitual husbandry, as it was hypothesized that there are major differences in the commensal microbiota present in the two locations of the adult bovine major forestomach. A surgically fitted rumen cannula was used to allow ruminal lumen contents and mucosal biopsies to be collected from six crossbred yearling steers. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was randomly sampled three times over a 3 week period. 16S rRNA sequencing was performed to provide a detailed descriptive analysis from phylum to genus taxonomic level. Significant differences were observed between luminal and epimural bacterial populations in the bovine rumen. As expected, a core microbiome composed by Firmicutes and Bacteroidetes represented over 90% of the microbiome, however, further analysis showed distinct diversity and distribution of the microbiome between the two locations. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty and the contribution of this study to the literature is the use of live cattle which allowed real-time sample collections and analysis of the rumen microbiome providing an understanding of what is normal in the live animal.
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Affiliation(s)
- Ricardo M. Stockler
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- *Correspondence: Ricardo M. Stockler
| | - Haley Hallowell
- Department of Biological Sciences, College of Sciences and Mathematics at Auburn University, Auburn, AL, United States
| | - Keah V. Higgins
- Department of Biological Sciences, College of Sciences and Mathematics at Auburn University, Auburn, AL, United States
| | - Erin S. Groover
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Elizabeth M. Hiltbold
- Department of Biological Sciences, College of Sciences and Mathematics at Auburn University, Auburn, AL, United States
| | - Benjamin Newcomer
- Veterinary Education, Research, and Outreach Program, Texas A&M and West Texas A&M Universities, Canyon, TX, United States
| | - Paul H. Walz
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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Corrêa PS, Jimenez CR, Mendes LW, Rymer C, Ray P, Gerdes L, da Silva VO, De Nadai Fernandes EA, Abdalla AL, Louvandini H. Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems. Front Microbiol 2021; 12:768480. [PMID: 34956130 PMCID: PMC8692951 DOI: 10.3389/fmicb.2021.768480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Caroline Rymer
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Luciana Gerdes
- Reference Laboratory on Classification and Evaluation of Animal Products, Institute of Zootechnics, Nova Odessa, Brazil
| | - Vagner Ovani da Silva
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
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Fregulia P, Neves ALA, Dias RJP, Campos MM. A review of rumen parameters in bovines with divergent feed efficiencies: What do these parameters tell us about improving animal productivity and sustainability? Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Castro DJ, Cerón-Cucchi ME, Ortiz-Chura A, Depetris GJ, Irazoqui JM, Amadio AF, Cravero S, Cantón GJ. Ruminal effects of excessive dietary sulphur in feedlot cattle. J Anim Physiol Anim Nutr (Berl) 2021; 106:978-987. [PMID: 34708462 DOI: 10.1111/jpn.13652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/28/2022]
Abstract
Sulphur (S) dietary excess can limit productive performance and increase polioencephalomalacia (PEM) incidence in feedlot cattle (FC). Sulphur excess ingested is transformed to hydrogen sulphide (H2 S) by sulfo-reducing ruminal bacteria (SRB), being high ruminal H2 S concentration responsible for aforementioned damages. As the ruminal mechanisms involved in H2 S concentrations increase have not been elucidated, this study aimed to evaluate the ruminal environment, and the association between ruminal H2 S and dissimilatory SRB (DSRB) concentration in FC experimentally subjected to S dietary excess. Twelve crossbred steers were randomly assigned to one of two dietary S levels (6 animals per treatment): low (LS, 0.19% S) and high (HS, 0.39% S obtained by sodium sulfate inclusion at 0.86%). The study lasted 38 days, and on days 0, 22 and 38, ruminal gas samples were taken to quantify H2 S concentration, and ruminal fluid to determine total bacteria, DSRB, protozoa, volatile fatty acid and ammonia nitrogen concentration. For ruminal H2 S concentration, S dietary × sampling day interaction was significant (p < 0.001), so that the greater concentration was observed on days 22 and 38 with the HS diet. The remaining ruminal parameters were not affected by dietary S level, and no significant correlation between H2 S and DSRB concentrations was observed. The ruminal adaptation that maximizes H2 S production in FC consuming S excess does not seem to be associated with biological or biochemical alterations, nor DSRB concentration changes. The microbial diversity and ruminal environment were resilient to the S excess evaluated, suggesting that 0.39% of dietary S achieved by 0.86% sodium sulfate addition, could be used without disturbances on digestion nor health of FC.
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Affiliation(s)
- Damián Jesús Castro
- National Institute of Agricultural Technology (INTA), EEA Marcos Juárez, Córdoba, Argentina
| | | | | | | | | | | | - Silvio Cravero
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), UEDD INTA-CONICET, Hurlingham, Argentina
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36
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Welch CB, Lourenco JM, Davis DB, Krause TR, Carmichael MN, Rothrock MJ, Pringle TD, Callaway TR. The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot. J Anim Sci 2020; 98:5873892. [PMID: 32687166 DOI: 10.1093/jas/skaa230] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023] Open
Abstract
Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these three locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n = 10) and low-RFI (n = 10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared with the cecal and fecal populations as revealed by beta diversity analysis (P < 0.001). Moreover, bacterial richness (Chao1) was greatest (P = 0.01) in the rumen of the high-RFI group compared with the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P = 0.01) in the cecum, and the Shannon diversity index was greater in both the cecum and feces of low-RFI compared with high-RFI steers (P = 0.01 and P < 0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P = 0.01); fecal Bifidobacteriaceae was more abundant in high-RFI steers (P = 0.03). No correlations (P ≥ 0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaceae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P < 0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P = 0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P = 0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers; therefore, the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.
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Affiliation(s)
- Christina B Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | | | - Dylan B Davis
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | - Taylor R Krause
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | - Mia N Carmichael
- 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
| | - T Dean Pringle
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
| | - Todd R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA
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Stockler RM, Higgins KV, Hallowell H, Groover ES, Hiltbold EM, Newcomer BW, Walz PH. In vivo Microbiome Profiling of the Luminal and Mucosal Surface of the Duodenum Using a Cannulated Yearling Bovine Model. Front Vet Sci 2020; 7:601874. [PMID: 33240966 PMCID: PMC7680733 DOI: 10.3389/fvets.2020.601874] [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: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
The gut microbiome provides important metabolic functions for the host animal. Bacterial dysbiosis as a result of bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health. The objective of this study is to characterize the commensal microbiome present in the lumen and the mucosal surface of the duodenum of cattle, as we hypothesize that due to metabolic processes and or host proprieties, there are differences in the natural microbiota present in the mucosal surface and luminal contents of the bovine duodenum. Duodenal lumen contents and mucosal biopsies were collected from six dairy crossbred yearling steers. A flexible video-endoscope was used to harvest biopsy samples via a T shaped intestinal cannula. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was sampled three times over a 6 week period. The DNA was extracted from the samples and submitted for16S rRNA gene Ion Torrent PGM bacterial sequencing. A detailed descriptive analysis from phylum to genus taxonomic level was reported. Differences in the microbiome population between two different sites within the duodenum were successfully characterized. A great and significant microbiota diversity was found between the luminal and mucosal biopsy At the phylum taxonomic level, Firmicutes, and Bacteroidetes composed over 80% of the microbiome. Further analysis at lower taxonomic levels, class, family, and genus, showed distinct diversity and distribution of the microbiome. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty of this study is the use of live cattle undergoing customary husbandry allowing real-time analysis of the duodenum microbiome contributing to the literature with respect to the bovine duodenum microbiome.
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Affiliation(s)
- Ricardo M Stockler
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Keah V Higgins
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Haley Hallowell
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Erin S Groover
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Elizabeth M Hiltbold
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Benjamin W Newcomer
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Paul H Walz
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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McLoughlin S, Spillane C, Claffey N, Smith PE, O’Rourke T, Diskin MG, Waters SM. Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency. Front Microbiol 2020; 11:1981. [PMID: 32983009 PMCID: PMC7477290 DOI: 10.3389/fmicb.2020.01981] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = -0.53; solid, rho = -0.56) and Olsenella (solid, rho = -0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.
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Affiliation(s)
- Steven McLoughlin
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Noel Claffey
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Paul E. Smith
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Tommy O’Rourke
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Michael G. Diskin
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Sinéad M. Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
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