1
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Wang L, Jin S, Wang P, Li X, Liu C, Sun S, Zhang G, Chang J, Yin Q, Zhang H, Zhu Q. Fermented total mixed ration enhances nutrient digestibility and modulates the milk components and fecal microbial community in lactating Holstein dairy cows. Front Vet Sci 2024; 11:1408348. [PMID: 39205803 PMCID: PMC11350115 DOI: 10.3389/fvets.2024.1408348] [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: 03/28/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
Fermented total mixed ration (FTMR) is an effective method of preserving high-moisture byproducts with higher aerobic stability after fermentation. FTMR has the potential to fulfill the daily nutritional requirements of cattle and enhance their production performance. The objective of this research was to examine the influence of FTMR on lactation performance, total tract apparent digestibility, fecal microbiota communities, and fermentation profiles in lactating dairy cows. A total of 12 cows were randomly assigned into two groups: the TMR group and the FTMR group. The TMR group was fed a total mixed ration (TMR) diet, and the FTMR group was fed an FTMR diet. The FTMR did not impact milk yield in dairy cows despite a decrease in dry matter intake, which increased the efficiency of the feed. In contrast to that in the TMR group, the milk fat content in the FTMR group was greater. The FTMR group showed greater digestibility of neutral detergent fiber (NDF), organic matter (OM), dry matter (DM), crude protein (CP), and acid detergent fiber (ADF) in the total digestive tract than did the TMR group. The FTMR increased the concentration of butyrate in the fecal matter and reduced the pH of the feces. The Chao1, ACE, and Shannon indices of the archaeal community in dairy cow feces were significantly higher in cow fed the FTMR compared to those fed the TMR. LefSe analysis revealed higher levels of Oscillospira, Lactobacillus, Prevotella, and Dehalobacterium in the feces of dairy cows fed the FTMR than in those fed the TMR. However, the abundances of Roseburia, rc4-4, Bulleidia and Sharpea exhibited the opposite trend. The abundances of Halobacteria, Halobacteriales, and Halobacteriaceae, which are biomarkers for distinguishing fecal archaea in the TMR from the FTMR, were substantially greater in the feces of dairy cows that consumed the TMR than in those that consumed the FTMR. Therefore, FTMR can improve the milk fat content, total tract apparent feed digestibility efficiency, and diversity of archaea in the feces. Additionally, this work provides a theoretical basis for the feasibility of FTMR feeding for dairy cows.
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Affiliation(s)
- Lijun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Sanjun Jin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Ping Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xinxin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Chaoqi Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Siying Sun
- Institute of International Education, Henan Agricultural University, Zhengzhou, China
| | - Guangning Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Juan Chang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Qingqiang Yin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Haiyang Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Qun Zhu
- Henan Delin Biological Products Co., Ltd., Xinxiang, China
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2
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Zhang X, Ma Z, Hao P, Ji S, Gao Y. Characteristics and health impacts of bioaerosols in animal barns: A comprehensive study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116381. [PMID: 38676963 DOI: 10.1016/j.ecoenv.2024.116381] [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: 08/23/2023] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
Bioaerosols produced during animal production have potential adverse effects on the health of workers and animals. Our objective was to investigate characteristics, antibiotic-resistance genes (ARGs), and health risks of bioaerosols in various animal barns. Poultry and swine barns had high concentrations of airborne bacteria (11156 and 10917 CFU/m3, respectively). Acinetobacter, Clostridium sensu stricto, Corynebacterium, Pseudomonas, Psychrobacter, Streptococcus, and Staphylococcus were dominant pathogenic bacteria in animal barns, with Firmicutes being the most abundant bacterial phylum. Based on linear discriminant analysis effect size (LEfSe), there were more discriminative biomarkers in cattle barns than in poultry or swine barns, although the latter had the highest abundance of bacterial pathogens and high abundances of ARGs (including tetM, tetO, tetQ, tetW sul1, sul2, ermA, ermB) and intI1). Based on network analyses, there were higher co-occurrence patterns between bacteria and ARGs in bioaerosol from swine barns. Furthermore, in these barns, relative abundance of bacteria in bioaerosol samples was greatly affected by environmental factors, mainly temperature, relative humidity, and concentrations of CO2, NH3, and PM2.5. This study provided novel data regarding airborne bio-contaminants in animal enclosures and an impetus to improve management to reduce potential health impacts on humans and animals.
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Affiliation(s)
- Xiqing Zhang
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Zhenhua Ma
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Peng Hao
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Shaoze Ji
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Yunhang Gao
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China.
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3
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Copeland DC, Ricigliano VA, Mott BM, Kortenkamp OL, Erickson RJ, Gorrochategui-Ortega J, Anderson KE. A longitudinal study of queen health in honey bees reveals tissue specific response to seasonal changes and pathogen pressure. Sci Rep 2024; 14:8963. [PMID: 38637564 PMCID: PMC11026438 DOI: 10.1038/s41598-024-58883-1] [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: 01/12/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
The health of honey bee queens is crucial for colony success, particularly during stressful periods like overwintering. To accompany a previous longitudinal study of colony and worker health, we explored niche-specific gut microbiota, host gene expression, and pathogen prevalence in honey bee queens overwintering in a warm southern climate. We found differential gene expression and bacterial abundance with respect to various pathogens throughout the season. Biologically older queens had larger microbiotas, particularly enriched in Bombella and Bifidobacterium. Both Deformed Wing Virus A and B subtypes were highest in the fat body tissue in January, correlating with colony Varroa levels, and Deformed Wing Virus titers in workers. High viral titers in queens were associated with decreased vitellogenin expression, suggesting a potential trade-off between immune function and reproductive capacity. Additionally, we found a complex and dynamic relationship between these viral loads and immune gene expression, indicating a possible breakdown in the coordinated immune response as the season progressed. Our study also revealed a potential link between Nosema and Melissococcus plutonius infections in queens, demonstrating that seasonal opportunism is not confined to just workers. Overall, our findings highlight the intricate interplay between pathogens, metabolic state, and immune response in honey bee queens. Combined with worker and colony-level metrics from the same colonies, our findings illustrate the social aspect of queen health and resilience over the winter dearth.
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Affiliation(s)
- Duan C Copeland
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA.
| | - Vincent A Ricigliano
- USDA-ARS Honey Bee Breeding, Genetics, and Physiology Laboratory, Baton Rouge, LA, 70820, USA
| | - Brendon M Mott
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
| | - Oliver L Kortenkamp
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Robert J Erickson
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA
| | - June Gorrochategui-Ortega
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940, Leioa, Spain
| | - Kirk E Anderson
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ, 85719, USA.
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA.
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Ruvalcaba-Gómez JM, Villaseñor-González F, Espinosa-Martínez MA, Gómez-Godínez LJ, Rojas-Anaya E, Villagrán Z, Anaya-Esparza LM, Buendía-Rodríguez G, Arteaga-Garibay RI. Growth Performance and Fecal Microbiota of Dairy Calves Supplemented with Autochthonous Lactic Acid Bacteria as Probiotics in Mexican Western Family Dairy Farming. Animals (Basel) 2023; 13:2841. [PMID: 37760240 PMCID: PMC10525134 DOI: 10.3390/ani13182841] [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: 07/07/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Probiotic supplementation in dairy cattle has achieved several beneficial effects (improved growth rate, immune response, and adequate ruminal microbiota). This study assessed the effects on the growth parameters and gut microbiota of newborn dairy calves supplemented with two Lactobacillus-based probiotics, individually (6BZ or 6BY) or their combination (6BZ + 6BY), administrated with the same concentration (1 × 109 CFU/kg weight) at three times, between days 5 and 19 after birth. The control group consisted of probiotic-unsupplemented calves. Growth parameters were recorded weekly until eight weeks and at the calves' ages of three, four, and five months. Fecal microbiota was described by high-throughput sequencing and bioinformatics. Although no significant effects were observed regarding daily weight and height gain among probiotic-supplemented and non-supplemented calves, correlation analysis showed that growth rate was maintained until month 5 through probiotic supplementation, mainly when the two-strain probiotics were supplied. Modulation effects on microbiota were observed in probiotic-supplemented calves, improving the Bacteroidota: Firmicutes and the Proteobacteria ratios. Functional prediction by PICRUSt also showed an increment in several pathways when the two-strain probiotic was supplemented. Therefore, using the three-administration scheme, the two-strain probiotic improved the growth rate and gut microbiota profile in newborn dairy calves. However, positive effects could be reached by applying more administrations of the probiotic during the first 20 days of a calf's life.
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Affiliation(s)
- José Martín Ruvalcaba-Gómez
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad 400, Tepatitlán de Morelos 47600, Jalisco, Mexico; (L.J.G.-G.); (E.R.-A.)
| | - Fernando Villaseñor-González
- Campo Experimental Centro Altos de Jalisco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Av. Biodiversidad 2470, Tepatitlán de Morelos 47600, Jalisco, Mexico;
| | - Mario Alfredo Espinosa-Martínez
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ajuchitlán Colón 76280, Querétaro, Mexico;
| | - Lorena Jacqueline Gómez-Godínez
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad 400, Tepatitlán de Morelos 47600, Jalisco, Mexico; (L.J.G.-G.); (E.R.-A.)
| | - Edith Rojas-Anaya
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad 400, Tepatitlán de Morelos 47600, Jalisco, Mexico; (L.J.G.-G.); (E.R.-A.)
| | - Zuamí Villagrán
- Centro Universitario de los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47600, Jalisco, Mexico; (Z.V.); (L.M.A.-E.)
| | - Luis Miguel Anaya-Esparza
- Centro Universitario de los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47600, Jalisco, Mexico; (Z.V.); (L.M.A.-E.)
| | - Germán Buendía-Rodríguez
- Sitio Experimental Hidalgo, Campo Experimental Valle de México, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Pachuca-Tulancingo 104ª, Pachuca de Soto 42090, Hidalgo, Mexico;
| | - Ramón Ignacio Arteaga-Garibay
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad 400, Tepatitlán de Morelos 47600, Jalisco, Mexico; (L.J.G.-G.); (E.R.-A.)
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Liang J, Ali S, Lv C, Yang H, Zhao X, Ni X, Li C, Danzeng B, Wang Y, Quan G. Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes. Front Endocrinol (Lausanne) 2023; 14:1194425. [PMID: 37621652 PMCID: PMC10446493 DOI: 10.3389/fendo.2023.1194425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/02/2023] [Indexed: 08/26/2023] Open
Abstract
In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.
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Affiliation(s)
- Jiachong Liang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Sikandar Ali
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
- Zhejiang Vegamax Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Chunrong Lv
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Hongyuan Yang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaoqi Zhao
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaojun Ni
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Chunyan Li
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Baiji Danzeng
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guobo Quan
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
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6
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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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7
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Russo N, Floridia V, D’Alessandro E, Lopreiato V, Pino A, Chiofalo V, Caggia C, Liotta L, Randazzo CL. Influence of olive cake dietary supplementation on fecal microbiota of dairy cows. Front Microbiol 2023; 14:1137452. [PMID: 37206333 PMCID: PMC10188969 DOI: 10.3389/fmicb.2023.1137452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
Olive by-products represent a valuable low-price feed supplement for animal nutrition. In the present study, the effect of the dietary destoned olive cake supplementation, on both composition and dynamics of the fecal bacterial biota of cow, was assessed by Illumina MiSeq analysis of the 16S rRNA gene. In addition, metabolic pathways were predicted by using the PICRUSt2 bioinformatic tool. Eighteen lactating cows, according to the body condition score, the days from calving, and the daily milk production were homogeneously allocated into two groups, control or experimental, and subjected to different dietary treatments. In detail, the experimental diet contained, along with the components of the control one, 8% of destoned olive cake. Metagenomics data revealed significant differences in abundance rather than in richness between the two groups. Results showed that Bacteroidota and Firmicutes were identified as the dominant phyla, accounting for over 90% of the total bacterial population. The Desulfobacterota phylum, able to reduce sulfur compounds, was detected only in fecal samples of cows allocated to the experimental diet whereas the Elusimicrobia phylum, a common endosymbiont or ectosymbiont of various flagellated protists, was detected only in cows subjected to the control diet. In addition, both Oscillospiraceae and Ruminococcaceae families were mainly found in the experimental group whereas fecal samples of control cows showed the presence of Rikenellaceae and Bacteroidaceae families, usually associated with the high roughage or low concentrate diet. Based on the PICRUSt2 bioinformatic tool, pathways related to carbohydrate, fatty acid, lipid, and amino acids biosynthesis were mainly up regulated in the experimental group. On the contrary, in the control group, the metabolic pathways detected with the highest occurrence were associated with amino acids biosynthesis and degradation, aromatic compounds degradation, nucleosides and nucleotides biosynthesis. Hence, the present study confirms that the destoned olive cake is a valuable feed supplement able to modulate the fecal microbiota of cows. Further studies will be conducted in order to deepen the inter-relationships between the GIT microbiota and the host.
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Affiliation(s)
- Nunziatina Russo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- ProBioEtna SRL, Spin-Off of University of Catania, Catania, Italy
| | - Viviana Floridia
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Enrico D’Alessandro
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Vincenzo Lopreiato
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Alessandra Pino
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- ProBioEtna SRL, Spin-Off of University of Catania, Catania, Italy
- CERNUT, Interdepartmental Research Centre in Nutraceuticals and Health Products, University of Catania, Catania, Italy
- *Correspondence: Alessandra Pino,
| | - Vincenzo Chiofalo
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Messina, Italy
- Consortium Research of Meat and Agribusiness Chain, Messina, Italy
| | - Cinzia Caggia
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- ProBioEtna SRL, Spin-Off of University of Catania, Catania, Italy
- CERNUT, Interdepartmental Research Centre in Nutraceuticals and Health Products, University of Catania, Catania, Italy
| | - Luigi Liotta
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Cinzia Lucia Randazzo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- ProBioEtna SRL, Spin-Off of University of Catania, Catania, Italy
- CERNUT, Interdepartmental Research Centre in Nutraceuticals and Health Products, University of Catania, Catania, Italy
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Sim S, Lee H, Yoon S, Seon H, Park C, Kim M. The impact of different diets and genders on fecal microbiota in Hanwoo cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:897-910. [PMID: 36287745 PMCID: PMC9574620 DOI: 10.5187/jast.2022.e71] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/05/2022]
Abstract
Bovine fecal microbiota is important for host health and its composition can be
affected by various factors, such as diet, age, species, breed, regions, and
environments. The objective of this study was to evaluate the impact of diet and
gender on fecal microbiota in Korean native Hanwoo cattle. The 16S rRNA gene
amplicon sequencing of fecal microbiota was conducted from 44 Hanwoo cattle
divided into four groups: (1) 11 heifers fed an oat hay plus total mixed ration
(TMR) diet for breeding (HOTB), (2) 11 heifers fed an early fattening TMR diet
(HEFT), (3) 11 steers fed the early fattening TMR diet (SEFT), and (4) 11 steers
fed the late fattening TMR diet (SLFT). Firmicutes and Bacteroidota were the
first and second most dominant phyla in all the samples, respectively. The
Firmicutes/Bacteroidota (F/B) ratio associated with feed efficiency was
significantly greater in the SLFT group than in the other groups. At the genus
level, Romboutsia, Paeniclostridium, and
Turicibacterwere the most abundant in the SLFT while
Akkermansia, Bacteroides, and
Monoglobus were the most abundant in the HOTB group.
Although the same early fattening TMR diet was fed to Hanwoo heifers and steers,
Marvinbryantia and Coprococcus were the
most abundant in the HEFT group while Alistipes and
Ruminococcus were the most abundant in the SEFT group.
Shannon and Simpson diversity indices were significantly lower in the SLFT group
than in the other groups. Distribution of fecal microbiota and functional
genetic profiles were significantly different among the four treatment groups.
The present study demonstrates that different diets and genders can affect fecal
microbiota and the F/B ratio may be associated with feed efficiency in Hanwoo
cattle. Our results may help develop strategies to improve gut health and
productivity through manipulation of fecal microbiota using the appropriate diet
considering Hanwoo cattle gender.
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Affiliation(s)
- Seunghyeun Sim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Huseong Lee
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea,Graduate School of Agricultural Science,
Tohoku University, Sendai 980-0845, Japan
| | - Sang Yoon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Hyeonsu Seon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Cheolju Park
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Minseok Kim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea,Corresponding author Minseok Kim,
Division of Animal Science, Chonnam National University, Gwangju 61186, Korea.
Tel: +82-62-530-2128, E-mail:
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9
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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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Zhang Z, Yang L, He Y, Luo X, Zhao S, Jia X. Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle. Animals (Basel) 2021; 11:ani11113167. [PMID: 34827898 PMCID: PMC8614352 DOI: 10.3390/ani11113167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary This study is to investigate the difference of bovine fecal microbiota between grazing and feedlot Angus cattle. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. A total of 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while species diversity was higher in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At the genus level, five microbiotas were significantly different microbiotas between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef. Abstract This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while higher species diversity was observed in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At a genus level, five microbiotas were significantly different between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef.
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Affiliation(s)
- Zhimin Zhang
- College of Animal Science, Xichang University, Xichang 615000, China;
| | - Li Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (L.Y.); (Y.H.); (X.L.); (S.Z.)
| | - Yang He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (L.Y.); (Y.H.); (X.L.); (S.Z.)
| | - Xinmao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (L.Y.); (Y.H.); (X.L.); (S.Z.)
| | - Shaokang Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (L.Y.); (Y.H.); (X.L.); (S.Z.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (L.Y.); (Y.H.); (X.L.); (S.Z.)
- Correspondence:
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11
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Beauchemin J, Fréchette A, Thériault W, Dufour S, Fravalo P, Thibodeau A. Comparison of microbiota of recycled manure solids and straw bedding used in dairy farms in eastern Canada. J Dairy Sci 2021; 105:389-408. [PMID: 34656347 DOI: 10.3168/jds.2021-20523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022]
Abstract
Recycled manure solids (RMS) bedding is an alternative bedding option that is growing in popularity on Canadian dairy farms. However, the microbiological characteristics and production of RMS bedding are poorly documented under on-farm conditions in eastern Canada. This bedding could support the presence of pathogens and could have an effect on cow and human health. The aim of this study was to describe the RMS microbiota when used under dairy cows and compare it with straw bedding. Unused and used bedding from 27 RMS and 61 straw-bedded dairy farms were collected and compared using 16S amplicon sequencing, bacterial counts, and Salmonella spp. and Listeria monocytogenes detection. Microbiota composition of unused RMS and unused straw were different. After use, both bedding microbiota were similar in their bacterial composition, structure, and diversity. Unused RMS generally contained higher bacterial counts than did unused straw, except for Klebsiella spp. counts. Salmonella spp. and L. monocytogenes were more frequently detected in unused RMS (Salmonella spp.: 11%; L. monocytogenes: 30%), than in unused straw (Salmonella spp.: 0%; L. monocytogenes: 11%). Finally, 2 RMS production systems (extraction of the liquid fraction followed by maturation in an opened or enclosed container vs. in a heap) did not influence the microbiota richness and bacteria distribution (α-diversity), but did influence the microbiota structure (β-diversity). In conclusion, animal and human pathogens were found in greater numbers and more frequently in unused RMS than unused straw, and this could eventually affect dairy cow or human health.
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Affiliation(s)
- Jessika Beauchemin
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Chaire de recherche en salubrité des viandes (CRSV), Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Regroupement FRQ-NT Op+Lait, Saint-Hyacinthe, Québec J2S 2M2 Canada.
| | - Annie Fréchette
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Regroupement FRQ-NT Op+Lait, Saint-Hyacinthe, Québec J2S 2M2 Canada
| | - William Thériault
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Chaire de recherche en salubrité des viandes (CRSV), Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada
| | - Simon Dufour
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Regroupement FRQ-NT Op+Lait, Saint-Hyacinthe, Québec J2S 2M2 Canada
| | - Philippe Fravalo
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Chaire de recherche en salubrité des viandes (CRSV), Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Pole Agro-alimentaire, Conservatoire national des arts et métiers, Le Cnam, 22440 Ploufragan, France
| | - Alexandre Thibodeau
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Chaire de recherche en salubrité des viandes (CRSV), Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2 Canada; Centre de recherche en infectiologie porcine et avicole (CRIPA-FRQNT), Saint-Hyacinthe, Québec J2S 2M2 Canada.
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12
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Characteristics of faecal bacterial flora and volatile fatty acids in Min pig, Landrace pig, and Yorkshire pig. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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13
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Efficacy of corn dried distillers grains with solubles as a replacement for soybean meal in Boer-cross goat finishing diets. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Lawrence M, Polukis S, Barnard AM, Miller MA, Kung L, Gressley TF. Evaluating the effects of Lactobacillus animalis and Propionibacterium freudenreichii on performance and rumen and fecal measures in lactating dairy cows. J Dairy Sci 2021; 104:4119-4133. [PMID: 33612206 DOI: 10.3168/jds.2020-19291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/23/2020] [Indexed: 11/19/2022]
Abstract
Two experiments evaluated the effect of supplementation with a bacterial direct-fed microbial on performance and apparent total-tract nutrient digestion of dairy cows. In experiment 1, 30 multiparous cows (75 ± 32 d in milk) were randomly assigned to 1 of 2 treatments fed for 10 wk. All cows were fed a diet containing 23.8% starch. Treatments were top dressed to rations twice daily and consisted of a combination of Lactobacillus animalis (1 × 109 cfu/d) and Propionibacterium freudenreichii (2 × 109 cfu/d; LAPF) or carrier alone (CON). In experiment 2, 6 ruminally cannulated cows (123 ± 129 d in milk) were randomly assigned to a crossover design with two 6-wk periods. Cows received the same CON or LAPF treatment as in experiment 1. Cows were fed the same 23.8% starch diet as experiment 1 during wk 1 through 5 of each period, and then cows were abruptly switched to a 31.1% starch diet for wk 6. For both experiments, intake and milk yield were measured daily, and milk samples were collected weekly. In experiment 1, fecal grab samples were collected every 6 h on d 7 of experimental wk 1, 2, 4, 6, 8, and 10. Fecal consistency was scored, and fecal starch was measured in daily composite samples. Fecal composites from a subset of 7 cows per treatment were used to measure apparent total-tract nutrient digestion. In experiment 2, rumen pH was continuously recorded during wk 5 and 6. On d 7 of wk 5 (the final day of feeding the 23.8% starch ration), d 1 of wk 6 (the day of diet transition), and d 7 of wk 6 (the final day of feeding the 31.1% starch ration), rumen in situ digestion was determined. Samples of rumen fluid and feces were collected every 6 h on those days for measurement of fecal starch (composited by cow within day), rumen volatile fatty acids, and fecal pH. Rumen and fecal samples were collected at one time point on those days for microbiota assessment. In experiment 1, treatment did not affect intake, milk yield, milk composition, or fecal score. The LAPF treatment decreased fecal starch percentage and tended to increase starch digestion compared with CON, but the differences were very small (0.59 vs. 0.78% and 98.74 vs. 98.46%, respectively). Digestion of other nutrients was unaffected. In experiment 2, LAPF increased rumen pH following the abrupt switch to the high-starch diet, but milk yield was lower for LAPF compared with CON (35.7 vs. 33.2 kg/d). Contrary to the decrease in fecal starch with LAPF observed in experiment 1, fecal starch tended to be increased by LAPF following the abrupt ration change in experiment 2 (2.97 vs. 2.15%). Few effects of treatment on rumen and fecal microbial populations were detectable. Under the conditions used in our experiments, addition of the bacterial direct-fed microbials did not have a marked effect on animal performance, ruminal measures, or total-tract nutrient digestion.
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Affiliation(s)
- M Lawrence
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - S Polukis
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - A M Barnard
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - M A Miller
- Phaseolus Consulting, Wyndmoor, PA 19308
| | - L Kung
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - T F Gressley
- Department of Animal and Food Sciences, University of Delaware, Newark 19716.
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Cendron F, Niero G, Carlino G, Penasa M, Cassandro M. Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing. J Appl Genet 2020; 61:593-605. [PMID: 32851593 PMCID: PMC7652803 DOI: 10.1007/s13353-020-00575-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/29/2020] [Accepted: 08/11/2020] [Indexed: 11/28/2022]
Abstract
The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy.
| | - Giovanni Niero
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Gabriele Carlino
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
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Albonico F, Barelli C, Albanese D, Manica M, Partel E, Rosso F, Ripellino S, Pindo M, Donati C, Zecconi A, Mortarino M, Hauffe HC. Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet. PLoS One 2020; 15:e0237262. [PMID: 32760129 PMCID: PMC7410245 DOI: 10.1371/journal.pone.0237262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.
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Affiliation(s)
- Francesca Albonico
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Veterinary Medicine, Universiy of Milan, Milan, Italy
| | - Claudia Barelli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Mattia Manica
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Erika Partel
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Fausta Rosso
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Silvia Ripellino
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Massimo Pindo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’ Adige (TN), Trento, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
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Effects of Paper Mulberry Silage on the Milk Production, Apparent Digestibility, Antioxidant Capacity, and Fecal Bacteria Composition in Holstein Dairy Cows. Animals (Basel) 2020; 10:ani10071152. [PMID: 32645955 PMCID: PMC7401539 DOI: 10.3390/ani10071152] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Paper mulberry (Broussonetia papyrifera; PM) is a type of roughage rich in bioactive substances, such as phenolics and flavonoids, which are beneficial for animal health. This study evaluated the apparent digestibility of PM silage in Holstein dairy cows and its effect on the milk production, antioxidant capacity, and fecal bacteria composition of the animals. The results showed that the PM silage had no significant influence on the milk yield, apparent digestibility, and fecal bacteria composition of dairy cows. However, diets with PM silage can enhance the antioxidant and immune capacity of dairy cows, mainly due to the bioactive substance in PM. Today, faced with a shortage of feedstuff resources in ruminants, PM can be a useful feed resource for ruminants. Simultaneously, with the ban on antibiotics, PM may become an important functional feed for protecting animal health. Abstract Paper mulberry (Broussonetia papyrifera; PM) is an excellent and extensive type of roughage in Asia. This study aimed to evaluate the effects of PM silage on the milk production, apparent digestibility, antioxidant capacity, and fecal bacteria composition in Holstein dairy cows. Forty-five lactating Holstein dairy cows with a similar milk yield and parity were selected and randomly assigned to three groups. The control group was fed a non-PM silage diet, and the PM-treated groups were fed 4.5 and 9.0% PM silage supplementary diets for 28 days. Then, treatment groups were fed diets containing 13.5 and 18.0% PM silage for the next 28 days, respectively. PM silage increased the milk urea nitrogen and decreased the somatic cell count (p < 0.05), but did not affect the dry matter intake, milk yield, apparent digestibility, and energy balance of dairy cows. PM silage can enhance the blood total antioxidant capacity, superoxide dismutase, and immune globulin content (p < 0.05). The PM silage significantly decreased the relative abundance of the genera Ruminococcaceae UCG-013 and Tyzzerella-4 (p < 0.05). In conclusion, PM silage enhanced the antioxidant capacity and immunity of dairy cows, but did not influence the milk yield, dry matter digestibility, and fecal bacteria composition.
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Lim SK, Kim D, Moon DC, Cho Y, Rho M. Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle. Gigascience 2020; 9:5829833. [PMID: 32369165 PMCID: PMC7317084 DOI: 10.1093/gigascience/giaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. Results In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. Conclusions Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.
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Affiliation(s)
- Suk-Kyung Lim
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Dongjun Kim
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Dong-Chan Moon
- Animal and Plant Quarantine Agency, Bacterial Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Youna Cho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering
| | - Mina Rho
- Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Computer Science and Engineering.,Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea, Department of Biomedical Informatics
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Ran T, Jiao P, AlZahal O, Xie X, Beauchemin KA, Niu D, Yang W. Fecal bacterial community of finishing beef steers fed ruminally protected and non-protected active dried yeast. J Anim Sci 2020; 98:skaa058. [PMID: 32068850 PMCID: PMC7105065 DOI: 10.1093/jas/skaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 02/17/2020] [Indexed: 12/11/2022] Open
Abstract
Our previous study suggested that supplementation of high-grain diets with ruminally protected and non-protected active dried yeast (ADY) may potentially reduce manure pathogen excretion by feedlot cattle. We hypothesized that feeding ruminally protected ADY might change the fecal bacterial community of finishing cattle. The objective of this study was to investigate the effects of feeding ruminally protected and non-protected ADY to finishing beef steers on their fecal bacterial community. Fresh fecal samples were collected on day 56 from 50 steers fed one of five treatments: 1) control (no monensin, tylosin, or ADY), 2) antibiotics (ANT, 330 mg monensin + 110 mg tylosin·steer-1d-1), 3) ADY (1.5 g·steer-1d-1), 4) encapsulated ADY (EDY; 3 g·steer-1d-1), and 5) a mixture of ADY and EDY (MDY; 1.5 g ADY + 3 g EDY·steer-1d-1). Bacterial DNA was extracted from fecal samples and sequenced using a MiSeq high-throughput sequencing platform. A total number of 2,128,772 high-quality V4 16S rRNA sequences from 50 fecal samples were analyzed, and 1,424 operational taxonomic units (OTU) were detected based on 97% nucleotide sequence identity among reads, with 769 OTU shared across the five treatments. Alpha diversity indices, including species observed, Chao estimate, abundance-based coverage estimator, Shannon, Simpson, and coverage, did not differ among treatments, and principal coordinate analysis revealed a high similarity among treatments without independent distribution. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) for greater relative abundance of Bacteroidetes but lesser Firmicutes with ANT, EDY, and MDY compared with control steers. Prevotella was the dominant genus in all treatments and steers supplemented with ANT, EDY, and MDY had greater (P < 0.05) relative abundance of Prevotella than control steers, but lesser (P < 0.03) relative abundance of Oscillospira. No differences between ADY and control were observed for the aforementioned variables. Fecal starch contents were not different among treatments, but the relative abundance of Bacteroidetes, as well as Prevotella at genera level, tended (P < 0.06) to be positively correlated to fecal starch content. We conclude that supplementing ruminally protected or non-protected ADY or ANT had no effect on diversity and richness of fecal bacteria of finishing beef cattle, whereas feeding protected ADY or ANT to finishing beef steers altered the dominant fecal bacteria at phylum and genus levels. Therefore, supplementation of ruminally protected ADY may potentially improve intestinal health by stimulating the relative abundance of Prevotella.
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Affiliation(s)
- Tao Ran
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
- Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, Hunan, China
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Peixin Jiao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | | | - Xiaolai Xie
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Karen A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Dongyan Niu
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Wenzhu Yang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
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Effects of fermented corn gluten meal on growth performance, plasma metabolites, rumen fermentation and bacterial community of Holstein calves during the pre-weaning period. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Weinroth MD, Martin JN, Doster E, Geornaras I, Parker JK, Carlson CR, Metcalf JL, Morley PS, Belk KE. Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1. J Anim Sci 2019; 97:4567-4578. [PMID: 31563955 PMCID: PMC6827412 DOI: 10.1093/jas/skz306] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022] Open
Abstract
Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.
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Affiliation(s)
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Enrique Doster
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO
| | - Ifigenia Geornaras
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO
| | - Clay R Carlson
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
| | - Paul S Morley
- Veterinary Education, Research and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO
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Metagenomic analysis of the fecal microbiomes from Escherichia coli O157:H7-shedding and non-shedding cows on a single dairy farm. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue. Appl Environ Microbiol 2019; 85:AEM.00032-19. [PMID: 31126949 DOI: 10.1128/aem.00032-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Epichloë coenophialum Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n = 6) or nontoxic (Max-Q; n = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the Firmicutes and Bacteroidetes phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the Erysipelotrichaceae family and delayed increases of the Ruminococcaceae and Lachnospiraceae families were among the major effects of E+ grazing. E+ also increased abundances within the Planctomycetes, Chloroflexi, and Proteobacteria phyla and the Clostridiaceae family. Multiple operational taxonomic units classified as Ruminococcaceae and Lachnospiraceae were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT.IMPORTANCE Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.
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Hagey JV, Bhatnagar S, Heguy JM, Karle BM, Price PL, Meyer D, Maga EA. Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows. Front Microbiol 2019; 10:1093. [PMID: 31156599 PMCID: PMC6532609 DOI: 10.3389/fmicb.2019.01093] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
Improved sequencing and analytical techniques allow for better resolution of microbial communities; however, the agriculture field lacks an updated analysis surveying the fecal microbial populations of dairy cattle in California. This study is a large-scale survey to determine the composition of the bacterial community present in the feces of lactating dairy cattle on commercial dairy operations. For the study, 10 dairy farms across northern and central California representing a variety of feeding and management systems were enrolled. The farms represented three typical housing types including five freestall, two drylot and three pasture-based management systems. Fresh feces were collected from 15 randomly selected cows on each farm and analyzed using 16S rRNA gene amplicon sequencing. This study found that housing type, individual farm, and dietary components significantly affected the alpha diversity of the fecal microbiota. While only one Operational Taxonomic Unit (OTU) was common among all the sampled individuals, 15 bacterial families and 27 genera were shared among 95% of samples. The ratio of the families Coriobacteriaceae to Bifidobacteriaceae was significantly different between housing types and farms with pasture fed animals having a higher relative abundance of Coriobacteriaceae. A majority of samples were positive for at least one OTU assigned to Enterobacteriaceae and 31% of samples contained OTUs assigned to Campylobacter. However, the relative abundance of both taxa was <0.1%. The microbial composition displays individual farm specific signatures, but housing type plays a role. These data provide insights into the composition of the core fecal microbiota of commercial dairy cows in California and will further generate hypotheses for strategies to manipulate the microbiome of cattle.
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Affiliation(s)
- Jill V. Hagey
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer M. Heguy
- Division of Agriculture and Natural Resources, University of California Cooperative Extension, Hayward, CA, United States
| | - Betsy M. Karle
- Division of Agriculture and Natural Resources, University of California Cooperative Extension, Hayward, CA, United States
| | - Patricia L. Price
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Deanne Meyer
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Elizabeth A. Maga
- Department of Animal Science, University of California, Davis, Davis, CA, United States
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Zhang J, Shi H, Wang Y, Cao Z, Yang H, Li S. Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers. Front Microbiol 2018; 9:976. [PMID: 29867879 PMCID: PMC5962747 DOI: 10.3389/fmicb.2018.00976] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/25/2018] [Indexed: 11/25/2022] Open
Abstract
Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haitao Shi
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongjian Yang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Chaney WE, Maloney R, Johnson BJ, Brooks JC, Brashears MM, Loneragan GH. Corn-Based Distillers' Grains in Diets for Feedlot Cattle Are Associated with the Burden of Escherichia coli O157 in Feces. Foodborne Pathog Dis 2018; 15:398-405. [PMID: 29620957 DOI: 10.1089/fpd.2017.2395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Inclusion of distillers' grains (DGs) has been associated with increased prevalence of Escherichia coli O157:H7 in cattle housed in research settings. Our objective was to quantify the relationship between inclusion of DGs in commercial feedlot rations and the burden of E. coli O157. A convenience sample of 10 feedlots was enrolled based on DG use in finishing diets; 1 cohort included 5 feedlots in which DGs were greater than 15% of the dietary dry matter and the other cohort consisted of 5 feedlots at a concentration less than 8%. Sampling occurred at each feedlot on four occasions at ∼6-week intervals. At each feedlot visit, 4 pens of cattle within 3 weeks of slaughter were selected and 24 freshly voided fecal pats were sampled. Ten-gram samples were enriched in 90 mL of modified tryptic soy broth with novobiocin (20 mg/L) for 14 h at 42°C. Enrichments were subjected to immunomagnetic separation, plating onto chromogenic agar with novobiocin (5 mg/L) and potassium tellurite (2.5 mg/L), incubation for 18 h at 37°C, and latex agglutination of morphologically typical colonies. E. coli O157 was recovered from 16.7% of 3840 samples. Adjusted prevalence was 14.3% after controlling for within-feedlot and within-pen clustering. Prevalence during each sampling period was 19.9% (round 1), 21.0% (round 2), 14.1% (round 3), and 11.7% (round 4). Prevalence varied between cohorts, but this difference varied over time (p = 0.06). Among those with greater than 15% of the diet as DGs, prevalence was greater than those with less than 8% inclusion for all rounds of sampling (p < 0.01). Averaged across time, prevalence was 23.9% and 9.4% for those with greater than 15% and those with less than 8% of DGs, respectively. While observational, these data provide real-world support of reports of increased E. coli O157:H7 burden associated with DG use in cattle diets.
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Affiliation(s)
- W Evan Chaney
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
| | - Rebecca Maloney
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
| | - Bradley J Johnson
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
| | - J Chance Brooks
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
| | - Mindy M Brashears
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
| | - Guy H Loneragan
- Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University , Lubbock, Texas
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Kim M, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle. J Appl Microbiol 2017; 123:1027-1042. [PMID: 28736954 DOI: 10.1111/jam.13545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
Abstract
AIMS The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration. METHODS AND RESULTS Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P < 0·001) with prevalence or enumeration, explaining as much as 50% of variability in E. coli O157:H7 prevalence or enumeration. CONCLUSIONS Individual colonic bacterial species have little impact on E. coli O157:H7 shedding but collectively groups of bacteria were strongly associated with pathogen shedding. SIGNIFICANCE AND IMPACT OF THE STUDY Bacterial groups in the bovine colon may impact faecal shedding of the zoonotic pathogen E. coli O157:H7, and manipulation of the intestinal microbiota to alter these bacteria may reduce shedding of this pathogen and foodborne illnesses.
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Affiliation(s)
- M Kim
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - L A Kuehn
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - J L Bono
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - E D Berry
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - N Kalchayanand
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - H C Freetly
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - A K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - J E Wells
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
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Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers. BMC Microbiol 2017; 17:97. [PMID: 28431497 PMCID: PMC5401608 DOI: 10.1186/s12866-017-1011-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/17/2017] [Indexed: 11/21/2022] Open
Abstract
Background Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community. Results Most of the sequences were assigned to Firmicutes (56.67%) and Bacteroidetes (35.90%), followed by Proteobacteria (1.87%), Verrucomicrobia (1.80%) and Tenericutes (1.37%). The predominant genera were 5-7 N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia (1.11%). No significant differences were observed in the numbers of Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17), and Tenericutes (p = 0.75) populations between the treatment groups. At the genus level, genera classified with high abundance (more than 0.1%) belonged primarily to Bacteroidetes and Firmicutes. Furthermore, no differences were observed at the genus level: 5-7 N15, CF231, Oscillospira, Paludibacter, and Akkermansia (p > 0.05 in all cases), except that rc4–4 was lower in the CON and SMFP groups than in the EML group (p = 0.02). There were no significant differences in the richness estimate and diversity indices between the groups (p > 0.16), and the different diets did not significantly influence most selected fecal bacterial species (p > 0.06), except for Ruminococcus albus, which was higher in the EML group (p < 0.01) and Streptococcus bovis, which was lower in the CON group (p < 0.01) relative to the other groups. Conclusions In conclusion, diets supplemented with EML and SMFP have little influence on the fecal bacterial community composition in finishing steers. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1011-9) contains supplementary material, which is available to authorized users.
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Impacts of dietary forage and crude protein levels on the shedding of Escherichia coli O157:H7 and Listeria in dairy cattle feces. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Haley BJ, Pettengill J, Gorham S, Ottesen A, Karns JS, Van Kessel JAS. Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows. Front Microbiol 2016; 7:691. [PMID: 27313565 PMCID: PMC4887466 DOI: 10.3389/fmicb.2016.00691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/26/2016] [Indexed: 01/06/2023] Open
Abstract
In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut.
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Affiliation(s)
- Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - James Pettengill
- Division of Public Health Informatics and Analytics, Center for Food Safety and Nutrition, Office of Analytics and Outreach, U.S. Food and Drug Administration College Park, MD, USA
| | - Sasha Gorham
- Division of Microbiology, Center for Food Safety and Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration College Park, MD, USA
| | - Andrea Ottesen
- Division of Microbiology, Center for Food Safety and Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration College Park, MD, USA
| | - Jeffrey S Karns
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Agricultural Research Service Beltsville, MD, USA
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Kim M, Wells JE. A Meta-analysis of Bacterial Diversity in the Feces of Cattle. Curr Microbiol 2015; 72:145-151. [PMID: 26542532 DOI: 10.1007/s00284-015-0931-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/26/2015] [Indexed: 12/29/2022]
Abstract
In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13,663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13,447 sequences were assigned to 10 phyla, 17 classes, 28 orders, 59 families, and 110 genera, while the remaining 216 sequences could not be assigned to a known phylum. Firmicutes and Bacteroidetes were the first and the second predominant phyla, respectively. About 41 % of the total sequences could not be assigned to a known genus. The total sequences were assigned to 1252 OTUs at 97 % sequence similarity. A small number of OTUs shared among datasets indicate that fecal bacterial communities of cattle are greatly affected by various factors, specifically diet. This study may guide future studies to further analyze fecal bacterial communities of cattle.
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Affiliation(s)
- Minseok Kim
- U.S. Department of Agriculture, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, NE, 68933, USA
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - James E Wells
- U.S. Department of Agriculture, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, NE, 68933, USA.
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Sato S. Pathophysiological evaluation of subacute ruminal acidosis (SARA) by continuous ruminal pH monitoring. Anim Sci J 2015; 87:168-77. [PMID: 26279060 PMCID: PMC5042035 DOI: 10.1111/asj.12415] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 02/09/2015] [Accepted: 02/27/2015] [Indexed: 11/29/2022]
Abstract
Evaluation of the radio‐transmission pH‐measurement system for monitoring the ruminal pH and subacute ruminal acidosis (SARA) in cattle is described. This is done in order to reveal the possible application of this system for detection and pathophysiological research of SARA by continuous ruminal pH measurement. The possibility of using this system for assessment of the ruminal pH in SARA cattle, and the presence of negative correlation between the ruminal pH and ruminal temperature in heathy and SARA cattle were determined. In addition, the 16S rRNA gene pyrosequencing analysis showed that the ruminal microbial community was simpler in SARA cattle, and the bacterial numbers in SARA cattle were lower than those in healthy hay‐fed cattle. Concentrate feeding might have reduced the diversity of the ruminal microbial community. Changes in the ruminal microbial community of SARA cattle might be related to the changes in ruminal pH followed by the decrease in the number of some bacteria. Continuous monitoring of the ruminal pH using the radio‐transmission pH‐measurement system would be applied for detection and prevention of SARA in the field and pathophysiological research of SARA, including ruminal zymology and bacteriology, which have been determined previously by sampling of the ruminal fluid and measuring of ruminal pH.
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Affiliation(s)
- Shigeru Sato
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Japan
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McEachran AD, Blackwell BR, Hanson JD, Wooten KJ, Mayer GD, Cox SB, Smith PN. Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:337-43. [PMID: 25633846 PMCID: PMC4383574 DOI: 10.1289/ehp.1408555] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 01/14/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Emergence and spread of antibiotic resistance has become a global health threat and is often linked with overuse and misuse of clinical and veterinary chemotherapeutic agents. Modern industrial-scale animal feeding operations rely extensively on veterinary pharmaceuticals, including antibiotics, to augment animal growth. Following excretion, antibiotics are transported through the environment via runoff, leaching, and land application of manure; however, airborne transport from feed yards has not been characterized. OBJECTIVES The goal of this study was to determine the extent to which antibiotics, antibiotic resistance genes (ARG), and ruminant-associated microbes are aerially dispersed via particulate matter (PM) derived from large-scale beef cattle feed yards. METHODS PM was collected downwind and upwind of 10 beef cattle feed yards. After extraction from PM, five veterinary antibiotics were quantified via high-performance liquid chromatography with tandem mass spectrometry, ARG were quantified via targeted quantitative polymerase chain reaction, and microbial community diversity was analyzed via 16S rRNA amplification and sequencing. RESULTS Airborne PM derived from feed yards facilitated dispersal of several veterinary antibiotics, as well as microbial communities containing ARG. Concentrations of several antibiotics in airborne PM immediately downwind of feed yards ranged from 0.5 to 4.6 μg/g of PM. Microbial communities of PM collected downwind of feed yards were enriched with ruminant-associated taxa and were distinct when compared to upwind PM assemblages. Furthermore, genes encoding resistance to tetracycline antibiotics were significantly more abundant in PM collected downwind of feed yards as compared to upwind. CONCLUSIONS Wind-dispersed PM from feed yards harbors antibiotics, bacteria, and ARGs.
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Affiliation(s)
- Andrew D McEachran
- Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas, USA
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Klein-Jöbstl D, Schornsteiner E, Mann E, Wagner M, Drillich M, Schmitz-Esser S. Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Front Microbiol 2014; 5:622. [PMID: 25452753 PMCID: PMC4233928 DOI: 10.3389/fmicb.2014.00622] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/31/2014] [Indexed: 01/01/2023] Open
Abstract
From birth to the time after weaning the gastrointestinal microbiota of calves must develop into a stable, autochthonous community accompanied by pivotal changes of anatomy and physiology of the gastrointestinal tract. The aim of this pilot study was to examine the fecal microbiota of six Simmental dairy calves to investigate time-dependent dynamics of the microbial community. Calves were followed up from birth until after weaning according to characteristic timepoints during physiological development of the gastrointestinal tract. Pyrosequencing of 16S rRNA gene amplicons from 35 samples yielded 253,528 reads clustering into 5410 operational taxonomic units based on 0.03 16S rRNA distance. Operational taxonomic units were assigned to 296 genera and 17 phyla with Bacteroidetes, Firmicutes, and Proteobacteria being most abundant. An age-dependent increasing diversity and species richness was observed. Highest similarities between fecal microbial communities were found around weaning compared with timepoints from birth to the middle of the milk feeding period. Principal coordinate analysis revealed a high variance particularly in samples taken at the middle of the milk feeding period (at the age of approximately 40 days) compared to earlier timepoints, confirming a unique individual development of the fecal microbiota of each calf. This study provides first deep insights into the composition of the fecal microbiota of Simmental dairy calves and might be a basis for future more detailed studies.
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Affiliation(s)
- Daniela Klein-Jöbstl
- Clinical Unit for Herd Health Management, Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna Vienna, Austria ; Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria
| | - Elisa Schornsteiner
- Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Evelyne Mann
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Martin Wagner
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
| | - Marc Drillich
- Clinical Unit for Herd Health Management, Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna Vienna, Austria
| | - Stephan Schmitz-Esser
- Research Cluster "Animal Gut Health," University of Veterinary Medicine Vienna Vienna, Austria ; Department for Farm Animals and Veterinary Public Health, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine Vienna Vienna, Austria
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Xu Y, Dugat-Bony E, Zaheer R, Selinger L, Barbieri R, Munns K, McAllister TA, Selinger LB. Escherichia coli O157:H7 super-shedder and non-shedder feedlot steers harbour distinct fecal bacterial communities. PLoS One 2014; 9:e98115. [PMID: 24858731 PMCID: PMC4032279 DOI: 10.1371/journal.pone.0098115] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/28/2014] [Indexed: 02/01/2023] Open
Abstract
Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed "super-shedders". A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a "normal" microbiota prevents E. coli O157:H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157:H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7.
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Affiliation(s)
- Yong Xu
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Eric Dugat-Bony
- AgroParisTech National Institute for Agricultural Research, Thiverval, Grignon France
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Lorna Selinger
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Ruth Barbieri
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Krysty Munns
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - L. Brent Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- * E-mail:
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Wells JE, Kim M, Bono JL, Kuehn LA, Benson AK. MEAT SCIENCE AND MUSCLE BIOLOGY SYMPOSIUM:Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle12. J Anim Sci 2014; 92:1345-55. [DOI: 10.2527/jas.2013-7282] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- J. E. Wells
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 689334
| | - M. Kim
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 689334
| | - J. L. Bono
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 689334
| | - L. A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 689334
| | - A. K. Benson
- Department of Food Science and Technology, University of Nebraska, Lincoln 68583
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Kim M, Kim J, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE. Investigation of bacterial diversity in the feces of cattle fed different diets. J Anim Sci 2013; 92:683-94. [PMID: 24352967 DOI: 10.2527/jas.2013-6841] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.
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Affiliation(s)
- M Kim
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933
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Song S, Jarvie T, Hattori M. Our second genome-human metagenome: how next-generation sequencer changes our life through microbiology. Adv Microb Physiol 2013; 62:119-44. [PMID: 23481336 DOI: 10.1016/b978-0-12-410515-7.00003-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Next-generation sequencing has greatly expanded our ability to query the identity and genetic composition of entire communities of microbial organisms. This area of research, known as metagenomics, does not rely upon culturing the individual organisms. Rather, the genetic material from the entire community is processed and sequenced simultaneously. From this sequence data, researchers are able to determine the relative population of organisms within the community as well as determine which genes and metabolic pathways are present and expressed in the microbial community. While these techniques have been applied to a wide range of environmental samples, metagenomics is also the focus of intensive research on human-associated microbial communities. The scope of these human metagenomics studies are quite varied, but all have a common goal of attempting to understand the important role that human commensal microbial communities play in health and disease. The early results from studying the human metagenome indicate a vital role that microbial communities play in immunity, health, and disease. Going forward, human metagenomics is a wide open field of research with many unanswered questions such as which factors are responsible for the variation of composition of an individual's microbiome, how does the microbiome respond to disturbance, and what beneficial functions are the microorganisms performing?
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Affiliation(s)
- Shuolin Song
- Genome Sequencing Department, Applied Science, Roche Diagnostics K. K., Tokyo, Japan.
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40
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Durso LM, Wells JE, Harhay GP, Rice WC, Kuehn L, Bono JL, Shackelford S, Wheeler T, Smith TPL. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers' grain with solubles. Lett Appl Microbiol 2012; 55:109-14. [PMID: 22583366 DOI: 10.1111/j.1472-765x.2012.03265.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AIM The mammalian intestinal microflora has been shown to impact host physiology. In cattle, intestinal bacteria are also associated with faecal contamination of environmental sources and human illness via foodborne pathogens. Use of wet distillers' grains with solubles (WDGS) in cattle feed creates a gastrointestinal environment where some bacterial species are enriched. Here, we examine if a diet containing 40% WDGS results in fundamentally different microbial community structures. METHODS AND RESULTS The 20,002 16S r-RNA gene sequences from 20 beef cattle were analysed using Sanger sequencing methods. At the genus level, Prevotella (Gram negative) and Anaerobacter (Gram positive) were the most frequently occurring bacteria in our beef cattle faecal samples. Diet-associated differences in prevalence were noted for Prevotella but not Anaerobacter. CONCLUSIONS Diet affects community structure. Faecal communities of co-housed beef cattle are not identical. SIGNIFICANCE AND IMPACT OF THE STUDY It is known that a diet of 40% corn-based WDGS increases the generic Escherichia coli in the faeces and enriches E. coli O157:H7. The results from the current study suggest that in addition to previously observed changes in E. coli, the entire bacterial community structure is different for animals fed 40% corn-based WDGS compared to a traditional corn-finishing diet.
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Affiliation(s)
- L M Durso
- USDA, ARS, Agroecosystem Management Resource Unit, Lincoln, NE 68583, USA.
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