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Thacharodi A, Hassan S, Ahmed ZHT, Singh P, Maqbool M, Meenatchi R, Pugazhendhi A, Sharma A. The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis. ENVIRONMENTAL RESEARCH 2024; 261:119661. [PMID: 39043353 DOI: 10.1016/j.envres.2024.119661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/17/2024] [Accepted: 07/20/2024] [Indexed: 07/25/2024]
Abstract
Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.
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Affiliation(s)
- Aswin Thacharodi
- Dr. Thacharodi's Laboratories, Department of Research and Development, Puducherry, 605005, India
| | - Saqib Hassan
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India; Future Leaders Mentoring Fellow, American Society for Microbiology, Washington, 20036, USA
| | - Z H Tawfeeq Ahmed
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India
| | - Prabhakar Singh
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India
| | - Mohsin Maqbool
- Sidney Kimmel Cancer Center, Jefferson Health, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Ramu Meenatchi
- Department of Biotechnology, SRM Institute of Science and Technology, Chengalpattu, Tamil Nadu, 603203, India
| | - Arivalagan Pugazhendhi
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, AgroInnovationLab, School of Engineering and Sciences, Queretaro, 76130, Mexico
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, AgroInnovationLab, School of Engineering and Sciences, Queretaro, 76130, Mexico.
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2
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Lu Z, Kong L, Ren S, Aschenbach JR, Shen H. Acid tolerance of lactate-utilizing bacteria of the order Bacteroidales contributes to prevention of ruminal acidosis in goats adapted to a high-concentrate diet. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 14:130-140. [PMID: 37397354 PMCID: PMC10314236 DOI: 10.1016/j.aninu.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2023] [Accepted: 05/11/2023] [Indexed: 07/04/2023]
Abstract
The rapid accumulation of organic acids, particularly lactate, has been suggested as the main cause of ruminal acidosis (RA) for ruminants fed high-concentrate diets. Previous research has shown that a gradual shift from low-to high-concentrate diets within 4 to 5 weeks effectively reduces the risk for RA. However, the mechanisms remain unknown. In this study, 20 goats were randomly allocated into four groups (n = 5) and fed with a diet containing a weekly increasing concentrate portion of 20%, 40%, 60%, and 80% over 28 d. At d 7, 14, 21, and 28, one group (named C20, C40, C60, and C80 according to the last concentrate level that they received) was killed and the ruminal microbiome was collected. Ruminal acidosis was not detected in any of the goats during the experiment. Nonetheless, ruminal pH dropped sharply from 6.2 to 5.7 (P < 0.05) when dietary concentrate increased from 40% to 60%. A combined metagenome and metatranscriptome sequencing approach identified that this was linked to a sharp decrease in the abundance and expression of genes encoding nicotinamide adenine dinucleotide (NAD)-dependent lactate dehydrogenase (nLDH), catalyzing the enzymatic conversion of pyruvate to lactate (P < 0.01), whereas the expression of two genes encoding NAD-independent lactate dehydrogenase (iLDH), catalyzing lactate oxidation to pyruvate, showed no significant concomitant change. Abundance and expression alterations for nLDH- and iLDH-encoding genes were attributable to bacteria from Clostridiales and Bacteroidales, respectively. By analyzing the gene profiles of 9 metagenome bins (MAG) with nLDH-encoding genes and 5 MAG with iLDH-encoding genes, we identified primary and secondary active transporters as being the major types of sugar transporter for lactate-producing bacteria (LPB) and lactate-utilizing bacteria (LUB), respectively. Furthermore, more adenosine triphosphate was required for the phosphorylation of sugars to initiate their catabolic pathways in LPB compared to LUB. Thus, the low dependence of sugar transport systems and catabolic pathways on primary energy sources supports the acid tolerance of LUB from Bacteroidales. It favors ruminal lactate utilization during the adaptation of goats to a high-concentrate diet. This finding has valuable implications for the development of measures to prevent RA.
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Affiliation(s)
- Zhongyan Lu
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lingmeng Kong
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shenhao Ren
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jörg R. Aschenbach
- Institute of Veterinary Physiology, Freie Universität Berlin, Berlin, Germany
| | - Hong Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu, China
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3
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Lobo RR, Arce-Cordero JA, Agustinho BC, Ravelo AD, Vinyard JR, Johnson ML, Monteiro HF, Sarmikasoglou E, Roesch LFW, Jeong KCC, Faciola AP. Can dietary magnesium sources and buffer change the ruminal microbiota composition and fermentation of lactating dairy cows? J Anim Sci 2023; 101:skad211. [PMID: 37350733 PMCID: PMC10355366 DOI: 10.1093/jas/skad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023] Open
Abstract
Magnesium oxide (MgO) is one of the most used Mg supplements in livestock. However, to avoid relying upon only one Mg source, it is important to have alternative Mg sources. Therefore, the objective of this study was to evaluate the effects of the interaction of two Mg sources with buffer use on the ruminal microbiota composition, ruminal fermentation, and nutrient digestibility in lactating dairy cows. Twenty lactating Holstein cows were blocked by parity and days in milk into five blocks with four cows each, in a 2 × 2 factorial design. Within blocks, cows were assigned to one of four treatments: 1) MgO; 2) MgO + Na sesquicarbonate (MgO+); 3) calcium-magnesium hydroxide (CaMgOH); 4) CaMgOH + Na sesquicarbonate (CaMgOH+). For 60 d, cows were individually fed a corn silage-based diet, and treatments were top-dressed. Ruminal fluid was collected via an orogastric tube, for analyses of the microbiota composition, volatile fatty acids (VFA), lactate, and ammonia nitrogen (NH3-N). The microbiota composition was analyzed using V4/16S rRNA gene sequencing, and taxonomy was assigned using the Silva database. Statistical analysis was carried out following the procedures of block design analysis, where block and cow were considered random variables. Effects of Mg source, buffer, and the interaction between Mg Source × Buffer were analyzed through orthogonal contrasts. There was no interaction effect of the two factors evaluated. There was a greater concentration of NH3-N, lactate, and butyrate in the ruminal fluid of cows fed with CaMg(OH)2, regardless of the buffer use. The increase in these fermentation intermediates/ end-products can be explained by an increase in abundance of micro-organisms of the genus Prevotella, Lactobacillus, and Butyrivibrio, which are micro-organisms mainly responsible for proteolysis, lactate-production, and butyrate-production in the rumen, respectively. Also, dietary buffer use did not affect the ruminal fermentation metabolites and pH; however, an improvement of the apparent total tract digestibility of dry matter (DM), organic matter (OM), neutral fiber detergent (NDF), and acid fiber detergent (ADF) were found for animals fed with dietary buffer. In summary, there was no interaction effect of buffer use and Mg source, whereas buffer improved total tract apparent digestibility of DM and OM through an increase in NDF and ADF digestibility and CaMg(OH)2 increased ruminal concentration of butyrate and abundance of butyrate-producing bacteria.
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Affiliation(s)
- Richard R Lobo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Jose A Arce-Cordero
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
- Escuela de Zootecnia, Universidad de Costa Rica, San Jose 11501-2060, Costa Rica
| | - Bruna C Agustinho
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Ana D Ravelo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
- College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
| | - James R Vinyard
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Mikayla L Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Hugo F Monteiro
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - Luiz Fernando W Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32608, USA
| | - Kwang Cheol C Jeong
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Antonio P Faciola
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
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4
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Ricci S, Pacífico C, Castillo-Lopez E, Rivera-Chacon R, Schwartz-Zimmermann HE, Reisinger N, Berthiller F, Zebeli Q, Petri RM. Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation. Front Microbiol 2022; 13:920427. [PMID: 35935232 PMCID: PMC9354822 DOI: 10.3389/fmicb.2022.920427] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.
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Affiliation(s)
- Sara Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
- *Correspondence: Sara Ricci
| | - Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Ezequias Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Raul Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Heidi E. Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Renee M. Petri
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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5
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Ban Y, Guan LL. Implication and challenges of direct-fed microbial supplementation to improve ruminant production and health. J Anim Sci Biotechnol 2021; 12:109. [PMID: 34635155 PMCID: PMC8507308 DOI: 10.1186/s40104-021-00630-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/08/2021] [Indexed: 01/03/2023] Open
Abstract
Direct-fed microbials (DFMs) are feed additives containing live naturally existing microbes that can benefit animals' health and production performance. Due to the banned or strictly limited prophylactic and growth promoting usage of antibiotics, DFMs have been considered as one of antimicrobial alternatives in livestock industry. Microorganisms used as DFMs for ruminants usually consist of bacteria including lactic acid producing bacteria, lactic acid utilizing bacteria and other bacterial groups, and fungi containing Saccharomyces and Aspergillus. To date, the available DFMs for ruminants have been largely based on their effects on improving the feed efficiency and ruminant productivity through enhancing the rumen function such as stabilizing ruminal pH, promoting ruminal fermentation and feed digestion. Recent research has shown emerging evidence that the DFMs may improve performance and health in young ruminants, however, these positive outcomes were not consistent among studies and the modes of action have not been clearly defined. This review summarizes the DFM studies conducted in ruminants in the last decade, aiming to provide the new knowledge on DFM supplementation strategies for various ruminant production stages, and to identify what are the potential barriers and challenges for current ruminant industry to adopt the DFMs. Overall literature research indicates that DFMs have the potential to mitigate ruminal acidosis, improve immune response and gut health, increase productivity (growth and milk production), and reduce methane emissions or fecal shedding of pathogens. More research is needed to explore the mode of action of specific DFMs in the gut of ruminants, and the optimal supplementation strategies to promote the development and efficiency of DFM products for ruminants.
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Affiliation(s)
- Yajing Ban
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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6
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Wongkuna S, Ghimire S, Janvilisri T, Doerner K, Chankhamhaengdecha S, Scaria J. Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken. F1000Res 2020; 9:1103. [PMID: 33024551 PMCID: PMC7520715 DOI: 10.12688/f1000research.25823.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165
T. Methods: For the possible novel strain SW165
T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was
Olsenella profusa DSM 13989
T (96.33% similarity) within the family
Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45
oC and pH 6.0-7.5 respectively. This strain produced acetic acid as the primary fermentation product. Major fatty acids were C
12:0, C
14:0, C
14:0 DMA and summed feature 1 (C
13:1 at 12-13 and C
14:0 aldehyde). Strain SW165
T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus
Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165
T and DSM 13989
T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus
Olsenella, and name it
Olsenella lakotia SW165
T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.
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Affiliation(s)
- Supapit Wongkuna
- Doctor of Philosophy Program in Biochemistry (International Program), Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, 57007, USA
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kinchel Doerner
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, 57007, USA
| | | | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, 57007, USA
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7
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Guo L, Yao D, Li D, Lin Y, Bureenok S, Ni K, Yang F. Effects of Lactic Acid Bacteria Isolated From Rumen Fluid and Feces of Dairy Cows on Fermentation Quality, Microbial Community, and in vitro Digestibility of Alfalfa Silage. Front Microbiol 2020; 10:2998. [PMID: 31998275 PMCID: PMC6962301 DOI: 10.3389/fmicb.2019.02998] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022] Open
Abstract
The objective of this study was to select lactic acid bacteria (LAB) isolated from the rumen fluid and feces of dairy cows, and evaluate their effects on silage quality of alfalfa after 30 or 60 days of ensiling. One hundred and four LAB strains were isolated from rumen fluid and feces of six dairy cows, of which four strains (Lactobacillus plantarum F1, L. plantarum F50, Lactobacillus salivarius L100, and Lactobacillus fermentum L120) and one commercial inoculant (GFG) isolated from forage were employed for further study. The silages treated with F1 had the lowest (P < 0.05) pH value and the highest (P < 0.05) lactic acid (LA) content in all treatments. Besides, higher (P < 0.05) in vitro digestibility was also observed in F1-treated silage after 60 days of ensiling. The microbial analysis showed that the Lactobacillus abundance in the F1-treated silages increased to 60.32%, higher than other treatments (5.12–47.64%). Our research indicated that strain F1 could be an alternative silage inoculant, and dairy cows could be a source for obtaining excellent LAB for ensiling.
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Affiliation(s)
- Linna Guo
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Dandan Yao
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dongxia Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanli Lin
- Beijing Sure Academy of Biosciences, Beijing, China
| | - Smerjai Bureenok
- Department of Agricultural Technology and Environment, Rajamangala University of Technology Isan, Nakhon Ratchasima, Thailand
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
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8
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Teoh R, Caro E, Holman DB, Joseph S, Meale SJ, Chaves AV. Effects of Hardwood Biochar on Methane Production, Fermentation Characteristics, and the Rumen Microbiota Using Rumen Simulation. Front Microbiol 2019; 10:1534. [PMID: 31354652 PMCID: PMC6635593 DOI: 10.3389/fmicb.2019.01534] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022] Open
Abstract
Biochar is a novel carbonized feed additive sourced from pyrolyzed biomass. This compound is known to adsorb gasses and carbon, participate in biological redox reactions and provide habitat biofilms for desirable microbiota proliferation. Therefore, biochar holds potential to modify rumen fermentation characteristics and reduce enteric CH4 emissions. The objective of this study was to investigate the effect of hardwood biochar supplementation on fermentation parameters, methane (CH4) production and the ruminal archaeal, bacterial, and fungal microbiota using the in vitro RUSITEC (rumen simulation technique) system. Treatments consisted of a control diet (oaten pasture: maize silage: concentrate, 35:35:30 w/w) and hardwood biochar included at 400 or 800 mg per day (3.6 and 7.2% of substrate DM, respectively), over a 15-day period. Biochar supplementation had no effect (P ≥ 0.37) on pH, effluent (mL/d), total gas (mL/d), dry matter (DM) digestibility or CH4 production (mg/d). The addition of 800 mg biochar per day had the tendency (P = 0.10) to lower the % of CH4 released in fermentation compared to 400 mg/d biochar treatment. However, no effect (P ≥ 0.44) was seen on total VFA, acetate, propionate, butyric, branched-chain VFA, valerate and caproate production and the ratio of acetate to propionate. No effect (P > 0.05) was observed on bacterial, archaeal or fungal community structure. However, biochar supplementation at 800 mg/d decreased the abundance of one Methanomethylophilaceae OTU (19.8-fold, P = 0.046) and one Lactobacillus spp. OTU (31.7-fold, P < 0.01), in comparison to control treatments. Two fungal OTUs classified as Vishniacozyma victoriae (5.4 × 107 increase) and Sporobolomyces ruberrimus (5.4 × 107-fold increase) were more abundant in the 800 mg/d biochar samples. In conclusion, hardwood biochar had no effects on ruminal fermentation characteristics and may potentially lower the concentration of enteric CH4 when included at higher dosages by manipulating ruminal microbiota abundances.
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Affiliation(s)
- Rebecca Teoh
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Eleonora Caro
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
- Department of Agricultural, Forestry and Food Science, University of Turin, Turin, Italy
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Stephen Joseph
- School of Materials Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Sarah J. Meale
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, QLD, Australia
| | - Alex V. Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
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9
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Liu J, Li H, Zhu W, Mao S. Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants. FASEB J 2019; 33:8453-8467. [PMID: 30973755 DOI: 10.1096/fj.201802456r] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Over the years, rumen fluid transplantation (RT) has been successfully applied to treat acute rumen acidosis in ruminants, but how it functions in the ruminal microbial homeostasis and host function remains largely unknown. Here, we investigated the dynamic changes of rumen fermentation and bacterial communities following RT and its beneficial effects on rumen epithelial morphology and function in a sheep model of rumen acidosis. The results showed that RT resulted in dynamic changes in rumen fermentation and increased the concentrations of total volatile fatty acid, acetate, propionate, and butyrate, but it decreased the levels of lactate and LPS in the rumen. Illumina MiSeq Sequencing data showed that RT facilitated rapid rebuilt of ruminal bacterial homeostasis (8 d in control vs. 2 d in RT) from a markedly dysbiotic acidosis state to a healthy level (similar with those of donors). At the genus level, RT increased the relative abundance of unclassified Bacteroidales, unclassified Prevotellaceae, unclassified Ruminococcaceae, and Acetitomaculum. Additionally, RT also accelerated recovery of the predicted metagenomic function of ruminal bacteria. Rumen papillae morphology results showed that RT alleviated the damage of rumen epithelia induced by acute rumen acidosis and increased the length of rumen papillae. Furthermore, real-time PCR results showed that RT modulated mRNA expression of genes related to cytokines and tight junctions in the rumen epithelia. In summary, these results reveal that RT accelerates recovery of rumen fermentation and bacterial homeostasis and modulates rumen epithelial morphology and function for sheep suffering from rumen acidosis.-Liu, J., Li, H., Zhu, W., Mao, S. Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants.
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Affiliation(s)
- Junhua Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongwei Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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10
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Amare T, Goshu G, Tamir B. Flock composition, breeding strategies and farmers' traits of interest evaluation of Wollo highland sheep and their F 1 crosses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:14. [PMID: 29796288 PMCID: PMC5963035 DOI: 10.1186/s40781-018-0173-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/25/2018] [Indexed: 11/29/2022]
Abstract
Background Sheep production is a major component of the livestock sector in Ethiopia. The country owing to the large population of 30.70 million estimated numbers of sheep in the country and out of which about 72.14% are females, and 27.86% are males with diverse genetic resources. The real value of indigenous breeds was often under-estimated mostly due to their poor appearance and relatively low productivity. Developing countries in most cases opt for exotic breeds to increase animal productivity through crossbreeding or breed substitution without properly investigating the production potential of the indigenous breeds. The main objective of the research was to identify sheep flock composition and structure, farmers’ traits of interest and breeding objective of Wollo highland sheep, and their F1 crossbreed progenies. Results Smallholder farmers’ flock synthesized from breeding ewes, breeding rams, pre-weaned ewe lambs, pre-weaned ram lambs, unproductive ewes, castrated and fattened rams, with the percentage coverage of 29.2, 13.3, 15.5, 16.5, 12.4, and 12.5%, respectively. The maximum number of flock size was 289.0 sheep per flock and higher in the third stratum. The off-take rate percentage of the three strata presented as 21.9% in 1st stratum, 12% in the 2nd stratum, and 16.4% in the 3rd stratum and higher off-take rate recorded in the first stratum. Sheep producer’s traits of interest ranked by growth rate (first), body size (second) and marketing value was third rank. Communal breeding (random mating), village based controlled breeding, mixed type and private ram controlled breeding practice were comprised of 39.7, 61.7, 52 and 71.3%, respectively. The percentages of ewes per flock composition were presented as 36.5, 27.1 and 25.5%, respectively in the 3rd stratum, 2nd stratum and 3rd stratum in the order of their importance’s. Conclusion Genetic improvement practices at smallholder sheep producers situation was showing promising outcome with indigenous Washera F1 crossbred lambs and which designated for weaning rate, body size, marketing age, age at first lambing, good temperament and large litter size in the order of their rank. The contemporary breeding practice tendency indicated that, reduced flock size to improve flock productivity via crossbreeding practices.
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Affiliation(s)
- Tadesse Amare
- 1Department of Animal Science, College of Agriculture, Wollo University, POBox 1145, Dessie, Ethiopia.,2Department of Animal Production Studies and College of Veterinary Medicine and Agriculture, Addis Ababa University, POBox 34, Bishoftu, Ethiopia
| | - Gebeyehu Goshu
- 2Department of Animal Production Studies and College of Veterinary Medicine and Agriculture, Addis Ababa University, POBox 34, Bishoftu, Ethiopia
| | - Berhan Tamir
- 2Department of Animal Production Studies and College of Veterinary Medicine and Agriculture, Addis Ababa University, POBox 34, Bishoftu, Ethiopia
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11
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Yang HE, Zotti CA, McKinnon JJ, McAllister TA. Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn. Front Microbiol 2018; 9:718. [PMID: 29692773 PMCID: PMC5902705 DOI: 10.3389/fmicb.2018.00718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
The chemical composition of barley grain can vary among barley varieties (Fibar, Xena, McGwire, and Hilose) and result in different digestion efficiencies in the rumen. It is not known if compositional differences in barley can affect the microbiota involved in the ruminal digestion of barley. The objective of this study was to characterize the in situ rumen degradability and microbiota of four barley grain varieties and to compare these to corn. Three ruminally cannulated heifers were fed a low (60% barley silage, 37% barley grain, and 3% supplement) or high grain (37% barley silage, 60% barley grain, and 3% supplement) diet. One set of bags was used to estimate dry matter (DM), starch and crude protein (CP) degradability. A second set was used to extract DNA from the adherent microbiota and visualize grain after incubation using scanning electron microscopy (SEM). DNA was subjected to amplicon 16S rRNA gene sequencing followed by analysis using QIIME. In the low grain diet, McGwire had the highest effective degradability (ED) of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Fibar, McGwire, and Xena, but the ED of CP was not affected by variety. For the high grain diet, Xena and McGwire had the highest ED of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Xena and Fibar. The ED of protein was highest (P < 0.01) for Xena and McGwire. Although the microbiota did not differ among barley varieties, they did differ from corn and with incubation time. Lactobacilli were dominant members of the mature biofilms associated with corn and barley and were accompanied by a notable increase in the lactic acid utilizing genera, Megasphaera. As none of the cattle exhibited subclinical or clinical acidosis during the study, our results suggest that lactobacilli play a more prominent role in routine starch digestion than presently surmised.
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Affiliation(s)
- Hee E. Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claiton A. Zotti
- Department of Animal Science, Universidade do Oeste de Santa Catarina, Xanxerê, Xanxerê, Brazil
| | - John J. McKinnon
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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12
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Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TJ, Dewhurst RJ, Walker AW, Roehe R, Watson M. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun 2018; 9:870. [PMID: 29491419 PMCID: PMC5830445 DOI: 10.1038/s41467-018-03317-6] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/05/2018] [Indexed: 12/15/2022] Open
Abstract
The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 69,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 913 genomes presented here improves metagenomic read classification by sevenfold against our own data, and by fivefold against other publicly available rumen datasets. Thus, our dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.
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Affiliation(s)
- Robert D Stewart
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | | | - Amanda Warr
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Andrew H Wiser
- Phase Genomics, 4000 Mason Road, Seattle, WA, 98195, USA
| | | | | | - Ivan Liachko
- Phase Genomics, 4000 Mason Road, Seattle, WA, 98195, USA
| | | | | | - Alan W Walker
- The Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Rainer Roehe
- Scotland's Rural College, Edinburgh, EH25 9RG, UK
| | - Mick Watson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK.
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13
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In vitro rumen fermentation of soluble and non-soluble polymeric carbohydrates in relation to ruminal acidosis. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1307-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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14
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Han H, Wang C, Li Y, Yu Z, Xu Q, Li G, Minh TT, Nishino N. Identification of lactic acid bacteria in the feces of dairy cows fed whole crop maize silage to assess the survival of silage bacteria in the gut. Anim Sci J 2017; 89:97-104. [DOI: 10.1111/asj.12896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Hongyan Han
- The Research Center for Laboratory Animal Science College of Life Science Inner Mongolia University Hohhot Inner Mongolia China
| | - Chao Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences Hohhot Inner MongoliaChina
| | - Yanbing Li
- College of Animal Science and Veterinary Medicine Heilongjiang Bayi Agricultural University Daqing HeilongjiangChina
| | - Zhu Yu
- Institute of Grassland Science China Agricultural University BeijingChina
| | - Qingfang Xu
- Department of Grassland Science Shanxi Agricultural University Shanxi Taigu China
| | - Guangpeng Li
- The Research Center for Laboratory Animal Science College of Life Science Inner Mongolia University Hohhot Inner Mongolia China
| | - Tang Thuy Minh
- Department of Animal Science Okayama University Okayama Japan
| | - Naoki Nishino
- Department of Animal Science Okayama University Okayama Japan
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15
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Han H, Ogata Y, Yamamoto Y, Nagao S, Nishino N. Identification of lactic acid bacteria in the rumen and feces of dairy cows fed total mixed ration silage to assess the survival of silage bacteria in the gut. J Dairy Sci 2014; 97:5754-62. [DOI: 10.3168/jds.2014-7968] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/10/2014] [Indexed: 11/19/2022]
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16
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de Aguiar SC, Zeoula LM, do Prado OPP, Arcuri PB, Forano E. Characterization of rumen bacterial strains isolated from enrichments of rumen content in the presence of propolis. World J Microbiol Biotechnol 2014; 30:2917-26. [PMID: 25172217 DOI: 10.1007/s11274-014-1719-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 08/07/2014] [Indexed: 01/20/2023]
Abstract
Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml(-1). C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.
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Affiliation(s)
- Sílvia Cristina de Aguiar
- Departamento de Zootecnia, Universidade Estadual de Maringá, Avenida Colombo 5790, Maringá, PR, 87020-900, Brazil
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Han H, Takase S, Nishino N. Survival of silage lactic acid bacteria in the goat gastrointestinal tract as determined by denaturing gradient gel electrophoresis. Lett Appl Microbiol 2012; 55:384-9. [DOI: 10.1111/j.1472-765x.2012.03305.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa. Int J Syst Evol Microbiol 2011; 61:795-803. [DOI: 10.1099/ijs.0.022954-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Strain A2 is an anaerobic, variably Gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of ‘Olsenella (basonym Atopobium) oviles’. Three phenotypically similar bacterial strains (lac15, lac16 and lac31T) were isolated in concert with Veillonella magna lac18T from the mucosal jejunum of a pig. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strains A2, lac15, lac16 and lac31T formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella–Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31T were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA–DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31T represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31T ( = CCUG 58604T = DSM 22620T = JCM 16156T) as the type strain and A2 ( = CCUG 58212 = DSM 22619 = JCM 16157) as an additionally available reference strain. Also, based on our data, we propose emended descriptions of the genus Olsenella and the species Olsenella uli and Olsenella profusa.
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Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 2008; 8:125. [PMID: 18652685 PMCID: PMC2515157 DOI: 10.1186/1471-2180-8-125] [Citation(s) in RCA: 756] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 07/24/2008] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. RESULTS Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). CONCLUSION Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.
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Affiliation(s)
- Scot E Dowd
- USDA-ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA.
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