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Quirino DF, Marcondes MI, de Oliveira KR, Guimarães SEF, da Silva JS, Suen G, Rossi LE, Cunha CS, Mantovani HC, Rotta PP. Comparison of ruminal microbiota, IL-1β gene variation, and tick incidence between Holstein × Gyr and Holstein heifers in grazing system. Front Microbiol 2024; 15:1132151. [PMID: 38468851 PMCID: PMC10925795 DOI: 10.3389/fmicb.2024.1132151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The variation in bacterial communities among breeds has been previously reported and may be one of the reasons why Holstein × Gyr dairy heifers have better development in grazing systems in tropical conditions. This study aimed to explore the ruminal microbiota composition, the IL-1β gene variation, tick incidence, and blood parameters of Holstein × Gyr (½ Holstein × ½ Gyr) and Holstein heifers grazing intensely managed Guinea grass (Panicum maximum Jacq. cv. Mombaça). Methods Sixteen heifers were divided into two groups consisting of 8 Holstein × Gyr and 8 Holstein heifers. The experimental period was comprised of 3 periods of 21 days. Ruminal samples were taken via the stomach tube technique. The sequencing of the V4 hypervariable region of the 16S rRNA gene was performed using the Illumina MiSeq platform. Counting and collection of ticks were conducted each 21 days. Blood and skeletal muscle tissue biopsies were performed at the end of the experiment. Results Firmicutes were the most abundant phyla present in both breed rumen samples and Bacteroidota showed differences in relative abundance between breed groups, with greater values for Holstein heifers (p < 0.05 with FDR correction). The 10 most abundant unique OTUs identified in each breed included several OTUs of the genus Prevotella. Holstein heifers had a greater tick count and weight (9.8 ticks/animal and 1.6 g/animal, respectively) than Holstein × Gyr (2.56 ticks/animal and 0.4 g/animal, respectively). We found nucleotide substitutions in the IL-1β gene that might be related to adaptation and resistance phenotypes to tick infestation in Holstein × Gyr heifers. Blood concentrations of urea, albumin, insulin-like growth factor 1, triiodothyronine, and thyroxine were greater in Holstein × Gyr than in Holstein heifers. Conclusion Adaptations in Holstein × Gyr heifers such as ruminal microbiota, tick resistance, nucleotide substitutions in IL-1β gene, and hormone concentration suggest a better energy metabolism and thermoregulation resulting in better performance in tropical grazing systems.
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Affiliation(s)
| | | | | | | | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Letícia Elisa Rossi
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila Soares Cunha
- School of Veterinary Medicine and Animal Science, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Polyana Pizzi Rotta
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Yang S, Zheng J, He S, Yuan Z, Wang R, Wu D. Exploring the elevation dynamics of rumen bacterial communities in Barn feeding cattle from 900 to 3,600 meters by full-length 16S sequencing. Front Vet Sci 2023; 10:1169573. [PMID: 37533459 PMCID: PMC10390322 DOI: 10.3389/fvets.2023.1169573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
The diversity and abundance of rumen microorganisms serve as indicators not only of the host's digestive and metabolic capacity but also of its health status. The complex microbial communities in the rumen are influenced to varying degrees by environmental adaptability. In this study, we collected 24 rumen fluid samples from 24 healthy male cattle in three regions of Yunnan, China. Using 16S rRNA amplicon sequencing data analysis, we examined the variations in rumen microorganisms among cattle fed at altitudes of 900 m, 1800 m, and 3,600 m. Altitude-related environmental factors did not surpass phylogeny as the main driving force behind the convergent evolution of yellow cattle rumen microbiome composition. However, they did have an impact on the alpha diversity of the rumen microbiome and the coevolution of the core microbiome. The change in altitude noticeably influenced the diversity and richness of the rumen microbiota, highlighting the environmental effect of altitude. As altitude increased, there was an observed increase in the abundance of Firmicutes and Bacteroidetes, while the abundance of ruminal Proteobacteria and Kiritimatiellaeota decreased. Importantly, at the genus level, the core genus exhibited distinct dynamic changes as altitude increased. Ruminants exhibit the ability to adapt their gut type in accordance with altitude, thereby optimizing energy utilization, especially in high-altitude settings. These discoveries offer valuable insights into the coevolution of host-microbe interactions during ruminant adaptation to various altitudinal environments.
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Affiliation(s)
- Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Jieyi Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Shichun He
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Zaimei Yuan
- Kunming Animal Disease Prevention and Control Center, Kunming, China
| | - Rongjiao Wang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dongwang Wu
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
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3
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Yang S, Zhang G, Yuan Z, He S, Wang R, Zheng J, Mao H, Chai J, Wu D. Exploring the temporal dynamics of rumen bacterial and fungal communities in yaks ( Bos grunniens) from 5 days after birth to adulthood by full-length 16S and 18S rRNA sequencing. Front Vet Sci 2023; 10:1166015. [PMID: 37415968 PMCID: PMC10321131 DOI: 10.3389/fvets.2023.1166015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The rumen of ruminants is inhabited by complex and diverse microorganisms. Young animals are exposed to a variety of microorganisms from their mother and the environment, and a few colonize and survive in their digestive tracts, forming specific microflora as the young animals grow and develop. In this study, we conducted full-length sequencing of bacterial and fungal communities in the rumen of pastured yaks of different ages (from 5 days after birth to adulthood) using amplified sequencing technology. The results showed that the rumen microflora of Zhongdian yaks changed gradually from 5 to 180 days after birth and tended to stabilize at 2 years of age. The rumen of adult yaks was the most suitable for the growth and reproduction of most bacteria. Bactria diversity of the yak rumen increased gradually from 5 days after birth to adulthood. With the growth of yaks, different dominated bacteria were enriched in different groups, but Prevotella remained highly abundant in all groups. The yak rumen at 90 days of age was the most suitable for the growth and reproduction of most fungi, and 90 days of age could be a cut-off point for the distribution of fungal communities. Fungal Thelebolus was the firstly reported in yak rumen and was enriched in the yak rumen of 90 days after birth. The most abundant and balanced fungal genera were found in adult yaks, and most of them were only detected in adult yaks. Our study reported on the rumen bacterial and fungal communities of Zhongdian yaks grazed at different ages and provided insights into the dynamic changes of dominant microflora with yak growth.
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Affiliation(s)
- Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Guangrong Zhang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Zaimei Yuan
- Kunming Animal Disease Prevention And Control Center, Kunming, China
| | - Shichun He
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Rongjiao Wang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Jieyi Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Huaming Mao
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Dongwang Wu
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
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Mahoney-Kurpe SC, Palevich N, Noel SJ, Gagic D, Biggs PJ, Soni P, Reid PM, Koike S, Kobayashi Y, Janssen PH, Attwood GT, Moon CD. Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37170869 DOI: 10.1099/ijsem.0.005831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order 'Christensenellales', were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6-99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order 'Christensenellales'. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.
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Affiliation(s)
- Sam C Mahoney-Kurpe
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nikola Palevich
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Samantha J Noel
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- Present address: Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Dragana Gagic
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Priya Soni
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter M Reid
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yasuo Kobayashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Peter H Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T Attwood
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Christina D Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
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Cunha CS, Marcondes MI, Veloso CM, Mantovani HC, Pereira LGR, Tomich TR, Dill-McFarland KA, Suen G. Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production. J Sci Food Agric 2019; 99:210-218. [PMID: 29851082 DOI: 10.1002/jsfa.9162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Heifers emit more enteric methane (CH4 ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for these pre-production animals. Given its direct role in CH4 production, altering the rumen microbiota is another potential avenue for reducing CH4 production by ruminants. However, to identify effective microbial targets, a better understanding of the rumen microbiota and its relationship to CH4 production across heifer development is needed. RESULTS Here, we investigate the relationship between rumen bacterial, archaeal, and fungal communities as well as CH4 emissions and a number of production traits in prepubertal (PP), pubertal (PB), and pregnant heifers (PG). Overall, PG heifers emitted the most CH4 , followed by PB and PP heifers. The bacterial genus Acetobacter and the archaeal genus Methanobrevibacter were positively associated, while Eubacterium and Methanosphaera were negatively associated with raw CH4 production by heifers. When corrected for dietary intake, both Eubacterium and Methanosphaera remained negatively associated with CH4 production. CONCLUSION We suggest that Eubacterium and Methanosphaera represent likely targets for CH4 mitigation efforts in heifers as they were negatively associated with CH4 production and not significantly associated with production traits. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Camila S Cunha
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcos I Marcondes
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Cristina M Veloso
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Thierry R Tomich
- Brazilian Agricultural Research Corporation, EMBRAPA Dairy Cattle, Juiz de Fora, Brazil
| | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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6
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Abstract
Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.
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Affiliation(s)
- Tamar Zehavi
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Maraike Probst
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Itzhak Mizrahi
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
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7
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Lei Y, Zhang K, Guo M, Li G, Li C, Li B, Yang Y, Chen Y, Wang X. Exploring the Spatial-Temporal Microbiota of Compound Stomachs in a Pre-weaned Goat Model. Front Microbiol 2018; 9:1846. [PMID: 30158908 PMCID: PMC6104157 DOI: 10.3389/fmicb.2018.01846] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/24/2018] [Indexed: 12/16/2022] Open
Abstract
Ruminant animals possess a characteristic four-compartment stomach (rumen, reticulum, omasum, and abomasum) that is specialized for pre-intestinal digestion of plant materials. Of these four compartments, the rumen is the largest. The rumen's diverse microbial community has been well studied. However, the current understanding of microbial profiles in the reticulum, omasum and abomasum are lacking. In the present study, fluid samples from the reticulum, omasum, and abomasum of goats at 3, 7, 14, 21, 28, 42, and 56 days after birth, as well as the negative controls (NC) used for microbial DNA extraction, were subjected to 16S rRNA sequencing. By filtering operational taxonomic units (OTUs) in NC, distinct temporal distributions of microbes were observed in the different compartments, we showed that the OTUs in control samples had a large effect to the samples with low microbial density. In addition, Proteobacteria gradually decreased with age from days 3 to 56 in all three compartments, and the relative abundance of Bacteroidetes increased from 24.15% (Day 3) to 52.03% (Day 56) in abomasum. Network analysis revealed that Prevotellaceae_UGG-03 and Rikenellaceae_RC9 were positively correlated with Prevotella_1, lending support to the well understood fact that cellulose is well digested in compound stomachs prior to the rumen. Pathway analysis revealed that gene expression in abomasum at Day 3 were primarily related to Glycolysis/Gluconeogenesis and Pyruvate metabolism, suggesting that colostrum digestion is the dominant function of the abomasum at an early age. These findings combined with other recent rumen microbiota data show that the microbiome landscape represents three distinct stages in ruminant stomachs. The first stage is to gain access to external microorganisms at Day 0-14, the secondary stage is for microbial transition at Day 14-28, and the third stage is for exogenous and endogenous microbial colonization beyond Day 28 of age. Our results provide insight into microbiota dynamics in ruminant stomachs, and will facilitate efforts for the maintenance of gastrointestinal balance and intervention with starter diets in juvenile ruminants during early development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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Flythe MD, Kagan IA, Wang Y, Narvaez N. Hops ( Humulus lupulus L.) Bitter Acids: Modulation of Rumen Fermentation and Potential As an Alternative Growth Promoter. Front Vet Sci 2017; 4:131. [PMID: 28871284 PMCID: PMC5566628 DOI: 10.3389/fvets.2017.00131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/31/2017] [Indexed: 01/26/2023] Open
Abstract
Antibiotics can improve ruminant growth and efficiency by altering rumen fermentation via selective inhibition of microorganisms. However, antibiotic use is increasingly restricted due to concerns about the spread of antibiotic-resistance. Plant-based antimicrobials are alternatives to antibiotics in animal production. The hops plant (Humulus lupulus L.) produces a range of bioactive secondary metabolites, including antimicrobial prenylated phloroglucinols, which are commonly called alpha- and beta-acids. These latter compounds can be considered phyto-ionophores, phytochemicals with a similar antimicrobial mechanism of action to ionophore antibiotics (e.g., monensin, lasalocid). Like ionophores, the hop beta-acids inhibit rumen bacteria possessing a classical Gram-positive cell envelope. This selective inhibition causes several effects on rumen fermentation that are beneficial to finishing cattle, such as decreased proteolysis, ammonia production, acetate: propionate ratio, and methane production. This article reviews the effects of hops and hop secondary metabolites on rumen fermentation, including the physiological mechanisms on specific rumen microorganisms, and consequences for the ruminant host and ruminant production. Further, we propose that hop beta-acids are useful model natural products for ruminants because of (1) the ionophore-like mechanism of action and spectrum of activity and (2) the literature available on the plant due to its use in brewing.
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Affiliation(s)
- Michael D Flythe
- USDA, Agricultural Research Service, Forage-Animal Production Research Unit, Lexington, KY, United States.,Department of Animal and Food Sciences, University of Kentucky, Lexington, KY, United States
| | - Isabelle A Kagan
- USDA, Agricultural Research Service, Forage-Animal Production Research Unit, Lexington, KY, United States.,Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Yuxi Wang
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Nelmy Narvaez
- SGS Canada Inc., Agricultural Services, Guelph, ON, Canada
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Anderson CL, Schneider CJ, Erickson GE, MacDonald JC, Fernando SC. Rumen bacterial communities can be acclimated faster to high concentrate diets than currently implemented feedlot programs. J Appl Microbiol 2016; 120:588-99. [PMID: 26726754 PMCID: PMC4785609 DOI: 10.1111/jam.13039] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/09/2015] [Accepted: 12/19/2015] [Indexed: 11/29/2022]
Abstract
Aims Recent studies have demonstrated RAMP®, a complete starter feed, to have beneficial effects for animal performance. However, how RAMP may elicit such responses is unknown. To understand if RAMP adaptation results in changes in the rumen bacterial community that can potentially affect animal performance, we investigated the dynamics of rumen bacterial community composition in corn‐adapted and RAMP‐adapted cattle. Methods and Results During gradual acclimation of the rumen bacterial communities, we compared the bacterial community dynamics in corn and RAMP‐adapted using 16S rRNA gene amplicon sequencing. Significant shifts in bacterial populations across diets were identified. The shift in corn‐adapted animals occurred between adaptation step3 and step4, whereas in RAMP‐adapted cattle, the shift occurred between step2 and step3. As the adaptation program progressed, the abundance of OTUs associated with family Prevotellaceae and S24‐7 changed in corn‐adapted animals. In RAMP‐adapted animals, OTUs belonging to family Ruminococcaceae and Lachnospiraceae changed in abundance. Conclusions Rumen bacteria can be acclimated faster to high concentrate diets, such as RAMP, than traditional adaptation programs and the speed of bacterial community acclimation depends on substrate composition. Significance and Impact of the Study These findings may have implications for beef producers to reduce feedlot costs, as less time adapting animals would result in lower feed costs. However, animal feeding behavior patterns and other factors must be considered.
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Affiliation(s)
- C L Anderson
- School of Biological Science, University of Nebraska, Lincoln, NE, USA
| | - C J Schneider
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - G E Erickson
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - J C MacDonald
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - S C Fernando
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
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St-Pierre B, Cersosimo LM, Ishaq SL, Wright ADG. Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animalsr. Front Microbiol 2015; 6:776. [PMID: 26284054 PMCID: PMC4519756 DOI: 10.3389/fmicb.2015.00776] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023] Open
Abstract
In herbivores, enteric methane is a by-product from the digestion of plant biomass by mutualistic gastrointestinal tract (GIT) microbial communities. Methane is a potent greenhouse gas that is not assimilated by the host and is released into the environment where it contributes to climate change. Since enteric methane is exclusively produced by methanogenic archaea, the investigation of mutualistic methanogen communities in the GIT of herbivores has been the subject of ongoing research by a number of research groups. In an effort to uncover trends that would facilitate the development of efficient methane mitigation strategies for livestock species, we have in this review summarized and compared currently available results from published studies on this subject. We also offer our perspectives on the importance of pursuing current research efforts on the sequencing of gut methanogen genomes, as well as investigating their cellular physiology and interactions with other GIT microorganisms.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Brookings SD, USA
| | - Laura M Cersosimo
- Department of Animal and Veterinary Sciences, The University of Vermont, Burlington VT, USA
| | - Suzanne L Ishaq
- Department of Animal and Range Sciences, Montana State University, Bozeman MT, USA
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA
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11
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Hackmann TJ, Firkins JL. Electron transport phosphorylation in rumen butyrivibrios: unprecedented ATP yield for glucose fermentation to butyrate. Front Microbiol 2015; 6:622. [PMID: 26157432 PMCID: PMC4478896 DOI: 10.3389/fmicb.2015.00622] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/08/2015] [Indexed: 12/19/2022] Open
Abstract
From a genomic analysis of rumen butyrivibrios (Butyrivibrio and Pseudobutyrivibrio sp.), we have re-evaluated the contribution of electron transport phosphorylation (ETP) to ATP formation in this group. This group is unique in that most (76%) genomes were predicted to possess genes for both Ech and Rnf transmembrane ion pumps. These pumps act in concert with the NifJ and Bcd-Etf to form a electrochemical potential (ΔμH+ and ΔμNa+), which drives ATP synthesis by ETP. Of the 62 total butyrivibrio genomes currently available from the Hungate 1000 project, all 62 were predicted to possess NifJ, which reduces oxidized ferredoxin (Fdox) during pyruvate conversion to acetyl-CoA. All 62 possessed all subunits of Bcd-Etf, which reduces Fdox and oxidizes reduced NAD during crotonyl-CoA reduction. Additionally, 61 genomes possessed all subunits of the Rnf, which generates ΔμH+ or ΔμNa+ from oxidation of reduced Fd (Fdred) and reduction of oxidized NAD. Further, 47 genomes possessed all six subunits of the Ech, which generates ΔμH+ from oxidation of Fdred. For glucose fermentation to butyrate and H2, the electrochemical potential established should drive synthesis of ∼1.5 ATP by the F0F1-ATP synthase (possessed by all 62 genomes). The total yield is ∼4.5 ATP/glucose after accounting for three ATP formed by classic substrate-level phosphorylation, and it is one the highest yields for any glucose fermentation. The yield was the same when unsaturated fatty acid bonds, not H+, served as the electron acceptor (as during biohydrogenation). Possession of both Ech and Rnf had been previously documented in only a few sulfate-reducers, was rare in other rumen prokaryotic genomes in our analysis, and may confer an energetic advantage to rumen butyrivibrios. This unique energy conservation system might enhance the butyrivibrios’ ability to overcome growth inhibition by unsaturated fatty acids, as postulated herein.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
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12
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Abstract
Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen.
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Affiliation(s)
| | - Jeffrey L. Firkins
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
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13
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Mohammed R, Brink GE, Stevenson DM, Neumann AP, Beauchemin KA, Suen G, Weimer PJ. Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay. Front Microbiol 2014; 5:689. [PMID: 25538699 PMCID: PMC4260508 DOI: 10.3389/fmicb.2014.00689] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/21/2014] [Indexed: 02/01/2023] Open
Abstract
The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-day periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23% of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins.
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Affiliation(s)
- Riazuddin Mohammed
- Lethbridge Research Center, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Geoffrey E. Brink
- US Department of Agriculture, United States Dairy Forage Research Center, Agricultural Research ServiceMadison, WI, USA
| | | | | | - Karen A. Beauchemin
- Lethbridge Research Center, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Garret Suen
- Department of Bacteriology, University of WisconsinMadison, WI, USA
| | - Paul J. Weimer
- US Department of Agriculture, United States Dairy Forage Research Center, Agricultural Research ServiceMadison, WI, USA
- Department of Bacteriology, University of WisconsinMadison, WI, USA
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14
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Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front Microbiol 2014; 5:307. [PMID: 25101058 PMCID: PMC4106096 DOI: 10.3389/fmicb.2014.00307] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023] Open
Abstract
The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.
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Affiliation(s)
- Hailan Piao
- Systems Microbiology and Biotechnology Group, School of Molecular Biosciences, Washington State University Richland, WA, USA
| | - Medora Lachman
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA
| | - Stephanie Malfatti
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division Livermore, CA, USA
| | - Alexander Sczyrba
- Faculty of Technology and Center for Biotechnology, Bielefeld University Bielefeld, Germany
| | - Bernhard Knierim
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Susannah G Tringe
- Prokaryote Super Program, DOE Joint Genome Institute Walnut Creek, CA, USA
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana-Champaign IL, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University Bozeman, MT, USA
| | - Matthias Hess
- Systems Microbiology and Biotechnology Group, School of Molecular Biosciences, Washington State University Richland, WA, USA ; Prokaryote Super Program, DOE Joint Genome Institute Walnut Creek, CA, USA ; Energy and Efficiency Division, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory Richland, WA, USA
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