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Sauers LA, Bassingthwaite T, Sierra-Rivera B, Hampton KJ, Duffield KR, Gore H, Ramirez JL, Sadd BM. Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction. Microbiol Spectr 2024:e0086124. [PMID: 39373496 DOI: 10.1128/spectrum.00861-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/26/2024] [Indexed: 10/08/2024] Open
Abstract
Understanding factors influencing the composition and maintenance of beneficial host-associated microbial communities is central to understanding their ecological, evolutionary, and health consequences for hosts. Host immunity is often implicated as a regulator of these microbiota, but immunity may also play a disruptive role, with responses to infection perturbing beneficial communities. Such effects may be more prominent from innate immune responses, with more rapid-acting and often non-specific components, compared to adaptive responses. We investigated how upregulation of antibacterial immunity in the bumble bee Bombus impatiens affects its core gut microbiota, testing the hypothesis that immunity-induced perturbation impacts the microbiota structure. Freshly emerged adult bees were fed a microbiota inoculum before receiving a non-pathogenic immune stimulation injection. We quantified microbial communities using 16S rRNA amplicon sequencing and targeted quantitative PCR. Coarse community membership shows apparent robustness, but we find that immune stimulation alters the abundance of two core community members, Gilliamella and Snodgrassella. Moreover, a positive association in communities between these bacteria is perturbed following a Gram-negative challenge. The observed changes in the gut microbial community are suggestive of immune response-induced dysbiosis, linking ecological interactions across levels between hosts, their pathogens, and their beneficial gut microbiota. The potential for collateral perturbation of the natural gut microbiota following an innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment depending on the ecological context. IMPORTANCE Our work demonstrates how innate immunity may influence the host-associated microbiota. While previous work has demonstrated the role of adaptive immunity in regulating the microbiota, we show that stimulation of an innate immune response in bumble bees may disrupt the native gut microbial community by shifting individual abundances of some members and pairwise associations. This work builds upon previous work in bumble bees demonstrating factors determining microbe colonization of hosts and microbiota membership, implicating immune response-induced changes as a factor shaping these important gut communities. While some microbiota members appear unaffected, changes in others and the community overall suggests that collateral perturbation of the native gut microbiota upon an innate immune response may serve as an additional selective pressure that shapes the evolution of host innate immunity.
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Affiliation(s)
- Logan A Sauers
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Toby Bassingthwaite
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Bryan Sierra-Rivera
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Kylie J Hampton
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Kristin R Duffield
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Haley Gore
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - José L Ramirez
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
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Davoudkhani M, Rubino F, Creevey CJ, Ahvenjärvi S, Bayat AR, Tapio I, Belanche A, Muñoz-Tamayo R. Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling. PLoS One 2024; 19:e0298930. [PMID: 38507436 PMCID: PMC10954177 DOI: 10.1371/journal.pone.0298930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic models and rumen microbiota data is lacking. The objective of this work was to integrate rumen microbiota time series determined by 16S rRNA gene amplicon sequencing into a dynamic modelling framework to link microbial data to the dynamics of the volatile fatty acids (VFA) production during fermentation. For that, we used the theory of state observers to develop a model that estimates the dynamics of VFA from the data of microbial functional proxies associated with the specific production of each VFA. We determined the microbial proxies using CowPi to infer the functional potential of the rumen microbiota and extrapolate their functional modules from KEGG (Kyoto Encyclopedia of Genes and Genomes). The approach was challenged using data from an in vitro RUSITEC experiment and from an in vivo experiment with four cows. The model performance was evaluated by the coefficient of variation of the root mean square error (CRMSE). For the in vitro case study, the mean CVRMSE were 9.8% for acetate, 14% for butyrate and 14.5% for propionate. For the in vivo case study, the mean CVRMSE were 16.4% for acetate, 15.8% for butyrate and 19.8% for propionate. The mean CVRMSE for the VFA molar fractions were 3.1% for acetate, 3.8% for butyrate and 8.9% for propionate. Ours results show the promising application of state observers integrated with microbiota time series data for predicting rumen microbial metabolism.
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Affiliation(s)
- Mohsen Davoudkhani
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
| | - Francesco Rubino
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Christopher J. Creevey
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Seppo Ahvenjärvi
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ali R. Bayat
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Alejandro Belanche
- Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Zaragoza, Spain
| | - Rafael Muñoz-Tamayo
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
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Li Z, Wang X, Wang W, An R, Wang Y, Ren Q, Xuan J. Benefits of tributyrin on growth performance, gastrointestinal tract development, ruminal bacteria and volatile fatty acid formation of weaned Small-Tailed Han lambs. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 15:187-196. [PMID: 38023378 PMCID: PMC10679854 DOI: 10.1016/j.aninu.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/23/2023] [Accepted: 08/08/2023] [Indexed: 12/01/2023]
Abstract
This study aimed to determine the effects of tributyrin on growth performance, gastrointestinal tract development, ruminal bacteria and volatile fatty acid (VFA) formation. Thirty healthy weaned Small-Tailed Han female lambs at 3 months old with BW 27.5 ± 4.1 kg (mean ± SD) were randomly assigned to five groups of six lambs each, and each group received tributyrin at 0, 0.5, 1.0, 2.0 and 4.0 g/kg in feed. Weights were measured before the start and end of the study. After 15 d adaptation, DMI, feed, faeces and urine were recorded every week. Lambs were sacrificed at d 75. Compared to lambs fed no tributyrin, lambs fed 4.0 g/kg tributyrin had higher average daily BW gain (P = 0.04) and DMI (P < 0.01). Tributyrin reduced nitrogen (P < 0.01), Ca (P < 0.01) and P (P < 0.01) losses derived from faeces and urine. The mostly important, tributyrin increased dorsal sac thickness (P < 0.01), papillae length (P = 0.04) and width (P < 0.01), ventral sac papillae length (P < 0.01) and width (P < 0.01), caudodorsal blind sac thickness (P = 0.02), papillae length (P < 0.01) and width (P < 0.01). Furthermore, tributyrin increased thicknesses of both the duodenum (P < 0.01) and ileum (P = 0.01), and villus heights of the duodenum (P = 0.01), ileum (P < 0.01), jejunum (P < 0.01) and caecum (P = 0.02), but tributyrin decreased duodenal (P < 0.01) and caecal crypt depths (P < 0.01). Tributyrin reduced rumen pH (P < 0.01) while promoting total VFA concentration (P < 0.01). Tributyrin improved the structure of rumen bacteria by enhancing Clostridium (P = 0.04), Butyrivibrio (P < 0.01), Streptococcus (P = 0.04), Prevotella (P = 0.04), Ruminobacter (P = 0.02) and Fibrobacter (P = 0.03). In conclusion, tributyrin could stimulate gastrointestinal tract development by enhancing colonization of rumen VFA-producing bacteria, and dietary supplementation of tributyrin at 4.0 g/kg of DM was recommended for the weaned lambs.
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Affiliation(s)
- Zhiwei Li
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Xueer Wang
- College of Animal Science and Technology, Tarim University, Alae, 843300, China
| | - Wei Wang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Ran An
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Yaxin Wang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Qingchang Ren
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Anhui Science and Technology University, Fengyang, 233100, China
| | - Jingjing Xuan
- School of Finance and Economics, Anhui Science and Technology University, Bengbu, 233030, China
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Świerk S, Przybyło M, Wajsman I, Molik E, Miltko R, Górka P. Effect of increased intake of concentrates and sodium butyrate supplementation on reticulorumen macroanatomy and reticulorumen fermentation in growing rams. Animal 2023; 17:100899. [PMID: 37558584 DOI: 10.1016/j.animal.2023.100899] [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: 04/26/2022] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 08/11/2023] Open
Abstract
Increased ruminal butyrate production is considered to have mostly positive impacts on rumen macro- and microanatomy and its functions. However, excessive ruminal butyrate production may also affect the rumen negatively. Forty-two growing rams were allocated into six treatments and fed a diet with low (22.5% of diet DM; LOW) or high (60% of diet DM; HIGH) inclusion of concentrates in combination with no, low (1.6% of diet DM) or high (3.2% of diet DM) sodium butyrate (SB) supplementation to obtain low or high reticuloruminal (RR) pH with different concentrations of butyrate. Both absolute (L/day) and relative (% of BW) water intake increased linearly with increasing dose of SB (P ≤ 0.02). The RR fluid pH was lower for HIGH compared to LOW treatments (P < 0.01) but was not affected by SB supplementation (P = 0.35). Total short-chain fatty acid concentration, propionate and valerate concentrations in the RR fluid were higher for HIGH compared to LOW treatments (P ≤ 0.01), but were not affected by SB supplementation (P ≥ 0.22). Reticuloruminal butyrate was higher for HIGH compared to LOW treatments and increased linearly with increasing dose of SB (P < 0.01). High concentrate inclusion in the diet (P < 0.01) decreased and SB supplementation tended to (P = 0.10) decrease fibrolytic activity in the RR. Increasing doses of SB linearly decreased acetate, isovalerate and NH3-N concentrations in RR fluid, and RR digesta DM weight (g DM/kg BW; P ≤ 0.02). Relative RR and rumen tissue weights (g/kg BW) were higher for LOW compared to HIGH (P ≤ 0.03) treatments but were not affected by SB inclusion in the diet (P ≥ 0.35). Also, there was no impact of concentrates or SB inclusion in the diet on ruminal epithelium DM weight (mg/cm2), either in the ventral or dorsal sac of the rumen (P ≥ 0.14). Under conditions of the current study, SB supplementation in the diet decreased RR digesta DM concentration and weight, acetate, isovalerate and NH3-N concentration in the RR fluid, and tended to reduce fibrolytic activity in the RR. At least part of this response could be due to increased intake of water, and consequently passage of digesta from the RR to lower regions of the gastrointestinal tract.
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Affiliation(s)
- S Świerk
- Department of Animal Nutrition and Biotechnology, and Fisheries, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - M Przybyło
- Department of Animal Nutrition and Biotechnology, and Fisheries, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - I Wajsman
- Department of Animal Nutrition and Biotechnology, and Fisheries, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - E Molik
- Department of Animal Nutrition and Biotechnology, and Fisheries, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - R Miltko
- The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, ul. Instytucka 3, 05-110 Jabłonna, Poland
| | - P Górka
- Department of Animal Nutrition and Biotechnology, and Fisheries, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
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Huang Q, Chen Y, Wang X, Wei Y, Pan M, Zhao G. Effects of Phlorotannins from Sargassum on In Vitro Rumen Fermentation, Microbiota and Fatty Acid Profile. Animals (Basel) 2023; 13:2854. [PMID: 37760253 PMCID: PMC10525790 DOI: 10.3390/ani13182854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The fatty acid profiles of ruminant-derived products are closely associated with human health. Ruminal microbiota play a vital role in modulating rumen biohydrogenation (BH). The aim of this study was to assess the influence of dietary supplementation with phlorotannins (PTs) extracted from Sargassum on rumen fermentation, fatty acid composition and bacterial communities by an in vitro culture study. The inclusion of PTs in the diet increased dry matter digestibility and gas production, and reduced ammonia-N concentration and pH. PT extract inhibited rumen BH, increasing the content of trans-9 C18:1, cis-9 C18:1, trans-9 and trans-12 C18:2 and reducing C18:0 concentration. 16S rRNA sequencing revealed that PTs caused an obvious change in rumen bacterial communities. The presence of Prevotella decreased while carbohydrate-utilizing bacteria such as Prevotellaceae_UCG-001, Ruminococcus, Selenomonas, Ruminobacter and Fibrobacter increased. Correlation analysis between rumen FA composition and the bacterial microbiome revealed that Prevotellaceae_UCG-001, Anaerovorax, Ruminococcus, Ruminobacter, Fibrobacter, Lachnospiraceae_AC2044_group and Clostridia_UCG-014 might have been involved in the BH process. In conclusion, the results suggest that the inclusion of PTs in the diet improved rumen fermentation and FA composition through modulating the rumen bacterial community.
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Affiliation(s)
- Qianqian Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yuhua Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
| | - Xingxing Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
| | - Yuanhao Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
| | - Min Pan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
| | - Guoqi Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.C.)
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Ma L, Yang Y, Liu W, Bu D. Sodium butyrate supplementation impacts the gastrointestinal bacteria of dairy calves before weaning. Appl Microbiol Biotechnol 2023; 107:3291-3304. [PMID: 37042986 DOI: 10.1007/s00253-023-12485-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 04/13/2023]
Abstract
The objective of this study was to systematically investigate how sodium butyrate (SB) affects the gastrointestinal bacteria in newborn calves at different stages before weaning. Forty female newborn Holstein calves (4-day-old, 40 ± 5 kg of body weight) were randomly divided into four groups; each group was supplemented with four SB doses: 0, 15, 30, and 45 g/day (ten replicates) in SB0, SB15, SB30, and SB45 groups, respectively. SB was fed with milk replacer from day 4 to day 60. Rumen fluid and feces were collected on days 2, 14, 28, 42, and 60 for 16S rRNA high-throughput sequencing. Data were analyzed in a complete randomized design and analyzed on the online platform of Majorbio Cloud Platform. The results showed that SB significantly increased the α-diversity in feces, especially Shannon and Chao indices in SB45 and SB30 at day 60 more than in SB15 (P < 0.05). Additionally, SB significantly enhanced Firmicutes growth from day 2 to 28 and also increased Bacteroides abundance from day 28 to 42 in rumen and feces (P < 0.05). SB also significantly inhibited Proteobacteria abundance in rumen and feces during the study period (P < 0.05). SB also promoted some potential beneficial bacterial abundance, including Prevotella, Lachnospiraceae, Clostridium, Ruminococcus, and Muribaculaceae (P < 0.05). Additionally, Escherichia-Shigella abundance at SB0 was significantly lower than in the other groups (P < 0.05). In conclusion, this study firstly reported a dynamic curve showing of the SB effects on bacteria in calves before weaning. This study provides valuable evidence for the development of the gastrointestinal tract of the calves in the early stage of the life. SB supplementation improved the gastrointestinal health by regulating the bacterial populations. KEY POINTS: • The gastrointestinal tract of calves has been improved after the SB supplementation. • Microbes were the vital influential factor in the development of calves. • Intervention before weaning is an effective strategy for calf health.
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Affiliation(s)
- Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yi Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wenhui Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
- Joint Laboratory On Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR) and World Agroforestry Center (ICRAF), Beijing, 100193, People's Republic of China.
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Cui X, Wang Z, Guo P, Li F, Chang S, Yan T, Zheng H, Hou F. Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season. Microbiol Spectr 2023; 11:e0281622. [PMID: 36809032 PMCID: PMC10100778 DOI: 10.1128/spectrum.02816-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/22/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.
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Affiliation(s)
- Xiongxiong Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhaofeng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Penghui Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fuhou Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tianhai Yan
- Livestock Production Science Branch, Agri-Food and Biosciences Institute, Hillsborough, County Down, United Kingdom
| | - Huiru Zheng
- School of Computing, University of Ulster, Belfast, United Kingdom
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Effect of whole oilseeds in the diet on bacterial diversity in the solid fraction of the ruminal content of steers. Trop Anim Health Prod 2023; 55:32. [PMID: 36602697 DOI: 10.1007/s11250-022-03442-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023]
Abstract
Our hypothesis was that different whole oilseeds included in the diet for steers confined could alter the diversity of rumen bacteria compared to a diet without oilseeds or an exclusively forage diet. It was aimed to evaluate the effects of oilseeds inclusion in the diet on bacterial diversity in the solid fraction of the ruminal content of steers, by gene sequences of the conserved 16S rDNA region. Six crossbred steers castrated males, fitted with ruminal cannula were used in a 6 × 6 Latin square design, using 21-day period. At the start of the experiment, the live weight of the animals averaged 416 ± 9.7 kg (mean ± SD). A total of 2,180,562 16S rDNA sequences were generated for the Bacteria domain by MiSeq sequencing. The bacterial diversity was composed of 24 bacterial phyla, with the most abundant being Firmicutes, Bacteroidetes, and Proteobacteria. Other phyla with less diversity were also identified including Eurychaeota, Tenericutes, SR1 Absconditalbacteria, Synergistetes, Actinobacteria, Saccharibacteria, Elusimicrobia, Cyanobacteria, Verrucomicrobia, Fusobacteria, Lentisphaerae. The similarity in the bacterial community averaged 50% for all the experimental diets. Steers-fed corn silage exhibited a great diversity of bacteria of the Firmicutes phylum. The steers-fed oilseeds in the diet had a great diversity of bacteria from the phylum Bacteroidetes and Proteobacteria. The inclusion of whole oilseeds in the steer diets can alter the rumen bacteria population by up to 50% of total diversity.
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Costa-Roura S, Villalba D, Balcells J, De la Fuente G. First Steps into Ruminal Microbiota Robustness. Animals (Basel) 2022; 12:2366. [PMID: 36139226 PMCID: PMC9495070 DOI: 10.3390/ani12182366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.
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Arce-Cordero JA, Liu T, Ravelo A, Lobo RR, Agustinho BC, Monteiro HF, Jeong KC, Faciola AP. Effects of calcium-magnesium carbonate and calcium-magnesium hydroxide as supplemental sources of magnesium on ruminal microbiome. Transl Anim Sci 2022; 6:txac092. [PMID: 35912064 PMCID: PMC9335223 DOI: 10.1093/tas/txac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Our objective was to evaluate the inclusion of calcium-magnesium carbonate [CaMg(CO3)2] and calcium-magnesium hydroxide [CaMg(OH)4] in corn silage-based diets and their impact on ruminal microbiome. Our previous work showed a lower pH and molar proportion of butyrate from diets supplemented with [CaMg(CO3)2] compared to [CaMg(OH)4]; therefore, we hypothesized that ruminal microbiome would be affected by Mg source. Four continuous culture fermenters were arranged in a 4 × 4 Latin square with the following treatments defined by the supplemental source of Mg: 1) Control (100% MgO, plus sodium sesquicarbonate as a buffer); 2) CO3 [100% CaMg(CO3)2]; 3) OH [100% CaMg(OH)4]; and 4) CO3/OH [50% Mg from CaMg(CO3)2, 50% Mg from CaMg(OH)4]. Diet nutrient concentration was held constant across treatments (16% CP, 30% NDF, 1.66 MCal NEl/kg, 0.67% Ca, and 0.25% Mg). We conducted four fermentation periods of 10 d, with the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 16 solid and 16 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R and SAS to determine treatment effects on taxa relative abundance of liquid and solid fractions. Correlation of butyrate molar proportion with taxa relative abundance was also analyzed. Treatments did not affect alpha and beta diversities or relative abundance of phylum, class and order in either liquid or solid fractions. At the family level, relative abundance of Lachnospiraceae in solid fraction was lower for CO3 and CO3/OH compared to OH and Control (P < 0.01). For genera, abundance of Butyrivibrio (P = 0.01) and Lachnospiraceae ND3007 (P < 0.01) (both from Lachnospiraceae family) was lower and unclassified Ruminococcaceae (P = 0.03) was greater in CO3 than Control and OH in solid fraction; while abundance of Pseudobutyrivibrio (P = 0.10) and Lachnospiraceae FD2005 (P = 0.09) (both from Lachnospiraceae family) and Ruminobacter (P = 0.09) tended to decrease in CO3 compared to Control in liquid fraction. Butyrate molar proportion was negatively correlated to Ruminococcaceae (r = –0.55) in solid fraction and positively correlated to Pseudobutyrivibrio (r = 0.61) and Lachnospiraceae FD2005 (r = 0.61) in liquid. Our results indicate that source of Mg has an impact on bacterial taxa associated with ruminal butyrate synthesis, which is important for epithelial health and fatty acid synthesis.
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Affiliation(s)
- Jose A Arce-Cordero
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
- Escuela de Zootecnia, Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Ting Liu
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Anay Ravelo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Richard R Lobo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Bruna C Agustinho
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Hugo F Monteiro
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kwang C Jeong
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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11
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Khairunisa BH, Susanti D, Loganathan U, Teutsch CD, Campbell BT, Fiske D, Wilkinson CA, Aylward FO, Mukhopadhyay B. Dominant remodelling of cattle rumen microbiome by Schedonorus arundinaceus (tall fescue) KY-31 carrying a fungal endophyte. Access Microbiol 2022; 4:000322. [PMID: 35355877 PMCID: PMC8941964 DOI: 10.1099/acmi.0.000322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Tall fescue KY-31 is an important primary forage for beef cattle. It carries a fungal endophyte that produces ergovaline, the main cause of tall fescue toxicosis that leads to major revenue loss for livestock producers. The MaxQ, an engineered cultivar, hosts an ergovaline nonproducing strain of the fungus and consequently is nontoxic. However, it is less attractive economically. It is not known how rumen microbiome processes these two forages towards nutrient generation and ergovaline transformation. We have analysed the rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period using the 16S rRNA-V4 element as an identifier and found that KY-31 remodelled the microbiome substantially, encompassing both cellulolytic and saccharolytic functions. The effect was not evident at the whole microbiome levels but was identified by analysing the sessile and planktonic fractions separately. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. The abundances of Fibrobacter , which degrades less degradable fibres, and certain cellulolytic Firmicutes such as Pseudobutyrivibrio and Butyrivibrio 2, dropped in the sessile fraction, and these losses were apparently compensated by increased occurrences of Eubacterium and specific Ruminococcaceae and Lachnospiraceae . A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, several KY-31 induced changes, such as the low abundance of Fibrobacter and Butyrivibrio two remained in place, and their substitutes maintained significant presence. The rumen microbiome was distinct from previously reported faecal microbiomes. In summary, KY-31 and MaxQ were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study also identified candidate ergovaline transforming bacteria. It highlighted the importance of analysing sessile and planktonic fractions separately.
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Affiliation(s)
- Bela Haifa Khairunisa
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Present address: Elanco Animal Health, Greenfield, IN, USA
| | - Usha Loganathan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christopher D Teutsch
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
- Present address: University of Kentucky Research and Education Center, Princeton, KY, USA
| | - Brian T Campbell
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
- Present address: Archer Daniels Midland Company, Decatur, IL, USA
| | - David Fiske
- Shennandoah Valley Agricultural Research and Extension Center, Virginia Tech, Raphine, VA, 24472, USA
| | - Carol A Wilkinson
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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12
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Corrêa PS, Jimenez CR, Mendes LW, Rymer C, Ray P, Gerdes L, da Silva VO, De Nadai Fernandes EA, Abdalla AL, Louvandini H. Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems. Front Microbiol 2021; 12:768480. [PMID: 34956130 PMCID: PMC8692951 DOI: 10.3389/fmicb.2021.768480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Caroline Rymer
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Luciana Gerdes
- Reference Laboratory on Classification and Evaluation of Animal Products, Institute of Zootechnics, Nova Odessa, Brazil
| | - Vagner Ovani da Silva
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
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13
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Karoor V, Strassheim D, Sullivan T, Verin A, Umapathy NS, Dempsey EC, Frank DN, Stenmark KR, Gerasimovskaya E. The Short-Chain Fatty Acid Butyrate Attenuates Pulmonary Vascular Remodeling and Inflammation in Hypoxia-Induced Pulmonary Hypertension. Int J Mol Sci 2021; 22:9916. [PMID: 34576081 PMCID: PMC8467617 DOI: 10.3390/ijms22189916] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/01/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Pulmonary hypertension (PH) is a progressive cardiovascular disorder in which local vascular inflammation leads to increased pulmonary vascular remodeling and ultimately to right heart failure. The HDAC inhibitor butyrate, a product of microbial fermentation, is protective in inflammatory intestinal diseases, but little is known regarding its effect on extraintestinal diseases, such as PH. In this study, we tested the hypothesis that butyrate is protective in a Sprague-Dawley (SD) rat model of hypoxic PH. Treatment with butyrate (220 mg/kg intake) prevented hypoxia-induced right ventricular hypertrophy (RVH), hypoxia-induced increases in right ventricular systolic pressure (RVSP), pulmonary vascular remodeling, and permeability. A reversal effect of butyrate (2200 mg/kg intake) was observed on elevated RVH. Butyrate treatment also increased the acetylation of histone H3, 25-34 kDa, and 34-50 kDa proteins in the total lung lysates of butyrate-treated animals. In addition, butyrate decreased hypoxia-induced accumulation of alveolar (mostly CD68+) and interstitial (CD68+ and CD163+) lung macrophages. Analysis of cytokine profiles in lung tissue lysates showed a hypoxia-induced upregulation of TIMP-1, CINC-1, and Fractalkine and downregulation of soluble ICAM (sICAM). The expression of Fractalkine and VEGFα, but not CINC-1, TIMP-1, and sICAM was downregulated by butyrate. In rat microvascular endothelial cells (RMVEC), butyrate (1 mM, 2 and 24 h) exhibited a protective effect against TNFα- and LPS-induced barrier disruption. Butyrate (1 mM, 24 h) also upregulated tight junctional proteins (occludin, cingulin, claudin-1) and increased the acetylation of histone H3 but not α-tubulin. These findings provide evidence of the protective effect of butyrate on hypoxic PH and suggest its potential use as a complementary treatment for PH and other cardiovascular diseases.
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Affiliation(s)
- Vijaya Karoor
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
| | - Derek Strassheim
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
| | - Timothy Sullivan
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
| | - Alexander Verin
- Vascular Biology Center, Augusta University, Augusta, GA 30912, USA; (A.V.); (N.S.U.)
| | - Nagavedi S. Umapathy
- Vascular Biology Center, Augusta University, Augusta, GA 30912, USA; (A.V.); (N.S.U.)
- Center for Blood Disorders, Augusta University, Augusta, GA 30912, USA
| | - Edward C. Dempsey
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
- Rocky Mountain Regional VA Center, Aurora, CO 80045, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Denver, Denver, CO 80204, USA;
| | - Kurt R. Stenmark
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
- Division of Critical Care Medicine, Department of Pediatrics, University of Colorado Denver, Denver, CO 80204, USA
| | - Evgenia Gerasimovskaya
- Department of Medicine Cardiovascular and Pulmonary Research Laboratory, University of Colorado Denver, Denver, CO 80204, USA; (V.K.); (D.S.); (T.S.); (E.C.D.); (K.R.S.)
- Division of Critical Care Medicine, Department of Pediatrics, University of Colorado Denver, Denver, CO 80204, USA
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14
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Matthews C, Cotter PD, O’ Mahony J. MAP, Johne's disease and the microbiome; current knowledge and future considerations. Anim Microbiome 2021; 3:34. [PMID: 33962690 PMCID: PMC8105914 DOI: 10.1186/s42523-021-00089-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.
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Affiliation(s)
- Chloe Matthews
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
| | - Paul D. Cotter
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Jim O’ Mahony
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
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15
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Islam M, Kim SH, Son AR, Ramos SC, Jeong CD, Yu Z, Kang SH, Cho YI, Lee SS, Cho KK, Lee SS. Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration. Animals (Basel) 2021; 11:1184. [PMID: 33924248 PMCID: PMC8074768 DOI: 10.3390/ani11041184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 01/16/2023] Open
Abstract
Seasonal effects on rumen microbiome and enteric methane (CH4) emissions are poorly documented. In this study, 6 Holstein and 6 Jersey steers were fed the same total mixed ration diet during winter, spring, and summer seasons under a 2 × 3 factorial arrangement for 30 days per season. The dry matter intake (DMI), rumen fermentation characteristics, enteric CH4 emissions and rumen microbiota were analyzed. Holstein had higher total DMI than Jersey steers regardless of season. However, Holstein steers had the lowest metabolic DMI during summer, while Jersey steers had the lowest total DMI during winter. Jersey steers had higher CH4 yields and intensities than Holstein steers regardless of season. The pH was decreased, while ammonia nitrogen concentration was increased in summer regardless of breed. Total volatile fatty acids concentration and propionate proportions were the highest in winter, while acetate and butyrate proportion were the highest in spring and in summer, respectively, regardless of breed. Moreover, Holstein steers produced a higher proportion of propionate, while Jersey steers produced a higher proportion of butyrate regardless of season. Metataxonomic analysis of rumen microbiota showed that operational taxonomic units and Chao 1 estimates were lower and highly unstable during summer, while winter had the lowest Shannon diversity. Beta diversity analysis suggested that the overall rumen microbiota was shifted according to seasonal changes in both breeds. In winter, the rumen microbiota was dominated by Carnobacterium jeotgali and Ruminococcus bromii, while in summer, Paludibacter propionicigenes was predominant. In Jersey steers, Capnocytophaga cynodegmi, Barnesiella viscericola and Flintibacter butyricus were predominant, whereas in Holstein steers, Succinivibrio dextrinosolvens and Gilliamella bombicola were predominant. Overall results suggest that seasonal changes alter rumen microbiota and fermentation characteristics of both breeds; however, CH4 emissions from steers were significantly influenced by breeds, not by seasons.
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Affiliation(s)
- Mahfuzul Islam
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
- Department of Microbiology and Parasitology, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Seon-Ho Kim
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
| | - A-Rang Son
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
| | - Sonny C. Ramos
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
| | - Chang-Dae Jeong
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
| | - Seung Ha Kang
- Faculty of Medicine, Diamantina Institute, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Yong-Il Cho
- Animal Disease and Diagnostic Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea;
| | - Sung-Sill Lee
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju 52828, Korea;
| | - Kwang-Keun Cho
- Department of Animal Resources Technology, Gyeongnam National University of Science and Technology, Jinju 52725, Korea;
| | - Sang-Suk Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.I.); (S.-H.K.); (A-R.S.); (S.C.R.); (C.-D.J.)
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16
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Corrêa PS, Mendes LW, Lemos LN, Crouzoulon P, Niderkorn V, Hoste H, Costa-Júnior LM, Tsai SM, Faciola AP, Abdalla AL, Louvandini H. Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes. FEMS Microbiol Ecol 2020; 96:5735434. [PMID: 32053145 DOI: 10.1093/femsec/fiaa024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
This study was carried out to evaluate the effects of tannin supplementation on ruminal microbiota of sixteen lambs infected and non-infected with Haemonchus contortus and Trichostrongylus colubriformis. Animals were fed with hay, concentrate and supplemented with Acacia mearnsii (A. mearnsii). The animals were divided into four treatments: two control groups without infection, either receiving A. mearnsii (C+) or not (C-), and two infected groups, one with A. mearnsii (I+) and another without A. mearnsii (I-). Ruminal short-chain fatty acids (SCFA) and metagenome sequencing of ruminal microbiota were used to evaluate the effect of tannin and infection on ruminal microbiome. For SCFA, differences were observed only with A. mearnsii. Total SCFA and acetate molar percentage were decreased in C+ and I+ (P<0.05). Butyrate, valerate and isovalerate were higher in lambs that received A. mearnsii in the diet (P<0.05). The infection changed the microbiome structure and decreased the abundance of butyrate-producing microorganisms. In addition, A. mearnsii supplementation also affected the structure the microbial community, increasing the diversity and abundance of the butyrate-producing and probiotics bacteria, amino acid metabolic pathways, purine, pyrimidine and sphingolipid metabolism. Together, our findings indicate that A. mearnsii supplementation modulates important groups related to nitrogen, amino acid, purine and pyrimidine metabolism, in rumen microbiome, affected by gastrointestinal nematodes infection in lambs.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Department of Animal Sciences, University of Florida, Gainesville 32611, United States
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Leandro Nascimento Lemos
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Pierre Crouzoulon
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Vincent Niderkorn
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Hervé Hoste
- INRAE, UMR, Chemin des Capelles - BP 87614 - 31 076 - Toulouse, France
| | - Livio Martins Costa-Júnior
- Biological and Health Center, Federal University of Maranhao, Avenida dos Portugueses, 1966 - Vila Bacanga, 65080-805, São Luís - Maranhao, Brazil
| | - Siu Mui Tsai
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Department of Animal Sciences, University of Florida, Gainesville 32611, United States
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17
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Kobayashi R, Nagaoka K, Nishimura N, Koike S, Takahashi E, Niimi K, Murase H, Kinjo T, Tsukahara T, Inoue R. Comparison of the fecal microbiota of two monogastric herbivorous and five omnivorous mammals. Anim Sci J 2020; 91:e13366. [PMID: 32285557 PMCID: PMC7216987 DOI: 10.1111/asj.13366] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Fecal microbiota in seven different monogastric animal species, elephant, horse, human, marmoset, mouse, pig and, rat were compared using the same analytical protocol of 16S rRNA metagenome. Fecal microbiota in herbivores showed higher alpha diversity than omnivores except for pigs. Additionally, principal coordinate analysis based on weighted UniFrac distance demonstrated that herbivores and pigs clustered together, whereas other animal species were separately aggregated. In view of butyrate- and lactate-producing bacteria, predominant genera were different depending on animal species. For example, the abundance of Faecalibacterium, a known butyrate producer, was 8.02% ± 3.22% in human while it was less than 1% in other animal species. Additionally, Bifidobacterium was a predominant lactate producer in human and marmoset, while it was rarely detected in other omnivores. The abundance of lactate-producing bacteria in herbivores was notably lower than omnivores. On the other hand, herbivores as well as pig possess Fibrobacter, a cellulolytic bacterium. This study demonstrated that fecal microbiota in herbivorous animals is similar, sharing some common features such as higher alpha diversity and higher abundance of cellulolytic bacterium. On the other hand, omnivorous animals seem to possess unique fecal microbiota. It is of interest that pigs, although omnivore, have fecal microbiota showing some common features with herbivores.
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Affiliation(s)
- Rana Kobayashi
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Naomichi Nishimura
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Eiki Takahashi
- Research Resources Division, RIKEN Center for Brain Science, Wako, Japan
| | - Kimie Niimi
- Research Resources Division, RIKEN Center for Brain Science, Wako, Japan
| | - Harutaka Murase
- Japan Racing Association, Hidaka Training and Research Center, Urakawa-cho, Japan
| | - Teruo Kinjo
- Okinawa Zoo and Museum, Okinawa Zoo Animal Hospital, Okinawa, Japan
| | | | - Ryo Inoue
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
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18
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Fan Q, Wanapat M, Hou F. Chemical Composition of Milk and Rumen Microbiome Diversity of Yak, Impacting by Herbage Grown at Different Phenological Periods on the Qinghai-Tibet Plateau. Animals (Basel) 2020; 10:ani10061030. [PMID: 32545764 PMCID: PMC7341253 DOI: 10.3390/ani10061030] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Native values of herbage grown at different phenological periods and rumen diversity of microbial population would impact rumen fermentation end-products and milk compositions of yaks (Bos grunniens). The research was conducted in 12 female yaks grazing on the Qinghai-Tibet Plateau (QTP). The results revealed that the phenological periods (VS: Vegetative stage, May; BS: Bloom stage, August; SS: Senescent stage, December) significantly influenced the nutritive values of herbages, microbial diversity and, as a consequence affected on the yak milk yield and compositions. We concluded that the observed differences resulted from the combined effects of phenological periods, herbage composition, and herbage availability. The findings of this study were of great value and useful for current understandings and onwards to conduct further research and for possible practical implementation for the yak cows grazing on QTP. Abstract To estimate how native herbage of three different phenological periods modify rumen performance and milk quality of yak grazing alpine meadow. In this study, milk composition and the diversity of the rumen microbial community were measured in 12 full-grazing female yaks on the Qinghai-Tibet Plateau (QTP). The nutrient composition of three phenological periods was determined: Vegetative stage (VS), bloom stage (BS), and senescent stage (SS). High-throughput sequencing of the bacterial 16S rRNA gene was used. The results showed that crude protein (CP) content of herbage in BS was higher than that in vs. and SS (p < 0.05), and neutral detergent fiber (NDF) content of herbage in SS was higher than that in vs. and BS (p < 0.05). Milk solids and fat contents were higher in the vs. and SS than in BS (p < 0.05). However, milk protein content was higher for the vs. and BS than those for SS (p < 0.05). The total volatile fatty acid (VFA), acetate, and propionate concentrations were higher in vs. and BS than in SS (p < 0.05). The community richness estimates (Chao1 estimator) of vs. were higher than that in BS and the SS (p < 0.05). The diversity indices (Shannon index) of the BS were higher than that vs. and the SS (p < 0.05). Spearman correlation analysis between the milk composition, ruminal fermentation parameters, and the relative abundances of the rumen bacteria showed that milk protein content, total VFA, acetate, and propionate concentrations were positively correlated with the relative abundances of the genera Desulfovibrio, Prevotella_1, and Butyrivibrio_2 and was negatively correlated with Olsenella, Ruminococcaceae_UCG.010, and Rikenellaceae_RC9_gut_group abundances. Collectively, the results revealed that there were significant differences in nutrient composition of herbage, chemical composition of yak milk, and microbial diversity in rumen at different phenological stages. The correlations between ruminal fermentation parameters, chemical constituents of yak milk, and some genera of ruminal bacteria might be indicative that the ruminal fermentation parameters and chemical constituents of yak milk are strongly influenced by the rumen bacterial community composition.
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Affiliation(s)
- Qingshan Fan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu, China;
| | - Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu, China;
- Correspondence:
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Vaidya JD, van Gastelen S, Smidt H, Plugge CM, Edwards JE. Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets. PLoS One 2020; 15:e0229887. [PMID: 32119709 PMCID: PMC7051090 DOI: 10.1371/journal.pone.0229887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The objective of the present study was to characterize the rumen bacterial and archaeal communities in dairy cows fed different ratios of maize silage (MS) and grass silage (GS), and place the findings in the context of ruminal fermentation as well as previously reported methane (CH4) emissions. Rumen fluid from 12 rumen cannulated dairy cows was collected after 10 and 17 days of feeding one of four diets, all of which had the same roughage to concentrate ratio of 80:20 based on dry matter (DM). Roughage in the four diets (GS100, GS0, GS67, GS33) consisted of either 1000 g/kg DM GS (GS100), 1000 g/kg DM MS (GS0), or a mixture of both silages in different proportions [667 g/kg DM GS and 333 g/kg DM MS (GS67); 333 g/kg DM GS and 677 g/kg DM MS (GS33)]. Total volatile fatty acid (VFA) concentrations and the molar proportions of the ruminal VFA were not affected by diet. Only the molar proportion of isovalerate was affected by time, being lower on day 17 than on day 10. Bacterial and archaeal concentrations were not affected by diet but increased from day 10 to day 17. The bacterial community composition was affected by diet, time and diet × time, whereas the archaeal community composition was only affected by diet. Several bacterial and archaeal genus level groups were associated with diet, but not with time. Analysis indicated the increased use of hydrogen by succinate and lactate producing bacteria is likely to at least partially explain the previously reported lower CH4 emissions from MS fed dairy cows. Furthermore, time had a significant effect on both bacterial and archaeal concentrations, and also bacterial community composition. This indicates that the rumen microbiota had not stabilized after 10 days of feeding the experimental diets.
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Affiliation(s)
- Jueeli D. Vaidya
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sanne van Gastelen
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- * E-mail:
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Joan E. Edwards
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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20
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Górka P, Sliwinski B, Flaga J, Olszewski J, Nawrocka P, Sobkowiak K, Miltko R, Godlewski MM, Zabielski R, Kowalski ZM. Effect of exogenous butyrate on the gastrointestinal tract of sheep. II. Hydrolytic activity in the rumen and structure and function of the small intestine. J Anim Sci 2019; 96:5325-5335. [PMID: 30321354 DOI: 10.1093/jas/sky368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/03/2018] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to determine the effect of exogenous butyrate on the activity of carbohydrate-digesting enzymes in the reticuloruminal digesta and structure and selected functions of the small intestine in sheep. Eighteen rams (30.8 ± 2.1 kg; 12 to 15 mo of age) were fed for 14 d a diet without (CTRL) or with sodium butyrate (BUT; 36 g/kg of offered DM). Butyrate concentration in the reticuloruminal fluid and proximal small intestinal digesta was greater for BUT compared with CTRL (P ≤ 0.05). Amylolytic activity was greater, whereas cellulolytic and xylanolytic activity in the reticuloruminal digesta was less for BUT compared with CTRL (P ≤ 0.04). Relative to BW, small intestinal tissue mass and small intestine length did not differ between treatments (P ≥ 0.15); however, absolute length of the small intestine was greater for BUT compared with CTRL (P = 0.04). In the duodenum, crypt depth tended (P = 0.10) to be greater, whereas in the ileum, crypt depth and muscularis thickness tended (P = 0.10) to be less for BUT compared with CTRL. Mitosis-to-apoptosis ratio in the proximal jejunum was greater for CTRL compared with BUT (P = 0.02). Expression of G-protein-coupled receptor 43 mRNA in the duodenal epithelium was greater for BUT compared with CTRL (P < 0.01). On the other hand, peptide transporter 1 mRNA expression in the distal sections of the small intestine, as well as activity of aminopeptidase A and dipeptidylpeptidase IV, were greater for CTRL (P ≤ 0.05). In summary, exogenous butyrate supplementation in feed affects hydrolytic activity in the rumen, and increased butyrate flow out of the reticulorumen affects both proximal and distal sections of the small intestine in sheep.
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Affiliation(s)
- Pawel Górka
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza, Krakow, Poland
| | - Bogdan Sliwinski
- Department of Animal Nutrition and Feed Science, National Research Institute of Animal Production, ul. Krakowska, Balice, Poland
| | - Jadwiga Flaga
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza, Krakow, Poland
| | - Jaroslaw Olszewski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Paulina Nawrocka
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza, Krakow, Poland
| | - Klaudyna Sobkowiak
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza, Krakow, Poland
| | - Renata Miltko
- The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, ul. Instytucka, Jablonna, Poland
| | - Michal M Godlewski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Romuald Zabielski
- Department of Large Animal Diseases with Clinic, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Zygmunt M Kowalski
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza, Krakow, Poland
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Abstract
Identification of differentially expressed genes has been a high priority task of downstream analyses to further advances in biomedical research. Investigators have been faced with an array of issues in dealing with more complicated experiments and metadata, including batch effects, normalization, temporal dynamics (temporally differential expression), and isoform diversity (isoform-level quantification and differential splicing events). To date, there are currently no standard approaches to precisely and efficiently analyze these moderate or large-scale experimental designs, especially with combined metadata. In this report, we propose comprehensive analytical pipelines to precisely characterize temporal dynamics in differential expression of genes and other genomic features, i.e., the variability of transcripts, isoforms and exons, by controlling batch effects and other nuisance factors that could have significant confounding effects on the main effects of interest in comparative models and may result in misleading interpretations.
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22
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Effects of Saccharomyces Cerevisiae Fermentation Products on the Microbial Community throughout the Gastrointestinal Tract of Calves. Animals (Basel) 2018; 9:ani9010004. [PMID: 30577678 PMCID: PMC6356610 DOI: 10.3390/ani9010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/01/2018] [Accepted: 12/13/2018] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Saccharomyces cerevisiae fermentation products (SCFP) are widely used for dairy cows and have been suggested to improve calf performance and health. However, the changes in microbial community along the gut in calves supplemented with SCFP have not been investigated extensively. This manuscript exhibited that calves supplemented with Saccharomyces cerevisiae fermentation products changed the microbial community of GIT and stimulated fibrolytic bacteria (Lachnospiraceae and Ruminococcaceae) colonization in early rumen and large intestine, respectively. Those alternations of microbiota in GIT might explain how SCFP works in calves. Abstract The effect of Saccharomyces cerevisiae fermentation products (SCFP) on improving growth and health of calves could be attributed to the ability of SCFP to modulate the microbiota in the gastrointestinal tract (GIT). However, the changes in microbial community along the gut in calves supplemented with SCFP have not been investigated extensively. The aims of this study were to investigate the effect of SCFP on microbial communities in each sites of GIT using high-throughput sequencing technique. Fifteen Holstein male calves were used and randomly assigned to 1 of the 3 treatments including a calf starter containing 0 (Control, CON), 0.5 (SCFP1) or 1% SCFP (SCFP2, Original XPC, Diamond V, Cedar Rapids, IA, USA) of dry matter from day 4 to 56. The supplemented calves were fed with an additional 1 g/d SCFP (SmartCare, Diamond V, Cedar Rapids, IA, USA) in milk from day 2 to 30. Rumen fluid was sampled at day 28 of age via esophageal tube. All calves were slaughtered and gastrointestinal samples collected on day 56. Inclusion of SCFP increased the microbial species richness in the large intestine. The SCFP also affected the bacterial community at an early age in the rumen and later in rectum microbiota. Supplementation of SCFP stimulated colonization by fibrolytic bacteria (Lachnospiraceae and Ruminococcaceae) in rumen and large intestine, respectively. No differences were found between SCFP1 and SCFP2. This is the first study to analyze the effect of SCFP on bacterial community of the GIT microbiota in calves. The results provide the basic bacterial community information, which helps us understand the mechanism of action of SCFP for improving the health and performance of pre-weaning calf.
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23
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O'Hara E, Kelly A, McCabe MS, Kenny DA, Guan LL, Waters SM. Effect of a butyrate-fortified milk replacer on gastrointestinal microbiota and products of fermentation in artificially reared dairy calves at weaning. Sci Rep 2018; 8:14901. [PMID: 30297834 PMCID: PMC6175921 DOI: 10.1038/s41598-018-33122-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022] Open
Abstract
Enrichment of calf diets with exogenous butyrate has shown promise as a promotor of calf growth and intestinal development. However, the impact of dietary derived butyrate on the gut microbiota and their potential role, in turn, as mediators of its effect on calf growth and development is not known. Here, the effects of butyrate supplementation on rumen and hindgut microbiota and fermentation profiles were assessed in 16 Holstein-Friesian bull calves randomly assigned to one of two groups: Control (CON) fed conventional milk replacer or Sodium-Butyrate (SB – added to milk replacer) from days 7 to 56 of life. In the colon, total short chain fatty acid (SCFA), propionate and acetate concentrations were increased by SB (P < 0.05). 16S rRNA gene amplicon sequencing showed cecal abundance of butyrate producers Butyrivibrio and Shuttleworthia were decreased by SB (P < 0.05), while that of the propionate producer Phascolarctobacterium was higher (P < 0.05). Mogibacterium is associated with impaired gut health and was reduced in the cecum of SB calves (P < 0.05). These data show that the beneficial effects of SB on growth and performance occur in tandem with changes in the abundance of important SCFA producing and health-associated bacteria in the hindgut in milk-fed calves.
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Affiliation(s)
- Eóin O'Hara
- Teagasc Animal & Bioscience Research Department, Teagasc Grange, Dunsany, Co Meath, Ireland. .,Faculty of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Alan Kelly
- UCD School of Agricultural and Food Science, University College Dublin, Belfield, Co, Dublin, Ireland
| | - Matthew S McCabe
- Teagasc Animal & Bioscience Research Department, Teagasc Grange, Dunsany, Co Meath, Ireland
| | - David A Kenny
- Teagasc Animal & Bioscience Research Department, Teagasc Grange, Dunsany, Co Meath, Ireland.,UCD School of Agricultural and Food Science, University College Dublin, Belfield, Co, Dublin, Ireland
| | - Le Luo Guan
- Faculty of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Sinéad M Waters
- Teagasc Animal & Bioscience Research Department, Teagasc Grange, Dunsany, Co Meath, Ireland.
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24
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Latham EA, Weldon KK, Wickersham TA, Coverdale JA, Pinchak WE. Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein. J Anim Sci 2018; 96:1032-1044. [PMID: 29617868 DOI: 10.1093/jas/sky023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/13/2018] [Indexed: 02/01/2023] Open
Abstract
Bos indicus typically perform better than Bos taurus when consuming a low-quality diet; however, the response to supplementation is generally greater in B. taurus. The underlying mechanisms supporting these responses have not been fully elucidated. Characterization of differences in rumen prokaryotic populations and their functional role in the two subspecies may provide additional insight. Ten cannulated steers (5 Angus and 5 Brahman) were used in concurrent 5 × 5 Latin squares. Animals were offered ad libitum access to rice straw (4.7% CP). Treatments consisted of an unsupplemented control diet and two levels (50 or 120 mg N/kg BW) of isonitrogenous supplements (30% CP), that were either high (H; 74%) or low (L; 26%) in undegradable intake protein. Rumen samples were collected at 0 and 4 h postfeeding and separated into liquid and solid fractions. Rumen bacterial taxa were sequenced utilizing a Roche 454 platform based on the 16s rRNA gene. At 97% sequence similarity, 97,826 operational taxonomic units were identified, which included 24 phyla, 108 families, and 255 genera. Analysis included SAS PROC mixed model, QIIME, and PICRUSt. Across all samples, Bacteroidetes and Firmicutes accounted for 65% and 28% of total bacterial abundance, respectively. The families Prevotellaceae (P = 0.05) and Ruminococcaceae (P = 0.004) and the genera Prevotellaceae (family; P = 0.003) within the phyla Bacteroidetes differed significantly in relative abundance with added protein when compared to the control. Consistent differences in the relative abundance of family and genus taxa between B. indicus and B. taurus suggest roles the symbiotic rumen microbiome may have in the capacity of B. indicus to utilize low-quality forage over a range of supplement types and levels including (Prevotella, Ruminococcus [family], Sphingobacteriaceae [family], Bacteroidales [order], Pontibacter, Bacteroides, Succiclasticum, Barnesiella, and Xylanibacter). Overall bacterial community diversity differences across parameters were limited. Rice straw is recalcitrant to bacterial digestion because of high levels of silica in the epidermis making this straw more resistant to bacterial attachment. Thus, this analysis represents the bacterial diversity and function of the rumen under conditions depleted CP, recalcitrant fiber matrix and restricted digestibility which appear to limit the microbial population to those capable of attaching and digesting complexed structural carbohydrates, resulting in reduced plasticity, and more evenness in diversity across parameters.
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Affiliation(s)
- E A Latham
- Texas A&M University, College Station, TX.,Texas A&M Agrilife Research, Vernon, TX
| | - K K Weldon
- Texas A&M University, College Station, TX
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25
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Wirth R, Kádár G, Kakuk B, Maróti G, Bagi Z, Szilágyi Á, Rákhely G, Horváth J, Kovács KL. The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing. Front Microbiol 2018; 9:2285. [PMID: 30319585 PMCID: PMC6165872 DOI: 10.3389/fmicb.2018.02285] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022] Open
Abstract
The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Balázs Kakuk
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - József Horváth
- Faculty of Agriculture, University of Szeged, Hódmezövásárhely, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
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26
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Elliott CL, Edwards JE, Wilkinson TJ, Allison GG, McCaffrey K, Scott MB, Rees-Stevens P, Kingston-Smith AH, Huws SA. Using 'Omic Approaches to Compare Temporal Bacterial Colonization of Lolium perenne, Lotus corniculatus, and Trifolium pratense in the Rumen. Front Microbiol 2018; 9:2184. [PMID: 30283417 PMCID: PMC6156263 DOI: 10.3389/fmicb.2018.02184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.
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Affiliation(s)
- Christopher L Elliott
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Toby J Wilkinson
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Gordon G Allison
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Kayleigh McCaffrey
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Mark B Scott
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Pauline Rees-Stevens
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Sharon A Huws
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, United Kingdom
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27
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Ma N, Abaker JA, Bilal MS, Dai H, Shen X. Sodium butyrate improves antioxidant stability in sub-acute ruminal acidosis in dairy goats. BMC Vet Res 2018; 14:275. [PMID: 30200953 PMCID: PMC6131738 DOI: 10.1186/s12917-018-1591-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/22/2018] [Indexed: 01/10/2023] Open
Abstract
Background Currently, little is known about the effect of sodium butyrate (NaB) on oxidative stress following grain-induced sub-acute ruminal acidosis in dairy goats. In the present study, 18 lactating dairy goats implanted with a ruminal cannula and permanent indwelling catheters in the portal and hepatic veins were randomly allocated into 3 treatment groups over 20 weeks: low grain (LG, 40% grain; n = 6), high grain (HG, 60% grain; n = 6) and high grain with sodium butyrate (HG + NaB, 60% grain + NaB; n = 6). Results When added to the HG diet, NaB increased the mean ruminal pH and reduced the levels of ruminal, portal and hepatic LPS; Additionally, we observed an increase in SOD1, SOD2, SOD3, GPX1 and CAT mRNA expression, increased levels of TSOD and CAT enzyme activity as well as increased total antioxidant capacity (T-AOC) and decreased malondialdehyde (MDA) in both the liver and plasma, while GPx activity increased in the liver of goats fed the HG + NaB diet. The mRNA expression of UGT1A1, NQO1, MGST3, and Nrf2, as well as total Nrf2 protein levels were increased in goats fed the HG + NaB diet. Conclusions Our study indicates that sodium butyrate could improve the oxidative status in sub-acute ruminal acidosis through the partial activation of Nrf2-dependent genes.
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Affiliation(s)
- Nana Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Juma Ahamed Abaker
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Muhammad Shahid Bilal
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Hongyu Dai
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xiangzhen Shen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Bi Y, Zeng S, Zhang R, Diao Q, Tu Y. Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition. BMC Microbiol 2018; 18:69. [PMID: 29996759 PMCID: PMC6042446 DOI: 10.1186/s12866-018-1213-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022] Open
Abstract
Background The rumen bacterial community plays a critical role in feeds degradation and productivity. The effects of different forage to concentrate ratios on the ruminal microbial population structure have been studied extensively; however, research into changes in the ruminal bacterial community composition in heifers fed different energy level diets, with the same forage to concentrate ratio, has been very limited. The purpose of this study was to investigate the effects of different dietary energy levels, with the same forage to concentrate ratio, on ruminal bacterial community composition of heifers. Furthermore, we also determine the relationship between rumen bacteria and ruminal fermentation parameters. Results The 16S rRNA gene sequencing showed that, under the same forage to concentrate ratio of 50:50, an 8% difference in dietary energy level had no significant impact on the alpha diversity and the relative abundance of the major phyla and most of the major genera in heifers. In all the treatments groups, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla. Spearman correlation analysis between the relative abundances of the rumen bacteria at the genus level and the fermentation parameters showed that the relative abundances of Prevotella and BF311 were positively correlated with the ammonia nitrogen and butyrate concentrations, and these two genera were negatively correlated with the propionate and isovalerate concentrations, respectively, and the genus Bifidobacterium was positively correlated with the butyrate concentration and was negatively correlated with propionate and isovalerate concentration. The total volatile fatty acid concentration was positively correlated with BF311 abundances, and was negatively correlated with Trichococcus and Facklamia abundances. Conclusions Under the same forage to concentrate ratio condition of 50:50, an 8% difference in dietary energy levels had little impact on rumen bacterial community composition in heifers. The correlations between some genera of ruminal bacteria and the concentrations of volatile fatty acids and ammonia nitrogen might be indicative that the ruminal fermentation parameters are strongly influenced by the rumen bacterial community composition.
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Affiliation(s)
- Yanliang Bi
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Shuqin Zeng
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Rong Zhang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Qiyu Diao
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Yan Tu
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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Ren QC, Xuan JJ, Wang LK, Zhan QW, Yin DZ, Hu ZZ, Yang HJ, Zhang W, Jiang LS. Effects of tributyrin supplementation on ruminal microbial protein yield, fermentation characteristics and nutrients degradability in adult Small Tail ewes. Anim Sci J 2018; 89:1271-1279. [PMID: 29851189 DOI: 10.1111/asj.13033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/20/2018] [Indexed: 12/30/2022]
Abstract
Two trials were conducted to assess the effects of tributyrin (TB) supplementation on ruminal microbial protein yield and fermentation characteristics in adult sheep. In an in vitro trial, substrate was made to offer TB at 0, 2, 4, 6, and 8 g/kg on a dry matter (DM) basis and incubated for 48 hr. In an in vivo trial, 45 adult ewes were randomly assigned by initial body weight (55 ± 5 kg) to five treatments of nine animals over an 18-day period. Total mixed ration was made to offer TB to ewes at 0, 2, 4, 6, and 8 g/kg on a DM basis. The in vitro trial showed that TB enhanced apparent degradation of DM (p = .009), crude protein (p < .001), neutral detergent fiber (p = .007) and acid detergent fiber (p = .010) and increased methanogenesis (p < .001), respectively. The in vivo trial showed that TB decreased DM intake (p < .001) and enhanced rumen microbial N synthesis (p < .001), respectively. Both in vitro and in vivo trials showed that TB increased total volatile fatty acid concentration and enhanced fibrolytic enzyme activity. The results indicated that TB might exert positive effects on microbial protein yield and fermentation in the rumen.
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Affiliation(s)
- Qing-Chang Ren
- Anhui Science and Technology University, Fengyang, China
| | - Jing-Jing Xuan
- Anhui Science and Technology University, Fengyang, China
| | - Li-Ke Wang
- Anhui Science and Technology University, Fengyang, China
| | - Qiu-Wen Zhan
- Anhui Science and Technology University, Fengyang, China
| | - Ding-Zhong Yin
- Anhui Science and Technology University, Fengyang, China
| | - Zhong-Ze Hu
- Anhui Science and Technology University, Fengyang, China
| | - Hong-Jian Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University (CAU), Beijing, China
| | - Wei Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University (CAU), Beijing, China
| | - Lin-Shu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, China
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30
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Soomro J, Lu Z, Gui H, Zhang B, Shen Z. Synchronous and Time-Dependent Expression of Cyclins, Cyclin-Dependant Kinases, and Apoptotic Genes in the Rumen Epithelia of Butyrate-Infused Goats. Front Physiol 2018; 9:496. [PMID: 29875672 PMCID: PMC5974050 DOI: 10.3389/fphys.2018.00496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
In our previous study, we demonstrated that butyrate induced ruminal epithelial growth through cyclin D1 upregulation. Here, we investigated the influence of butyrate on the expression of genes associated with cell cycle and apoptosis in rumen epithelium. Goats (n = 24) were given an intra ruminal infusion of sodium butyrate at 0.3 (group B, n = 12) or 0 (group A, n = 12) g/kg of body weight (BW) per day before morning feeding for 28 days and were slaughtered (4 goat/group) at 5,7 and 9 h after butyrate infusion. Rumen fluid was analyzed for short chain fatty acids (SCFAs) concentration. Ruminal tissues were analyzed for morpho-histrometry and the expressions of genes associated with cell cycle and apoptosis. The results revealed that the ruminal butyrate concentration increased (P < 0.05) in B compared to group A. Morphometric analysis showed increased (P < 0.05) papillae size associated with higher number of cell layers in epithelial strata in B compared to A. Butyrate-induced papillae enlargement was coupled with enhanced mRNA expression levels (P < 0.05) of cyclin D1, CDK2, CDK4, and CDK6 (G0/G1 phase regulators) at 5 h, cyclin E1 (G1/S phase regulator) at 7 h and cyclin A and CDK1 (S phase regulators) at 9 h post-infusion compared to A group. In addition, the mRNA expression levels of apoptotic genes, i.e., caspase 3, caspase 9 and Bax at 5 h post-infusion were upregulated (P < 0.05) in group B compared to group A. The present study demonstrated that butyrate improved ruminal epithelial growth through concurrent and time-dependent changes in the expressions of genes involved in cell proliferation and apoptosis. It seems that the rate of proliferation was higher than the apoptosis which was reflected in epithelial growth.
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Affiliation(s)
- Jamila Soomro
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Department of Veterinary Physiology and Biochemistry, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Pakistan
| | - Zhongyan Lu
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hongbing Gui
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bei Zhang
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zanming Shen
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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31
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Baldwin RL, Li RW, Jia Y, Li CJ. Transcriptomic Impacts of Rumen Epithelium Induced by Butyrate Infusion in Dairy Cattle in Dry Period. GENE REGULATION AND SYSTEMS BIOLOGY 2018; 12:1177625018774798. [PMID: 29785087 PMCID: PMC5954180 DOI: 10.1177/1177625018774798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/09/2018] [Indexed: 01/14/2023]
Abstract
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function. Ruminal infusion of butyrate was following 0-hour sampling (baseline controls) and continued for 168 hours at a rate of 5.0 L/day of a 2.5 M solution as a continuous infusion. Following the 168-hour infusion, the infusion was stopped, and cows were maintained on the basal lactation ration for an additional 168 hours for sampling. Rumen epithelial samples were serially collected via biopsy through rumen fistulae at 0-, 24-, 72-, and 168-hour (D1, D3, D7) and 168-hour post-infusion (D14). In comparison with pre-infusion at 0 hours, a total of 3513 genes were identified to be impacted in the rumen epithelium by butyrate infusion at least once at different sampling time points at a stringent cutoff of false discovery rate (FDR) < 0.01. The maximal effect of butyrate was observed at day 7. Among these impacted genes, 117 genes were responsive consistently from day 1 to day 14, and another 42 genes were lasting through day 7. Temporal effects induced by butyrate infusion indicate that the transcriptomic alterations are very dynamic. Gene ontology (GO) enrichment analysis revealed that in the early stage of rumen butyrate infusion (on day 1 and day 3 of butyrate infusion), the transcriptomic effects in the rumen epithelium were involved with mitotic cell cycle process, cell cycle process, and regulation of cell cycle. Bioinformatic analysis of cellular functions, canonical pathways, and upstream regulator of impacted genes underlie the potential mechanisms of butyrate-induced gene expression regulation in rumen epithelium. The introduction of transcriptomic and bioinformatic technologies to study nutrigenomics in the farm animal presented a new prospect to study multiple levels of biological information to better apprehend the whole animal response to nutrition, physiological state, and their interactions. The nutrigenomics approach may eventually lead to more precise management of utilization of feed resources in a more effective approach.
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Affiliation(s)
- Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Yankai Jia
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, USA
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
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32
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Yang W, Xin H, Cao F, Hou J, Ma L, Bao L, Wang F, Yu Z, Cao B. The significance of the diversity and composition of the cecal microbiota of the Tibetan swine. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1329-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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33
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Górka P, Kowalski ZM, Zabielski R, Guilloteau P. Invited review: Use of butyrate to promote gastrointestinal tract development in calves. J Dairy Sci 2018. [PMID: 29525310 DOI: 10.3168/jds.2017-14086] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Promotion of microbial butyrate production in the reticulorumen is a widely used method for enhancing forestomach development in calves. Additional acceleration of gastrointestinal tract (GIT) development, both the forestomach and lower parts of the GIT (e.g., abomasum, intestine, and also pancreas), can be obtained by dietary butyrate supplementation. For this purpose, different sources (e.g., butyrate salts or butyrins), forms (e.g., protected or unprotected), methods (e.g., in liquid feed or solid feed), and periods (e.g., before or after weaning) of butyrate administration can be used. The aim of this paper was to summarize the knowledge in the field of butyrate supplementation in feeds for newborn calves in practical situations, and to suggest directions of future studies. It has been repeatedly shown that supplementation of unprotected salts of butyrate (primarily sodium salt) in milk replacer (MR) stimulates the rumen, small intestine, and pancreas development in calves, with a supplementation level equating to 0.3% of dry matter being sufficient to exert the desired effect on both GIT development and growth performance. On the other hand, the effect of unprotected butyrins and protected forms of butyrate supplementation in MR has not been extensively investigated, and few studies have documented the effect of butyrate addition into whole milk (WM), with those available focusing mainly on the growth performance of animals. Protected butyrate supplementation at a low level (0.3% of protected product in DM) in solid feed was shown to have a potential to enhance GIT development and performance of calves fed MR during the preweaning period. Justification of this form of butyrate supplementation in solid feed when calves are fed WM or after weaning needs to be documented. After weaning, inclusion of unprotected butyrate salts in solid feed was shown to increase solid feed intake, but the effect on GIT development and function has not been determined in detail, and optimal levels of supplementation are also difficult to recommend based on available reports. Future studies should focus on comparing different sources (e.g., salts vs. esters), forms (e.g., protected vs. unprotected), and doses of supplemental butyrate in liquid feeds and solid feeds and their effect not only on the development of rumen, abomasum, and small intestine but also the omasum and large intestine. Furthermore, the most effective source, form, and dose of supplemental butyrate in solid feed depending on the liquid feed program (e.g., MR or WM), stage of rearing (e.g., pre- or postweaning), and solid composition (e.g., lack or presence of forage in the diet) need to be determined.
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Affiliation(s)
- P Górka
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
| | - Z M Kowalski
- Department of Animal Nutrition and Dietetics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - R Zabielski
- Veterinary Research Center, Department of Large Animal Diseases with Clinic, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska 100, 02-787 Warsaw, Poland
| | - P Guilloteau
- INRA, Institut National de la Santé et de la Recherche Médicale, Université de Rennes, Université Bretagne Loire, Nutrition, Métabolismes et Cancer, Rennes, 35000, France
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34
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Górka P, Śliwiński B, Flaga J, Wieczorek J, Godlewski MM, Wierzchoś E, Zabielski R, Kowalski ZM. Effect of butyrate infusion into the rumen on butyrate flow to the duodenum, selected gene expression in the duodenum epithelium, and nutrient digestion in sheep. J Anim Sci 2017; 95:2144-2155. [PMID: 28726987 DOI: 10.2527/jas.2016.1218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The aim of the study was to determine the effect of butyrate infusion into the rumen on butyrate flow to the duodenum, expression of short-chain fatty acid (SCFA) transporters (monocarboxylate transporter-1, -2, and -4) and receptors (G protein coupled receptor-41 and -43) in the duodenal epithelium and nutrient digestion in sheep. Eight wethers (39.0 ± 3.00 kg; mean ± SD) with ruminal and T-shape duodenal cannulas were allocated to 4 × 4 replicated Latin square design with each experimental period lasting for 21 d (12 d of adaptation and 9 d for data and sample collection). Experimental treatments were: 1) distilled water infusion into the rumen (CONT); 2) 15 g/d of butyric acid infusion into the rumen (BUT15); 3) 30 g/d of butyric acid infusion into the rumen (BUT30); and 4) 45 g/d of butyric acid infusion into the rumen (BUT45). The daily dose of butyrate was infused into the rumen via the rumen cannula, with 200 mL of solution of butyric acid and distilled water, at a constant rate (0.1389 mL/min) throughout the day using a peristaltic pump. Correspondingly, 200 mL/d of distilled water was infused into the rumen of CONT. The wethers were fed daily 900 g of chopped meadow hay and 200 g of concentrate in two equal meals at 0600 and 1800 h. Butyrate infusion into the rumen did not affect total SCFA concentration in the rumen fluid ( > 0.11). Molar proportion of butyrate in total SCFA linearly increased, and molar proportion of acetate and isovalerate linearly decreased ( ≤ 0.02) with an increasing amount of butyrate infused into the rumen. The molar proportion of butyrate in total SCFA in the duodenal digesta linearly increased ( < 0.01), and butyrate flow to duodenum tended to linearly increase ( = 0.06) with an increasing dose of exogenous butyrate delivered to the rumen. Butyrate infusion into the rumen did not affect ( ≥ 0.14) the mRNA expression of monocarboxylate transporter-2 and -4 and G protein coupled receptor-43 in the duodenal epithelium. The G protein coupled receptor-41 and monocarboxylate transporter-1 mRNA expression in the duodenal epithelium was very low in many of the analyzed samples. Digestibility of organic matter, neutral detergent fiber, and acid detergent fiber in the stomach (forestomach and abomasum) decreased for BUT15 and BUT30 and then increased for BUT45 (quadratic, ≤ 0.04); however, neither digestibility in the intestine nor total tract digestibility differed between treatments ( ≥ 0.10).
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35
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Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions. Sci Rep 2017; 7:6783. [PMID: 28754911 PMCID: PMC5533764 DOI: 10.1038/s41598-017-05860-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
Chondroitin sulfate (CS) has been widely used for medical and nutraceutical purposes due to its roles in maintaining tissue structural integrity. We investigated if CS disaccharides may act as a bioactive compound and modulate gut microbial composition in mice. Our data show that CS disaccharides supplementation for 16 days significantly reduced blood LPS in the mice experiencing exhaustive exercise stress. CS disaccharides partially restored total fecal short-chain fatty acids from the level significantly repressed in mice under the stress. Our findings demonstrated that CS was likely butyrogenic and resulted in a significant increase in fecal butyrate concentration. CS disaccharides had a profound impact on gut microbial composition, affecting the abundance of 13.6% and 7.3% Operational Taxonomic Units in fecal microbial communities in healthy and stressed mice, respectively. CS disaccharides reduced the prevalence of inflammatory Proteobacteria. Together, our findings demonstrated that CS may ameliorate stress-induced intestinal inflammation. Furthermore, CS significantly increased intestinal Bacteroides acidifaciens population, indirectly exerting its immunomodulatory effect on the intestine. CS disaccharides had a significant impact on a broad range of biological pathways under stressed condition, such as ABC transporters, two-component systems, and carbohydrate metabolism. Our results will facilitate the development of CS as a bioactive nutraceutical.
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Wilkinson TJ, Cowan AA, Vallin HE, Onime LA, Oyama LB, Cameron SJ, Gonot C, Moorby JM, Waddams K, Theobald VJ, Leemans D, Bowra S, Nixey C, Huws SA. Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys. Front Microbiol 2017; 8:1089. [PMID: 28690591 PMCID: PMC5479886 DOI: 10.3389/fmicb.2017.01089] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/30/2017] [Indexed: 12/11/2022] Open
Abstract
The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.
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Affiliation(s)
- Toby J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - A A Cowan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - H E Vallin
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - L A Onime
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Linda B Oyama
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - S J Cameron
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom.,Department of Surgery and Cancer, Faculty of Medicine, Imperial College LondonLondon, United Kingdom
| | - Charlotte Gonot
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - J M Moorby
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - K Waddams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - V J Theobald
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - D Leemans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - S Bowra
- Phytatec (UK) Ltd.-Plas GogerddanAberystwyth, United Kingdom
| | - C Nixey
- British Poultry CouncilLondon, United Kingdom
| | - Sharon A Huws
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
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Noel SJ, Attwood GT, Rakonjac J, Moon CD, Waghorn GC, Janssen PH. Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture. PLoS One 2017; 12:e0173819. [PMID: 28296930 PMCID: PMC5351972 DOI: 10.1371/journal.pone.0173819] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/26/2017] [Indexed: 11/19/2022] Open
Abstract
The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a ‘snapshot’ in time. We monitored the diversity of rumen bacteria in four New Zealand dairy cows, grazing a rye-grass and clover pasture over five consecutive seasons, using high throughput pyrosequencing of bacterial 16S rRNA genes. We chose to focus on the digesta-adherent bacterial community to learn more about the stability of this community over time. 16S rRNA gene sequencing showed a high level of bacterial diversity, totalling 1539 operational taxonomic units (OTUs, grouped at 96% sequence similarity) across all samples, and ranging from 653 to 926 OTUs per individual sample. The nutritive composition of the pasture changed with the seasons as did the production phase of the animals. Sequence analysis showed that, overall, the bacterial communities were broadly similar between the individual animals. The adherent bacterial community was strongly dominated by members of Firmicutes (82.1%), followed by Bacteroidetes (11.8%). This community differed between the seasons, returning to close to that observed in the same season one year later. These seasonal differences were only small, but were statistically significant (p < 0.001), and were probably due to the seasonal differences in the diet. These results demonstrate a general invariability of the ruminal bacterial community structure in these grazing dairy cattle.
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Affiliation(s)
- Samantha J. Noel
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Department of Animal Science, Aarhus University, Tjele, Denmark
- * E-mail:
| | - Graeme T. Attwood
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Christina D. Moon
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | | | - Peter H. Janssen
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
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Dai H, Liu X, Yan J, Aabdin ZU, Bilal MS, Shen X. Sodium Butyrate Ameliorates High-Concentrate Diet-Induced Inflammation in the Rumen Epithelium of Dairy Goats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:596-604. [PMID: 28032994 DOI: 10.1021/acs.jafc.6b04447] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To investigate the effect of sodium butyrate on high-concentrate diet-induced local inflammation of the rumen epithelium, 18 midlactating dairy goats were randomly assigned to 3 groups: a low-concentrate diet group as the control (concentrate:forage = 4:6), a high-concentrate (HC) diet group (concentrate:forage = 6:4), and a sodium butyrate (SB) group (concentrate:forage = 6:4, with 1% SB by weight). The results showed that, with the addition of sodium butyrate, the concentration of lipopolysaccharide (LPS) in rumen fluid (2.62 × 104 ± 2.90 × 103 EU/mL) was significantly lower than that in the HC group (4.03 × 104 ± 2.77 × 103 EU/mL). The protein abundance of pp65, gene expression of proinflammatory cytokines, and activity of myeloperoxidase (MPO) and matrix metalloproteinase (MMP)-2,9 in the rumen epithelium were significantly down-regulated by SB compared with those in the HC group. With sodium butyrate administration, the concentration of NH3-N (19.2 ± 0.890 mM) in the rumen fluid was significantly higher than that for the HC group (12.7 ± 1.38 mM). Severe disruption of the rumen epithelium induced by HC was also ameliorated by dietary SB. Therefore, local inflammation and disruption of the rumen epithelium induced by HC were alleviated with SB administration.
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Affiliation(s)
- Hongyu Dai
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
| | - Xinxin Liu
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
| | - Jinyu Yan
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
| | - Zain Ul Aabdin
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
| | - Muhammad Shahid Bilal
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
| | - Xiangzhen Shen
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing 210095, P. R. China
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Shen H, Chen Z, Shen Z, Lu Z. Maintaining stability of the rumen ecosystem is associated with changes of microbial composition and epithelial TLR signaling. Microbiologyopen 2017; 6. [PMID: 28109059 PMCID: PMC5458463 DOI: 10.1002/mbo3.436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 02/01/2023] Open
Abstract
We used the goat as a model to study the effects of rumen microbial composition and epithelial TLR signaling on maintaining rumen stability during exogenous butyrate interference. Six cannulated goats received a rapid intraruminal infusion of 0.1 mol/L potassium phosphate buffer with (BT, n = 3) or without (CO, n = 3) 0.3 g/kg·BW·day sodium butyrate for 28 days. The ruminal pH and the concentration of total SCFA were not affected by the interference. 16S rRNA gene amplicon sequencing revealed a change in microbial composition after the butyrate infusion. LEfSe analysis showed a shift of the biomarker species from butyrate‐producing bacteria to acetate‐and propionate‐producing bacteria. Quantitative PCR‐based comparisons showed that significant increases in TLR2, TLR5, and MyD88 expression were accompanied by a significant decrease in IL‐1β and IFN‐γ expression in the ruminal epithelium. Constrained correlation analysis showed that the relative abundance of Roseburia was positively correlated with the expression of TLR5. Taken together, our study shows that microbial composition plays an important role in maintaining the stability of the microbial ecosystem in rumen, and indicates that the microbe‐TLR‐cytokine axis was involved in maintaining the stability of the gastrointestinal ecosystem.
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Affiliation(s)
- Hong Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhan Chen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zanming Shen
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhongyan Lu
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Review: Exogenous butyrate: implications for the functional development of ruminal epithelium and calf performance. Animal 2017; 11:1522-1530. [DOI: 10.1017/s1751731117000167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Effects of Early Intervention with Sodium Butyrate on Gut Microbiota and the Expression of Inflammatory Cytokines in Neonatal Piglets. PLoS One 2016; 11:e0162461. [PMID: 27611998 PMCID: PMC5017769 DOI: 10.1371/journal.pone.0162461] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/23/2016] [Indexed: 11/19/2022] Open
Abstract
Butyrate in the gut of animals has potential properties including regulating the innate immune, modulating the lipid metabolism, and protecting gut healthy. So far, only limited information on the impact of butyrate on the neonatal is available. This study aimed to investigate effects of oral administration of sodium butyrate (SB) on gut microbiota and the expression of inflammatory cytokine in neonatal piglets. Ten litters of crossbred newborn piglets were randomly allocated to the SB and control (CO) groups, each group consisted of five litters (replicates). Piglets in the SB group were orally administrated with 7 to 13 ml sodium butyrate solution (150 mmol/l) per day from the age of 1 to 7 days, respectively; piglets in the CO group were treated with the same dose of physiological saline. On days 8 and 21 (of age), gut digesta and tissues were collected for the analysis of microbiota, butyrate concentration and gene expression of inflammatory cytokine. Results showed that there was no difference in the butyrate concentration in the gut of piglets on days 8 and 21 between two groups. Real-time PCR assay showed that SB had no effect on the numbers of total bacteria in the stomach, ileum, and colon. MiSeq sequencing of the V3-V4 region of the 16S rRNA gene revealed that SB increased the richness in the stomach and colon, and the diversity of colonic microbiota on day 8 (P < 0.05). Genera Acinetobacter, Actinobacillus, Facklamia, Globicatella, Kocuria, Rothia, unclassified Leptotrichiaceae, unclassified Neisseriaceae, and unclassified Prevotellaceae in the stomach were increased in relative abundance by SB treatment, whereas the abundances of Lactobacillus decreased on day 8 (P < 0.05). At the genus and operational taxonomic unit (OTU) levels, SB had low impact on bacterial community in the ileum and colon on days 8 and 21. SB treatment decreased the expression of IL-6, IL-8, IFN-γ, IL-10, TGF-β, and histone deacetylase 1 (HDAC1) in the ileum of piglets on day 8 (P < 0.05). SB treatment down-regulated the expression of IL-8, IFN-γ, and IL-1β on day 21 (P < 0.05). Correlation analysis on the combined datasets revealed some potential relationships between gut microbiota and the expression of inflammatory cytokines. The results show that early intervention with sodium butyrate can modulate the ileum inflammatory cytokine in neonatal piglets with low impact on intestinal microbial structure, which suggests oral administration of SB may have a benefit role in the health of neonatal piglets.
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Wang J, Fan H, Han Y, Zhao J, Zhou Z. Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:100-110. [PMID: 27383798 PMCID: PMC5205584 DOI: 10.5713/ajas.16.0166] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/22/2016] [Accepted: 06/28/2016] [Indexed: 11/27/2022]
Abstract
Objective The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep’s health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. Methods This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. Results The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). Conclusion This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.
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Affiliation(s)
- Jin Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Fan
- Tianjin Institute of Animal Husbandry and Veterinary Research, Tianjin 300384, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China
| | - Ye Han
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jinzhao Zhao
- Tianjin Kuntai Environment & Energy Science and Technology Development Co., Ltd, Tianjin 300191, China
| | - Zhijiang Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Abrar A, Watanabe H, Kitamura T, Kondo M, Ban-Tokuda T, Matsui H. Diversity and fluctuation in ciliate protozoan population in the rumen of cattle. Anim Sci J 2016; 87:1188-92. [PMID: 27197634 DOI: 10.1111/asj.12591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 09/28/2015] [Accepted: 11/24/2015] [Indexed: 11/28/2022]
Abstract
The purpose of this study was to investigate the diversity and fluctuation in the ciliate protozoan population in the rumen of cattle. DNA was extracted from the rumen of three ruminally cannulated, crossbred cattle and a polymerase chain reaction (PCR)-derived clone library was constructed, using a specific primer set targeting 18S ribosomal RNA genes of ciliate protozoa. DNA fragments of seven selected clones were validated for standard DNA of the protozoa-specific real-time PCR assay. Furthermore, population fluctuation of ciliate protozoa and methanogens in the cattle rumen was determined by real-time PCR. A total of 60 clones were sequenced, phylogenetically analyzed, and classified into 24 operational taxonomic units (OTUs) based on a 99% similarity criterion. More than 80% sequences were phylogenetically placed in the genus Entodinium. The rest of the sequences were placed in the genus Diploplastron (5%), Dasytricha (8.3%) and Isotricha (3.3%). The results suggest that Entodinium was the dominant group in the rumen of cattle used in this study. The ciliate protozoan population showed no significant change in numbers during the monitoring period and reached a peak at 3 h after feeding. Changes in the protozoa population were lower than those of the methanogens.
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Affiliation(s)
- Arfan Abrar
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | | | - Makoto Kondo
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | - Hiroki Matsui
- Graduate School of Bioresources, Mie University, Tsu, Japan
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The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome. Sci Rep 2016; 6:20606. [PMID: 26853110 PMCID: PMC4757478 DOI: 10.1038/srep20606] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/08/2016] [Indexed: 01/22/2023] Open
Abstract
Haemonchus contortus is arguably the most injurious helminth parasite for small ruminants. We characterized the impact of H. contortus infection on the caprine abomasal microbiome. Fourteen parasite naive goats were inoculated with 5,000 H. contortus infective larvae and followed for 50 days. Six age-matched naïve goats served as uninfected controls. Reduced bodyweight gain and a significant increase in the abosamal pH was observed in infected goats compared to uninfected controls. Infection also increased the bacterial load while reducing the abundance of the Archaea in the abomasum but did not appear to affect microbial diversity. Nevertheless, the infection altered the abundance of approximately 19% of the 432 species-level operational taxonomic units (OTU) detected per sample. A total of 30 taxa displayed a significantly different abundance between control and infected goats. Furthermore, the infection resulted in a distinct difference in the microbiome structure. As many as 8 KEGG pathways were predicted to be significantly affected by infection. In addition, H. contortus-induced changes in butyrate producing bacteria could regulate mucosal inflammation and tissue repair. Our results provided insight into physiological consequences of helminth infection in small ruminants and could facilitate the development of novel control strategies to improve animal and human health.
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Janarthanan OM, Laycock B, Montano-Herrera L, Lu Y, Arcos-Hernandez MV, Werker A, Pratt S. Fluxes in PHA-storing microbial communities during enrichment and biopolymer accumulation processes. N Biotechnol 2016; 33:61-72. [DOI: 10.1016/j.nbt.2015.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/15/2015] [Accepted: 07/29/2015] [Indexed: 10/23/2022]
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Sun X, Wang Y, Chen B, Zhao X. Partially replacing cornstarch in a high-concentrate diet with sucrose inhibited the ruminal trans-10 biohydrogenation pathway in vitro by changing populations of specific bacteria. J Anim Sci Biotechnol 2015; 6:57. [PMID: 26705470 PMCID: PMC4690235 DOI: 10.1186/s40104-015-0051-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/30/2015] [Indexed: 11/20/2022] Open
Abstract
Background The positive influence of replacing dietary starch with sugar on milk fat production has been proposed to be partially attributed to the inhibition of the rumen trans-10 biohydrogenation pathway. However, whether and how sucrose inhibits the rumen trans-10 biohydrogenation pathway remains elusive. Results A batch in vitro incubation system was used to evaluate effects of replacing cornstarch in a high-concentrate diet (forage to concentrate ratio = 40:60) with 0 (control), 3, 6 and 9 % of sucrose on rumen fermentation pattern, fatty acid (FA) biohydrogenation pathways and bacterial populations relating to trans-11 to trans-10 biohydrogenation pathways. Replacing dietary cornstarch with sucrose did not alter rumen pH or concentrations of total volatile fatty acids (VFA) in comparison with the control but significantly influenced the profiles of individual VFA. The molar proportions of butyrate and valerate were linearly increased, while that of acetate was quadratically decreased and those of propionate, isobutyrate and isovalerate were linearly decreased with increasing concentrations of sucrose in the diet. Furthermore, replacing cornstarch with sucrose led to a linear decrease in C18:1 trans-10, linear increases in the proportions of C18:1 trans-11, C18:2n-6 and the ratio of trans-11 to trans-10, and linear decreases in biohydrogenation of C18:2n-6 and C18:3n-3. The abundance of Butyrivibrio fibrisolvens, a butyrate and CLA cis-9, trans-11 producer, was increased with the increasing inclusion of sucrose in the diet, while the population of Megasphaera elsdenii, a CLA trans-10, cis-12 producer, was significantly decreased by all levels of sucrose replacements. Conclusions These results indicate that replacing starch in a high-concentrate diet with sucrose increased butyrate production and inhibited the rumen trans-10 biohydrogenation pathway, which was at least partially due to increased abundance of Butyrivibrio fibrisolvens and decreased abundance of Megasphaera elsdenii.
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Affiliation(s)
- Xiaoqin Sun
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100 People's Republic of China
| | - Yaping Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100 People's Republic of China
| | - Bo Chen
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100 People's Republic of China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100 People's Republic of China ; Department of Animal Science, McGill University, 21,111 Lakeshore, Ste. Anne de Bellevue, QC H9X 3V9 Canada
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Harder H, Khol-Parisini A, Metzler-Zebeli BU, Klevenhusen F, Zebeli Q. Treatment of grain with organic acids at 2 different dietary phosphorus levels modulates ruminal microbial community structure and fermentation patterns in vitro. J Dairy Sci 2015; 98:8107-20. [PMID: 26299164 DOI: 10.3168/jds.2015-9913] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 07/05/2015] [Indexed: 12/21/2022]
Abstract
Recent data indicate positive effects of treating grain with citric (CAc) or lactic acid (LAc) on the hydrolysis of phytate phosphorus (P) and fermentation products of the grain. This study used a semicontinuous rumen simulation technique to evaluate the effects of processing of barley with 50.25 g/L (wt/vol) CAc or 76.25 g/L LAc on microbial composition, metabolic fermentation profile, and nutrient degradation at low or high dietary P supply. The low P diet [3.1g of P per kg of dry matter (DM) of dietary P sources only] was not supplemented with inorganic P, whereas the high P diet was supplemented with 0.5 g of inorganic P per kg of DM through mineral premix and 870 mg of inorganic P/d per incubation fermenter via artificial saliva. Target microbes were determined using quantitative PCR. Data showed depression of total bacteria but not of total protozoa or short-chain fatty acid (SCFA) concentration with the low P diet. In addition, the low P diet lowered the relative abundance of Ruminococcus albus and decreased neutral detergent fiber (NDF) degradation and acetate proportion, but increased the abundance of several predominantly noncellulolytic bacterial species and anaerobic fungi. Treatment of grain with LAc increased the abundance of total bacteria in the low P diet only, and this effect was associated with a greater concentration of SCFA in the ruminal fluid. Interestingly, in the low P diet, CAc treatment of barley increased the most prevalent bacterial group, the genus Prevotella, in ruminal fluid and increased NDF degradation to the same extent as did inorganic P supplementation in the high P diet. Treatment with either CAc or LAc lowered the abundance of Megasphaera elsdenii but only in the low P diet. On the other hand, CAc treatment increased the proportion of acetate in the low P diet, whereas LAc treatment decreased this variable at both dietary P levels. The propionate proportion was significantly increased by LAc at both P levels, whereas butyrate increased only with the low P diet. Treatments with CAc or LAc reduced the degradation of CP and ammonia concentration compared with the control diet at both P levels. In conclusion, the beneficial effects of CAc and LAc treatment on specific ruminal microbes, fermentation profile, and fiber degradation in the low P diet suggest the potential for the treatment to compensate for the lack of inorganic P supplementation in vitro. Further research is warranted to determine the extent to which the treatment can alleviate the shortage of inorganic P supplementation under in vivo conditions.
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Affiliation(s)
- H Harder
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; Research Cluster Animal Gut Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - A Khol-Parisini
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; Research Cluster Animal Gut Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - B U Metzler-Zebeli
- Research Cluster Animal Gut Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - F Klevenhusen
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; Research Cluster Animal Gut Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; Research Cluster Animal Gut Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
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Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen. Appl Environ Microbiol 2015; 81:7470-83. [PMID: 26276109 DOI: 10.1128/aem.02385-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/09/2015] [Indexed: 11/20/2022] Open
Abstract
Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.
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Agarwal U, Hu Q, Baldwin RL, Bequette BJ. Role of rumen butyrate in regulation of nitrogen utilization and urea nitrogen kinetics in growing sheep1. J Anim Sci 2015; 93:2382-90. [DOI: 10.2527/jas.2014-8738] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kowalski Z, Górka P, Flaga J, Barteczko A, Burakowska K, Oprządek J, Zabielski R. Effect of microencapsulated sodium butyrate in the close-up diet on performance of dairy cows in the early lactation period. J Dairy Sci 2015; 98:3284-91. [DOI: 10.3168/jds.2014-8688] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022]
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