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Microbial patterns in rumen are associated with gain of weight in beef cattle. Antonie Van Leeuwenhoek 2020; 113:1299-1312. [PMID: 32577920 DOI: 10.1007/s10482-020-01440-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil. We aimed to detect microbial patterns in the rumen that could be correlated with the gain of weight. We hypothesized that microorganisms important to digestion process are increased in animals with a higher gain of weight. The gain of weight of seventeen healthy animals was monitored for 60 days. Ruminal samples were obtained and the 16S and ITS1 genes were amplified and sequenced to identify the closest microbial relatives within the microbial communities. A predictive model based on microbes responsible for the gain of weight was build and further tested using the entire dataset., The main differential abundant microbes between groups included the bacterial taxa RFN20, Prevotella, Anaeroplasma and RF16 and the fungal taxa Aureobasidium, Cryptococcus, Sarocladium, Pleosporales and Tremellales. The predictive model detected some of these taxa associated with animals with the high gain of weight group, most of them being organisms that have been correlated to the production of substances that improve the ruminal digestion process. These findings provide new insights about cattle nutrition and suggest the use of these microbes to improve beef cattle breeding.
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McMullen C, Alexander TW, Léguillette R, Workentine M, Timsit E. Topography of the respiratory tract bacterial microbiota in cattle. MICROBIOME 2020; 8:91. [PMID: 32522285 PMCID: PMC7288481 DOI: 10.1186/s40168-020-00869-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung microbiota. METHODS Seventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations. RESULTS Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma. Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar. Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella, Fusobacterium, and Streptococcus, respectively. CONCLUSIONS The nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory microbiota research. Video abstract.
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Affiliation(s)
| | - Trevor W. Alexander
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, Alberta Canada
| | - Renaud Léguillette
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Matthew Workentine
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Edouard Timsit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
- Simpson Ranch Chair in Beef Cattle Health and Wellness, University of Calgary, Calgary, Alberta Canada
- Ceva Santé Animale, 10 Avenue de la Ballastière, 33500 Libourne, France
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Bowen JM, Cormican P, Lister SJ, McCabe MS, Duthie CA, Roehe R, Dewhurst RJ. Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation. PLoS One 2020; 15:e0231759. [PMID: 32330150 PMCID: PMC7182223 DOI: 10.1371/journal.pone.0231759] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/31/2020] [Indexed: 01/07/2023] Open
Abstract
Ruminant methane production is a significant energy loss to the animal and major contributor to global greenhouse gas emissions. However, it also seems necessary for effective rumen function, so studies of anti-methanogenic treatments must also consider implications for feed efficiency. Between-animal variation in feed efficiency represents an alternative approach to reducing overall methane emissions intensity. Here we assess the effects of dietary additives designed to reduce methane emissions on the rumen microbiota, and explore relationships with feed efficiency within dietary treatment groups. Seventy-nine finishing steers were offered one of four diets (a forage/concentrate mixture supplemented with nitrate (NIT), lipid (MDDG) or a combination (COMB) compared to the control (CTL)). Rumen fluid samples were collected at the end of a 56 d feed efficiency measurement period. DNA was extracted, multiplexed 16s rRNA libraries sequenced (Illumina MiSeq) and taxonomic profiles were generated. The effect of dietary treatments and feed efficiency (within treatment groups) was conducted both overall (using non-metric multidimensional scaling (NMDS) and diversity indexes) and for individual taxa. Diet affected overall microbial populations but no overall difference in beta-diversity was observed. The relative abundance of Methanobacteriales (Methanobrevibacter and Methanosphaera) increased in MDDG relative to CTL, whilst VadinCA11 (Methanomassiliicoccales) was decreased. Trimethylamine precursors from rapeseed meal (only present in CTL) probably explain the differences in relative abundance of Methanomassiliicoccales. There were no differences in Shannon indexes between nominal low or high feed efficiency groups (expressed as feed conversion ratio or residual feed intake) within treatment groups. Relationships between the relative abundance of individual taxa and feed efficiency measures were observed, but were not consistent across dietary treatments.
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Affiliation(s)
- Jenna M. Bowen
- Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
- IBERS, Aberystwyth University, Aberystwyth, Wales, United Kingdom
| | - Paul Cormican
- Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Susan J. Lister
- IBERS, Aberystwyth University, Aberystwyth, Wales, United Kingdom
| | - Matthew S. McCabe
- Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
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Huang S, Ji S, Yan H, Hao Y, Zhang J, Wang Y, Cao Z, Li S. The day-to-day stability of the ruminal and fecal microbiota in lactating dairy cows. Microbiologyopen 2020; 9:e990. [PMID: 32175695 PMCID: PMC7221419 DOI: 10.1002/mbo3.990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
In this study, we examined differences between the microbiota of the ruminal fluid (DR) and feces (DF) from five lactating dairy cows over three consecutive days using 16S rRNA gene sequence-based analysis. Results showed significant differences between the microbial communities of the DR and DF. In particular, the relative abundance of the phyla Firmicutes and Actinobacteria was significantly lower (q < 0.001) in DR compared with DF, while the relative abundance of Bacteroidetes was significantly higher in DF than that of DR (q < 0.001). A significantly higher relative abundance of the genera Bifidobacterium, 5-7N15, Clostridium, Epulopiscium, SMB53, Turicibacter, Dorea, Roseburia, and Akkermansia was observed in the DF, while a higher relative abundance of the genera Prevotella, Butyrivibrio, CF231, RFN20, and Succiniclasticum was observed in the DR. A further analysis using the functional prediction program PICRUSt showed that sequences belonging to the 5-7N15, Akkermansia, Bifidobacterium, Clostridium, Dorea, Epulopiscium, Roseburia, and Turicibacter were significantly and positively correlated with glycan biosynthesis and metabolism, while CF231, Prevotella, RFN20, and Succiniclasticum were significantly and positively correlated with amino acid, lipid, carbohydrate, other amino acid, cofactors, and vitamins metabolism. No significant differences were observed across the three consecutive days in either the DR or DF ecosystems, with no significant differences in the diversity or abundance at the phylum and genus levels suggested that there is a limited day-to-day variability in the gut microbiota.
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Affiliation(s)
- Shuai Huang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shoukun Ji
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Hui Yan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Yangyi Hao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jun Zhang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Yu S, Zhang G, Liu Z, Wu P, Yu Z, Wang J. Repeated inoculation with fresh rumen fluid before or during weaning modulates the microbiota composition and co-occurrence of the rumen and colon of lambs. BMC Microbiol 2020; 20:29. [PMID: 32028889 PMCID: PMC7006167 DOI: 10.1186/s12866-020-1716-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background Many recent studies have gravitated towards manipulating the gastrointestinal (GI) microbiome of livestock to improve host nutrition and health using dietary interventions. Few studies, however, have evaluated if inoculation with rumen fluid could effectively reprogram the development of GI microbiota. We hypothesized that inoculation with rumen fluid at an early age could modulate the development of GI microbiota because of its low colonization resistance. Results In this study, we tested the above hypothesis using young lambs as a model. Young lambs were orally inoculated repeatedly (four times before or twice during gradual weaning) with the rumen fluid collected from adult sheep. The oral inoculation did not significantly affect starter intake, growth performance, or ruminal fermentation. Based on sequencing analysis of 16S rRNA gene amplicons, however, the inoculation (both before and during weaning) affected the assemblage of the rumen microbiota, increasing or enabling some bacterial taxa to colonize the rumen. These included operational taxonomic units (OTUs) belonging to Moryella, Acetitomaculum, Tyzzerella 4, Succiniclasticum, Prevotella 1, Lachnospiraceae, Christensenellaceae R-7 group, Family XIII AD3011, and Bacteroidales S24–7 corresponding to inoculation before weaning; and OTUs belonging to Succiniclasticum, Prevotellaceae UCG-003, Erysipelotrichaceae UCG-004, Prevotella 1, Bacteroidales S24–7 gut group uncultured bacterium, and candidate Family XIII AD3011 corresponding to inoculation during weaning. Compared to the inoculation during weaning, the inoculation before weaning resulted in more co-occurrences of OTUs that were exclusively predominant in the inoculum. However, inoculation during weaning appeared to have more impacts on the colonic microbiota than the inoculation before weaning. Considerable successions in the microbial colonization of the GI tracts accompanied the transition from liquid feed to solid feed during weaning. Conclusions Repeated rumen fluid inoculation during early life can modulate the establishment of the microbiota in both the rumen and the colon and co-occurrence of some bacteria. Oral inoculation with rumen microbiota may be a useful approach to redirect the development of the microbiota in both the rumen and colon.
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Affiliation(s)
- Shaobo Yu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Guangyu Zhang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhibo Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Peng Wu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
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Abstract
This review aims to explain the influence and characterization of the microbiome in the ruminant digestive system by presenting the knowledge collected so far. The knowledge presented in this work is focused on the main factors affecting the microbiome and the main dependencies that have been found in it so far. The microbiome in the rumen is the first to come into contact with the biomass of the forage and its main purpose is to decompose into smaller particles or compounds. With the gradual increase in knowledge about the microbiome, there is a chance to manipulate it so that the animal continues to live in a symbiotic relationship with it, while reducing greenhouse gas emissions to the environment as well as increasing feed efficiency. Therefore, understanding the influence of the ruminant microbiome is the main step to achieve such results. However, learning the relationship between microorganisms is only at an early stage, because research focuses mainly on taxonomy. Future research should focus on interactions in the ecosystem which is the microbiome, on explaining individual functions and on influence of environmental factors.
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Sofronov V, Fayzrakhmanov R, Yamaev E, Danilova N, Kuznetsova E, Sofronov P. Effect of extruded grain feed, with the preliminary germination of rapeseed, on the cicatricial digestion of dairy cows and calves. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20201700132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This article describes the scientific and production experience conducted in the Druzhba LLC, of the Buinsky district of the Republic of Tatarstan. The purpose of the scientific and production experiment is to study the effect of extruded feed, with the preliminary germination of rapeseed in a 0.05 % nicotinic acid solution, on the cicatricial digestion of calves and dairy cows. During the experiment, it is found that feeding calves and dairy cows with extruded feed with preliminary germination of rapeseed in a 0.05 % nicotinic acid solution had a positive effect on cicatricial digestion, contributing to an increase in ammonia to 8.7 and 7.9 %, acetic acid – 12, 6 and 11.5 % and propionic – 13.4 and 12.6 % acids, with a decrease in butyric acid – 12.8 and 10.4 %, an increase in the total microbial number – 8 4.0 and 16.3 %, in including cellulolytic bacteria – 11.6 and 14.3 %, ciliates – 13.4 and 12.9 %, as well as the enzymatic activity of cicatricial microflora, respectively accordingly, in comparison with the control and the group where the grain feed is subjected to only one extrusion. Thus, the use of extruded feed with pre-germinated rapeseed in feeding calves and dairy cows improved the underlying indices of cicatricial digestion compared with the control group of animals fed with non-extruded feed and the group of animals fed with extruded feed.
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Albakri NN, Bouqellah NA, Shabana II. A metagenomic survey of lamb's pre- and post-weaning fecal microbiomes. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2020. [DOI: 10.1080/16583655.2020.1816000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- N. N. Albakri
- Biology Department, Faculty of Science, Taibah University, Al- madinah Al-munawarah, Saudi Arabia
| | - N. A. Bouqellah
- Biology Department, Faculty of Science, Taibah University, Al- madinah Al-munawarah, Saudi Arabia
| | - I. I. Shabana
- Faculty of Veterinary Medicine, Department of Bacteriology, Immunology and Mycology, Suez Canal University, Ismailia, Egypt
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Temporal Dynamics in Rumen Bacterial Community Composition of Finishing Steers during an Adaptation Period of Three Months. Microorganisms 2019; 7:microorganisms7100410. [PMID: 31581417 PMCID: PMC6843415 DOI: 10.3390/microorganisms7100410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/18/2019] [Accepted: 09/29/2019] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary treatments were either standard energy and standard protein (C) or low energy and low protein (L). Rumen samples were obtained on day 30, day 60 and day 90 from both dietary treatments and were analyzed by using 16S rRNA gene sequencing. The results showed that monthly intervals had no effect on the richness and evenness of the rumen bacterial community in the two diets. However, taxonomic difference analysis (relative abundance >0.5%) revealed that the relative abundance of three phyla (Proteobacteria, Fibrobacteres and Cyanobacteria) and six genera (Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Fibrobacter, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-010 and Ruminobacter) were significantly different between monthly sampling intervals, and the difference was prominent between sampling in the first month and the subsequent two months. Moreover, the differences in abundances of phyla and genera between monthly sampling intervals were affected by diets. Analysis of similarity (ANOSIM) showed no significant differences between monthly sampling intervals in the C diet. However, ANOSIM results revealed that significant differences between the first month and second month and between the first month and third month were present in the L diet. These results indicated that temporal dynamics in rumen bacterial community composition did occur even after an adaptation period of three months. This study tracked the changes in rumen bacterial populations of finishing cattle after a shift in diet with the passage of time. This study may provide insight into bacterial adaptation time to dietary transition in finishing steers.
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60
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Mamuad LL, Kim SH, Biswas AA, Yu Z, Cho KK, Kim SB, Lee K, Lee SS. Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation. AMB Express 2019; 9:123. [PMID: 31363877 PMCID: PMC6667549 DOI: 10.1186/s13568-019-0848-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Supplementation of appropriate probiotics can improve the health and productivity of ruminants while mitigating environmental methane production. Hence, this study was conducted to determine the effects of Enterococcus faecium SROD on in vitro rumen fermentation, methane concentration, and microbial population structure. Ruminal samples were collected from ruminally cannulated Holstein–Friesian cattle, and 40:60 rice straw to concentrate ratio was used as substrate. Fresh culture of E. faecium SROD at different inclusion rates (0, 0.1%, 0.5%, and 1.0%) were investigated using in vitro rumen fermentation system. Addition of E. faecium SROD had a significant effect on total gas production with the greatest effect observed with 0.1% supplementation; however, there was no significant influence on pH. Supplementation of 0.1% E. faecium SROD resulted in the highest propionate (P = 0.005) but the lowest methane concentration (P = 0.001). In addition, acetate, butyrate, and total VFA concentrations in treatments were comparatively higher than control. Bioinformatics analysis revealed the predominance of the bacterial phyla Bacteroidetes and Firmicutes and the archaeal phylum Euryarchaeota. At the genus level, Prevotella (15–17%) and Methanobrevibacter (96%) dominated the bacterial and archaeal communities of the in vitro rumen fermenta, respectively. Supplementation of 0.1% E. faecium SROD resulted in the highest quantities of total bacteria and Ruminococcus flavefaciens, whereas 1.0% E. faecium SROD resulted in the highest contents of total fungi and Fibrobacter succinogenes. Overall, supplementation of 0.1% E. faecium SROD significantly increased the propionate and total volatile fatty acids concentrations but decreased the methane concentration while changing the microbial community abundance and composition.
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Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue. Appl Environ Microbiol 2019; 85:AEM.00032-19. [PMID: 31126949 DOI: 10.1128/aem.00032-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Epichloë coenophialum Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n = 6) or nontoxic (Max-Q; n = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the Firmicutes and Bacteroidetes phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the Erysipelotrichaceae family and delayed increases of the Ruminococcaceae and Lachnospiraceae families were among the major effects of E+ grazing. E+ also increased abundances within the Planctomycetes, Chloroflexi, and Proteobacteria phyla and the Clostridiaceae family. Multiple operational taxonomic units classified as Ruminococcaceae and Lachnospiraceae were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT.IMPORTANCE Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.
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Liu C, Wu H, Liu S, Chai S, Meng Q, Zhou Z. Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type. Front Microbiol 2019; 10:1116. [PMID: 31191470 PMCID: PMC6538947 DOI: 10.3389/fmicb.2019.01116] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/02/2019] [Indexed: 01/07/2023] Open
Abstract
Current knowledge about the relationships between ruminal bacterial communities and metabolite profiles in the yak rumen is limited. This is due to differences in the nutritional and metabolic features between yak and other ordinary cattle combined with difficulties associated with farm-based research and a lack of technical guidance. A comprehensive analysis of the composition and alterations in ruminal metabolites is required to advance the development of modern yak husbandry. In the current study, we characterized the effect of feed type on the ruminal fluid microbiota and metabolites in yak using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS). Bacteroidetes and Firmicutes were the predominant bacterial phyla in the yak rumen. At the genus level, the relative abundance of Bacteroidales BS11 gut group, Prevotellaceae UCG-003, Ruminococcaceae UCG-011, Bacteroidales RF16 group and Ruminococcaceae UCG-010 was significantly (P < 0.01) higher in the forage group compared to that in the concentrate group, while the concentrate group harbored higher proportions of Bacteroidales S24-7 group, Ruminococcaceae NK4A214, Succiniclasticum and Ruminococcus 2. Yak rumen metabolomics analysis combined with enrichment analysis revealed that feed type altered the concentrations of ruminal metabolites as well as the metabolic pattern, and significantly (P < 0.01) affected the concentrations of ruminal metabolites involved in protein digestion and absorption (e.g., L-arginine, ornithine, L-threonine, L-proline and β-alanine), purine metabolism (e.g., xanthine, hypoxanthine, deoxyadenosine and deoxyadenosine monophosphate) and fatty acid biosynthesis (e.g., stearic acid, myristic acid and arachidonic acid). Correlation analysis of the association of microorganisms with metabolite features provides us with a comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified between affected microbiota and certain metabolites, and these findings will contribute to the direction of future research in yak.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shujie Liu
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining, China
| | - Shatuo Chai
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China,*Correspondence: Zhenming Zhou
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Characterization of the rumen and fecal microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat prevention strategies. Sci Rep 2019; 9:4272. [PMID: 30862851 PMCID: PMC6414552 DOI: 10.1038/s41598-019-41017-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 01/02/2023] Open
Abstract
Frothy bloat is an often fatal digestive disorder of cattle grazing alfalfa pastures. The aim of this study was to investigate ruminal and fecal microbiota dynamics associated with development of alfalfa-induced frothy bloat and to further explore how bloat prevention strategies influence the composition of these microbial communities. In a 3 × 3 crossover experiment, twelve rumen-cannulated steers were sequentially subjected to: (1) pure alfalfa pasture, (2) pure alfalfa pasture supplemented with the pluronic detergent ALFASURE, and (3) alfalfa – sainfoin mixed pasture. Eleven out of 12 steers in pure alfalfa pasture developed clinical bloat, whereas ALFASURE treatment prevented the development of bloat in all 12 steers and alfalfa – sainfoin prevented bloat in 5 out of 11 steers. Development of bloat was associated with considerable shifts in the microbiota profile of rumen contents. In particular, the microbiota of solid rumen contents from bloated steers contained higher species richness and diversity. Streptococcus, Succinivibrio and unclassified Myxococcales were enriched in the rumen microbiota of bloated steers, whereas Fibrobacter and Ruminococcus were overrepresented in the rumen contents of non-bloated steers. Our results provide novel insights into bloat-associated shifts in the composition and predicted functional properties of the rumen microbiota of cattle grazing alfalfa pasture.
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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Zhong Y, Xue M, Liu J. Composition of Rumen Bacterial Community in Dairy Cows With Different Levels of Somatic Cell Counts. Front Microbiol 2018; 9:3217. [PMID: 30619238 PMCID: PMC6312127 DOI: 10.3389/fmicb.2018.03217] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/11/2018] [Indexed: 11/28/2022] Open
Abstract
Mastitis is an inflammatory disease, affects the dairy industry and has a severe economic impact. During subclinical mastitis, milk production and milk quality deteriorates. Recently, rumen microbial composition has been linked to rumen health, but few studies have investigated the effect of rumen microbiota on mammary health in cows. This study was undertaken to identify the rumen microbial composition and associated microbial fermentation in cows with different somatic cell counts (SCC), with the speculation that cows with different health statuses of the mammary gland have different rumen bacterial composition and diversity. A total of 319 Holstein dairy cows fed the same diet and under the same management were selected and divided into four groups as SCC1 (N = 175), SCC2 (N = 49), SCC3 (N = 49), and SCC4 (N = 46) with < 200,000, 200,001–500,000, 500,001–1,000,000, and >1,000,000 somatic cells/mL, respectively. Further, 20 cows with the lowest SCC and 20 cows with the highest SCC were identified. The rumen microbial composition was profiled using 16S rRNA sequencing, along with measurement of rumen fermentation parameters and milking performance. Compared to low SCC, cows with high SCC showed poorer milk yield, milk composition, and rumen volatile fatty acids concentration, but higher rumen bacterial diversity. Although the predominant rumen bacterial taxa did not vary among the SCC groups, the relative abundance of phyla SR1 and Actinobacteria, unclassified family Clostridiales and genus Butyrivibrio were significantly different. In addition, Proteobacteria and family Succinivibrionaceae were enriched in cows with low SCC. Our results suggest that specific rumen microbes are altered in cows with high SCC.
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Affiliation(s)
- Yifan Zhong
- MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Institute of Diary Science, Zhejiang University, Hangzhou, China
| | - Mingyuan Xue
- MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Institute of Diary Science, Zhejiang University, Hangzhou, China
| | - Jianxin Liu
- MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Institute of Diary Science, Zhejiang University, Hangzhou, China
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Hayakawa T, Nathan SKSS, Stark DJ, Saldivar DAR, Sipangkui R, Goossens B, Tuuga A, Clauss M, Sawada A, Fukuda S, Imai H, Matsuda I. First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes? ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:655-662. [PMID: 29992728 DOI: 10.1111/1758-2229.12677] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Foregut fermentation is well known to occur in a wide range of mammalian species and in a single bird species. Yet, the foregut microbial community of free-ranging, foregut-fermenting monkeys, that is, colobines, has not been investigated so far. We analysed the foregut microbiomes in four free-ranging proboscis monkeys (Nasalis larvatus) from two different tropical habitats with varying plant diversity (mangrove and riverine forests), in an individual from a semi-free-ranging setting with supplemental feeding, and in an individual from captivity, using high-throughput sequencing based on 16S ribosomal RNA genes. We found a decrease in foregut microbial diversity from a diverse natural habitat (riverine forest) to a low diverse natural habitat (mangrove forest), to human-related environments. Of a total of 2700 bacterial operational taxonomic units (OTUs) detected in all environments, only 153 OTUs were shared across all individuals, suggesting that they were not influenced by diet or habitat. These OTUs were dominated by Firmicutes and Proteobacteria. The relative abundance of the habitat-specific microbial communities showed a wide range of differences among living environments, although such bacterial communities appeared to be dominated by Firmicutes and Bacteroidetes, suggesting that those phyla are key to understanding the adaptive strategy in proboscis monkeys living in different habitats.
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Affiliation(s)
- Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
- Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
| | - Senthilvel K S S Nathan
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Danica J Stark
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Diana A Ramirez Saldivar
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Rosa Sipangkui
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
- Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff, CF10 3BA, UK
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Marcus Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Akiko Sawada
- Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Ikki Matsuda
- Japan Monkey Centre, Inuyama, Aichi, 484-0081, Japan
- Chubu University Academy of Emerging Sciences, 1200, Matsumoto-cho, Kasugai-shi, Aichi, 487-8501, Japan
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
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67
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Biscarini F, Palazzo F, Castellani F, Masetti G, Grotta L, Cichelli A, Martino G. Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile. PLoS One 2018; 13:e0205670. [PMID: 30496201 PMCID: PMC6264861 DOI: 10.1371/journal.pone.0205670] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/29/2018] [Indexed: 01/10/2023] Open
Abstract
The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon's and Fisher's alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.
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Affiliation(s)
- Filippo Biscarini
- Institute for Biology and Biotechnology in Agriculture (IBBA), CNR, Milano, Italy
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Fiorentina Palazzo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, Università di Teramo, Teramo, Italy
| | - Federica Castellani
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, Università di Teramo, Teramo, Italy
| | - Giulia Masetti
- School of Medicine, Cardiff University, Cardiff, United Kingdom
- Bioinformatics Unit, PTP Science Park, Lodi, Italy
| | - Lisa Grotta
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, Università di Teramo, Teramo, Italy
| | - Angelo Cichelli
- Department of Medical and Oral Sciences and Biotechnologies, Università degli Studi “Gabriele d’Annunzio”, Chieti, Italy
| | - Giuseppe Martino
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, Università di Teramo, Teramo, Italy
- * E-mail:
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68
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Koringa PG, Thakkar JR, Pandit RJ, Hinsu AT, Parekh MJ, Shah RK, Jakhesara SJ, Joshi CG. Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing. Funct Integr Genomics 2018; 19:237-247. [DOI: 10.1007/s10142-018-0640-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/25/2018] [Accepted: 10/12/2018] [Indexed: 01/14/2023]
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Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen. J Clin Med 2018; 7:jcm7100346. [PMID: 30322074 PMCID: PMC6210133 DOI: 10.3390/jcm7100346] [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: 08/31/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022] Open
Abstract
Background: The purpose of this study was to profile the bacterium in the ascites and blood of patients with acute surgical abdomen by metagenome analysis. Methods: A total of 97 patients with acute surgical abdomen were included in this study. Accompanied with the standard culture procedures, ascites and blood samples were collected for metagenome analysis to measure the relative abundance of bacteria among groups of patients and between blood and ascites. Results: Metagenomic analysis identified 107 bacterial taxa from the ascites of patients. A principal component analysis (PCA) could separate the bacteria of ascites into roughly three groups: peptic ulcer, perforated or non-perforated appendicitis, and a group which included cholecystitis, small bowel lesion, and colon perforation. Significant correlation between the bacteria of blood and ascites was found in nine bacterial taxa both in blood and ascites with more than 500 sequence reads. However, the PCA failed to separate the variation in the bacteria of blood into different groups of patients, and the bacteria of metagenomic analysis is only partly in accordance with those isolated from a conventional culture method. Conclusion: This study indicated that the metagenome analysis can provide limited information regarding the bacteria in the ascites and blood of patients with acute surgical abdomen.
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70
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Duffy EM, Tietze SM, Knoell AL, Aluthge ND, Fernando SC, Schmidt TS, Yates DT, Petersen JL. Rumen bacterial composition in lambs is affected by β-adrenergic agonist supplementation and heat stress at the phylum level. Transl Anim Sci 2018; 2:S145-S148. [PMID: 32704761 PMCID: PMC7200979 DOI: 10.1093/tas/txy052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 04/14/2018] [Indexed: 12/05/2022] Open
Affiliation(s)
- Erin M Duffy
- Department of Animal Science, University of Nebraska-Lincoln, NE
| | - Shauna M Tietze
- Department of Animal Science, University of Nebraska-Lincoln, NE
| | - Allison L Knoell
- Department of Animal Science, University of Nebraska-Lincoln, NE
| | - Nirosh D Aluthge
- Department of Animal Science, University of Nebraska-Lincoln, NE
| | | | - Ty S Schmidt
- Department of Animal Science, University of Nebraska-Lincoln, NE
| | - Dustin T Yates
- Department of Animal Science, University of Nebraska-Lincoln, NE
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71
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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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72
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Matthews C, Crispie F, Lewis E, Reid M, O’Toole PW, Cotter PD. The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency. Gut Microbes 2018; 10:115-132. [PMID: 30207838 PMCID: PMC6546327 DOI: 10.1080/19490976.2018.1505176] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/08/2018] [Accepted: 06/26/2018] [Indexed: 02/03/2023] Open
Abstract
Methane is generated in the foregut of all ruminant animals by the microorganisms present. Dietary manipulation is regarded as the most effective and most convenient way to reduce methane emissions (and in turn energy loss in the animal) and increase nitrogen utilization efficiency. This review examines the impact of diet on bovine rumen function and outlines what is known about the rumen microbiome. Our understanding of this area has increased significantly in recent years due to the application of omics technologies to determine microbial composition and functionality patterns in the rumen. This information can be combined with data on nutrition, rumen physiology, nitrogen excretion and/or methane emission to provide comprehensive insights into the relationship between rumen microbial activity, nitrogen utilisation efficiency and methane emission, with an ultimate view to the development of new and improved intervention strategies.
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Affiliation(s)
- Chloe Matthews
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Eva Lewis
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Michael Reid
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul W. O’Toole
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland
- Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland
- Nutribio, Co. Cork
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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73
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Terry SA, Ribeiro GDO, Gruninger RJ, Hunerberg M, Ping S, Chaves AV, Burlet J, Beauchemin KA, McAllister TA. Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers1. J Anim Sci 2018; 96:3863-3877. [PMID: 30169754 PMCID: PMC6127782 DOI: 10.1093/jas/sky265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/05/2018] [Indexed: 11/13/2022] Open
Abstract
Ruminants play an important role in food security, but there is a growing concern about the impact of cattle on the environment, particularly regarding greenhouse gas emissions. The objective of this study was to examine the effect of humic substances (HS) on rumen fermentation, nutrient digestibility, methane (CH4) emissions, and the rumen microbiome of beef heifers fed a barley silage-based diet. The experiment was designed as a replicated 4 × 4 Latin square using 8 ruminally cannulated Angus × Hereford heifers (758 ± 40.7 kg initial BW). Heifers were offered a basal diet consisting of 60% barley silage and 40% concentrate (DM basis) with either 0- (control), 100-, 200- or 300-mg granulated HS/kg BW. Each period was 28 d with 14 d of adaptation. Rumen samples were taken on day 15 at 0, 3, 6, and 12 h postfeeding. Total urine and feces were collected from days 18 to 22. Blood samples were taken on day 22 at 0 and 6 h postfeeding. Between days 26 and 28, heifers were placed in open-circuit respiratory chambers to measure CH4. Ruminal pH was recorded continuously during the periods of CH4 measurement using indwelling pH loggers. Intake was similar (P = 0.47) across treatments. Concentration of ammonia-N and counts of rumen protozoa responded quadratically (P = 0.03), where both increased at H100 and then decreased for the H300 treatments. Apparent total tract digestibility of CP (P = 0.04) was linearly increased by HS and total N retention (g/d, % N intake, g/kg BW0.75) was improved (P = 0.04) for HS when compared with the control. There was no effect of HS on CH4 production (g/d; P = 0.83); however, HS decreased the relative abundance of Proteobacteria (P = 0.04) and increased the relative abundance of Synergistetes (P = 0.01) and Euryarchaeota (P = 0.04). Results suggest that HS included at up to 300 mg/kg BW may improve N retention and CP digestibility, but there was no impact on CH4 production.
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Affiliation(s)
- Stephanie A Terry
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Gabriel de Oliveira Ribeiro
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- University of Calgary, Department of Production Animal Health, Calgary, Alberta, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Martin Hunerberg
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- University of Goettingen, Department of Animal Sciences, Goettingen, Germany
| | - Sheng Ping
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, China
| | - Alex V Chaves
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
| | - Jake Burlet
- Venture West Veterinary Services Ltd, Edmonton, Alberta, Canada
| | - Karen Ann Beauchemin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Tim Angus McAllister
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
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Abstract
Due to their high energy requirements, high-yielding dairy cows receive high-grain diets. This commonly jeopardises their gastrointestinal health by causing subacute ruminal acidosis (SARA) and hindgut acidosis. These disorders can disrupt nutrient utilisations, impair the functionalities of gastrointestinal microbiota, and reduce the absorptive and barrier capacities of gastrointestinal epithelia. They can also trigger inflammatory responses. The symptoms of SARA are not only due to a depressed rumen pH. Hence, the diagnosis of this disorder based solely on reticulo-rumen pH values is inaccurate. An accurate diagnosis requires a combination of clinical examinations of cows, including blood, milk, urine and faeces parameters, as well as analyses of herd management and feed quality, including the dietary contents of NDF, starch and physical effective NDF. Grain-induced SARA increases acidity and shifts availabilities of substrates for microorganisms in the reticulo-rumen and hindgut and can result in a dysbiotic microbiota that are characterised by low richness, diversity and functionality. Also, amylolytic microorganisms become more dominant at the expense of proteolytic and fibrolytic ones. Opportunistic microorganisms can take advantage of newly available niches, which, combined with reduced functionalities of epithelia, can contribute to an overall reduction in nutrient utilisation and increasing endotoxins and pathogens in digesta and faeces. The reduced barrier function of epithelia increases translocation of these endotoxins and other immunogenic compounds out of the digestive tract, which may be the cause of inflammations. This needs to be confirmed by determining the toxicity of these compounds. Cows differ in their susceptibility to poor gastrointestinal health, due to variations in genetics, feeding history, diet adaptation, gastrointestinal microbiota, metabolic adaptation, stress and infections. These differences may also offer opportunities for the management of gastrointestinal health. Strategies to prevent SARA include balancing the diet for physical effective fibre, non-fibre carbohydrates and starch, managing the different fractions of non-fibre carbohydrates, and consideration of the type and processing of grain and forage digestibility. Gastrointestinal health disorders due to high grain feeding may be attenuated by a variety of feed supplements and additives, including buffers, antibiotics, probiotics/direct fed microbials and yeast products. However, the efficacy of strategies to prevent these disorders must be improved. This requires a better understanding of the mechanisms through which these strategies affect the functionality of gastrointestinal microbiota and epithelia, and the immunity, inflammation and 'gastrointestinal-health robustness' of cows. More representative models to induce SARA are also needed.
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Lillehoj H, Liu Y, Calsamiglia S, Fernandez-Miyakawa ME, Chi F, Cravens RL, Oh S, Gay CG. Phytochemicals as antibiotic alternatives to promote growth and enhance host health. Vet Res 2018; 49:76. [PMID: 30060764 PMCID: PMC6066919 DOI: 10.1186/s13567-018-0562-6] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/02/2018] [Indexed: 01/14/2023] Open
Abstract
There are heightened concerns globally on emerging drug-resistant superbugs and the lack of new antibiotics for treating human and animal diseases. For the agricultural industry, there is an urgent need to develop strategies to replace antibiotics for food-producing animals, especially poultry and livestock. The 2nd International Symposium on Alternatives to Antibiotics was held at the World Organization for Animal Health in Paris, France, December 12-15, 2016 to discuss recent scientific developments on strategic antibiotic-free management plans, to evaluate regional differences in policies regarding the reduction of antibiotics in animal agriculture and to develop antibiotic alternatives to combat the global increase in antibiotic resistance. More than 270 participants from academia, government research institutions, regulatory agencies, and private animal industries from >25 different countries came together to discuss recent research and promising novel technologies that could provide alternatives to antibiotics for use in animal health and production; assess challenges associated with their commercialization; and devise actionable strategies to facilitate the development of alternatives to antibiotic growth promoters (AGPs) without hampering animal production. The 3-day meeting consisted of four scientific sessions including vaccines, microbial products, phytochemicals, immune-related products, and innovative drugs, chemicals and enzymes, followed by the last session on regulation and funding. Each session was followed by an expert panel discussion that included industry representatives and session speakers. The session on phytochemicals included talks describing recent research achievements, with examples of successful agricultural use of various phytochemicals as antibiotic alternatives and their mode of action in major agricultural animals (poultry, swine and ruminants). Scientists from industry and academia and government research institutes shared their experience in developing and applying potential antibiotic-alternative phytochemicals commercially to reduce AGPs and to develop a sustainable animal production system in the absence of antibiotics.
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Affiliation(s)
- Hyun Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20705 USA
| | - Yanhong Liu
- University of California, Davis, CA 95616 USA
| | - Sergio Calsamiglia
- Animal Nutrition and Welfare Service, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Mariano E. Fernandez-Miyakawa
- Instituto de Patobiología, Centro Nacional de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, Castelar, 1712 Buenos Aires, Argentina
| | - Fang Chi
- Amlan International, Chicago, IL 60611 USA
| | | | - Sungtaek Oh
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20705 USA
| | - Cyril G. Gay
- National Program Staff-Animal Health, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20705 USA
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76
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Doster E, Rovira P, Noyes NR, Burgess BA, Yang X, Weinroth MD, Lakin SM, Dean CJ, Linke L, Magnuson R, Jones KI, Boucher C, Ruiz J, Belk KE, Morley PS. Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period. Front Microbiol 2018; 9:1715. [PMID: 30105011 PMCID: PMC6077226 DOI: 10.3389/fmicb.2018.01715] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/09/2018] [Indexed: 02/01/2023] Open
Abstract
The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.
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Affiliation(s)
- Enrique Doster
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Pablo Rovira
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Noelle R Noyes
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MI, United States
| | - Brandy A Burgess
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Xiang Yang
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States
| | - Margaret D Weinroth
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Steven M Lakin
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Christopher J Dean
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Lyndsey Linke
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Roberta Magnuson
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kenneth I Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, United States
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Jamie Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Keith E Belk
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Paul S Morley
- Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States.,Department of Clinical Sciences, Colorado State University, Fort Collins, CO, United States
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77
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Duque E, Daddaoua A, Cordero BF, Udaondo Z, Molina‐Santiago C, Roca A, Solano J, Molina‐Alcaide E, Segura A, Ramos J. Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. Microb Biotechnol 2018; 11:781-787. [PMID: 29663699 PMCID: PMC6011990 DOI: 10.1111/1751-7915.13269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/01/2022] Open
Abstract
The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.
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Affiliation(s)
- Estrella Duque
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Abdelali Daddaoua
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Faculty of PharmacyDepartment of PharmacologyUniversity of Granada18071GranadaSpain
| | - Baldo F. Cordero
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Zulema Udaondo
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Carlos Molina‐Santiago
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Amalia Roca
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | - Jennifer Solano
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | | | - Ana Segura
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
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78
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Pitta DW, Indugu N, Baker L, Vecchiarelli B, Attwood G. Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows. J Dairy Sci 2018; 101:7661-7679. [PMID: 29859694 DOI: 10.3168/jds.2017-13858] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/30/2018] [Indexed: 11/19/2022]
Abstract
Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.
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Affiliation(s)
- Dipti W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
| | - Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348
| | - Linda Baker
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348
| | - Graeme Attwood
- Rumen Microbial Genomics, Ag Research, Palmerston North, New Zealand 11222
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79
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Elolimy AA, Moisá SJ, Brennan KM, Smith AC, Graugnard D, Shike DW, Loor JJ. Skeletal muscle and liver gene expression profiles in finishing steers supplemented with Amaize. Anim Sci J 2018; 89:1107-1119. [PMID: 29808540 DOI: 10.1111/asj.13041] [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: 11/30/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022]
Abstract
Our main objective was to evaluate the effects of feeding α-amylase (Amaize, Alltech Inc., Nicholasville, KY, USA) for 140 days on skeletal muscle and liver gene transcription in beef steers. Steers fed Amaize had lower average daily gain (p = .03) and gain:feed ratio (p = .05). No differences (p > .10) in serum metabolites or carcass traits were detected between the two groups but Amaize steers tended (p < .15) to have increased 12th rib fat depth. Microarray analysis of skeletal muscle revealed 21 differentially expressed genes (DEG), where 14 were up-regulated and seven were down-regulated in Amaize-fed steers. The bioinformatics analysis indicated that metabolic pathways involved in fat formation and deposition, stress response, and muscle function were activated, while myogenesis was inhibited in Amaize-fed steers. The quantitative PCR results for liver revealed a decrease (p < .01) in expression of fatty acid binding protein 1 (FABP1) and 3-hydroxybutyrate dehydrogenase 1 (BDH1) with Amaize. Because these genes are key for intracellular fatty acid transport, oxidation and ketone body production, data suggest a reduction in hepatic lipid catabolism. Future work to investigate potential positive effects of Amaize on cellular stress response, muscle function, and liver function in beef cattle appears warranted.
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Affiliation(s)
- Ahmed A Elolimy
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois
| | - Sonia J Moisá
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, Auburn University, Auburn, Alabama
| | - Kristen M Brennan
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Allison C Smith
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Daniel Graugnard
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Daniel W Shike
- Department of Animal Sciences, University of Illinois, Urbana, Illinois
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, Illinois
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80
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Schären M, Frahm J, Kersten S, Meyer U, Hummel J, Breves G, Dänicke S. Interrelations between the rumen microbiota and production, behavioral, rumen fermentation, metabolic, and immunological attributes of dairy cows. J Dairy Sci 2018; 101:4615-4637. [DOI: 10.3168/jds.2017-13736] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
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81
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O’Callaghan TF, Vázquez-Fresno R, Serra-Cayuela A, Dong E, Mandal R, Hennessy D, McAuliffe S, Dillon P, Wishart DS, Stanton C, Ross RP. Pasture Feeding Changes the Bovine Rumen and Milk Metabolome. Metabolites 2018; 8:E27. [PMID: 29642378 PMCID: PMC6027121 DOI: 10.3390/metabo8020027] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to examine the effects of two pasture feeding systems-perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)-and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems. The microbiota present in rumen liquid and solid portions were analysed using 16S rRNA gene sequencing, while ¹H-NMR untargeted metabolomic analysis was performed on rumen fluid and raw milk samples. The rumen microbiota composition was not found to be significantly altered by any feeding system in this study, likely as a result of a shortened adaptation period (two weeks' exposure time). In contrast, feeding system had a significant effect on both the rumen and milk metabolome. Increased concentrations of volatile fatty acids including acetic acid, an important source of energy for the cow, were detected in the rumen of TMR and CLV-fed cows. Pasture feeding resulted in significantly higher concentrations of isoacids in the rumen. The ruminal fluids of both CLV and GRS-fed cows were found to have increased concentrations of p-cresol, a product of microbiome metabolism. CLV feeding resulted in increased rumen concentrations of formate, a substrate compound for methanogenesis. The TMR feeding resulted in significantly higher rumen choline content, which contributes to animal health and milk production, and succinate, a product of carbohydrate metabolism. Milk and rumen-fluids were shown to have varying levels of dimethyl sulfone in each feeding system, which was found to be an important compound for distinguishing between the diets. CLV feeding resulted in increased concentrations of milk urea. Milk from pasture-based feeding systems was shown to have significantly higher concentrations of hippuric acid, a potential biomarker of pasture-derived milk. This study has demonstrated that ¹H-NMR metabolomics coupled with multivariate analysis is capable of distinguishing both rumen-fluid and milk derived from cows on different feeding systems, specifically between indoor TMR and pasture-based diets used in this study.
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Affiliation(s)
- Tom F. O’Callaghan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (T.F.O.); (C.S.)
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
| | - Rosa Vázquez-Fresno
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G1C9, Canada; (R.V.-F.); (A.S.-C.); (E.D.); (R.M.); (D.S.W.)
| | - Arnau Serra-Cayuela
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G1C9, Canada; (R.V.-F.); (A.S.-C.); (E.D.); (R.M.); (D.S.W.)
| | - Edison Dong
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G1C9, Canada; (R.V.-F.); (A.S.-C.); (E.D.); (R.M.); (D.S.W.)
| | - Rupasri Mandal
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G1C9, Canada; (R.V.-F.); (A.S.-C.); (E.D.); (R.M.); (D.S.W.)
| | - Deirdre Hennessy
- Teagasc Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (D.H.); (S.M.); (P.D.)
| | - Stephen McAuliffe
- Teagasc Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (D.H.); (S.M.); (P.D.)
- School of Biological Sciences, Queens University, Belfast BT7 1NN, Northern Ireland, UK
| | - Pat Dillon
- Teagasc Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (D.H.); (S.M.); (P.D.)
| | - David S. Wishart
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G1C9, Canada; (R.V.-F.); (A.S.-C.); (E.D.); (R.M.); (D.S.W.)
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (T.F.O.); (C.S.)
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland; (T.F.O.); (C.S.)
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
- College of Science, Engineering and Food Science, University College Cork, T12 YT20 Cork, Ireland
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82
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Krizsan SJ, Mateos-Rivera A, Bertilsson S, Felton A, Anttila A, Ramin M, Vaga M, Gidlund H, Huhtanen P. An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods. Ecol Evol 2018; 8:4183-4196. [PMID: 29721290 PMCID: PMC5916270 DOI: 10.1002/ece3.3920] [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: 12/02/2016] [Revised: 10/18/2017] [Accepted: 12/06/2017] [Indexed: 12/14/2022] Open
Abstract
Evolutionary morphological and physiological differences between browsers and grazers contribute to species‐specific digestion efficiency of food resources. Rumen microbial community structure of browsers is supposedly adapted to characteristic nutrient composition of the diet source. If this assumption is correct, domesticated ruminants, or grazers, are poor model animals for assessing the nutritional value of food consumed by browsing game species. In this study, typical spring and summer foods of the European moose (Alces alces) were combined with rumen fluid collected from both dairy cows (Bos taurus) and from moose, with the aim of comparing fermentation efficiency and microbial community composition. The nutritional value of the food resources was characterized by chemical analysis and advanced in vitro measurements. The study also addressed whether or not feed evaluation based on in vitro techniques with cattle rumen fluid as inoculum could be a practical alternative when evaluating the nutritional value of plants consumed by wild browsers. Our results suggest that the fermentation characteristics of moose spring and summer food are partly host‐specific and related to the contribution of the bacterial phyla Firmicutes and Bacteriodetes to the rumen microbial community. Host‐specific adaptations of the ruminal microbial community structure could be explained from the evolutionary adaptations related to feeding habitats and morphophysiological differences between browsers and grazers. However, the observed overall differences in microbial community structure could not be related to ruminal digestion parameters measured in vitro. The in vitro evaluation of digestion efficiency reveals that equal amounts of methane were produced across all feed samples regardless of whether the ruminal fluid was from moose or dairy cow. The results of this study suggested that the nutritional value of browsers' spring and summer food can be predicted using rumen fluid from domesticated grazers as inoculum in in vitro assessments of extent of digestion when excluding samples of the white water lily root, but not of fermentation characteristics as indicated by the proportions of individual fermentation fatty acids to the total of volatile fatty acids.
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Affiliation(s)
- Sophie J Krizsan
- Department of Agricultural Research for Northern Sweden Swedish University of Agricultural Sciences Umeå Sweden
| | - Alejandro Mateos-Rivera
- Limnology and Science for Life Laboratory Department of Ecology and Genetics Uppsala University Uppsala Sweden.,Present address: Department of Science and Technology Høgskulen i Sogn og Fjordane Sogndal Norway
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Annika Felton
- Department of Southern Swedish Forest Research Centre Swedish University of Agricultural Sciences Alnarp Sweden
| | - Anne Anttila
- Department of Agricultural Sciences Helsinki University Helsinki Finland
| | - Mohammad Ramin
- Department of Agricultural Research for Northern Sweden Swedish University of Agricultural Sciences Umeå Sweden
| | - Merko Vaga
- Department of Agricultural Research for Northern Sweden Swedish University of Agricultural Sciences Umeå Sweden
| | - Helena Gidlund
- Department of Agricultural Research for Northern Sweden Swedish University of Agricultural Sciences Umeå Sweden
| | - Pekka Huhtanen
- Department of Agricultural Research for Northern Sweden Swedish University of Agricultural Sciences Umeå Sweden
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83
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Pandit RJ, Hinsu AT, Patel SH, Jakhesara SJ, Koringa PG, Bruno F, Psifidi A, Shah SV, Joshi CG. Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches. Syst Appl Microbiol 2018; 41:374-385. [PMID: 29555111 DOI: 10.1016/j.syapm.2018.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 01/17/2023]
Abstract
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.
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Affiliation(s)
- Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Shriram H Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Fosso Bruno
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK; Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - S V Shah
- Livestock Research Station, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India.
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84
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Cammack KM, Austin KJ, Lamberson WR, Conant GC, Cunningham HC. RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production. J Anim Sci 2018; 96:752-770. [PMID: 29385535 PMCID: PMC6140983 DOI: 10.1093/jas/skx053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Abstract
The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen microbiome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.
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Affiliation(s)
- Kristi M Cammack
- Department of Animal Science and West River Ag Center, South Dakota State University, Rapid City, SD
| | | | | | - Gavin C Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
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85
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Vaidya JD, van den Bogert B, Edwards JE, Boekhorst J, van Gastelen S, Saccenti E, Plugge CM, Smidt H. The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows. Front Microbiol 2018; 9:92. [PMID: 29445366 PMCID: PMC5797766 DOI: 10.3389/fmicb.2018.00092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/16/2018] [Indexed: 12/01/2022] Open
Abstract
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method (p < 0.001) and fraction (p < 0.001). The 260/280 ratio was not affected by extraction (p = 0.08) but was affected by fraction (p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method (p < 0.001) but not affected by fraction (p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction (p = 0.012), and that PBB (p = 0.012) and FDSS (p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both. In summary, the comprehensive assessment of observed communities of bacteria, archaea and anaerobic fungi described here provides insight into a rational basis for selecting an optimal methodology to obtain a representative picture of the rumen microbiota.
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Affiliation(s)
- Jueeli D. Vaidya
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Bartholomeus van den Bogert
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Joan E. Edwards
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Sanne van Gastelen
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Animal Nutrition Group, Wageningen University and Research, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
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86
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Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9610810. [PMID: 29445749 PMCID: PMC5763072 DOI: 10.1155/2017/9610810] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/03/2017] [Indexed: 11/29/2022]
Abstract
The use of phytogenic dietary additives is being evaluated as a means to improve animal productivity. The effect of tannins seems to be the influence not only directly on the digestive process through binding of dietary proteins but also indirectly over their effects on gastrointestinal microbiota. High-throughput sequencing of 16S rRNA gene was used to analyze the impact of dietary supplementation with a blend of chestnut and quebracho tannins on the rumen microbiota of Holstein steers. Bacterial richness was lower in tannins treated animals, while the overall population structure of rumen microbiota was not significantly disturbed by tannins. The ratio of the phyla Firmicutes and Bacteroidetes, a parameter associated with energy harvesting function, was increased in tannins supplemented animals, essentially due to the selective growth of Ruminococcaceae over members of genus Prevotella. Fibrolytic, amylolytic, and ureolytic bacterial communities in the rumen were altered by tannins, while methanogenic archaea were reduced. Furthermore, ruminal pH was significantly higher in animals supplemented with tannins than in the control group, while urease activity exhibited the opposite pattern. Further work is necessary to assess the relation between tannins impact on rumen microbiota and alteration of rumen fermentation parameters associated with bovine performance.
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87
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Oyama LB, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Privé F, Vallin HE, Wilkinson TJ, Golyshin PN, Golyshina OV, Mikut R, Hilpert K, Richards J, Wootton M, Edwards JE, Maresca M, Perrier J, Lundy FT, Luo Y, Zhou M, Hess M, Mantovani HC, Creevey CJ, Huws SA. The rumen microbiome: an underexplored resource for novel antimicrobial discovery. NPJ Biofilms Microbiomes 2017; 3:33. [PMID: 29214045 PMCID: PMC5711939 DOI: 10.1038/s41522-017-0042-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/04/2017] [Accepted: 11/06/2017] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application. Anti-microbial molecules made by microbes in the gut of ruminant animals could become new weapons against antibiotic-resistant infections. An international team of researchers led by Sharon Huws at Queen’s University Belfast, UK, identified three anti-microbial peptides in the rumen of animals such as cattle, sheep and goats. The peptides—short proteins—were highly active in laboratory trials against several clinically important drug-resistant infections. These included methicillin resistant Staphylococcus aureus (MRSA), a notorious cause of life-threatening infections, especially in patients with weakened immunity. There is growing interest in using peptides as alternatives to existing antibiotics. The findings, initiated by examining a ‘library’ of molecular data, suggest that the rumen is an under-explored resource that may harbor many medically useful antimicrobials. The possibilities should be investigated further, with promising molecules being tested in clinical conditions.
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Affiliation(s)
- Linda B Oyama
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Susan E Girdwood
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Alan R Cookson
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Florence Privé
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Hannah E Vallin
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Toby J Wilkinson
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | | | | | - Ralf Mikut
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein, Leopoldshafen, Germany
| | - Kai Hilpert
- Institute of Infection and Immunity, St. George's University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Jennifer Richards
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Joan E Edwards
- Wageningen University & Research, 6708 WE, Wageningen, Netherlands
| | - Marc Maresca
- Aix Marseille Université, CNRS, Central Marseille, iSm2, Marseille, France
| | - Josette Perrier
- Aix Marseille Université, CNRS, Central Marseille, iSm2, Marseille, France
| | - Fionnuala T Lundy
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL UK
| | - Yu Luo
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, BT9 7BL UK
| | - Mei Zhou
- School of Pharmacy, Queens's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK
| | - Matthias Hess
- UC Davis, College of Agricultural and Environmental Sciences, California, 95616 USA
| | - Hilario C Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, 36570-900 Brazil
| | - Christopher J Creevey
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA UK
| | - Sharon A Huws
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7BL UK
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88
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Humer E, Petri RM, Aschenbach JR, Bradford BJ, Penner GB, Tafaj M, Südekum KH, Zebeli Q. Invited review: Practical feeding management recommendations to mitigate the risk of subacute ruminal acidosis in dairy cattle. J Dairy Sci 2017; 101:872-888. [PMID: 29153519 DOI: 10.3168/jds.2017-13191] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/28/2017] [Indexed: 01/04/2023]
Abstract
Rumen health is of vital importance in ensuring healthy and efficient dairy cattle production. Current feeding programs for cattle recommend concentrate-rich diets to meet the high nutritional needs of cows during lactation and enhance cost-efficiency. These diets, however, can impair rumen health. The term "subacute ruminal acidosis" (SARA) is often used as a synonym for poor rumen health. In this review, we first describe the physiological demands of cattle for dietary physically effective fiber. We also provide background information on the importance of enhancing salivary secretions and short-chain fatty acid absorption across the stratified squamous epithelium of the rumen; thus, preventing the disruption of the ruminal acid-base balance, a process that paves the way for acidification of the rumen. On-farm evaluation of dietary fiber adequacy is challenging for both nutritionists and veterinarians; therefore, this review provides practical recommendations on how to evaluate the physical effectiveness of the diet based on differences in particle size distribution, fiber content, and the type of concentrate fed, both when the latter is part of total mixed ration and when it is supplemented in partial mixed rations. Besides considering the absolute amount of physically effective fiber and starch types in the diet, we highlight the role of several feeding management factors that affect rumen health and should be considered to control and mitigate SARA. Most importantly, transitional feeding to ensure gradual adaptation of the ruminal epithelium and microbiota; monitoring and careful management of particle size distribution; controlling feed sorting, meal size, and meal frequency; and paying special attention to primiparous cows are some of the feeding management tools that can help in sustaining rumen health in high-producing dairy herds. Supplementation of feed additives including yeast products, phytogenic compounds, and buffers may help attenuate SARA, especially during stress periods when the risk of a deficiency of physically effective fiber in the diet is high, such as during early lactation. However, the usage of feed additives cannot fully compensate for suboptimal feeding management.
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Affiliation(s)
- E Humer
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - R M Petri
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - J R Aschenbach
- Institute of Veterinary Physiology, Freie Universität Berlin, 14163 Berlin, Germany
| | - B J Bradford
- Department of Animal Sciences and Industry, Kansas State University, Manhattan 66506
| | - G B Penner
- Animal and Poultry Science, University of Saskatchewan, Saskatoon, Canada, S7N 5A8
| | - M Tafaj
- Department of Animal Science, Agriculture University of Tirana, Tirana 1000, Albania
| | - K-H Südekum
- Institute of Animal Science, University of Bonn, 53115 Bonn, Germany
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
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89
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Avramenko RW, Redman EM, Lewis R, Bichuette MA, Palmeira BM, Yazwinski TA, Gilleard JS. The use of nemabiome metabarcoding to explore gastro-intestinal nematode species diversity and anthelmintic treatment effectiveness in beef calves. Int J Parasitol 2017; 47:893-902. [DOI: 10.1016/j.ijpara.2017.06.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/12/2022]
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90
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Kim SH, Mamuad LL, Kim EJ, Sung HG, Bae GS, Cho KK, Lee C, Lee SS. Effect of different concentrate diet levels on rumen fluid inoculum used for determination of in vitro rumen fermentation, methane concentration, and methanogen abundance and diversity. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1394170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Seon-Ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
- Department of Animal Sciences Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
| | - Lovelia L. Mamuad
- Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Eun-Joong Kim
- Department of Animal Science, Kyungpook National University, Sangju, South Korea
| | - Ha-Guyn Sung
- Department of Animal Science and Technology, Sangji University, Gangwon-do, South Korea
| | - Gui-Seck Bae
- Department of Animal Science and Technology, Chung-Ang University, Ansung, South Korea
| | - Kwang-Keun Cho
- Gyeongnam National University of Science and Technology, Jinju, South Korea
| | - Chanhee Lee
- Department of Animal Sciences Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
| | - Sang-Suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
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91
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Vidal S, Kegler K, Posthaus H, Perreten V, Rodriguez-Campos S. Amplicon sequencing of bacterial microbiota in abortion material from cattle. Vet Res 2017; 48:64. [PMID: 29017611 PMCID: PMC5633877 DOI: 10.1186/s13567-017-0470-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/13/2017] [Indexed: 01/21/2023] Open
Abstract
Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.
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Affiliation(s)
- Sara Vidal
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, Theodor Kocher Institute, University of Bern, Freiestrasse 1, 3001, Bern, Switzerland
| | - Kristel Kegler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Horst Posthaus
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland.
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92
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Indugu N, Vecchiarelli B, Baker LD, Ferguson JD, Vanamala JKP, Pitta DW. Comparison of rumen bacterial communities in dairy herds of different production. BMC Microbiol 2017; 17:190. [PMID: 28854878 PMCID: PMC5577838 DOI: 10.1186/s12866-017-1098-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/22/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The purpose of this study was to compare the rumen bacterial composition in high and low yielding dairy cows within and between two dairy herds. Eighty five Holstein dairy cows in mid-lactation (79-179 days in milk) were selected from two farms: Farm 12 (M305 = 12,300 kg; n = 47; 24 primiparous cows, 23 multiparous cows) and Farm 9 (M305 = 9700 kg; n = 38; 19 primiparous cows, 19 multiparous cows). Each study cow was sampled once using the stomach tube method and processed for 16S rRNA gene amplicon sequencing using the Ion Torrent (PGM) platform. RESULTS Differences in bacterial communities between farms were greater (Adonis: R2 = 0.16; p < 0.001) than within farm. Five bacterial lineages, namely Prevotella (48-52%), unclassified Bacteroidales (10-12%), unclassified bacteria (5-8%), unclassified Succinivibrionaceae (1-7%) and unclassified Prevotellaceae (4-5%) were observed to differentiate the community clustering patterns among the two farms. A notable finding is the greater (p < 0.05) contribution of Succinivibrionaceae lineages in Farm 12 compared to Farm 9. Furthermore, in Farm 12, Succinivibrionaceae lineages were higher (p < 0.05) in the high yielding cows compared to the low yielding cows in both primiparous and multiparous groups. Prevotella, S24-7 and Succinivibrionaceae lineages were found in greater abundance on Farm 12 and were positively correlated with milk yield. CONCLUSIONS Differences in rumen bacterial populations observed between the two farms can be attributed to dietary composition, particularly differences in forage type and proportion in the diets. A combination of corn silage and alfalfa silage may have contributed to the increased proportion of Proteobacteria in Farm 12. It was concluded that Farm 12 had a greater proportion of specialist bacteria that have the potential to enhance rumen fermentative digestion of feedstuffs to support higher milk yields.
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Affiliation(s)
- Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Linda D Baker
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - James D Ferguson
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Jairam K P Vanamala
- Department of Food Science, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Penn State Hershey Cancer Institute, Hershey, PA, 17033, USA
| | - Dipti W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA.
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93
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Wauters J, Van Meulebroek L, Fichant E, Delahaut P, Vanhaecke L. Discrimination between Synthetically Administered and Endogenous Thiouracil Based on Monitoring of Urine, Muscle, and Thyroid Tissue: An in Vivo Study in Young and Adult Bovines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6231-6239. [PMID: 28692258 DOI: 10.1021/acs.jafc.7b01920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thiouracil (TU), synthesized for its thyroid-regulating capacities and alternatively misused in livestock for its weight-gaining effects, is acknowledged to have an endogenous origin. Discrimination between low-level abuse and endogenous occurrence is challenging and unexplored in an experimental setting. Therefore, cows (n = 16) and calves (n = 18) were subjected to a rapeseed-supplemented diet or treated with synthetic TU. Significant higher urinary TU levels were recorded after TU administration (<CCα, 15 642 μg L-1) compared to rapeseed supplementation (<CCα, 65.8 μg L-1), however, with overlapping values. TU was not detected in the edible meat; however, concentrations between the CCα and 10 μg kg-1 were noted in thyroid tissue of calves and cows following rapeseed supplementation. The latter concentrations were significantly higher in thyroid tissue of calves (22.9-41.8 μg kg-1) and cows (16.9-36.7 μg kg-1) after synthetic TU administration. These results strongly point toward thyroid analysis as a discriminatory tool.
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Affiliation(s)
- J Wauters
- Ghent University , Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - L Van Meulebroek
- Ghent University , Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - E Fichant
- CER Groupe , Health Department, 6900 Marloie, Belgium
| | - P Delahaut
- CER Groupe , Health Department, 6900 Marloie, Belgium
| | - L Vanhaecke
- Ghent University , Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
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94
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McCann JC, Elolimy AA, Loor JJ. Rumen Microbiome, Probiotics, and Fermentation Additives. Vet Clin North Am Food Anim Pract 2017; 33:539-553. [PMID: 28764865 DOI: 10.1016/j.cvfa.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Fermentation of a variety of feedstuffs by the ruminal microbiome is the distinctive feature of the ruminant digestive tract. The host derives energy and nutrients from microbiome activity; these organisms are essential to survival. Advances in DNA sequencing and bioinformatics have redefined the rumen microbial community. Current research seeks to connect our understanding of the rumen microbiome with nutritional strategies in ruminant livestock systems and their associated digestive disorders. These efforts align with a growing number of products designed to improve ruminal fermentation to benefit the overall efficiency of ruminant livestock production and health.
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Affiliation(s)
- Joshua C McCann
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
| | - Ahmed A Elolimy
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
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95
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Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Front Chem 2017; 5:51. [PMID: 28748180 PMCID: PMC5506224 DOI: 10.3389/fchem.2017.00051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/27/2017] [Indexed: 11/14/2022] Open
Abstract
Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.
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Affiliation(s)
- Linda B Oyama
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Jean-Adrien Crochet
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Joan E Edwards
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Susan E Girdwood
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Alan R Cookson
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Narcis Fernandez-Fuentes
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Kai Hilpert
- Institute of Infection and Immunity, St George's University of LondonLondon, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor UniversityBangor, United Kingdom
| | - Olga V Golyshina
- School of Biological Sciences, Bangor UniversityBangor, United Kingdom
| | - Florence Privé
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Matthias Hess
- College of Agricultural and Environmental Sciences, University of California, DavisDavis, CA, United States
| | | | - Christopher J Creevey
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Sharon A Huws
- Medical Biology Centre, School of Biological Sciences, Queen's University BelfastBelfast, United Kingdom
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96
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Schären M, Kiri K, Riede S, Gardener M, Meyer U, Hummel J, Urich T, Breves G, Dänicke S. Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring. Front Microbiol 2017; 8:744. [PMID: 28512453 PMCID: PMC5411454 DOI: 10.3389/fmicb.2017.00744] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/10/2017] [Indexed: 02/04/2023] Open
Abstract
In spring dairy cows are often gradually transitioned from a silage- and concentrate-based ration (total mixed ration, TMR) to pasture. Rumen microbiota adaptability is a key feature of ruminant survival strategy. However, only little is known on the temporal and spatial microbial alterations involved. This study aims to investigate how the rumen liquid (LAAB), particle (PAAB), and epithelium (EAAB) associated archaea and bacteria are influenced by this nutritional change. A 10-wk trial was performed, including 10 rumen-fistulated dairy cows, equally divided into a pasture- and a confinement- group (PG and CG). The CG stayed on a TMR-based ration, while the PG was gradually transitioned from TMR to pasture (wk 1: TMR-only, wk 2: 3 h/day on pasture, wk 3 & 4: 12 h/day on pasture, wk 5-10: pasture-only). In wk 1, wk 5, and wk 10 samples of solid and liquid rumen contents, and papillae biopsies were collected. The DNA was isolated, and PCR-SSCP and 16S rRNA gene amplicon sequencing analysis were performed. Cluster analysis revealed a higher similarity between LAAB and PAAB, compared to the EAAB, characterized by higher species diversity. At all three locations the microbiota was significantly influenced by the ration change, opposite the generally acknowledged hypothesis that the EAAB remain more consistent throughout dietary changes. Even though the animals in the PG were already on a full-grazing ration for 4-6 days in wk 5, the microbiota at all three locations was significantly different compared to wk 10, suggesting an adaptation period of several days to weeks. This is in line with observations made on animal level, showing a required time for adaptation of 2-3 weeks for production and metabolic variables. A large part of the rumen prokaryote species remained unaltered upon transition to pasture and exhibited a strong host influence, supporting the hypothesis that the rumen microbiota consists of a core and a variable microbiota. For the effect of the location as well as the ration change either very similar or opposite trends among member species of common taxa were observed, demonstrating that microbes that are phylogenetically close may still exhibit substantially different phenotypes and functions.
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Affiliation(s)
- Melanie Schären
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal HealthBrunswick, Germany
| | - Kerstin Kiri
- Department of Physiology, University of Veterinary Medicine HannoverHannover, Germany
| | - Susanne Riede
- Department of Physiology, University of Veterinary Medicine HannoverHannover, Germany
| | - Mark Gardener
- Environment, Earth & Ecosystems, The Open UniversityMilton Keynes, UK
| | - Ulrich Meyer
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal HealthBrunswick, Germany
| | - Jürgen Hummel
- Department of Animal Sciences, University of GoettingenGoettingen, Germany
| | - Tim Urich
- Institute of Microbiology, University of GreifswaldGreifswald, Germany
| | - Gerhard Breves
- Department of Physiology, University of Veterinary Medicine HannoverHannover, Germany
| | - Sven Dänicke
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal HealthBrunswick, Germany
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97
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Carvalho IPCD, Fiorentini G, Castagnino PDS, Jesus RBD, Messana JD, Granja-Salcedo YT, Detmann E, Padmanabha J, McSweeney CS, Berchielli TT. Supplementation with lipid sources alters the ruminal fermentation and duodenal flow of fatty acids in grazing Nellore steers. Anim Feed Sci Technol 2017. [DOI: 10.1016/j.anifeedsci.2017.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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98
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Liu C, Li XH, Chen YX, Cheng ZH, Duan QH, Meng QH, Tao XP, Shang B, Dong HM. Age-Related Response of Rumen Microbiota to Mineral Salt and Effects of Their Interactions on Enteric Methane Emissions in Cattle. MICROBIAL ECOLOGY 2017; 73:590-601. [PMID: 27924402 DOI: 10.1007/s00248-016-0888-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
Mineral salt bricks are often used in cow raising as compensation for mineral losses to improve milk yield, growth, and metabolic activity. Generally, effects of minerals are partially thought to result from improvement of microbial metabolism, but their influence on the rumen microbiota has rarely been documented to date. In this study, we investigated the response of microbiota to mineral salt in heifer and adult cows and evaluated ruminal fermentation and enteric methane emissions of cows fed mineral salts. Twelve lactating Holstein cows and twelve heifers fed a total mixed ration (TMR) diet were randomly allocated into two groups, respectively: a treatment group comprising half of the adults and heifers that were fed mineral salt and a control group containing the other half fed a diet with no mineral salt supplement. Enteric methane emissions were reduced by 9.6% (P < 0.05) in adults ingesting a mineral salt diet, while concentrations of ruminal ammonia, butyrate, and propionate were increased to a significant extent (P < 0.05). Enteric methane emissions were also reduced in heifers ingesting a mineral salt diet, but not to a significant extent (P > 0.05). Moreover, the concentrations of ammonia and volatile fatty acids (VFAs) were not significantly altered in heifers (P > 0.05). Based on these results, we performed high-throughput sequencing to explore the bacterial and archaeal communities of the rumen samples. Succiniclasticum and Prevotella, two propionate-producing bacteria, were predominant in samples of both adults and heifers. At the phylotype level, mineral salt intake led to a significant shift from Succiniclasticum to Prevotella and Prevotellaceae populations in adults. In contrast, reduced abundance of Succiniclasticum and Prevotella phylotypes was observed, with no marked shift in propionate-producing bacteria in heifers. Methanogenic archaea were not significantly abundant between groups, either in adult cows or heifers. The shift of Succiniclasticum to Prevotella and Prevotellaceae in adults suggests a response of microbiota to mineral salt that contributes to higher propionate production, which competes for hydrogen utilized by methanogens. Our data collectively indicate that a mineral salt diet can alter interactions of bacterial taxa that result in enteric methane reduction, and this effect is also influenced in an age-dependent manner.
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Affiliation(s)
- C Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China
| | - X H Li
- Agro-environmental Protection Institute, Ministry of Agriculture, Tianjin, 300191, China
- Rural Energy and Environment Agency, Ministry of Agriculture, Beijing, 100125, China
| | - Y X Chen
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China
| | - Z H Cheng
- Tianjin Agricultural Environmental Protection Management and Monitoring Station, Tianjin, 300061, China
| | - Q H Duan
- Rural Energy and Environment Agency, Ministry of Agriculture, Beijing, 100125, China
| | - Q H Meng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China
| | - X P Tao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China
| | - B Shang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China
| | - H M Dong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun Southern St. No. 12, 100081, Haidian District, Beijing, China.
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99
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Dieho K, van den Bogert B, Henderson G, Bannink A, Ramiro-Garcia J, Smidt H, Dijkstra J. Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance. J Dairy Sci 2017; 100:2695-2710. [DOI: 10.3168/jds.2016-11982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/28/2016] [Indexed: 11/19/2022]
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100
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Zhou Z, Fang L, Meng Q, Li S, Chai S, Liu S, Schonewille JT. Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak ( Bos grunniens). Front Microbiol 2017; 8:179. [PMID: 28223980 PMCID: PMC5293774 DOI: 10.3389/fmicb.2017.00179] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/24/2017] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the microbial community composition in the rumen of yaks under different feeding regimes. Microbial communities were assessed by sequencing bacterial and archaeal 16S ribosomal RNA gene fragments obtained from yaks (Bos grunniens) from Qinghai-Tibetan Plateau, China. Samples were obtained from 14 animals allocated to either pasture grazing (Graze), a grazing and supplementary feeding regime (GSF), or an indoor feeding regime (Feed). The predominant bacterial phyla across feeding regimes were Bacteroidetes (51.06%) and Firmicutes (32.73%). At genus level, 25 genera were shared across all samples. The relative abundance of Prevotella in the graze and GSF regime group were significantly higher than that in the feed regime group. Meanwhile, the relative abundance of Ruminococcus was lower in the graze group than the feed and GSF regime groups. The most abundant archaeal phylum was Euryarchaeota, which accounted for 99.67% of the sequences. Ten genera were detected across feeding regimes, seven genera were shared by all samples, and the most abundant was genus Methanobrevibacter (91.60%). The relative abundance of the most detected genera were similar across feeding regime groups. Our results suggest that the ruminal bacterial community structure differs across yak feeding regimes while the archaeal community structures are largely similar.
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Affiliation(s)
- Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Lei Fang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University Beijing, China
| | - Shatuo Chai
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University Xining, China
| | - Shujie Liu
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University Xining, China
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