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1
Flachowsky, Gerhard. "Rumen Microbiology." Animal Feed Science and Technology 113, no. 1-4 (March 2004): 253–54. http://dx.doi.org/10.1016/j.anifeedsci.2003.09.002.
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France, J., and J. Dijkstra. "Applications of biomathematics to rumen microbiology." Reproduction Nutrition Development 37, Suppl. 1 (1997): 59–60. http://dx.doi.org/10.1051/rnd:19970740.
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TKALCIC, SUZANA, CATHY A. BROWN, BARRY G. HARMON, ANANT V. JAIN, ERIC P. O. MUELLER, ANDREW PARKS, KAREN L. JACOBSEN, SCOTT A. MARTIN, TONG ZHAO, and MICHAEL P. DOYLE. "Effects of Diet on Rumen Proliferation and Fecal Shedding of Escherichia coli O157:H7 in Calves." Journal of Food Protection 63, no. 12 (December 1, 2000): 1630–36. http://dx.doi.org/10.4315/0362-028x-63.12.1630.
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Calves inoculated with Escherichia coli O157:H7 and fed either a high-roughage or high-concentrate diet were evaluated for rumen proliferation and fecal shedding of E. coli O157:H7. Calves fed the high-roughage diet had lower mean rumen volatile fatty acid concentrations and higher rumen pH values than did calves fed the high-concentrate diet. Despite these differences in rumen conditions, the calves fed the high-roughage diet did not have greater rumen populations of E. coli O157: H7 and did not exhibit increased or longer fecal shedding compared with the calves fed the high-concentrate diet. Two calves shedding the highest mean concentrations of E. coli O157:H7 were both fed the high-concentrate diet. There was a significant (P < 0.05) positive correlation between fecal shedding and rumen volatile fatty acid concentration in calves fed a high-concentrate diet. The effects of diet on E. coli O157:H7 proliferation and acid resistance were investigated using an in vitro rumen fermentation system. Rumen fluid collected from steers fed a high-roughage diet, but not from steers fed a high-concentrate diet, supported the proliferation of E. coli O157:H7. Rumen fluid from steers fed a high-concentrate diet rapidly induced acid resistance in E. coli O157:H7. The impact of diet on fecal shedding of E. coli O157:H7 is still unclear and may depend on dietary effects on fermentation in the colon and on diet-induced changes in the resident microflora. However, rapid development of acid tolerance by E. coli O157:H7 in the rumens of calves fed high-concentrate diets, allowing larger populations to survive passage through the acidic abomasum to proliferate in the colon, may be one factor that influences fecal shedding in cattle on feed.
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Wang, Yan-Lu, Wei-Kang Wang, Qi-Chao Wu, Fan Zhang, Wen-Juan Li, Sheng-Li Li, Wei Wang, Zhi-Jun Cao, and Hong-Jian Yang. "In Situ Rumen Degradation Characteristics and Bacterial Colonization of Corn Silages Differing in Ferulic and p-Coumaric Acid Contents." Microorganisms 10, no. 11 (November 15, 2022): 2269. http://dx.doi.org/10.3390/microorganisms10112269.
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In plant cell wall, ferulic acid (FA) and p-coumaric acid (pCA) are commonly linked with arabinoxylans and lignin through ester and ether bonds. These linkages were deemed to hinder the access of rumen microbes to cell wall polysaccharides. The attachment of rumen microbes to plant cell wall was believed to have profound effects on the rate and the extent of forage digestion in rumen. The objective of this study was to evaluate the effect of bound phenolic acid content and their composition in corn silages on the nutrient degradability, and the composition of the attached bacteria. Following an in situ rumen degradation method, eight representative corn silages with different FA and pCA contents were placed into nylon bags and incubated in the rumens of three matured lactating Holstein cows for 0, 6, 12, 24, 36, 48, and 72 h, respectively. Corn silage digestibility was assessed by in situ degradation methods. As a result, the effective degradability of dry matter, neutral detergent fibre, and acid detergent fibre were negatively related to the ether-linked FA and pCA, and their ratio in corn silages, suggesting that not only the content and but also the composition of phenolic acids significantly affected the degradation characteristics of corn silages. After 24 h rumen fermentation, Firmicutes, Actinobacteria, and Bacteroidota were observed as the dominant phyla in the bacterial communities attached to the corn silages. After 72 h rumen fermentation, the rumen degradation of ester-linked FA was much greater than that of ester-linked pCA. The correlation analysis noted that Erysipelotrichaceae_UCG-002, Olsenella, Ruminococcus_gauvreauii_group, Acetitomaculum, and Bifidobacterium were negatively related to the initial ether-linked FA content while Prevotella was positively related to the ether-linked FA content and the ratio of pCA to FA. In summary, the present results suggested that the content of ether-linked phenolic acids in plant cell walls exhibited a more profound effect on the pattern of microbial colonization than the fibre content.
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Li, Zhipeng, Gemma Henderson, Yahan Yang, and Guangyu Li. "Diversity of formyltetrahydrofolate synthetase genes in the rumens of roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed different diets." Canadian Journal of Microbiology 63, no. 1 (January 2017): 11–19. http://dx.doi.org/10.1139/cjm-2016-0424.
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Reductive acetogenesis by homoacetogens represents an alternative pathway to methanogenesis to remove metabolic hydrogen during rumen fermentation. In this study, we investigated the occurrence of homoacetogen in the rumens of pasture-fed roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed either oak-leaf-based (tannin-rich, 100 mg/kg dried matter), corn-stover-based, or corn-silage-based diets, by using formyltetrahydrofolate synthetase (FTHFS) gene sequences as a marker. The diversity and richness of FTHFS sequences was lowest in animals fed oak leaf, indicating that tannin-containing plants may affect rumen homoacetogen diversity. FTHFS amino acid sequences in the rumen of roe deer significantly differed from those of sika deer. The phylogenetic analyses showed that 44.8% of sequences in pasture-fed roe deer, and 72.1%, 81.1%, and 37.5% of sequences in sika deer fed oak-leaf-, corn-stover-, and corn-silage-based diets, respectively, may represent novel bacteria that have not yet been cultured. These results demonstrate that the rumens of roe deer and sika deer harbor potentially novel homoacetogens and that diet may influence homoacetogen community structure.
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Shakira, G., IH Mirza, and A. Latif. "Scope of common DNA based methods for the study of rumen bacterial population." Bangladesh Journal of Animal Science 41, no. 2 (March 10, 2013): 141–46. http://dx.doi.org/10.3329/bjas.v41i2.14134.
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Innovative methods in relation to rumen microbiology are mainly focused on the study of rumen microbial population. Rumen ecosystem is highly responsive to changes in diet, age, antibiotic use, health of the host animal, which varies according to geographical location, season, and feeding scheme. Until recently, knowledge of rumen fermentation was primarily studied using classical culture-based techniques, such as isolation, enumeration and nutritional characterization, which probably only account for 10 to 20% of the rumen microbial biomass. An increase in bacterial numbers recovered from the rumen is the most reproducible effect of dietary yeast supplementation, and it has been recognized that the increased bacterial population especially cellulolytic bacteria is central to the action of the yeast in improving ruminant productivity . Many DNA based methods have described the diet dependent shift in the diversity of rumen bacterial population. This paper is primarily aimed to see different DNA based methods for study rumen bacterial population.DOI: http://dx.doi.org/10.3329/bjas.v41i2.14134Bang. J. Anim. Sci. 2012. 41 (2): 141-146
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ORPIN, C. G., Y. GREENWOOD, F. J. HALL, and I. W. PATERSON. "The rumen microbiology of seaweed digestion in Orkney sheep." Journal of Applied Bacteriology 58, no. 6 (June 1985): 585–96. http://dx.doi.org/10.1111/j.1365-2672.1985.tb01715.x.
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KOSTYUKOVSKY, VLADIMIR, TAMIO INAMOTO, TASUKE ANDO, YUTAKA NAKAI, and KEIJI OGIMOTO. "Degradation of hay by rumen fungi in artificial rumen (RUSITEC)." Journal of General and Applied Microbiology 41, no. 1 (1995): 83–86. http://dx.doi.org/10.2323/jgam.41.83.
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Qiu, Xinjun, Xiaoli Qin, Liming Chen, Zhiming Chen, Rikang Hao, Siyu Zhang, Shunran Yang, et al. "Serum Biochemical Parameters, Rumen Fermentation, and Rumen Bacterial Communities Are Partly Driven by the Breed and Sex of Cattle When Fed High-Grain Diet." Microorganisms 10, no. 2 (January 30, 2022): 323. http://dx.doi.org/10.3390/microorganisms10020323.
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Hybridization in bovines is practiced with the main aim of improving production performance, which may imply the microbial variations in the rumen from the parental breed cross to their progeny. Besides, the interactions of offspring breed with sex in terms of rumen bacteria are not clear. This study aims to evaluate the variations in rumen bacterial communities in different breeds and sexes, and the correlations among fattening performance, serum biochemical parameters, and rumen fermentation. Forty-two 19.2 ± 0.67-month-old beef cattle (390 ± 95 kg of initial body weight) comprising two genetic lines (Yiling and Angus × Yiling) and two sexes (heifers and steers) were raised under the same high-grain diet for 120 d. On the last two days, blood samples were collected from each animal via the jugular vein before morning feeding for analyzing serum biochemical parameters; rumen fluid samples were obtained via esophageal intubation 2 h after morning feeding for analyzing rumen fermentation parameters and bacterial communities. The results show that both breed and sex had a certain impact on fattening performance, serum biochemical parameters, and rumen fermentation. No differences in the diversity and structure of rumen bacterial communities were observed. Significant interactions (p < 0.05) of breed and sex were observed for Succinivibrionaceae UCG-002 and Prevotellaceae UCG-001. The relative abundances of the Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Succinivibrio were different (p < 0.05) between breeds. Heifers had a higher (p = 0.008) relative abundance of the Rikenellaceae RC9 gut group than steers. Correlation analysis showed a significant relationship (p < 0.05) of rumen bacteria with serum biochemical parameters, rumen pH, and rumen fermentation patterns. Additionally, only two genera, Prevotellaceae UCG-003 and Prevotellaceae UCG-001, had positive correlations with feed efficiency. In conclusion, serum biochemical parameters, rumen fermentation, and rumen bacterial communities are partly driven by the breed and sex of cattle fed a high-grain diet.
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Rabee, Alaa Emara, Khalid Z. Kewan, Hassan M. El Shaer, Mebarek Lamara, and Ebrahim A. Sabra. "Effect of olive and date palm by-products on rumen methanogenic community in Barki sheep." AIMS Microbiology 8, no. 1 (2022): 26–41. http://dx.doi.org/10.3934/microbiol.2022003.
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<abstract> <p>Rumen methanogens prevent the accumulation of fermentation gases in the rumen and generate methane that increases global warming and represents a loss in animals' gross energy. Non-traditional feed resources such as the by-products of date palm (<italic>Phoenix dactylifera</italic>) and olive (<italic>Olea europaea</italic>) trees have received attention to be used in animal feeding. This study evaluated the impact of non-traditional feed resources including olive cake (OC), discarded dates (DD), and date palm frond (DPF) in sheep diet on rumen fermentation, diversity and relative abundance of rumen methanogens. Nine adult rams were assigned to three equal groups and fed three diets: traditional concentrates mixture (S1); non-traditional concentrate mixture (S2) based on DD and OC; and (S3) composed of the same S2 concentrate supplemented with DPF as a roughage part. The results showed that rumen pH was higher with S3 diet than the other two diets. However, the S1 diet showed the highest values of total volatile fatty acids (TVFA) and rumen ammonia. In addition, the proportions of acetic and butyric acids were increased, whereas propionic acid declined in S2 and S3 compared to the S1 diet. Rumen methanogens were dominated by <italic>Methanobrevibacter</italic> that showed a numeric decline by including DD, OC, and DPF in the animal diets. Principal component analysis (PCA) based on rumen fermentation parameters and relative abundances of methanogens genera showed three distinct clusters. Also, positive and negative correlations were revealed between methanogens genera and rumen metabolites. This study expands the knowledge regarding the effect of agricultural byproducts on rumen fermentation and the methanogenic community.</p> </abstract>
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Malmuthuge, Nilusha, Philip J. Griebel, and Le Luo Guan. "Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves." Applied and Environmental Microbiology 80, no. 6 (January 17, 2014): 2021–28. http://dx.doi.org/10.1128/aem.03864-13.
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ABSTRACTBacterial colonization in the gastrointestinal tracts (GIT) of preweaned calves is very important, since it can influence early development and postweaning performance and health. This study investigated the composition of the bacteria along the GIT (rumen, jejunum, ileum, cecum, and colon) of preweaned bull calves (3 weeks old) using pyrosequencing to understand the segregation of bacteria between the mucosal surface and digesta. Phylogenetic analysis revealed that a total of 83 genera belonging to 13 phyla were distributed throughout the GIT of preweaned calves, with theFirmicutes,Bacteroidetes, andProteobacteriapredominating. Quantitative PCR (qPCR) analysis of selected abundant bacterial genera (Prevotella,Bacteroides,Lactobacillus, andFaecalibacterium) revealed that their prevalence was significantly different among the GIT regions and between mucosa- and digesta-associated communities. Rumens contained the most diverse bacterial population, consisting of 47 genera, including 16 rumen-specific genera, followed by the large intestine and then the small intestine. Bacterial species richness was higher at the mucosal surface than in the local digesta, with the exception of the rumen. The majority of bacteria found on the rumen epithelial surface and within the small intestine could not be identified due to a lack of known genus-level information. Thus, future studies will be required to fully characterize the microbiome during the development of the rumens and the mucosal immune systems of newborn calves. This is the first study to analyze in depth the bacterial composition of the GIT microbiome in preweaned calves, which extends previous findings regarding early rumen colonization and bacterial segregation between mucosa- and digesta-associated microbial communities.
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Attwood, G. T., W. J. Kelly, E. H. Altermann, C. D. Moon, S. Leahy, and A. L. Cookson. "Application of rumen microbial genome information to livestock systems in the postgenomic era." Australian Journal of Experimental Agriculture 48, no. 7 (2008): 695. http://dx.doi.org/10.1071/ea07408.
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Sequencing the genomes of individual rumen microbes and determining the function of their encoded genes promises to transform our understanding of the microbiology of the rumen. The diversity and density of microbes in the rumen, and our inability to culture the majority of rumen microbes, limit current genome studies to only a small fraction of the microbes present in this environment. Nevertheless, genomes of fibre-degrading organisms are beginning to reveal a previously unexpected abundance of genes encoding glycosyl hydrolases and carbohydrate esterases, which could be used to enhance fibre digestion in the rumen. Additionally, genome sequencing of a rumen methanogen is identifying conserved genes within the methanogenic archaea that may serve as targets for their inhibition and therefore reduction of methane emissions from ruminants. The problem of rumen microbe culturability can be overcome by a new approach called metagenomics, in which microbial DNAs are extracted from rumen samples and sequenced independent of cultivation. In the future, sequencing individual genomes and metagenomic libraries is likely to capture much more of the microbial DNA in the rumen and, coupled with postgenomic studies on gene and protein expression, is likely to enhance our knowledge of the microbial component of ruminant digestion.
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Sirohi, S. K., Neha Pandey, B. Singh, and A. K. Puniya. "Rumen methanogens: a review." Indian Journal of Microbiology 50, no. 3 (September 2010): 253–62. http://dx.doi.org/10.1007/s12088-010-0061-6.
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Joshi, Akshay, Diana Young, Liren Huang, Lona Mosberger, Bernhard Munk, Julia Vinzelj, Veronika Flad, et al. "Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats." Microorganisms 10, no. 10 (October 5, 2022): 1972. http://dx.doi.org/10.3390/microorganisms10101972.
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Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski’s horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.
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Hook, S. E., K. S. Northwood, A. D. G. Wright, and B. W. McBride. "Long-Term Monensin Supplementation Does Not Significantly Affect the Quantity or Diversity of Methanogens in the Rumen of the Lactating Dairy Cow." Applied and Environmental Microbiology 75, no. 2 (November 21, 2008): 374–80. http://dx.doi.org/10.1128/aem.01672-08.
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ABSTRACT A long-term monensin supplementation trial involving lactating dairy cattle was conducted to determine the effect of monensin on the quantity and diversity of rumen methanogens in vivo. Fourteen cows were paired on the basis of days in milk and parity and allocated to one of two treatment groups, receiving (i) a control total mixed ration (TMR) or (ii) a TMR with 24 mg of monensin premix/kg of diet dry matter. Rumen fluid was obtained using an ororuminal probe on day −15 (baseline) and days 20, 90, and 180 following treatment. Throughout the 6-month experiment, the quantity of rumen methanogens was not significantly affected by monensin supplementation, as measured by quantitative real-time PCR. The diversity of the rumen methanogen population was investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA clone gene libraries. DGGE analysis at each sampling point indicated that the molecular diversity of rumen methanogens from monensin-treated cattle was not significantly different from that of rumen methanogens from control cattle. 16S rRNA gene libraries were constructed from samples obtained from the rumen fluids of five cows, with a total of 166 clones examined. Eleven unique 16S rRNA sequences or phylotypes were identified, five of which have not been recognized previously. The majority of clones (98.2%) belonged to the genus Methanobrevibacter, with all libraries containing Methanobrevibacter strains M6 and SM9 and a novel phylotype, UG3322.2. Overall, long-term monensin supplementation was not found to significantly alter the quantity or diversity of methanogens in the rumens of lactating dairy cattle in the present study.
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HARMON, BARRY G., CATHY A. BROWN, SUZANA TKALCIC, P. O. E. MUELLER, ANDREW PARKS, ANANT V. JAIN, TONG ZHAO, and MICHAEL P. DOYLE. "Fecal Shedding and Rumen Growth of Escherichia coli O157:H7 in Fasted Calves." Journal of Food Protection 62, no. 6 (June 1, 1999): 574–79. http://dx.doi.org/10.4315/0362-028x-62.6.574.
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Nine weaned calves aged from 8 to 12 weeks were fitted with rumen cannulas and were inoculated by cannula with 1010 CFU of a five-strain mixture of nalidixic acid-resistant Escherichia coli O157:H7. Six calves were fasted for 48 h on days 15 and 16 and days 22 and 23 after inoculation. Samples of rumen contents and feces were obtained daily to enumerate E. coli O157:H7 populations and to determine rumen volatile fatty acid (VFA) concentrations and rumen pH. Fasting resulted in a marked decrease in rumen VFA concentrations from a mean of 135 mmol/liter before the fast to a mean of 35 mmol/liter during the second day of the fast. However, there was no correlation between daily VFA concentration and daily rumen or fecal numbers of E. coli O157:H7 in any of the calves. Fasting generally had no significant effect on the rumen or fecal numbers of E. coli O157:H7. The exception was a single fasted calf that experienced a 3-log10 CFU/g increase in fecal shedding during and after the first fast. Despite the consistent changes in VFA concentrations in fasted calves, the fluctuations in rumen numbers of E. coli O157:H7 in the rumen of fasted calves were minimal. At the end of the experiment, E. coli O157:H7 was detected in either the rumen or omasum in two of three control calves at necropsy and in either the rumen or reticulum in five of six fasted calves. E. coli O157:H7 was detected in the colon in two of three control calves and in six of six fasted calves at necropsy. These results suggest that in cattle already shedding E. coli O157:H7, feed withdrawal and the associated changes in rumen pH and VFA concentrations have little effect on fecal shedding and rumen proliferation of E. coli O157:H7.
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Hook, Sarah E., André-Denis G. Wright, and Brian W. McBride. "Methanogens: Methane Producers of the Rumen and Mitigation Strategies." Archaea 2010 (2010): 1–11. http://dx.doi.org/10.1155/2010/945785.
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Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effectivein vivo.
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ELLIS, J. L., J. DIJKSTRA, E. KEBREAB, A. BANNINK, N. E. ODONGO, B. W. McBRIDE, and J. FRANCE. "Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle." Journal of Agricultural Science 146, no. 2 (March 26, 2008): 213–33. http://dx.doi.org/10.1017/s0021859608007752.
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SUMMARYMethane, in addition to being a significant source of energy loss to the animal that can range from 0·02 to 0·12 of gross energy intake, is one of the major greenhouse gases being targeted for reduction by the Kyoto protocol. Thus, one of the focuses of recent research in animal science has been to develop or improve existing methane prediction models in order to increase overall understanding of the system and to evaluate mitigation strategies for methane reduction. Several dynamic mechanistic models of rumen function have been developed which contain hydrogen gas balance sub-models from which methane production can be predicted. These models predict methane production with varying levels of success and in many cases could benefit from further development. Central to methane prediction is accurate volatile fatty acid prediction, representation of the competition for substrate usage within the rumen, as well as descriptions of protozoal dynamics and pH. Most methane models could also largely benefit from an expanded description of lipid metabolism and hindgut fermentation. The purpose of the current review is to identify key aspects of rumen microbiology that could be incorporated into, or have improved representation within, a model of ruminant digestion and environmental emissions.
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Guo, Yanxia, Faiz-ul Hassan, Mengwei Li, Huade Xie, Lijuan Peng, Zhenhua Tang, and Chengjian Yang. "Effect of Sodium Nitrate and Cysteamine on In Vitro Ruminal Fermentation, Amino Acid Metabolism and Microbiota in Buffalo." Microorganisms 10, no. 10 (October 14, 2022): 2038. http://dx.doi.org/10.3390/microorganisms10102038.
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Nitrate is used as a methane inhibitor while cysteamine is considered as a growth promoter in ruminants. The present study evaluated the effect of sodium nitrate and cysteamine on methane (CH4) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. Four treatments containing a 0.5 g of substrate were supplemented with 1 mg/mL sodium nitrate (SN), 100 ppm cysteamine hydrochloride (CS), and a combination of SN 1 mg/mL and CS 100 ppm (CS+SN), and a control (no additive) were applied in a completely randomized design. Each treatment group had five replicates. Two experimental runs using in vitro batch culture technique were performed for two consecutive weeks. Total gas and CH4 production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, and 72 h of incubation. The results showed that SN and CS+SN reduced the production of total gas and CH4, increased the rumen pH, acetate, acetate to propionate ratio (A/P), and microbial protein (MCP) contents (p < 0.05), but decreased other volatile fatty acids (VFA) and total VFA (p = 0.001). The CS had no effect on CH4 production and rumen fermentation parameters except for increasing A/P. The CSN increased the populations of total bacteria, fungi, and methanogens but decreased the diversity and richness of rumen microorganisms. In conclusion, CS+SN exhibited a positive effect on rumen fermentation by increasing the number of fiber degrading and hydrogen-utilizing bacteria, with a desirable impact on rumen fermentation while reducing total gas and CH4 production.
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Wang, Shiqin, Jianmin Chai, Guohong Zhao, Naifeng Zhang, Kai Cui, Yanliang Bi, Tao Ma, Yan Tu, and Qiyu Diao. "The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs." Microorganisms 10, no. 1 (January 11, 2022): 144. http://dx.doi.org/10.3390/microorganisms10010144.
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Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.
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LOWE, S. E., M. K. THEODOROU, A. P. J. TRINCI, and R. B. HESPELL. "Growth of Anaerobic Rumen Fungi on Defined and Semi-defined Media Lacking Rumen Fluid." Microbiology 131, no. 9 (September 1, 1985): 2225–29. http://dx.doi.org/10.1099/00221287-131-9-2225.
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WANG, HOUFU, PENGFEI LI, XUCHUAN LIU, CHUNYONG ZHANG, QIONGFEN LU, DONGMEI XI, RENHUI YANG, et al. "The Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)." Polish Journal of Microbiology 68, no. 4 (December 2019): 505–14. http://dx.doi.org/10.33073/pjm-2019-050.
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The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Mccann, Joshua C., Tryon A. Wickersham, and Juan J. Loor. "High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism." Bioinformatics and Biology Insights 8 (January 2014): BBI.S15389. http://dx.doi.org/10.4137/bbi.s15389.
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Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function.
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Rabee, Alaa Emara, Robert Forster, and Ebrahim A. Sabra. "Lignocelluloytic activities and composition of bacterial community in the camel rumen." AIMS Microbiology 7, no. 3 (2021): 354–67. http://dx.doi.org/10.3934/microbiol.2021022.
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<abstract> <p>The camel is well-adapted to utilize the poor-quality forages in the harsh desert conditions as the camel rumen sustains fibrolytic microorganisms, mainly bacteria that are capable of breaking down the lignocellulosic biomass efficiently. Exploring the composition of the bacterial community in the rumen of the camel and quantifying their cellulolytic and xylanolytic activities could lead to understanding and improving fiber fermentation and discovering novel sources of cellulases and xylanases. In this study, Illumina MiSeq sequencing of the V4 region on 16S rRNA was applied to identify the bacterial and archaeal communities in the rumen of three camels fed wheat straw and broom corn. Furthermore, rumen samples were inoculated into bacterial media enriched with xylan and different cellulose sources, including filter paper (FP), wheat straw (WS), and alfalfa hay (AH) to assess the ability of rumen bacteria to produce endo-cellulase and endo-xylanase at different fermentation intervals. The results revealed that the phylum Bacteroidetes dominated the bacterial community and <italic>Candidatus Methanomethylophilus</italic> dominated the archaeal community. Also, most of the bacterial community has fibrolytic potential and the dominant bacterial genera were <italic>Prevotella</italic>, <italic>RC9_gut_group</italic>, <italic>Butyrivibrio</italic>, <italic>Ruminococcus</italic>, <italic>Fibrobacteres</italic>, and <italic>Treponema</italic>. The highest xylanase production (884.8 mU/mL) was observed at 7 days. The highest cellulase production (1049.5 mU/mL) was observed when rumen samples were incubated with Alfalfa hay for 7 days.</p> </abstract>
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Krause, D. O., T. G. Nagaraja, A. D. G. Wright, and T. R. Callaway. "Board-invited review: Rumen microbiology: Leading the way in microbial ecology1,2." Journal of Animal Science 91, no. 1 (January 1, 2013): 331–41. http://dx.doi.org/10.2527/jas.2012-5567.
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Tokura, Mitsunori, Kazunari Ushida, Kohji Miyazaki, and Yoichi Kojima. "Methanogens associated with rumen ciliates." FEMS Microbiology Ecology 22, no. 2 (January 17, 2006): 137–43. http://dx.doi.org/10.1111/j.1574-6941.1997.tb00365.x.
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Wang, Wei-Kang, Wen-Juan Li, Qi-Chao Wu, Yan-Lu Wang, Sheng-Li Li, and Hong-Jian Yang. "Isolation and Identification of a Rumen Lactobacillus Bacteria and Its Degradation Potential of Gossypol in Cottonseed Meal during Solid-State Fermentation." Microorganisms 9, no. 11 (October 21, 2021): 2200. http://dx.doi.org/10.3390/microorganisms9112200.
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Cottonseed meal (CSM) is an important protein feed source for dairy cows. Its inclusion in ruminant diets is limited due to the presence of the highly toxic gossypol though rumen microorganisms are believed to be capable of gossypol degrading and transforming. The objective of the present study was to isolate the gossypol-degrading bacteria from the rumen contents and to assess its potential for gossypol degradation in vitro. A strain named Lactobacillus agilis WWK129 was anaerobically isolated from dairy cows after mixed rumen microorganisms were grown on a substrate with gossypol as the sole carbon source. Furthermore, the strain was applied at 5% inoculum concentration in vitro to continuously ferment CSM at 39 °C for five days, and it presented gossypol degradability as high as 83%. Meanwhile, the CSM contents of crude protein, essential amino acids increased significantly along with the increase of lactic acid yield (p < 0.01). Compared with the original CSM, the fermented CSM contents of neutral detergent fiber and acid detergent fiber was remarkably decreased after the anaerobic fermentation (p < 0.01). In brief, the Lactobacillus strain isolated from the rumen is not only of great importance for gossypol biodegradation of CSM, but it could also be used to further explore the role of rumen microorganisms in gossypol degradation by the ruminants.
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Muck, Richard. "Recent advances in silage microbiology." Agricultural and Food Science 22, no. 1 (March 27, 2013): 3–15. http://dx.doi.org/10.23986/afsci.6718.
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Recent advances in silage microbiology are reviewed. Most new techniques in silage microbiology use the polymerase chain reaction (PCR) to make copies of a portion of the DNA in microorganisms. These techniques allow us to identify and quantify species as well as do community analysis. The PCR-based techniques are uncovering new species, both bacteria and fungi, during storage and feeding. Silage inoculants are widely available, but of greater interest has been research investigating why inoculants are so successful. Various inoculant strains have been found to produce bacteriocins and other compounds that inhibit other bacteria and fungi, improving their chances for success. In vitro ruminal fermentation research is showing that some inoculated silages affect rumen microorganisms, reducing methane in some cases and increasing microbial biomass production in others. Better understanding of silage microbiology will allow us to better manage silos and develop better inoculants to improve silage quality.
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Qian, Wenxi, ZhiPeng Li, Weiping Ao, Guangyong Zhao, Guangyu Li, and JianPing Wu. "Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)." Canadian Journal of Microbiology 63, no. 5 (May 2017): 375–83. http://dx.doi.org/10.1139/cjm-2016-0596.
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The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.
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Lockwood, B. C., G. H. Coombs, and A. G. Williams. "Proteinase Activity in Rumen Ciliate Protozoa." Microbiology 134, no. 9 (September 1, 1988): 2605–14. http://dx.doi.org/10.1099/00221287-134-9-2605.
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Hao, Yangyi, Yue Gong, Shuai Huang, Shoukun Ji, Wei Wang, Yajing Wang, Hongjian Yang, Zhijun Cao, and Shengli Li. "Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle." Microorganisms 9, no. 8 (August 23, 2021): 1788. http://dx.doi.org/10.3390/microorganisms9081788.
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To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.
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Williams, A. G. "Rumen holotrich ciliate protozoa." Microbiological Reviews 50, no. 1 (1986): 25–49. http://dx.doi.org/10.1128/mmbr.50.1.25-49.1986.
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Williams, A. G. "Rumen holotrich ciliate protozoa." Microbiological Reviews 50, no. 1 (1986): 25–49. http://dx.doi.org/10.1128/mr.50.1.25-49.1986.
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Mountfort, Douglas O. "The rumen anaerobic fungi." FEMS Microbiology Letters 46, no. 4 (October 1987): 401–8. http://dx.doi.org/10.1111/j.1574-6968.1987.tb02476.x.
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Li, Long-Ping, Ke-Lan Peng, Ming-Yuan Xue, Sen-Lin Zhu, Jian-Xin Liu, and Hui-Zeng Sun. "An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics." Microorganisms 10, no. 8 (July 25, 2022): 1491. http://dx.doi.org/10.3390/microorganisms10081491.
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Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3–5 years old), E (6–8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.
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CHEN, YA-BING, DAO-LIANG LAN, CHENG TANG, XIAO-NONG YANG, and JIAN LI. "Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing." Polish Journal of Microbiology 64, no. 1 (2015): 29–36. http://dx.doi.org/10.33073/pjm-2015-004.
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To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.
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FAN, Y. Y., S. C. RICKE, C. M. SCANLAN, D. J. NISBET, A. A. VARGAS-MOSKOLA, D. E. CORRIER, and J. R. DELOACH. "Use of Differential Rumen Fluid-Based Carbohydrate Agar Media for Culturing Lactose-Selected Cecal Bacteria from Chickens." Journal of Food Protection 58, no. 4 (April 1, 1995): 361–67. http://dx.doi.org/10.4315/0362-028x-58.4.361.
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A rumen fluid-based differential carbohydrate agar medium for enumerating chicken cecal carbohydrate-utilizing bacteria was tested. Eleven bacteria isolated from a continuous-flow culture that had been seeded with chicken cecal contents were inoculated on fifteen different media in an anaerobic environment. These media included various levels of rumen fluid (0%, 5%, 10%, 16%) and carbohydrate (glucose [GLU], galactose [GAL], lactose[LAC]). Viable cell recovery (colony-forming units [CFU]/direct cell counts × 100%) was higher for 16% rumen fluid-supplemented carbohydrate media than the lower concentrations of rumen fluid-supplemented carbohydrate media. In addition, average viable cell recovery of all 11 bacteria on differential carbohydrate media were significantly (P &lt; 0.05) higher in galactose and lactose media than on the glucose media. Data indicated that 16% rumen-fluid based media can be used to enumerate anaerobic, lactose-fermenting subgroups of chicken cecal bacteria.
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Malgwi, Isaac, János Tossenberger, Veronika Halas, György Végvári, Melinda Kovács, and Ildikó Jócsák. "PCR and qPCR-based applications in rumen microbiology research: a review." Acta Agraria Kaposváriensis 23, no. 1 (September 27, 2019). http://dx.doi.org/10.31914/aak.2330.
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The rumen and its microbial ecosystem play a central role in the overall nutrition and health of ruminant animals. However, development and homeostatic state of the entire gut system is influenced by different interrelated factors. Recent developments in molecular diagnostic tools by using amplicon sequencing of 16S ribosomal RNA and use of high-throughput data generated through applications of pyrosequencing is a promising approach to defining the rumen microbial genome. Several procedures such as genome-wide shotgun sequencing for metagenomic data generation to predict how the rumen microbiota works, bacterial DNA integration in order to construct or edit genomes of isolated microbes and several other “omic”-based technologies based on PCR and real-time PCR (qPCR), have elucidated the complexity of the rumen microbiota. These tools are more sensitive and precise in quantitation, identification and functional characterisation of the entire rumen microbiome. PCR/qPCR enables investigations of changes in the microbiome and microbiota with respect to age, diet, species and environmental variations thus providing new information about rumen microbial genome. In this review, we will highlight recent findings using PCR and qPCR-based procedures in investigating the complex nature of the rumen microbial population which has advanced our knowledge and understanding of the rumen microbiome.
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Park, Tansol, Laura M. Cersosimo, Wenli Li, Wendy Radloff, and Geoffrey I. Zanton. "Pre-weaning Ruminal Administration of Differentially-Enriched, Rumen-Derived Inocula Shaped Rumen Bacterial Communities and Co-occurrence Networks of Post-weaned Dairy Calves." Frontiers in Microbiology 12 (February 26, 2021). http://dx.doi.org/10.3389/fmicb.2021.625488.
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Adult rumen fluid inoculations have been considered to facilitate the establishment of rumen microbiota of pre-weaned dairy calves. However, the sustained effects of the inoculations remain to be explored. In our previous study, 20 pre-weaned dairy calves had been dosed with four types of adult rumen inoculums [autoclaved rumen fluid, bacterial-enriched rumen fluid (BE), protozoal-enriched (PE), and BE + PE] weekly at 3 to 6 weeks of age. To verify the sustained effect of adult rumen inoculation, the rumen bacterial communities, fermentation characteristics, and animal performance measurements were measured after sacrifice from 20 post-weaned dairy bull calves (9 weeks of age). Ruminal pH tended to be lower in BE treated calves (n = 10). All PE treated calves had rumen ciliates (&gt;104 cells per ml of rumen fluid). PE treated calves had greater VFA concentrations (P = 0.052), lower molar proportions of isobutyrate (P = 0.073), and butyrate (P = 0.019) compared to those of control calves. No treatment differences were found in all animal performance measurements. Both PE and BE inocula increased bacterial species richness, Faith’s phylogenetic diversity, and Shannon’s index in rumen liquid fractions. However, the relative proportion of those bacterial taxa possibly transferred from the donor’s rumen was minor. Microbial network analysis showed different co-occurrence and mutually exclusive interactions between treatments of microbial inoculations. Collectively, adult rumen inoculations in pre-weaned dairy calves slightly altered the rumen bacteriome of post-weaned calves without changing fermentation and animal performance.
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Liu, Xiaozhen, Qinmeng Liu, Sihuai Sun, Hengxi Sun, Yao Wang, Xihui Shen, and Lei Zhang. "Exploring AI-2-mediated interspecies communications within rumen microbial communities." Microbiome 10, no. 1 (October 7, 2022). http://dx.doi.org/10.1186/s40168-022-01367-z.
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Abstract Background The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients and energy via microbial processes. Quorum sensing (QS) is a cell-to-cell communication mechanism that allows microbes to synchronize the expression of multiple genes in the group to perform social behaviors such as chemotaxis and biofilm formation using self-synthesized QS signaling molecules. Whereas QS has been extensively studied in model microorganisms under pure culture conditions, QS mechanisms are poorly understood in complex bacterial communities, such as the rumen microflora, in which cell-to-cell communication may be common. Results Here, we analyzed 981 rumens bacterial and archaeal genomes from the Joint Genome Institute (JGI) and GenBank databases and identified 15 types of known QS signaling molecule-related genes. The analysis of the prevalence and abundance of genes involved in QS showed that 767 microbial genomes appeared to possess QS-related genes, including 680 bacterial genomes containing autoinducer-2 (AI-2) synthase- or receptor-encoding genes. Prevotella, Butyivibrio, Ruminococcus, Oribacterium, Selenomonas, and Treponema, known abundant bacterial genera in the rumen, possessed the greatest numbers of AI-2-related genes; these genes were highly expressed within the metatranscriptome dataset, suggesting that intra- and interspecies communication mediated by AI-2 among rumen microbes was universal in the rumen. The QS processes mediated by the dCache_1-containing AI-2 receptors (CahRs) with various functional modules may be essential for degrading plants, digesting food, and providing energy and nutrients to the host. Additionally, a universal natural network based on QS revealed how rumen microbes coordinate social behaviors via the AI-2-mediated QS system, most of which may potentially function via AI-2 binding to the extracellular sensor dCache_1 domain to activate corresponding receptors involved in different signal transduction pathways, such as methyl-accepting chemotaxis proteins, histidine kinases, serine phosphatases, c-di-GMP synthases and phosphodiesterases, and serine/threonine kinases in the rumen. Conclusions The exploration of AI-2-related genes, especially CahR-type AI-2 receptors, greatly increased our insight into AI-2 as a potentially “universal” signal mediating social behaviors and will help us better understand microbial communication networks and the function of QS in plant-microbe interactions in complex microecosystems.
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Jin, Di, Shengguo Zhao, Pengpeng Wang, Nan Zheng, Dengpan Bu, Yves Beckers, and Jiaqi Wang. "Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System." Frontiers in Microbiology 7 (June 28, 2016). http://dx.doi.org/10.3389/fmicb.2016.01006.
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Fan, Qingshan, Metha Wanapat, Tianhai Yan, and Fujiang Hou. "Altitude influences microbial diversity and herbage fermentation in the rumen of yaks." BMC Microbiology 20, no. 1 (December 2020). http://dx.doi.org/10.1186/s12866-020-02054-5.
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Abstract Background Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level. Results The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks. Conclusions Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.
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Gao, Kai, and Chunyin Geng. "Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture." Frontiers in Microbiology 13 (December 20, 2022). http://dx.doi.org/10.3389/fmicb.2022.908244.
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This study investigated the effects of active dry yeast (ADY) and yeast culture (YC) supplementation on rumen bacteria and metabolites in finishing bulls fed high-concentrate diets using the full-length 16S rDNA gene sequencing and liquid chromatography-mass spectrometry. Supplementation with ADY improved the alpha diversity and relative abundance of rumen bacteria, while YC only affected relative abundance of rumen bacteria at the genus level. Sixty-three differential metabolites were identified in rumen fluid after ADY supplementation, and 17 after YC. PICRUSt2 functional prediction showed that ADY supplementation improved the capacity of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of terpenoids and polyketides, and energy metabolism in rumen bacteria (all P &lt; 0.05). Correlation analysis showed that the rumen differential metabolites following ADY supplementation were mainly related to Oligosphaera, Verruc, Mycoplasma, and Anaeroplasma. Supplementation with ADY was more effective than YC in remodeling the rumen bacterial flora structure and metabolite composition under high-concentrate diets.
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Anderson, Chiron J., Lucas R. Koester, and Stephan Schmitz-Esser. "Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets." Frontiers in Microbiology 12 (March 15, 2021). http://dx.doi.org/10.3389/fmicb.2021.625400.
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In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.
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Altermann, Eric, Kerri Reilly, Wayne Young, Ron S. Ronimus, and Stefan Muetzel. "Tailored Nanoparticles With the Potential to Reduce Ruminant Methane Emissions." Frontiers in Microbiology 13 (March 11, 2022). http://dx.doi.org/10.3389/fmicb.2022.816695.
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Agricultural methane produced by archaea in the forestomach of ruminants is a key contributor to rising levels of greenhouse gases leading to climate change. Functionalized biological polyhydroxybutyrate (PHB) nanoparticles offer a new concept for the reduction of enteric methane emissions by inhibiting rumen methanogens. Nanoparticles were functionalized in vivo with an archaeal virus lytic enzyme, PeiR, active against a range of rumen Methanobrevibacter species. The impact of functionalized nanoparticles against rumen methanogens was demonstrated in pure cultures, in rumen batch and continuous flow rumen models yielding methane reduction of up to 15% over 11 days in the most complex system. We further present evidence of biological nanoparticle fermentation in a rumen environment. Elevated levels of short-chain fatty acids essential to ruminant nutrition were recorded, giving rise to a promising new strategy combining methane mitigation with a possible increase in animal productivity.
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Cui, Xiongxiong, Zhaofeng Wang, Yuhui Tan, Shenghua Chang, Huiru Zheng, Haiying Wang, Tianhai Yan, Tsedan Guru, and Fujiang Hou. "Selenium Yeast Dietary Supplement Affects Rumen Bacterial Population Dynamics and Fermentation Parameters of Tibetan Sheep (Ovis aries) in Alpine Meadow." Frontiers in Microbiology 12 (July 2, 2021). http://dx.doi.org/10.3389/fmicb.2021.663945.
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Selenium (Se) deficiency is a widespread and seasonally chronic phenomenon observed in Tibetan sheep (Ovis aries) traditionally grazed on the Qinghai–Tibet Plateau (QTP). Effects of the dietary addition of Se-enriched yeast (SeY) on the bacterial community in sheep rumen and rumen fermentation were evaluated with the aim of gaining a better understanding of the rumen prokaryotic community. Twenty-four yearling Tibetan rams [initial average body weight (BW) of 31.0 ± 0.64 kg] were randomly divided into four treatment groups, namely, control (CK), low Se (L), medium Se (M), and high Se (H). Each group comprised six rams and was fed a basic diet of fresh forage cut from the alpine meadow, to which SeY was added at prescribed dose rates. This feed trial was conducted for over 35 days. On the final day, rumen fluid was collected using a transesophageal sampler for analyzing rumen pH, NH3-N content, volatile fatty acid (VFA) level, and the rumen microbial community. Our analyses showed that NH3-N, total VFA, and propionate concentrations in the M group were significantly higher than in the other groups (P &lt; 0.05). Both the principal coordinates analysis (PCoA) and the analysis of similarities revealed that the bacterial population structure of rumen differed among the four groups. The predominant rumen bacterial phyla were found to be Bacteroidetes and Firmicutes, and the three dominant genera in all the samples across all treatments were Christensenellaceae R7 group, Rikenellaceae RC9 gut group, and Prevotella 1. The relative abundances of Prevotella 1, Rikenellaceae RC9 gut group, Ruminococcus 2, Lachnospiraceae XPB1014 group, Carnobacterium, and Hafnia-Obesumbacterium were found to differ significantly among the four treatment groups (P &lt; 0.05). Moreover, Tax4fun metagenome estimation revealed that gene functions and metabolic pathways associated with carbohydrate and other amino acids were overexpressed in the rumen microbiota of SeY-supplemented sheep. To conclude, SeY significantly affects the abundance of rumen bacteria and ultimately affects the rumen microbial fermentation.
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Yin, Xuejiao, Shoukun Ji, Chunhui Duan, Peizhi Tian, Sisi Ju, Hui Yan, Yingjie Zhang, and Yueqin Liu. "Age-Related Changes in the Ruminal Microbiota and Their Relationship With Rumen Fermentation in Lambs." Frontiers in Microbiology 12 (September 20, 2021). http://dx.doi.org/10.3389/fmicb.2021.679135.
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The rumen microbiota is vital for the health and growth performance of the host animal, mainly due to its role in the fermentation of ingested feed within the rumen. Attaining a better understanding of the development of the bacterial community and fermentation in the rumen can provide the theoretical basis for regulating feed utilization. This study analyzed the development of rumen bacteria in lambs from birth to 4 months of age using 16S-rRNA amplicon sequencing data and studied its relationship with ruminal fermentation. Serum levels of metabolites were monitored at 30, 60, 90, and 120 days of age, and the RandomForest approach was used to determine age-related changes in rumen bacteria. Levels of blood metabolites, ruminal fermentation, the rumen bacterial community and its functions were all affected by the age of the lambs (P &lt; 0.05). Based on the Bray-Curtis distance within the age groups of the rumen microbiota, the similarity increased sharply after the lambs were weaned at 60 days of age (P &lt; 0.05). The similarity between the samples collected from birth to 90 days of age and those collected at 120 days of age, increased after 20 days of age, reaching a maximum at 90 days vs. 120 days (P &lt; 0.05). Some age-associated changes in the microbial genera were correlated with changes in the concentrations of volatile fatty acids and the levels of microbial crude protein in the rumen, including positive correlations between main volatile fatty acids and the genera of Prevotella 1, Lachnospiraceae NK3A20 group, Ruminococcus gauvreauii group, Ruminococcaceae UCG-014, and Ruminococcus 2 (P &lt; 0.05). These results indicated that the microbial community and the function of rumen was not well-established before 20 days of age, so there is a degree of plasticity in the rumen bacterial community during the first 20 days of post-natal development in lambs, and this might provide an opportunity for interventions to improve rumen fermentation and, thus, increase their growth performance.
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Cheng, Zhiqiang, Zitong Meng, Dejin Tan, Osmond Datsomor, Kang Zhan, Miao Lin, and Guoqi Zhao. "Effects of supplementation of sodium acetate on rumen fermentation and microbiota in postpartum dairy cows." Frontiers in Microbiology 13 (November 21, 2022). http://dx.doi.org/10.3389/fmicb.2022.1053503.
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The primary product of rumen fermentation is acetic acid, and its sodium salt is an excellent energy source for post-partum cows to manage negative energy balance (NEB). However, it is unknown how adding sodium acetate (NAc) may affect the rumen bacterial population of post-partum cows. Using the identical nutritional total mixed ration (TMR), this research sought to characterize the impact of NAc supplementation on rumen fermentation and the composition of bacterial communities in post-partum cows. After calving, 24 cows were randomly assigned to two groups of 12 cows each: a control group (CON) and a NAc group (ACE). All cows were fed the same basal TMR with 468 g/d NaCl added to the TMR for the CON group and 656 g/d NAc added to the TMR for the ACE group for 21 days after calving. Ruminal fluid was collected before morning feeding on the last day of the feeding period and analyzed for rumen bacterial community composition by 16S rRNA gene sequencing. Under the identical TMR diet conditions, NAc supplementation did not change rumen pH but increased ammonia nitrogen (NH3-N) levels and microbial crude protein (MCP) concentrations. The administration of NAc to the feed upregulated rumen concentrations of total volatile fatty acids (TVFA), acetic, propionic, isovaleric and isobutyric acids without affecting the molar ratio of VFAs. In the two experimental groups, the Bacteroidota, Firmicutes, Patescibacteria and Proteobacteria were the dominant rumen phylum, and Prevotella was the dominant rumen genus. The administration of NAc had no significant influence on the α-diversity of the rumen bacterial community but upregulated the relative abundance of Prevotella and downregulated the relative abundance of RF39 and Clostridia_UCG_014. In conclusion, the NAc supplementation in the post-peripartum period altered rumen flora structure and thus improved rumen fermentation in dairy cows. Our findings provide a reference for the addition of sodium acetate to alleviate NEB in cows during the late perinatal period.
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Smith, Paul E., Alan K. Kelly, David A. Kenny, and Sinéad M. Waters. "Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions." Frontiers in Microbiology 13 (April 29, 2022). http://dx.doi.org/10.3389/fmicb.2022.855565.
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With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of ruminant livestock divergently ranked for enteric emissions. Recently, the residual methane emissions (RME) concept has been identified as the optimal phenotype for assessing the methanogenic potential of ruminant livestock due to the trait’s independence from animal productivity but strong correlation with daily methane emissions. However, there is currently a dearth of data available on the bacterial and archaeal microbial communities residing in the rumens of animals divergently ranked for RME. Therefore, the objective of this study was to investigate the relationship between the rumen microbiota and RME in a population of finishing beef cattle. Methane emissions were estimated from individual animals using the GreenFeed Emissions Monitoring system for 21 days over a mean feed intake measurement period of 91 days. Residual methane emissions were calculated for 282 crossbred finishing beef cattle, following which a ∼30% difference in all expressions of methane emissions was observed between high and low RME ranked animals. Rumen fluid samples were successfully obtained from 268 animals during the final week of the methane measurement period using a trans-oesophageal sampling device. Rumen microbial DNA was extracted and subjected to 16S rRNA amplicon sequencing. Animals ranked as low RME had the highest relative abundances (P &lt; 0.05) of lactic-acid-producing bacteria (Intestinibaculum, Sharpea, and Olsenella) and Selenomonas, and the lowest (P &lt; 0.05) proportions of Pseudobutyrivibrio, Butyrivibrio, and Mogibacterium. Within the rumen methanogen community, an increased abundance (P &lt; 0.05) of the genus Methanosphaera and Methanobrevibacter RO clade was observed in low RME animals. The relative abundances of both Intestinibaculum and Olsenella were negatively correlated (P &lt; 0.05) with RME and positively correlated with ruminal propionate. A similar relationship was observed for the abundance of Methanosphaera and the Methanobrevibacter RO clade. Findings from this study highlight the ruminal abundance of bacterial genera associated with the synthesis of propionate via the acrylate pathway, as well as the methanogens Methanosphaera and members of the Methanobrevibacter RO clade as potential microbial biomarkers of the methanogenic potential of beef cattle.
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Huang, Yongliang, Guoxiu Wang, Qian Zhang, Zhanyu Chen, Chong Li, Weimin Wang, Xiaoxue Zhang, et al. "Effects of milk replacer feeding level on growth performance, rumen development and the ruminal bacterial community in lambs." Frontiers in Microbiology 13 (January 10, 2023). http://dx.doi.org/10.3389/fmicb.2022.1069964.
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Feeding with a suitable level of milk replacer (MR) can improve the survival rate and stimulate the growth potential of early lambs. However, feeding excessive MR might be detrimental to rumen development and microbial colonization. Herein, we investigated the effects of feeding different levels of MR on rumen digestive function and ruminal microorganisms. Fourteen healthy male Hu lambs with similar birth weights and detailed pedigree records were divided into two groups to receive low (2% of average body weight per day) and high (4% of average body weight per day) levels of MR. We analyzed the effects of the MR feeding level on growth performance, fiber degradation rates, rumen fermentation parameters, enzyme activities and rumen histomorphology. We found that feeding with a high level of MR improved the average daily gain of early lambs, but decreased the starter intake, rumen weight and papillae length. We also analyzed the effects of the MR feeding level on the rumen microbiota using 16S-rRNA amplicon sequencing data. The results showed that high a MR feeding level increased the rumen microbial diversity but decreased the abundance of many carbohydrate degrading bacteria. Several bacterial genera with significant differences correlated positively with rumen cellulase activity and the acid detergent fiber degradation rate. Our results suggested that a high level of MR could improve the growth performance of early lambs in the short term; however, in the long term, it would be detrimental to rumen development and have adverse effects on the adaptation process of the microbiota to solid feed.