Initial effects of supplemental forages and feedstuffs on bovine rumen ecology in vitro as determined by DNA-based molecular procedures

References

• Abberton MT, MacDuff JH, Marshall AH, Humphreys MW. 2007. The genetic improvement of forage grasses and legumes to reduce greenhouse gas emissions. Rome, Italy: Food and Agricultural Organization of the United Nations; pp. 1–15. Available at: https://www.uncclearn.org/sites/default/files/inventory/fao143.pdf.
   Google Scholar
• Acamovic T, Brooker JD. 2005. Biochemistry of plant secondary metabolites and their effects on animals. Proc Nutr Soc. 64:403–412.
   PubMed Web of Science ®Google Scholar
• Aerts RJ, McNabb WC, Molan A, Brand A, Peters JS, Barry TN. 1999. Condensed tannins from Lotus corniculatus and Lotus pedunculatus affect the degradation of ribulose 1,5-bisphosphate carboxylase (Rubisco) protein in the rumen differently. J Sci Food Agric. 79:79–85.
   Web of Science ®Google Scholar
• AOAC. 1990. Association of Official Analytical Chemists. Official methods of analysis, 15th ed. Washington, DC, USA: AOAC. 1298 p.
   Google Scholar
• Bannink A, France J, Lopez S, Gerrits WJJ, Kebreab E, Tamminga S, Dijkstra J. 2008. Modelling the implications of feeding strategy on rumen fermentation and functioning of the rumen wall. Anim Feed Sci Technol. 143:3–26.
   Web of Science ®Google Scholar
• Bauchop T. 1981. The anaerobic fungi in rumen fibre digestion. Agric Environ. 6:339–348.
   Google Scholar
• Belanche A, Doreau M, Edwards JE, Moorby JM, Pinloche E, Newbold CJ. 2012. Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. J Nutr. 142:1684–1692.
   PubMed Web of Science ®Google Scholar
• Bowman JGP, Firkins JL. 1993. Effects of forage species and particle size on bacterial cellulolytic activity and colonization in situ. J Anim Sci. 71:1623–1633.
   PubMed Web of Science ®Google Scholar
• Bowman JGP, Sanson DW. 1996. Starch- or fiber-based energy supplements for grazing ruminants. In: Judkins MB and McCollum III FT (Ed.) Proc 3rd Grazing Livestock Nutrition Conf, West Sect Am Soc Anim Sci (suppl 1):118-135 (abstr).
   Google Scholar
• Cheng YF, Edwards JE, Allison GG, Zhu W-Y, Theodorou MK. 2009. Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture. Bioresour Technol. 100:4821–4828.
   PubMed Web of Science ®Google Scholar
• Christie BR, McElroy AR. 1995. Orchardgrass. In: Barnes RF, Miller DA, Nelson CJ, editor. Forages, Vol I. An introduction to grassland agriculture. 5th ed. Ames, IA, USA: Iowa State University Press; p. 325–344.
   Google Scholar
• Colwell RK. 2019. User’s guide to EstimateS 9.1.0. Statistical estmation of species richness and shared species from samples. [accessed 2020 Apr 9]. http://viceroy.colorado.edu/estimates.
   Google Scholar
• Culman SW, Gauch HG, Blackwood CB, Thies JE. 2008. Analysis of T-RFLP data using analysis of variance and ordination method: A comparative study. J Microbiol Methods. 75:55–63.
   PubMed Web of Science ®Google Scholar
• de la Fuente G, Belanche A, Girwood SE, Pinloche E, Wilkinson T, Newbold CJ. 2014. Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community. PLoS ONE. 9(7):e101435. doi:10.1371/journal.pone.0101435.
   PubMed Web of Science ®Google Scholar
• Denison RF, Fedders JM, Tong CBS. 1990. Amyloglucosidase hydrolysis can over estimate starch concentration of plants. Agron J. 82:869–873.
   Web of Science ®Google Scholar
• Dijkstra J, Ellis JL, Kebreab E, Strathe AB, Lopez S, France J, Bannink A. 2012. Rumial pH regulation and nutritional consequences of low pH. Anim Feed Sci Technol. 172:22–33.
   Web of Science ®Google Scholar
• Egan AR. 2005. Experimental designs for rumen microbiology. In: Makkar HP, McSweeney CS, editor. Methods in gut microbial ecology for ruminants. Dordrecht, Netherlands: Springer; p. 3–19.
   Google Scholar
• Erdman RA. 1988. Dietary buffering requirements of the lactating dairy cow: A review. J Dairy Sci. 71:3246–3266.
   Web of Science ®Google Scholar
• Fang H, Al-Marashdeh O, Zhou H, Podolyan A, Hickford JG, Edwards GR, Cameron KC, Cheng L. 2018. Ex-vivo rumen fluid fermentation: changes in microbial populations and fermentation products with different forages. J Appl Anim Res. 46:1272–1279. doi:10.1080/09712119.2018.1495082.
   Web of Science ®Google Scholar
• FASS. 2010. Guide for care and Use of Agricultural animals in Research and Teaching, 3rd ed. Champaign, IL, USA: Federation of Animal Science Societies.
   Google Scholar
• Feng Y, Barry TN, Moughan PJ, Wilson GF. 1993. Condensed tannin and gossypol concentrations in cottonseed and in processes cottonseed meal. J Sci Food Agric. 63:7–15.
   Web of Science ®Google Scholar
• Fliegerova K, Mrazek J, Voigt K. 2006. Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP. Folia Microbiol. 51(4):273–277.
   PubMed Web of Science ®Google Scholar
• Firkins JL. 1996. Maximizing microbial protein synthesis in the rumen. J Nutr. 126:1347S–1354S.
   PubMed Web of Science ®Google Scholar
• Firkins JL, Karnati SKR, Yu Z. 2008. Linking rumen function to animal response by application of metagenomics techniques. Austral J Exp Agric. 48:711–721.
   Google Scholar
• Firkins JL, Yu Z. 2006. Characterisation and quantification of the microbial populations in the rumen. In: Sejrsen K, Hvelplund T, Nielsen MO, editor. Ruminant physiology, digestion, metabolism and impact of nutrition on gene expression, immunology and stress. Wageningen, The Netherlands: Academic Publishers; p. 19–54.
   Google Scholar
• Flythe M, Kagan I. 2010. Antimicrobial effect of red clover (Trifolium pratense) phenolic extract on the rumen hyper ammonia-producing bacterium, Clostridium sticklandii. Curr Microbiol. 61:125–131.
   PubMed Web of Science ®Google Scholar
• Foster JG, Cassida KA, Turner KE. 2011. In vitro analysis of anthelmintic activity of forage chicory (Cichorium intybus L.) sesquiterpene lactones against a predominately Haemonchus contortus egg population. Vet Parasitol. 180:298–306.
   PubMed Web of Science ®Google Scholar
• Goering H, Van Soest PJ. 1970. Forage fiber analysis (apparatus, reagents, procedures, and some applications). Agric. Handbook 379. Washington, DC, USA: USDA-ARS; pp. 1–20.
   Google Scholar
• Goetsch AL, Galyean ML. 1993. Influence of feeding frequency on passage of fluid and particle markers in steers fed a concentrate diet. Can J Anim Sci. 63:727–730.
   Google Scholar
• Grosskopf R, Janssen PH, Liesack W. 1998. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence analysis. Appl Environ Microbiol. 64:668–675.
   Web of Science ®Google Scholar
• Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 68:669–685.
   PubMed Web of Science ®Google Scholar
• Hanson CH, Kohler GO, Dudley JW, Sorensen EL, Van Atta GR, Taylor KW, Pedersen MW, Carnahan HL, Wilsie CP, Kehr WR, et al. 1963. Saponin content of alfalfa as related to location, cutting, variety, and other variables. USDA Res Rep ARS. 1963:34–44.
   Google Scholar
• Horn GW, McCollum FT. 1987. Energy supplementation of grazing ruminants. In: Judkins M, editor. Proc grazing livestock Nutrition Conf. Jackson, WY: Univ. of Wyoming, Laramie; p. 125–136.
   Google Scholar
• Hristov AN, Callaway TR, Lee C, Dowd SE. 2012. Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid. J Anim Sci. 90:4449–4457.
   PubMed Web of Science ®Google Scholar
• Hristov AN, Jouany J-P. 2005. Factors affecting the efficiency of nitrogen utilization in the rumen. In: Hristov AN, Pfeffer E, editor. Nitrogen and phosphorus nutrition of cattle and environment. Wallingford, UK: CAB International; p. 117–166.
   Google Scholar
• Huntington GB. 1997. Starch utilization by ruminants: from basics to the bunk. J Anim Sci. 75:852–867.
   PubMed Web of Science ®Google Scholar
• Ivan M, Mir PS, Mir Z, Entz T, He ML, McAllister TA. 2004. Effects of dietary sunflower seeds on rumen protozoa and growth of lambs. Br J Nutr. 9:303–310.
   Google Scholar
• James TY, Porter D, Leander CA, Vilgalys R, Longcore JE. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can J Bot. 78:336–350.
   Google Scholar
• Jessing KK, Duke SO, Cedergreeen N. 2014. Potential ecological roles of artemisinin produced by artemisia annua L. J Chem Ecol. 40:100–117.
   PubMed Web of Science ®Google Scholar
• Johnson MC, Devine AA, Ellis JC, Grunden AM, Fellner V. 2009. Effects of antibiotics and oil on microbial profiles and fermentation in mixed cultures of ruminal microorganisms. J Dairy Sci. 92:4467–4480.
   PubMed Web of Science ®Google Scholar
• Jung HG, Varel VH. 1988. Influence of forage type on ruminal bacterial populations and subsequent in vitro fiber digestion. J Dairy Sci. 71:1526–1535.
   PubMed Web of Science ®Google Scholar
• Kamra DN. 2005. Rumen microbial ecosystem. Microbiology Section, Centre of Advanced Studies in animal Nutrition, India Veterinary Research Institute, Izatnagar 243 122, India. Curr Sci. 89(1):124–135.
   Google Scholar
• Kocherginskaya SA, Aminov RI, White BA. 2001. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe. 7:119–134.
   Web of Science ®Google Scholar
• Kong Y, Teather R, Forster R. 2010. Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiol Ecol. 74(3):612–622.
   PubMed Web of Science ®Google Scholar
• Krause DO, Easte RA, White BA, Mackie RI. 1995. Effect of weaning diet on the ecology of adherent lactobacilli in the gastrointestinal tract of the pig. J Anim Sci. 73:2347–2354.
   PubMed Web of Science ®Google Scholar
• Lee E-J, Johnson DE. 2006. AMMI macros for multiplicative interaction models. Proceedings, SAS Users Group International Conference; March 26-29; San Francisco, CA, USA. Paper 049-31. [Accessed 2018 Aug 21]. http://www2.sas.com/proceedings/sugi31/toc.html.
   Google Scholar
• Lee MRF. 2014. Forage polyphenol oxidase and ruminant livestock nutrition. Front Plant Sci. 5:694. doi:10.3389/fpls.2014.00694.
   PubMed Web of Science ®Google Scholar
• Lee S, Ha JK, Cheng K-J. 2000. Relative contributions of bacteria, protozoa, and fungi to in vitro degradation of orchardgrass cell walls and their interaction. Appl Environ Microbiol. 66(9):3807–3813.
   PubMedGoogle Scholar
• Lueders T, Friedrich M. 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl Environ Microbiol. 66:2732–2742.
   PubMed Web of Science ®Google Scholar
• Loor JJ, Ueda K, Ferlay A, Chilliard Y, Doreau M. 2004. Biohydrogenation, duodenal flow, and intestinal digestibility of trans fatty acids and conjugated linoleic acids in response to dietary forage:concentrate ratio and linseed oil in dairy cows. J Dairy Sci. 87:2472–2485.
   PubMed Web of Science ®Google Scholar
• Lu CD, Jorgensen NA. 1987. Alfalfa saponins affect site and extent of nutrient digestion in ruminants. J Nutr. 117:919–927.
   PubMed Web of Science ®Google Scholar
• McDougall EI. 1948. Studies on ruminant saliva. 1. The composition and output of sheep’s saliva. Biochem J. 43:99–109.
   PubMed Web of Science ®Google Scholar
• McGraw RL, Nelson CJ. 2003. Legumes for northern areas. In: Barnes RF, Nelson CJ, Collins M, Moore KJ, editor. Forages: An Introduction to grassland Agriculture. Vol 1. 6th Ed. Ames, IA: Iowa State Univ Press; p. 171–190.
   Google Scholar
• Miller TL. 1995. Ecology of methane production and hydrogen sinks in the rumen. In: Engelhardt WV, Leonhardt-Mark S, Breves G, Gieseke D, editor. Ruminant physiology: digestion, metabolism, growth and reproduction. Stuttgart, Germany: Ferdinand Enke Verlag; p. 317–331.
   Google Scholar
• Min BR, Attwood GT, Reilly K, Sun W, Peters JS, Barry TN, McNabb WC. 2002. Condensed tannins decrease in vivo populations of proteolytic bacteria and affect nitrogen metabolism in the rumen of sheep. Can J Microbiol. 48:911–921.
   PubMed Web of Science ®Google Scholar
• Min BR, Hart SP. 2003. Tannins for suppression of internal parasites. J Anim Sci. 81(E. Suppl):E102–E109.
   Google Scholar
• Moore JA, Swingle RS, Hale WH. 1986. Effects of whole cottonseed, cottonseed oil, or animal fat on digestibility of wheat straw diets by steers. J Anim Sci. 63:1267–1273.
   PubMed Web of Science ®Google Scholar
• Moore JE. 1970. Procedures for the two-stage in vitro digestion of forages. In: Harris LE, editor. Nutrition research techniques for domestic and wild animals. Vol. I. Logan, UT, USA: Utah State University; p. 5001.1–5001.3.
   Google Scholar
• Moore JE, Brant MH, Kunkle WE, Hopkins DI. 1999. Effects of supplementation on voluntary intake, diet digestibility, and animal performance. J Anim Sci. 77(Suppl 2):122–135.
   PubMedGoogle Scholar
• Mouriño F, Akkarawongsa RA, Weimer PJ. 2001. Initial pH as a determinant of cellulose digestion rate by mixed ruminal microorganisms in vitro. J Dairy Sci. 84:848–859.
   PubMed Web of Science ®Google Scholar
• Muir JP, Terrill TH, Mosjidis JA, Luginbuhl J-M, Miller JE, Burke JM, Coleman SW. 2018. Harvest regimen changes sericea lespedeza condensed tannin, fiber, and protein concentrations. Grassl Sci. 64:137–144.
   Web of Science ®Google Scholar
• Niderkorn V, Baumont R, LeMorvan A, Macheboeuf D. 2011. Occurrence of associative effects between grasses and legumes in binary mixtures on in vitro rumen fermentation characteristics. J Anim Sci. 89:1138–1145.
   PubMed Web of Science ®Google Scholar
• Ouwerkerk D, Turner AF, Klieve AV. 2008. Diversity of methanogens in ruminants in Queensland. Aust J Exp Agric. 48:722–725.
   Google Scholar
• Patra AK, Saxena J. 2009. The effect and mode of action of saponins on the microbial populations and fermentation in the rumen and ruminant production. Nutr Rep Rev. 22:204–219.
   PubMed Web of Science ®Google Scholar
• Picman AK. 1986. Biological activities of sesquiterpene lactones. Biochem Syst Ecol. 14:255–281.
   Web of Science ®Google Scholar
• Rochfort S, Parker AJ, Duhshea FR. 2008. Plant bioactives for ruminant health and productivity. Phytochem. 69:299–322.
   PubMed Web of Science ®Google Scholar
• Roger V, Fonty G, Komisarczuk-Bony S, Gouet P. 1990. Effects of physiochemical factors on the adhesion to cellulose avicel of the rumen bacteria Ruminococcus flavefaciens and Fibrobacter succinogenes subsp. succinogenes. Appl Environ Microbiol. 56:3081–3087.
   PubMed Web of Science ®Google Scholar
• Scully C, Collins G, O'Flaherty V. 2005. Assessment of anaerobic wastewater treatment failure using terminal restriction fragment length polymorphism analysis. J Appl Microbiol. 99(6):1463–1471.
   PubMed Web of Science ®Google Scholar
• Sen S, Makkar HPS, Becker K. 1998. Alfalfa saponins and their implication in animal nutrition. J Agric Food Chem. 46:131–140.
   PubMed Web of Science ®Google Scholar
• Shlimon A, Friedric MW, Niemann H, Ramsing NB, Finster K. 2004. Methanobacterium aarhusense sp. nov., a novel methanogen isolated from marine sediment (Aarhus Bay, Denmark). Int J Syst Evol Microbiol. 54:759–763.
   PubMed Web of Science ®Google Scholar
• Skillman LC, Toovey AF, Williams AJ, Wright A-DG. 2006. Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet. Appl Environ Microbiol. 72(1):200–206.
   PubMed Web of Science ®Google Scholar
• Smith CJ, Danoilowicz BS, Clear AK, Costello FJ, Wilson B, Meijer WG. 2005. T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol Ecol. 54:375–380.
   PubMed Web of Science ®Google Scholar
• Sun XZ, Joblin KN, Andrew IG, Hoskin SO, Harris PJ. 2008. Degradation of forage chicory by ruminal fibrolytic bacteria. J Appl Microbiol. 105:1286–1297.
   PubMed Web of Science ®Google Scholar
• Sollenberger LE, Collins M. 2003. Legumes for northern areas. In: Barnes RF, Nelson CJ, Collins M, Moore KJ, editor. Forages: An Introduction to grassland Agriculture. Vol 1. 6th Ed. Ames, IA: Iowa State Univ Press; p. 191–213.
   Google Scholar
• Tavendale MH, Meagher LP, Pacheco D, Walker N, Attwood GT, Sivakumaran S. 2005. Methane production from in vitro rumen incubations with Lotus pedunculatus and Medicago sativa, and effects of extractable condensed tannin fractions on methanogenesis. Anim Feed Sci Technol. 123-124:403–419.
   Web of Science ®Google Scholar
• Terrill TH, Rowan AM, Douglas GB, Barry TN. 1992. Determination of extractable and bound condensed tannin concentrations in forage plants, protein concentrate meals, and cereal grain. J Sci Food Agric. 58:321–329.
   Web of Science ®Google Scholar
• Theurer CB. 1986. Grain processing effects on starch utilization by ruminants. J Anim Sci. 63:1649–1662.
   PubMed Web of Science ®Google Scholar
• Tilley JMA, Terry RA. 1963. A two-stage technique for the in vitro digestion of forage crops. J Br Grassl Soc. 18:104–111.
   Google Scholar
• Tukey JW. 1962a. The future of data analysis. Ann of Math Stat. 33(1):1–67.
   Google Scholar
• Tukey JW. 1962b. Correction notes: Correction to “The future of data analysis”. Ann Math Stat. 33(2):812.
   Google Scholar
• Turner KE, Belesky DP. 2010. Terminology revisited: effective communications for the agricultural community. J Extension [On-line]. 48(2): Article No. 2FEA5. http://www.joe.org/joe/2010april/a5.php.
   Google Scholar
• Van Soest PJ. 1983. Rumen microbes. In: Van Soest PJ, editor. Nutritional ecology of the ruminant. Corvallis, OR: O&B Books, Inc.; p. 152–177.
   Google Scholar
• Van Soest PJ, Robertson JB, Lewis BA. 1991. Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition. J Dairy Sci. 74:3583–3597.
   PubMed Web of Science ®Google Scholar
• Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol. 172:4238–4246.
   PubMed Web of Science ®Google Scholar
• Waghorn GC, Shelton ID. 1995. Effect of condensed tannins in Lotus pedunculatus on the nutritive value of ryegrass (Lolium perenne) fed sheep. J Agric Sci (Camb.). 125:291–297.
   Web of Science ®Google Scholar
• Waghorn GC, Shelton ID. 1997. Effect of condensed tannins in Lotus corniculatus on the nutritive value of pasture for sheep. J Agric Sci (Camb.). 128:365–372.
   Web of Science ®Google Scholar
• Wallace RJ, McEwan NR, McIntosh FM, Teferedegne B, Newbold CJ. 2002. Natural products as manipulators of rumen fermentation. Asian-Aust Anim Sci. 15:1458–1468.
   Web of Science ®Google Scholar
• White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand H, Sninsky JS, White T, editor. PCR-Protocols and applications: A laboratory manual. San Diego, CA, USA: Academic Press; p. 315–322.
   Google Scholar
• Winker S, Woese C R. 1991. A definition of the domains archaea, cacteria and eucarya in terms of small subunit ribosomal-RNA characteristics. Syst Appl Microbiol. 14(4):305–310.
   PubMed Web of Science ®Google Scholar
• Wright AJ. 1971. The analysis and prediction of some two factor interactions in grass breeding. J Agric Sci Camb. 76:301–306.
   Web of Science ®Google Scholar
• Yokoyama MT, Johnson KA. 1988. Microbiology of the rumen and intestine. In: Church DC, editor. The ruminant animal: Digestive physiology and nutrition. Englewood Cliffs, NJ, USA: Prentice Hall; p. 125–144.
   Google Scholar
• Yu F, Barry TN, Moughan PJ, Wilson GF. 1993. Condensed tannin and gossypol concentrations in cottonseed and in processed cottonseed meal. J Sci Food. 63:7–15.
   Google Scholar
• Zhu Z, Kristensen L, Difford GF, Poulsen M, Noel SJ, Al-Soud WA, Sørensen SJ, Lassen J, Løvendahl P, Højberg O. 2018. Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows. J Dairy Sci. 101:9847–9862.
   PubMed Web of Science ®Google Scholar
• Zobel RW, Wallace DH. 1995. AMMI statistical model and interaction analysis. In: Pessarakli M, editor. Handbook of plant and crop physiology. New York: Marcel Dekker, Inc; p. 849–862.
   Google Scholar