Probiotic Dosing of Ruminococcus flavefaciens Affects Rumen Microbiome Structure and Function in Reindeer

Microbial Ecology

Volumn 66, Issue 4, 2013, Pages 840-849

  Præsteng, Kirsti E ^a   Pope, Phillip B ^b   Cann, Isaac K O ^c,d   Mackie, Roderick I ^c   Mathiesen, Svein D ^b   Folkow, Lars P ^a   Eijsink, Vincent G H ^b   Sundset, Monica A ^a  

^a UNIVERSITY OF TROMSØ   (Norway)

^b NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BACTEROIDETES; PREVOTELLA; RANGIFER TARANDUS; RUMINOCOCCUS FLAVEFACIENS;

CELLULOSE; PROBIOTIC AGENT;

ANIMAL; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; DIGESTION; GENETICS; ISOLATION AND PURIFICATION; MALE; METABOLISM; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; REINDEER; RUMINANT STOMACH; RUMINOCOCCUS;

ANIMALS; BACTERIA; BIODIVERSITY; CELLULOSE; DIGESTION; MALE; MICROBIOTA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROBIOTICS; REINDEER; RUMEN; RUMINOCOCCUS;

EID: 84885906217     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-013-0279-z     Document Type: Article

References (39)

1. Abe F, Ishibashi N, Shimamura S (1995) Effect of administration of bifidobacteria and lactic acid bacteria to newborn calves and piglets. J Dairy Sci 78: 2838-2846.
2. Avgustin G, Wallace RJ, Flint HJ (1997) Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola. Int J Syst Bacteriol 47: 284-288.
3. Belenguer A, Toral PG, Frutos P, Hervás G (2010) Changes in the rumen bacterial community in response to sunflower oil and fish oil supplements in the diet of dairy sheep. J Dairy Sci 93: 3275-3286.
4. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267.
5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N (2010) QIIME allows integration and analysis of high-throughput community sequencing data. Nat Meth 7: 335-336.
6. Carberry CA, Kenny DA, Han S, McCabe MS, Waters SM (2012) Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Appl Environ Microbiol 78: 4949-4958.
7. Chiquette J, Talbot G, Markwell F, Nili N, Forster RJ (2007) Repeated ruminal dosing of Ruminococcus flavefaciens NJ along with a probiotic mixture in forage or concentrate-fed dairy cows: effect of ruminal fermentation, cellulolytic populations and in sacco digestibility. Can J Anim Sci 87: 237-249.
8. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
9. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
10. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
11. Eira IM, Jaedicke C, Magga OH, Maynard NG, Vikhamar-Schuler D, Mathiesen SD (2013) Traditional Sámi snow terminology and physical snow classification-two ways of knowing. Cold Reg Sci Technol 85: 117-130.
12. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
13. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Meth 5: 235-237.
14. Josefsen TD, Sørensen KK, Mørk T, Mathiesen SD, Ryeng KA (2007) Fatal inanition in reindeer (Rangifer tarandus tarandus): pathological findings in completely emaciated carcasses. Acta Vet Scand 49: 27.
15. Kang S, Denman SE, Morrison M, Yu Z, McSweeney CS (2009) An efficient RNA extraction method for estimating gut microbial diversity by polymerase chain reaction. Curr Microbiol 58: 464-471.
16. Kmet V, Flint HJ, Wallace RJ (1993) Probiotics and manipulation of rumen development and function. Arch Tierernahr 44: 1-10.
17. Krause DO, Bunch RJ, Colan LL, Kennedy PM, Smith WJ, Mackie RI, McSweeney CS (2001) Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes. Microbiology 147: 1719-1729.
18. Li RW, Connor EE, Li C, Baldwin VRL, Sparks ME (2012) Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol 14: 129-139.
19. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
20. Mackenzie AK, Pope PB, Pedersen HL, Gupta R, Morrison M, Willats WG, Eijsink VGH (2012) Two SusD-like proteins encoded within a polysaccharide utilization locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose. Appl Environ Microbiol 78: 5935-5937.
21. Mathiesen SD, Haga ØE, Kaino T, Tyler NJC (2000) Diet composition, rumen papillation and maintenance of carcas mass in female Norwegian reindeer (Rangifer tarandus tarandus) in winter. J Zool 251: 129-138.
22. Nilsson A, Åhman B, Murphy M, Soveri T (2006) Rumen function in reindeer (Rangifer tanandus tarandus) after sub-maintenance feed intake and subsequent feeding. Rangifer 26: 73-83.
23. Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VGH (2012) Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE 7: e38571.
24. Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
25. Rosewarne CP, Pope PB, Denman SE, McSweeney CS, O'Cuiv P, Morrison M (2010) High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut. Microb Ecol 61: 448-454.
26. Russell JB, Dombrowski DB (1980) Effect of pH on the efficiency of growth by pure cultures of rumen bacteria in continuous culture. Appl Environ Microbiol 39: 604-610.
27. Russell JB, Wilson DB (1996) Why are ruminal cellulolytic bacteria unable to digest cellulose at low pH? J Dairy Sci 79: 1503-1509.
28. Sletten H, Hove K (1990) Digestive studies with a feed developed for realimentation of starving reindeer. Rangifer 10: 31-37.
29. Sundset MA, Kohn A, Mathiesen SD, Præsteng KE (2008) Eubacterium rangiferina, a novel usnic acid resistant bacterium from the reindeer rumen. Naturwissenschaften 95: 741-749.
30. Sundset MA, Præsteng KE, Cann IK, Mathiesen SD, Mackie RI (2007) Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol 54: 424-438.
31. Tyler NJC, Turi JM, Sundset MA, Bull KS, Sara MN, Reinert E, Oskal N, Nellemann C, McCarthy JJ, Mathiesen SD, Martello ML, Magga OH, Hovelsrud GK, Hanssen-Bauer I, Eira NI, Eira IMG, Corell RW (2007) Saami reindeer pastoralism under climate change: applying a generalized framework for vulnerability studies to a sub-arctic social-ecological system. Global Env Change 17: 191-206.
32. Wallace RJ (2008) Gut microbiology-broad genetic diversity, yet specific metabolic niches. Animal 2: 661-668.
33. Welkie DG, Stevenson DM, Weimer PJ (2010) ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle. Anaerobe 16: 94-100.
34. Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT (2011) Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A 108: 4158-4163.
35. Whitehouse NL, Olson VM, Schwab CG, Chesbro WR, Cunningham KD, Lykos T (1994) Improved techniques for dissociating particle-associated mixed ruminal microorganisms from ruminal digesta solids. J Anim Sci 72: 1335-1343.
36. Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, De Vos P, Verstraete W, Boon N (2009) Initial community evenness favours functionality under selective stress. Nature 458: 623-626.
37. Yu Z, Morrison M (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36: 808-812.
38. Ørskov ER, Hovell FDD, Mould F (1980) The use of the nylon bag technique for the evaluation of feedstuffs. Trop Animal Prod 5: 195-213.
39. Aagnes TH, Sørmo W, Mathiesen SD (1995) Ruminal microbial digestion in free-living, in captive lichen-fed, and in starved reindeer (Rangifer tarandus tarandus) in winter. Appl Environ Microbiol 61: 583-591.