1 |
Kim, M., Yu, Z., 2012. Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets. J. Anim. Sci. Biotechnol. 3, 28.
DOI
ScienceOn
|
2 |
Kim, M., Wang, L., Morrison, M., Yu, Z., 2014a. Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities. J. Appl. Microbiol. 117, 949-960.
DOI
ScienceOn
|
3 |
Kim, M., Kim, J., Kuehn, L.A., Bono, J.L., Berry, E.D., Kalchayanand, N., Freetly, H.C., Benson, A.K., Wells, J.E., 2014b. Investigation of bacterial diversity in the feces of cattle fed different diets. J. Anim. Sci. 92, 683-694.
DOI
ScienceOn
|
4 |
Mosher, J.J., Bowman, B., Bernberg, E.L., Shevchenko, O., Kan, J., Korlach, J., Kaplan, L.A., 2014. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. J. Microbiol. Methods. 104, 59-60.
DOI
ScienceOn
|
5 |
Myer, P.R., Smith, T.P., Wells, J.E., Kuehn, L.A., Freetly, H.C., 2015. Rumen microbiome from steers differing in feed efficiency. PLoS One. 10, e0129174.
DOI
ScienceOn
|
6 |
Park, S.J., Kim, J., Lee, J.S., Rhee, S.K., Kim, H., 2014. Characterization of the fecal microbiome in different swine groups by high-throughput sequencing. Anaerobe. 28, 157-162.
DOI
ScienceOn
|
7 |
Schloss, P.D., Handelsman, J., 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68, 686-691.
DOI
ScienceOn
|
8 |
Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D. H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J., Weber, C. F., 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541.
DOI
ScienceOn
|
9 |
Wei, S., Morrison, M., Yu, Z., 2013. Bacterial census of poultry intestinal microbiome. 92, 671-683.
DOI
ScienceOn
|
10 |
Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., Glockner, F.O., 2014. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic. Acids. Res. 42, D643-D648.
DOI
ScienceOn
|
11 |
Yu, Z., Morrison, M., 2004a. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70, 4800-4806.
DOI
ScienceOn
|
12 |
Yu, Z., Morrison, M., 2004b. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 36, 808-812.
|
13 |
Zhou, M., Hernandez-Sanabria, E., Guan, L.L., 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl. Environ. Microbiol. 75, 6524-6533.
DOI
ScienceOn
|
14 |
Freetly HC, Lindholm-Perry AK, Hales KE, Brown-Brandl TM, Kim M, Myer PR, Wells JE. 2015. Methane production and methanogen levels in steers that differ in residual gain. J. Anim. Sci. 93, 2375-2381.
DOI
ScienceOn
|
15 |
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R., 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7, 335-336.
DOI
ScienceOn
|
16 |
Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A,, Turnbaugh, P.J., Fierer, N., Knight, R., 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U. S. A. 108 Suppl 1, 4516-4522.
DOI
ScienceOn
|
17 |
Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., Sun, Y., Brown, C.T., Porras-Alfaro, A., Kuske, C.R., Tiedje, J. M., 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic. Acids. Res. 42, D633- D642.
DOI
ScienceOn
|
18 |
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G.L., 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072.
DOI
ScienceOn
|
19 |
Eden, P.A., Schmidt, T.M., Blakemore, R. P., Pace, N.R., 1991. Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int. J. Syst. Bacteriol. 41, 324-325.
DOI
|
20 |
Kim, M., Morrison, M., Yu, Z., 2011a. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS. Microbiol. Ecol. 76, 49-63.
DOI
ScienceOn
|
21 |
Kim, M., Morrison, M., Yu, Z., 2011b. Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments. Folia. Microbiol. 56, 453-458.
DOI
ScienceOn
|
22 |
Kim, M., Morrison, M., Yu, Z., 2011c. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J. Microbiol. Methods. 84, 81-87.
DOI
ScienceOn
|
23 |
Ruff-Roberts, A.L., Kuenen, J.G., Ward, D.M., 1994. Distribution of cultivated and uncultivated cyanobacteria and Chloroflexuslike bacteria in hot spring microbial mats. Appl. Environ. Microbiol. 60, 697-704.
|
24 |
Kumari, P., Choi, H.L., Sudiarto, S.I., 2015. Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry. PLoS. One. 10, e0139437.
DOI
ScienceOn
|
25 |
Woese, C.R., Fox, G.E., 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U. S. A. 74, 5088-5090.
DOI
ScienceOn
|
26 |
Hwang, O.H., Raveendar, S., Kim, Y.J., Kim, J.H., Choi, J.W., Kim, T.H., Choi, D.Y., Jeon, C.O., Cho, S.B., Lee, K.T., 2014. Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis. J. Microbiol. 52, 918-929.
DOI
ScienceOn
|