Culture-Based and Denaturing Gradient Gel Electrophoresis Analysis of the Bacterial Community Structure from the Intestinal Tracts of Earthworms (Eisenia fetida) |
Hong, Sung-Wook
(Division of Biological Science and Technology, Yonsei University)
Kim, In-Su (Division of Biological Science and Technology, Yonsei University) Lee, Ju-Sam (Division of Biological Science and Technology, Yonsei University) Chung, Kun-Sub (Division of Biological Science and Technology, Yonsei University) |
1 | Ji, N., B. Peng, G. Wang, S. Wang, and X. Peng. 2004. Universal primer PCR with DGGE for rapid detection of bacterial pathogens. J. Microbiol. Methods 57: 409-413. DOI ScienceOn |
2 | Ju, D. H., M. K. Choi, J. H. Ahn, M. H. Kim, J. C. Cho, T. S. Kim, T. S. Kim, C. N. Seong, and J. O. Ka. 2007. Molecular and ecological analyses of microbial community structures in biofilms of a full-scale aerated up-flow biobead process. J. Microbiol. Biotechnol. 17: 253-261. |
3 | Jung, Y. R., I. G. Song, J. Y. Kim, S. G. Lee, and Y. J. Kim. 2005. Microbial diversity in the soil damaged by a forest fire. J. Korra 13: 85-90. |
4 | Gurtner, C., J. Heyrman, G. Pinar, W. Lubitz, J. Swings, and S. Rolleke. 2000 Comparative analyses of the bacterial diversity on two different biodeteriorated wall paintings by DGGE and 16S rDNA sequence analysis. Int. Biodeterior. Biodegrad. 46: 229-239. DOI ScienceOn |
5 | Hong, Y., T. H. Kim, and Y. E. Na. 2001. Identity of two earthworms used in vermiculture and vermicomposting in Korea. Kor. J. Soil Zool. 17: 185-190. |
6 | Furlong, M. A., D. R. Singleton, D. C. Coleman, and W. B. Whitman. 2002. Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl. Environ. Microbiol. 68: 1265-1279. DOI |
7 | Jany, J. L. and G. Barbier. 2008. Culture-independent methods for identifying microbial communities in cheese. Food Microbiol. 25: 839-848. DOI ScienceOn |
8 | Daniel, O. and J. M. Anderson. 1992. Microbial biomass and activity in contrasting soil materials after passage through the gut of the earthworm Lumbricus rubellus Hoffmeister. Soil Biol. Biochem. 24: 465-470. DOI ScienceOn |
9 | Edwards, C. A. and K. E. Fletcher. 1988. Interactions between earthworms and microorganisms in organic-matter breakdown. Agric. Ecosyst. Environ. 24: 235-247. DOI |
10 | Fasoli, S., M. Marzotto, L. Rizzotti, F. Rossi, F. Dellaglio, and S. Torriani. 2003. Bacterial composition of commercial probiotic products as evaluated by PCR-DGGE analysis. Int. J. Food Microbiol. 82: 59-70. DOI ScienceOn |
11 | Araya, R., K. Tani, T. Takagi, N. Yamaguchi, and M. Nasu. 2003. Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and DGGE analysis. FEMS Microbiol. Ecol. 43: 111-119. DOI ScienceOn |
12 | Clegg, C. D., R. D. L. Lovell, and P. J. Hobbs. 2003. The impact of grassland management regime on the community structure of selected bacterial groups in soils. FEMS Microbiol. Ecol. 43: 263-270. DOI ScienceOn |
13 | Leung, K. and E. Topp. 2001. Bacterial community dynamics in liquid swine manure during storage: Molecular analysis using DGGE/PCR of 16S rDNA. FEMS Microbiol. Ecol. 38: 169-177. DOI |
14 | Cocolin, L., D. Aggio, M. Manzano, C. Cantoni, and G. Comi. 2002. An application of PCR-DGGE analysis to profile the yeast populations in raw milk. Int. Dairy J. 12: 407-411. DOI ScienceOn |
15 | Cocolin, L., N. Innocente, M. Biasutti, and G. Comi. 2004. The late blowing in cheese: A new molecular approach based on PCR and DGGE to study the microbial ecology of the alteration process. Int. J. Food Microbiol. 90: 83-91. DOI ScienceOn |
16 | Aira, M., F. Monroy, and J. Dominguez. 2005. Eisenia fetida (Oligochaeta, Lumbricidae) activates fungal growth, triggering cellulose decomposition during vermicomposting. Microb. Ecol. 52: 738-746. |
17 | Albano, H., I. Henriques, A. Correia, T. Hogg, and P. Teixeira. 2008. Characterization of microbial population of 'Alheira' (a traditional Portuguese fermented sausage) by PCR-DGGE and traditional cultural microbiological methods. J. Appl. Microbiol. 105: 2187-2194. DOI ScienceOn |
18 | Kim, H. J., K. H. Shin, C. J. Cha, and H. G. Hur. 2004. Analysis of aerobic and culturable bacterial community structures in earthworm (Eisenia fetida) intestine. Agric. Chem. Biotechnol. 47: 137-142. |
19 | Kim, M. S., J. H. Ahn, M. K. Jung, J. H. Yu, D. H. Joo, M. C. Kim, et al. 2005. Molecular and cultivation-based characterization of bacterial community structure in rice field soil. J. Microbiol. Biotechnol. 15: 1087-1093. |
20 | LaPara, T. M., C. H. Nakatsu, L. M. Pantea, and J. E. Alleman. 2002. Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE. Water Res. 36: 638-646. DOI ScienceOn |
21 | Parle, J. N. 1963. Micro-organisms in the intestines of earthworms. J. Gen. Microbiol. 31: 1-11. DOI |
22 | Liew, P. W. Y. and B. C. Jong. 2008. Application of rDNA-PCR amplification and DGGE fingerprinting for detection of microbial diversity in a Malaysian crude oil. J. Microbiol. Biotechnol. 18: 815-820. |
23 | Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63: 4516-4522. |
24 | Lu, C. P. 1992. Pathogenic Aeromonas hydrophila and the fish diseases caused by it. J. Fisheries China 16: 282-288. |
25 | Miller, K. M., T. J. Ming, A. D. Schulze, and R. E. Withler. 1999. Denaturing gradient gel electrophoresis (DGGE): A rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques 27: 1016-1030. |
26 | Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700. |
27 | Muyzer, G. and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127-141. DOI ScienceOn |
28 | Nielsen, A. T., W. T. Liu, C. Filipe, L. Grady, S. Molin, and D. A. Stahl. 1999. Identification of a novel group of bacteria in sludge from a deteriorate biological phosphorus removal reactor. Appl. Environ. Microbiol. 65: 1251-1258. |
29 | Park, J. S., C. J. Sim, and K. D. An. 2009. Community structure of bacteria associated with two marine sponges from Jeju Island based on 16S rDNA-DGGE profiles. Kor. J. Microbiol. 45: 170-176. |
30 | Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, et al. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390-394. DOI ScienceOn |
31 | Rondon, M. R., R. M. Goodman, and J. Handelsman. 1999. The earth's bounty: Assessing and assessing soil microbial diversity. Trends Biotech. 17: 403-409. DOI ScienceOn |
32 | Possemiers, S., K. Verthe, S. Uyttendaela, and W. Verstraete. 2004. PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol. Ecol. 49: 495-507. DOI ScienceOn |
33 | Rantsiou, K., R. Urso, L. Iacumin, C. Cantoni, P. Cattaneo, G. Comi, and L. Cocolin. 2005. Culture-dependent and -independent methods to investigate the microbial ecology of Italian fermented sausages. Appl. Environ. Microbiol. 71: 1977-1986. DOI ScienceOn |
34 | Reeson, A. F., T. Jancovic, M. L. Kasper, S. Rogers, and A. D. Austin. 2003. Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp, Vespula germanica. Insect Mol. Biol. 12: 85-91. DOI ScienceOn |
35 | Toyota, K. and M. Kimura. 1994. Earthworm disseminate a soil-borne plant pathogen, Fusarium oxysporum f. sp. raphani. Biol. Fertil. Soils 18: 32-26. DOI ScienceOn |
36 | Weid, V. D., E. Korenblum, D. Jurelevicius, A. S. Rosado, R. Dino, G. V. Sebastian, and L. Seldin. 2008. Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil. J. Microbiol. Biotechnol. 18: 5-14. |
37 | Yoshie, S., N. Noda, T. Miyano, S. Tsuneda, A. Hirata, and Y. Inamori. 2001. Microbial community analysis in the denitrification process of saline-wastewater by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA and the cultivation method. J. Biosci. Bioeng. 92: 346-353. DOI |
38 | Shin, K. H., H. Yi, J. S. Chun, C. J. Cha, I. S. Kim, and H. G. Hur. 2004. Analysis of the anaerobic bacterial community in the earthworm (Eisenia fetida) intestine. Agric. Chem. Biotechnol. 47: 147-152. |
39 | Temmerman, R., I. Scheirlinck, G. Huys, and J. Swings. 2003. Culture-independent analysis of probiotic products by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69: 220-226. DOI ScienceOn |
40 | Tripathi, G. and P. Bhardwaj. 2004. Decomposition of kitchen waste amended with cow manure using an epigeic species (Eisenia fetida) and an anecic species (Lampito mauritii). Bioresour. Technol. 92: 215-218. DOI ScienceOn |
41 | Toyota, K. and M. Kimura. 2000. Microbial community indigenous to the earthworm Eisenia foetida. Biol. Fertil. Soils 31: 187-190. DOI ScienceOn |
42 | Walter, J., G. W. Tannock, A. Tilsala-Timisjarvi, S. Rodtong, D. M. Loach, K. Munro, and T. Alassatova. 2000. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species specific primers. Appl. Environ. Microbiol. 66: 297-303. DOI ScienceOn |
43 | Schabereiter-Gurtner, C., G. Pinar, W. Lubitz, and S. Rolleke. 2001. An advanced molecular strategy to identify bacterial communities on art objects. J. Microbiol. Methods 45: 77-87. DOI ScienceOn |