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Diversity Census of Fungi in the Ruminal Microbiome: A meta-analysis

반추위 곰팡이 다양성 조사 : 메타분석

  • Song, Jaeyong (Animal Nutrition and Physiology Team, National Institute of Animal Science) ;
  • Jeong, Jin Young (Animal Nutrition and Physiology Team, National Institute of Animal Science) ;
  • Kim, Minseok (Animal Nutrition and Physiology Team, National Institute of Animal Science)
  • 송재용 (국립축산과학원 영양생리팀) ;
  • 정진영 (국립축산과학원 영양생리팀) ;
  • 김민석 (국립축산과학원 영양생리팀)
  • Received : 2017.10.23
  • Accepted : 2017.12.08
  • Published : 2017.12.31

Abstract

This study was designed to examine the diversity census of fungi in rumen microbiome via meta-analysis of fungal 28S rDNA sequences. Both terms, "rumen" and "ruminal," were searched to retrieve the sequences of rumen fungi. As of September 2016, these sequences (n=165) of ruminal origin were retrieved from the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu), an archive of all 28S rDNA sequences and were assigned to the phyla Ascomycota, Neocallimastigomycota, and Basidiomycota, which accounted for 109, 48, and 8 of the 165 sequences, respectively. Ascomycota sequences were assigned to the genera Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium, and Davidiella, including fungal plant pathogens or mycotoxigenic species. Moreover, Basidiomycota sequences were assigned to the genera Thanatephorus and Cryptococcus, including fungal plant pathogens. Furthermore, Neocallimastigomycota sequences were assigned to the genera Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, and Piromyces, which may degrade the major structural carbohydrates of the ingested plant material. This study provided a collective view of the rumen fungal diversity using a meta-analysis of 28S rDNA sequences. The present results will provide a direction for further studies on ruminal fungi and be applicable to the development of new analytic tools.

본 연구의 목적은 곰팡이 28S rDNA 염기서열의 메타분석을 통하여 반추위 곰팡이의 다양성을 조사하는데 있다. 'rumen'과 'ruminal'이 반추위 곰팡이 유래 염기서열들을 회수하기 위한 검색어로 사용되었다. 2016년 9월부로 모든 28S rDNA 염기서열이 보관되어 있는 Ribosomal Database Project(RDP, http://rdp.cme.msu.edu) 데이터베이스에서 반추위 곰팡이 유래 28S rDNA 유전자 염기서열(n=165)을 획득하였다. 총 165개의 염기서열은 분류학상의 '문(phylum)'인 Ascomycota, Neocallimastigomycota 및 Basidiomycota로 분류되었고, 165개의 염기서열 중에서 각각 109개, 48개, 8개의 염기서열을 차지하였다. Ascomycota 염기서열은 식물병원성곰팡이나 마이코톡신을 생성하는 곰팡이를 포함하고 있는 '속(genus)' Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium 및 Davidiella로 분류되었다. 또한, Basidiomycota 염기서열은 식물병원성곰팡이를 포함하고 있는 '속(genus)' Thanatephorus와 Cryptococcus로 분류되었다. 뿐만 아니라, Neocallimastigomycota 염기서열의 경우 섭취된 조사료의 주요 구조탄수화물을 분해하는 '속(genus)' Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, Piromyces로 분류되었다. 본 연구는 처음으로 28S rDNA 염기서열의 메타분석을 통해 반추위 곰팡이 다양성에 대한 정보를 통합적으로 제공하였다. 본 연구의 결과는 향후 반추위 곰팡이 연구에 대한 방향을 제공할 것이고, 새로운 분석도구 개발에 응용될 수 있을 것이다.

Keywords

References

  1. H. G. Sung., "Study on Roughage Degradation and Adhesion of Rumen Fibrolytic Bacteria by Real-Time PCR", Journal of the Korean Society of Grassland and Forage Science, vol. 34, no. 1 pp. 60-67, 2014. DOI: https://doi.org/10.5333/KGFS.2014.34.1.60
  2. S. J. Lee, D. S. Oh, D. H. Kim, J. U. Ok, S. K. Lee, J. H. Lim, S. S. Lee., "Effects of long-chain fatty acids on in vitro rumen microbial population, dry matter degradability and methane production", Journal of Agriculture & Life Science, vol. 49, no. 2 pp. 47-56, 2015. DOI: https://doi.org/10.14397/jals.2015.49.2.47
  3. C. Ryu, H. R. Park, S. Cho, N. J. Choi., "Effects of Dietary formulated feed Additive on Growth Performance and Carcass Traits in Hanwoo Steers", Korean journal of organic agriculture, vol. 24, no. 4 pp. 869-879, 2016. https://doi.org/10.11625/KJOA.2016.24.4.869
  4. M. Kown, J. Song, J. K. Ha, H. S. Park, J. Chang., "Analysis of functional genes in carbohydrate metabolic pathway of anaerobic rumen fungus Neocallimastix frontalis PMA02", Asian-Australasian Journal of Animal Sciences, vol. 22, no. 11 pp. 1555-1565, 2009. DOI: https://doi.org/10.5713/ajas.2009.80371
  5. S. K. Sirohi, P. K. Choudhury, A. K. Puniya, D. Singh, S. S. Dagar, N. Singh., "Ribosomal ITS1 sequence-based diversity analysis of anaerobic rumen fungi in cattle fed on high fiber diet", Annals of Microbiology, vol. 63, no. 4 pp. 1571-1577, 2013. DOI: https://doi.org/10.1007/s13213-013-0620-2
  6. M. Kwon, J. Song, H. S. Park, H. Park, J. Chang., "Characterization of heterologously expressed actyl xylan esterase1 isolated from the anaerobic rumen fungus Neocallimastix frontalis PMA02", Asian-Australasian Journal of Animal Sciences, vol. 29, no. 11 pp. 1576-1584, 2016. DOI: https://doi.org/10.5713/ajas.16.0336
  7. J. B. Lee, J. K. Ha, W. Y. Kim, H. D. Kim, S. W. Kim, Y. G. Ko, S. S. Lee., "Studies on the improvement of utility value of silage by inoculating ruminal fungi. II. Effects of fungal inoculation on nutritive values and nutrient digestibilities of sudan grass silage", Korean Journal of Animal Nutrition & Feedstuffs, vol. 21, no. 2 pp. 197-206, 1997.
  8. S. J. Lee, I. D. Lee, S. K. Lee, D. H. Kim, S. M. Lee, C. H. Kim, S. S. Lee., "Effects of Unsaturated Fatty Acids on the Rumen Fermentation Characteristics and Carboxymethylcellulase Activity in vitro Culture with Rumen Fungus, Piromyces communis", Journal of Agriculture & Life Science, vol. 48, no. 3 pp. 217-226, 2014. DOI: https://doi.org/10.14397/jals.2014.48.4.217
  9. BA Dehority. Rumen microbiology. p.295-319, Nottingham University Press, 2003.
  10. C. H. Kim, S. S. Lee., "Isolation and Characterization of Cellulolytic Anaerobic Fungi from the Guts of the Hanwoo Cattle and the Korean Native Goat", Journal of Animal Science and Technology, vol. 45, no. 6 pp. 1019-1030, 2003. DOI: https://doi.org/10.5187/JAST.2003.45.6.1019
  11. I. S. Nam., "Isolation and Identification of Rumen Fungus and Its Produced Conjugated Linoleic Acid", Korean Journal of Microbiology, vol. 43, no. 2 pp. 111-115, 2007.
  12. M. Kim, M. Morrison, Z. Yu., "Status of the phylogenetic diversity census of ruminal microbiomes", FEMS Microbiology Ecology, vol. 76, no. 1 pp. 49-63, 2011. DOI: https://doi.org/10.1111/j.1574-6941.2010.01029.x
  13. C. R. Woese, G. E. Fox., "Phylogenetic structure of the prokaryotic domain: the primary kingdoms", Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 11, pp. 5088-5090, 1977. DOI: https://doi.org/10.1073/pnas.74.11.5088
  14. K. L. Liu, A. Porras-Alfaro, C. R. Kuske, S. A. Eichorst, G. Xie., "Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes", Applied and Environmental Microbiology, vol. 78, no. 5 pp. 1523-1533, 2012. DOI: https://doi.org/10.1128/AEM.06826-11
  15. J. Y. Jeong, M. Kim., "A meta-analysis of fecal bacterial diversity in dogs", Journal of the Korea Academia-Industrial Cooperation Society, vol. 18, no. 1 pp. 141-147, 2017. DOI: https://doi.org/10.5762/KAIS.2017.18.1.141
  16. F. Shi, T. Hsiang., "First Report of Pseudonectria buxi Causing Volutella Blight on Boxwood (Buxus sp.) in Beijing, China", Plant Disease, vol. 98, no. 9 pp. 1282-1282, 2014. DOI: https://doi.org/10.1094/PDIS-04-14-0434-PDN
  17. R.A. Dean, N. J. Talbot, D. J. Ebbole, M. L. Farman, T. K. Mitchell, M. J. Orbach, M. Thon, R. Kulkarni, J. R. Xu, H. Pan, N. D. Read, Y. H. Lee, I. Carbone, D. Brown, Y.Y. Oh, N. Donofrio, J. S. Jeong, D. M. Soanes, S. Djonovic, E. Kolomiets, C. Rehmeyer, W. Li, M. Harding, S. Kim, M. H. Lebrun, H. Bohnert H, S. Coughlan, J. Butler, S. Calvo, L. J. Ma, R. Nicol, S. Purcell, C. Nusbaum, J. E. Galagan, B. W. Birren., "The genome sequence of the rice blast fungus Magnaporthe grisea", Nature, vol. 434, no. 7036 pp. 980-986, 2005. DOI: https://doi.org/10.1038/nature03449
  18. D. H. Kim, H. S. Chun., "Influence of the climate change on growth of fungi and mycotoxin production", Food Science and Industry, vol. 42, no. 4 pp. 27-35, 2009.
  19. D. H. Kim, H. S. Jang, G. I. Choi, H. J. Kim, H. J. Kim, H. L. Kim, H. J. Cho, C. Lee., "Occurrence of Mycotoxins in Korean Grains and Their Simultaneous Analysis", Korean Journal of Food Science and Technology, vol. 45, no. 1 pp. 111-119, 2013. DOI: https://doi.org/10.9721/KJFST.2013.45.1.111
  20. H. G. Sung., "The Studies on Real Condition of Mycotoxin Contamination in the Fields before Harvest and by the Storage of Rice Straw using as Roughage in Korea", Journal of the Korean Society of Grassland and Forage Science, vol. 33, no. 1 pp. 21-29, 2013. DOI: https://doi.org/10.5333/KGFS.2013.33.1.21
  21. Y. J. Kim, M. R. Kim, T. S. Choi, Y. S. Kim, J. H. Lee., "Monitoring of 7 mycotoxins in pork", Korean Journal of Veterinary Service, vol. 36, no. 4 pp. 303-309, 2013. DOI: https://doi.org/10.7853/kjvs.2013.36.4.303
  22. A. Gallo, G. Giuberti, J. C. Frisvad, T. Bertuzzi, K. F. Nielsen., "Review on Mycotoxin Issues in Ruminants: Occurrence in Forages, Effects of Mycotoxin Ingestion on Health Status and Animal Performance and Practical Strategies to Counteract Their Negative Effects", Toxins, vol. 7, no. 8 pp. 3057-3111, 2015. DOI: https://doi.org/10.3390/toxins7083057
  23. Y. H. Moon, H. S. Kim, C. H. Kim, W. G. Cho, Y. B. Yoo, P. G. Shin, S. J. Cho., "Effect of dietary supplementation of fermented spent mushroom substrates from Pleurotus eryngii on Hanwoo Steers", Journal of Mushrooms, vol. 13, no. 2 pp. 108-113, 2015. DOI: https://doi.org/10.14480/JM.2015.13.2.108
  24. Y. M. Ro, G. H. Lee, I. C. Park, W. G. Kim, B. H. Han, J. You, J. H. Ahn., "Isolation and characterization of lactic acid bacteria for use as silage additives", Korean Journal of Microbiology, vol. 52, no. 4 pp. 444-454, 2016. DOI: https://doi.org/10.7845/kjm.2016.6060
  25. J. S. Ahn, J. I. Lee, B. K. Park, M. J. Kim, Y. G. Goh, Y. S. Choi, S. M. Kim, J. S. Shin., "Survey on General Status and Feed Safety Management for TMR Manufacturing Facility and Pollution Level of Harmful Factors in Feed", Annals of Animal Resource Sciences, vol. 28, no. 1 pp. 32-45, 2017. DOI: https://doi.org/10.12718/AARS.2017.28.1.32
  26. R. Wang, Y. Leng, S. Shrestha, S. Zhong., "Coordinated and independent functions of velvet-complex genes in fungal development and virulence of the fungal cereal pathogen Cochliobolus sativus", Fungal Biology, vol. 120, no. 8 pp. 940-960, 2016. DOI: https://doi.org/10.1016/j.funbio.2016.05.004
  27. U. K. Simon, M. Weiss., "Intragenomic variation of fungal ribosomal genes is higher than previously thought", Molecular Biology and Evolution, vol. 25, no. 11 pp. 2251-2254, 2008. DOI: https://doi.org/10.1093/molbev/msn188
  28. J. Almario, G. Jeena, J. Wunder, G. Langen, A. Zuccaro, G. Coupland, M. Bucher., "Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition", Proceedings of the National Academy of Sciences of the United States of America, In press, 2017. DOI: https://doi.org/10.1073/pnas.1710455114
  29. A. Lund., "Yeasts and moulds in the bovine rumen", Journal of General Microbiology, vol. 81, no. 2 pp. 453-462, 1974. DOI: https://doi.org/10.1099/00221287-81-2-453
  30. M. Sridhar, D. Kumar, S. Anandan, C. S. Prasad, K. T. Sampath., "Morphological and molecular characterization of polycentric rumen fungi belonging to the genus Orpinomyces isolated from Indian cattle and buffaloes", Research Journal of Microbiology, vol. 5, no. 7 pp. 581-594, 2010. DOI: https://doi.org/10.3923/jm.2010.581.594
  31. A. S. Liggenstoffer, N. H. Youssef, M. B. Couger, M. S. Elshahed., "Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores", ISME Journal, vol. 4, no. 10 pp. 1225-1235, 2010. DOI: https://doi.org/10.1038/ismej.2010.49
  32. M. W. Phillips, G. L. Gordon., "Sugar and polysaccharide fermentation by rumen anaerobic fungi from Australia, Britain and New Zealand", Biosystems, vol. 21, no. 3-4 pp. 377-383, 1988. DOI: https://doi.org/10.1016/0303-2647(88)90036-6
  33. J. Webb, M. K. Theodorou., "Neocallimastix hurleyensis sp. nov., an anaerobic fungus from the ovine rumen", Canadian Journal of Botany, vol. 69, no. 6 pp. 1220-1224, 1991. DOI: https://doi.org/10.1139/b91-156
  34. M. Gonzalez, M. Pujol, J. P. Metraux, V. Gonzalez-Garcia, M. D. Bolton, O. Borras-Hidalgo., "Tobacco leaf spot and root rot caused by Rhizoctonia solani Kuhn", Molecular Plant Pathology, vol. 12, no. 3 pp. 209-216, 2011. DOI: https://doi.org/10.1111/j.1364-3703.2010.00664.x
  35. H. M. Chapman, W. F. Robinson, J. R. Bolton, J. P. Robertson., "Cryptococcus neoformans infection in goats", Australian Veterinary Journal, vol. 67, no. 7 pp. 263-265, 1990. DOI: https://doi.org/10.1111/j.1751-0813.1990.tb07783.x
  36. A. Lund., "Yeasts in the rumen contents of musk oxen", Journal of General Microbiology, vol. 121, no. 1 pp. 273-276, 1980. DOI: https://doi.org/10.1099/00221287-121-1-273