Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing
The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and t...
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Language: | English |
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Frontiers Media S.A.
2017-11-01
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Series: | Frontiers in Microbiology |
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Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02165/full |
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doaj-7edf8c57551e4f0cb05f53d6f2328cfd |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yanfen Cheng Ying Wang Yuanfei Li Yipeng Zhang Tianyi Liu Yu Wang Thomas J. Sharpton Weiyun Zhu |
spellingShingle |
Yanfen Cheng Ying Wang Yuanfei Li Yipeng Zhang Tianyi Liu Yu Wang Thomas J. Sharpton Weiyun Zhu Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing Frontiers in Microbiology rice straw fiber degradation ruminal bacteria carbohydrate-active enzymes metagenome |
author_facet |
Yanfen Cheng Ying Wang Yuanfei Li Yipeng Zhang Tianyi Liu Yu Wang Thomas J. Sharpton Weiyun Zhu |
author_sort |
Yanfen Cheng |
title |
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
title_short |
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
title_full |
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
title_fullStr |
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
title_full_unstemmed |
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
title_sort |
progressive colonization of bacteria and degradation of rice straw in the rumen by illumina sequencing |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2017-11-01 |
description |
The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics. The diversity of bacteria loosely and tightly attached to the rice straw was investigated by scanning electron microscopy and Miseq sequencing of 16S rRNA genes. The predominant genus in the rumen fluid was Prevotella, followed by Bacteroides, Butyrivibrio, unclassified Desulfobulbaceae, Desulfovibrio, and unclassified Sphingobacteriaceae. The main enzymes were members of the glycosyl hydrolase family, divided into four categories (cellulases, hemicellulases, debranching enzymes, and oligosaccharide-degrading enzymes), with oligosaccharide-degrading enzymes being the most abundant. No significant degradation of rice straw was observed between 0.5 and 6 h, whereas the rice straw was rapidly degraded between 6 and 24 h. The degradation then gradually slowed between 24 and 72 h. A high proportion of unclassified bacteria were attached to the rice straw and that Prevotella, Ruminococcus, and Butyrivibrio were the predominant classified genera in the loosely and tightly attached fractions. The composition of the loosely attached bacterial community remained consistent throughout the incubation, whereas a significant shift in composition was observed in the tightly attached bacterial community after 6 h of incubation. This shift resulted in a significant reduction in numbers of Bacteroidetes and a significant increase in numbers of Firmicutes. In conclusion, the degradation pattern of rice straw in the dairy cow rumen indicates a strong contribution by tightly attached bacteria, especially after 6 h incubation, but most of these bacteria were not taxonomically characterized. Thus, these bacteria should be further identified and subjected to functional analysis to improve the utilization of crop residues in ruminants. |
topic |
rice straw fiber degradation ruminal bacteria carbohydrate-active enzymes metagenome |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2017.02165/full |
work_keys_str_mv |
AT yanfencheng progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT yingwang progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT yuanfeili progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT yipengzhang progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT tianyiliu progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT yuwang progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT thomasjsharpton progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing AT weiyunzhu progressivecolonizationofbacteriaanddegradationofricestrawintherumenbyilluminasequencing |
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spelling |
doaj-7edf8c57551e4f0cb05f53d6f2328cfd2020-11-24T22:59:39ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-11-01810.3389/fmicb.2017.02165279819Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina SequencingYanfen Cheng0Ying Wang1Yuanfei Li2Yipeng Zhang3Tianyi Liu4Yu Wang5Thomas J. Sharpton6Weiyun Zhu7Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaDepartments of Microbiology and Statistics, Oregon State University, Corvallis, OR, United StatesJiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, ChinaThe aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics. The diversity of bacteria loosely and tightly attached to the rice straw was investigated by scanning electron microscopy and Miseq sequencing of 16S rRNA genes. The predominant genus in the rumen fluid was Prevotella, followed by Bacteroides, Butyrivibrio, unclassified Desulfobulbaceae, Desulfovibrio, and unclassified Sphingobacteriaceae. The main enzymes were members of the glycosyl hydrolase family, divided into four categories (cellulases, hemicellulases, debranching enzymes, and oligosaccharide-degrading enzymes), with oligosaccharide-degrading enzymes being the most abundant. No significant degradation of rice straw was observed between 0.5 and 6 h, whereas the rice straw was rapidly degraded between 6 and 24 h. The degradation then gradually slowed between 24 and 72 h. A high proportion of unclassified bacteria were attached to the rice straw and that Prevotella, Ruminococcus, and Butyrivibrio were the predominant classified genera in the loosely and tightly attached fractions. The composition of the loosely attached bacterial community remained consistent throughout the incubation, whereas a significant shift in composition was observed in the tightly attached bacterial community after 6 h of incubation. This shift resulted in a significant reduction in numbers of Bacteroidetes and a significant increase in numbers of Firmicutes. In conclusion, the degradation pattern of rice straw in the dairy cow rumen indicates a strong contribution by tightly attached bacteria, especially after 6 h incubation, but most of these bacteria were not taxonomically characterized. Thus, these bacteria should be further identified and subjected to functional analysis to improve the utilization of crop residues in ruminants.http://journal.frontiersin.org/article/10.3389/fmicb.2017.02165/fullrice strawfiber degradationruminal bacteriacarbohydrate-active enzymesmetagenome |