RESEARCH PAPER

Amplicon Sequencing Analysis Based on QIIME2 Platform Evaluates Difference in Anaerobic Fungal Structure between Ruminal and Rectal Content of Beef Cattle

  • ZHANG Yawei ,
  • TAO Xinyan ,
  • ZHANG Yuejiao ,
  • WANG Yuehong ,
  • ZHANG Yuanqing
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  • College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China

Received date: 2022-02-17

  Online published: 2022-08-11

Abstract

This study aimed to introduce a processing pipeline for amplicon sequencing data of gastrointestinal anaerobic fungal community, and to investigate the difference in anaerobic fungal composition between ruminal and rectal content of beef cattle. Six Jinnan cattle fitted with permanent rumen cannula were offered the same experimental diet for 15 days, and then ruminal and rectal content samples were collected through the rumen fistulas and rectum respectively before morning feeding on the next day. The whole genomic DNA was extracted from all samples and used to internal transcribed spacer 1 (ITS1) amplicon sequencing. Results showed that the Faith phylogenetic diversity of fungal community in rectal content was higher than that in ruminal content (P<0.05), while the other alpha diversity indices were not affected by the gastrointestinal regions (P>0.05). The differential analysis of beta diversity metrics revealed a significant difference in anaerobic fungal profiles between ruminal and rectal content of beef cattle (P<0.05). Fungal differential abundance analysis indicated that the relative abundance of Caecomyces and unclassified fungi in rectal content had an increasing tendency compared with that in ruminal content (0.05≤P<0.10). In conclusion, there is a niche differentiation within anaerobic fungal community between rumen and rectum of beef cattle, which could be attributed to monocentric anaerobic fungal genus Caecomyces.

Cite this article

ZHANG Yawei , TAO Xinyan , ZHANG Yuejiao , WANG Yuehong , ZHANG Yuanqing . Amplicon Sequencing Analysis Based on QIIME2 Platform Evaluates Difference in Anaerobic Fungal Structure between Ruminal and Rectal Content of Beef Cattle[J]. Chinese Journal of Animal Nutrition, 2022 , 34(8) : 5107 -5115 . DOI: 10.3969/j.issn.1006-267x.2022.08.034

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