Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing
Objective To analyze the microflora structure and abundance of ileum and colon of SPF male SD rats by high-throughput sequencing technique.MethodsThe ileal and colonic lumen contents of 30 SPF male SD rats were collected, the total bacterial DNA in the contents was extracted and amplified by PCR. Th...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | zho |
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Editorial Office of Laboratory Animal and Comparative Medicine
2023-02-01
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| Series: | Shiyan dongwu yu bijiao yixue |
| Subjects: | |
| Online Access: | https://www.slarc.org.cn/dwyx/CN/10.12300/j.issn.1674-5817.2022.103 |
| _version_ | 1797871532061491200 |
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| author | XU Qin NI Yan SHI Wenhui LI Jianying LIU Jiangwei ZHAO Hongqiong XU Xinming |
| author_facet | XU Qin NI Yan SHI Wenhui LI Jianying LIU Jiangwei ZHAO Hongqiong XU Xinming |
| author_sort | XU Qin |
| collection | DOAJ |
| description | Objective To analyze the microflora structure and abundance of ileum and colon of SPF male SD rats by high-throughput sequencing technique.MethodsThe ileal and colonic lumen contents of 30 SPF male SD rats were collected, the total bacterial DNA in the contents was extracted and amplified by PCR. The V3-V4 region of bacterial 16S rRNA in the samples was sequenced using Illumina NovaSeq sequencing platform. Then the species structure and abundance of the intestinal flora were analyzed at the phylum and genus level based on validated data. The diversity and differences between ileal and colonic flora were analyzed using the QIIME software (amplicon) analysis tool. The Tax4Fun program was applied to predict the dominant gene enrichment pathways of ileal and colonic flora.ResultsAt the phylum level, the dominant microflora in the ileum of male SD rats were Firmicutes and Actinobacteria, accounting for more than 98%. The dominant colonic microbial community were mainly Firmicutes and Bacteroidetes, accounting for more than 95%. At the genus level, Lactobacillus and Alistipes were the predominant bacteria in the ileum. The colon was dominated by Lactobacillus and Romboutsia. In terms of flora diversity, the alpha diversity of colonic flora including richness index (Chao1 index) and diversity index (Shannon index) were significantly higher than those of ileum (P < 0.01), and the structural variability of the composition of its flora species was smaller than that of ileum; the ileal flora with significant structural variability were mainly of the phylum Firmicutes, Romboutsia, Peptostreptococcaceae, while the colonic flora had significant structural differences in Bacteroidales. In terms of flora function, the ileal flora dominant genes were significantly enriched in lipid-like metabolism, polyketide metabolism, membrane transport, biodegradation and other pathways, while the colonic flora dominant genes were significantly enriched in glycan biosynthesis metabolism, energy metabolism, biosynthesis of cofactor and vitamins and other products, and other pathways.ConclusionThere are significant differences in structure and abundance between the ileal and colonic flora of SPF male SD rats, and the abundance and diversity of colonic flora are higher than those of ileal flora. |
| first_indexed | 2024-04-10T00:44:18Z |
| format | Article |
| id | doaj.art-be826f8f265d4379a6a35947dbacc461 |
| institution | Directory Open Access Journal |
| issn | 1674-5817 |
| language | zho |
| last_indexed | 2024-04-10T00:44:18Z |
| publishDate | 2023-02-01 |
| publisher | Editorial Office of Laboratory Animal and Comparative Medicine |
| record_format | Article |
| series | Shiyan dongwu yu bijiao yixue |
| spelling | doaj.art-be826f8f265d4379a6a35947dbacc4612023-03-14T02:15:27ZzhoEditorial Office of Laboratory Animal and Comparative MedicineShiyan dongwu yu bijiao yixue1674-58172023-02-01431536010.12300/j.issn.1674-5817.2022.1031674-5817（2023）01-0053-08Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput SequencingXU Qin0NI Yan1SHI Wenhui2LI Jianying3LIU Jiangwei4ZHAO Hongqiong5XU Xinming6General Hospital of Xinjiang Military Districts, Key Laboratory of Special Environmental Medicines of Xinjiang, Urumqi 830000, ChinaGeneral Hospital of Xinjiang Military Districts, Key Laboratory of Special Environmental Medicines of Xinjiang, Urumqi 830000, ChinaGeneral Hospital of Xinjiang Military Districts, Key Laboratory of Special Environmental Medicines of Xinjiang, Urumqi 830000, ChinaGeneral Hospital of Xinjiang Military Districts, Key Laboratory of Special Environmental Medicines of Xinjiang, Urumqi 830000, ChinaGeneral Hospital of Xinjiang Military Districts, Key Laboratory of Special Environmental Medicines of Xinjiang, Urumqi 830000, ChinaVeterinary Medicine College of Xinjiang Agricultural University, Urumqi 830052, ChinaBiotechnology Research Institute of Xinjiang Animal Husbandry Sciences Academy, Urumqi 830000, ChinaObjective To analyze the microflora structure and abundance of ileum and colon of SPF male SD rats by high-throughput sequencing technique.MethodsThe ileal and colonic lumen contents of 30 SPF male SD rats were collected, the total bacterial DNA in the contents was extracted and amplified by PCR. The V3-V4 region of bacterial 16S rRNA in the samples was sequenced using Illumina NovaSeq sequencing platform. Then the species structure and abundance of the intestinal flora were analyzed at the phylum and genus level based on validated data. The diversity and differences between ileal and colonic flora were analyzed using the QIIME software (amplicon) analysis tool. The Tax4Fun program was applied to predict the dominant gene enrichment pathways of ileal and colonic flora.ResultsAt the phylum level, the dominant microflora in the ileum of male SD rats were Firmicutes and Actinobacteria, accounting for more than 98%. The dominant colonic microbial community were mainly Firmicutes and Bacteroidetes, accounting for more than 95%. At the genus level, Lactobacillus and Alistipes were the predominant bacteria in the ileum. The colon was dominated by Lactobacillus and Romboutsia. In terms of flora diversity, the alpha diversity of colonic flora including richness index (Chao1 index) and diversity index (Shannon index) were significantly higher than those of ileum (P < 0.01), and the structural variability of the composition of its flora species was smaller than that of ileum; the ileal flora with significant structural variability were mainly of the phylum Firmicutes, Romboutsia, Peptostreptococcaceae, while the colonic flora had significant structural differences in Bacteroidales. In terms of flora function, the ileal flora dominant genes were significantly enriched in lipid-like metabolism, polyketide metabolism, membrane transport, biodegradation and other pathways, while the colonic flora dominant genes were significantly enriched in glycan biosynthesis metabolism, energy metabolism, biosynthesis of cofactor and vitamins and other products, and other pathways.ConclusionThere are significant differences in structure and abundance between the ileal and colonic flora of SPF male SD rats, and the abundance and diversity of colonic flora are higher than those of ileal flora.https://www.slarc.org.cn/dwyx/CN/10.12300/j.issn.1674-5817.2022.103intestinal microflorabacteria abundanceileumcolonsd rats |
| spellingShingle | XU Qin NI Yan SHI Wenhui LI Jianying LIU Jiangwei ZHAO Hongqiong XU Xinming Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing Shiyan dongwu yu bijiao yixue intestinal microflora bacteria abundance ileum colon sd rats |
| title | Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing |
| title_full | Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing |
| title_fullStr | Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing |
| title_full_unstemmed | Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing |
| title_short | Analysis on Ileum and Colon Microflora of SPF Male SD Rats based on High-throughput Sequencing |
| title_sort | analysis on ileum and colon microflora of spf male sd rats based on high throughput sequencing |
| topic | intestinal microflora bacteria abundance ileum colon sd rats |
| url | https://www.slarc.org.cn/dwyx/CN/10.12300/j.issn.1674-5817.2022.103 |
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