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Establishing the first gene catalogue of Sprague-Dawley rat gut metagenome based on the BGISEQ-500 platform
Publish Date: 2018-07-06

Recently, the Institute of Metagenomics, BGI-Research, cooperating with the Liu Liang team of the State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health of Macao University of Science and China National GeneBank(CNGB), completed the first gene catalogue of the gut metagenome of male Sprague-Dawley rats in the world. The paper of this work was published online in Giga Science of Oxford Academic on May XX22, 2018.

Sprague-Dawley(SD) rat is an important model for biomedical studies in relation to human physiological or pathogenic processes. Therefore, in order to study the potential relationship between intestinal flora and rheumatoid arthritis, as well as the influence of drug intervention on the dynamics of intestinal flora and rheumatoid arthritis, the researchers selected49 SD rats. The adjuvant-induced arthritis model was performed and drug intervention experiments were conducted for 30 days, 5 time points, and 7 experimental groups. With advanced metagenomic shot-gun sequencing technology on the BGISEQ-500 platform, all rat fecal samples were sequenced with the strategy of SE100 and additional PE50 sequencing was performed to samples collected at the first and the last time points. 2512 Gb was gained from the SE sequencing of 245 samples and the PE sequencing of 98 samples. After quality controlling and host removing process, a total size of 2223 Gb (SE100: 1689Gb, PE50: 534Gb) high quality sequencing data was obtained, while the rates of host were 9.76% (SE100) and 11.2% (PE50) separately. Sequencing data of the first and the last time point was iterative assembled with the “PE50 + SE100” hybrid strategy and 22,329,515 scaffolds were obtained eventually. On average, each sample possesses 234,005 scaffolds and the average N50 reached 5,340 bps.

The team performed gene prediction based on assembly data to eliminate redundant gene sequences and eventually obtained 5.1 million non-redundant genes of SD rat gut metagenome, approximately 200 times that of the rats' own genes. Gene annotation analysis revealed that 64.6% and 26.7% were annotated to the phylum and genus levels, respectively. At the phylum level, most of the annotated genes belonged to Firmicutes(75.90%), followed by Bacteroidetes (10.83%) and Proteobacteria (6.77%). At the genus level, the annotated genes (5.30%) primarily belong to Clostridium (8.74%), followed by Bacteroides (6.25%), Roseburia (4.75%), Ruminococcus (4.44%), and Lachnoclostridium (2.58%), reflecting the paucity of the sequenced gut bacterial genomes. A further functional annotation analysis found that 53.1%, 21.8%, and 31% of the genes could be annotated to KEGG orthologous groups (KOs), modules, and pathways, respectively.

In addition, the team also conducted a comparative analysis of human, mouse, and rat gut microbial gene catalogues and found that the pairwise overlap at the gene level is modest, but wat substantially higher for rats and humans (2.47%) than for mouse and humans (1.19%). The gut microbiota of the three gene sets were more functionally similar at the gene level; at the same time, the human gut microbiota KOs (93.65%) was able to be found in rats, which was also higher than the mouse gut microbiota (80.03%).

"The results of this study indicate that the metagenomic sequencing data of the BGISEQ-500 platform demonstrated good assembly performance; at the same time, it demonstrated that the rat is suitable as an animal experimental model for studying the relationship between human diseases and gut microbiota, which will provide important reference data for future research." Guo Ruijin, head of the rat project at the Institute of Metagenomics, BGI-Research said: "Based on the rat's gut gene catalogue, we are working with the State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health of Macao University of Science and other collaborative units, to intervene the intestinal microecology of rats through probiotics, Chinese and Western medicines, and diets to conduct more in-depth research on anti-arthritis methods and molecular mechanisms.”