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Establishment of the first Macaca fascicularis gut microbiome gene catalog
Publish Date: 2018-08-24

Recently, a research group from Institute of Metagenomics of BGI Research successfully constructed the first Macaca fascicularis gut microbiome gene catalog, which was published online in GigaScience of Oxford Academic.

Macaca fascicularis is a primate mammal whose genetics and physiology are close to humans. Therefore, it has been widely used as an important model in biomedical research and drug development. However, detailed information of cynomolgus macaque gut microbiota had not been well developed. In order to construct the cynomolgus macaque gut microbial gene catalog and explore differences of cynomolgus macaque gut microbiome under different diet conditions, 20 cynomolgus macaques aged 13 to 16 years old were selected and separated into two groups. One group was fed with high-fat/low fiber diet (group A) and the other with a low-fat/high fiber (group B). After three months of feeding, fecal samples were collected and sequenced with metagenomic shotgun sequencing technology. In total, 140 gigabytes (Gb) of sequencing data were generated, with 131Gb of high quality data remaining after quality control and host genome DNA removal, in which each sample consists of 6.55Gb data on average.

Finally, the researchers constructed the first non-redundant Macaca fascicularis gene catalog comprising 1,991,169 genes, by performing assembly and open reading frames (ORF) prediction with SOAPdenovo and Metagene2, and used CD-HIT to remove redundant genes. By aligning against the NCBI-NR database, 65.68% of the macaque gut genes have the taxonomic annotation information, and 53.65% of the macaque gut genes could be annotated to the phylum level. Most of the annotated phylum contain Firmicutes (52.94%) and Bacteroidetes (21.25%). At the genus level, 276,920 (13.91%) of the macaque gut bacterial genes could be annotated, and most of the annotated genes belonged to Prevotella (34.55%), followed by Ruminococcus (9.91%), Clostridium (6.73%), Eubacterium (6.12%) and Bacteroides (6.00%). At the functional level, 53.09% of the macaque gut genes can be assigned to KEGG orthologous (KOs).

In order to explore the feasibility of cynomolgus macaque as an animal model for human gut microbiome research, the team compared macaque gut bacterial gene catalog with the human, pig and mouse catalog. The results showed that 39.49% of the cynomolgus macaque gut bacterial genes were included in the human gut bacterial gene catalog, and 25.45% of the genes were presented in the pig gut bacterial gene catalog, whereas only 0.6% of the genes were found in the mouse gut gene catalog. Additionally, high quality reads from each 20 fecal samples of cynomolgus macaque, pig and mouse were also mapped with the 9.9M human gut bacterial gene catalog. More reads of cynomolgus macaque gut microbiome (39.23%) could be mapped to the human gut bacterial gene catalog compared to reads from the pig (26.98%) and mouse (16.01%). These new findings revealed that cynomolgus macaque could become a promising model for human gut microbiome research due to its greater similarity in gut microbiomes compared with other mammals.

Furthermore, the cynomolgus macaques gut microbiome differences under different dieta were also compared. The results showed that alpha diversity of group A was lower than that of group B. Abundant differences were also found in genus, species, gene and KO levels between these two groups. Notably, compared with group B, the reads from group A showed significantly higher mapping rate to the human gut bacterial gene sets.

Xiaoping Li, head of this project at the Institute of Metagenomics, BGI-Research said: “This project successfully constructed the cynomolgus macaque gut microbiome gene catalog, and compared it with human, pig and mouse gut gene catalog, which provided important reference data for further research on the cynomolgus macaque gut microbiome.”


Further Reading:

https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giy100/5076037