Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta)

ABSTRACT

Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.

KEYWORDS:

• Macaca mulatta
• Metagenomic binning
• MAG
• non-human primate
• gut microbiome
• Campylobacter

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2188848

Authors’ contributions

SY and ZF wrote the manuscript. SY, ZF, JiaweiL, XW and YL performed the bioinformatics analyses. BY and MH revised the manuscript. AZ and JingL designed and supervised the study. All authors read and approved the final manuscript.

Data availability statement

The data that support the findings of this study are openly available in CNGB Sequence Archive (CNSA) of China National GeneBank DataBase (CNGBdb) with accession number CNP0001810 at https://db.cngb.org/.

Ethics

This study was approved by the Ethics Committee of College of Life Sciences, Sichuan University (No. 20210308001).

Additional information

Funding

This work was supported by Sichuan Science and Technology Program (No. 2023NSFSC1935), the National Natural Science Foundation of China (No. 32070413) and Key R&D Program of Sichuan Province (No. 22ZDZX0011).