1.动物肠道微生物与动物适应性性进化 

适应性进化是进化生物学领域的研究热点。一直以来，大多数研究都是利用动物自身基因组的变异来探讨动物适应性进化的分子机制。然而，除了动物自身基因组之外，动物的第二套基因组（肠道微生物组）在维持动物正常生理代谢、免疫、发育、认知等功能方面具有重要的作用，表明两套基因组（也被成为“全基因组-Hologenomes”）及其相互作用有利于动物对极端环境或新环境的适应。本研究方向重点是系统整合两套基因组信息（宿主自身基因组以及共生微生物组），结合代谢组、蛋白组、培养组等组学工具，利用进化基因组学、系统生物学等多学科交叉的优势，探讨自然选择和人工选择下哺乳动物适应性进化的全基因组机制。 

2.肠道微生物与多细胞动物宿主的协同进化 

本研究方向重点选择物种多样性较为丰富、具有社会性、肠菌简单的授粉昆虫作用模型动物，来探讨肠道微生物与动物宿主的协同进化机制，力求为靶向肠道微生物干预或调控动物复杂性状提供重要的进化生物学理论基础。 

3.以灵长类动物为模型，探索肠道微生物干预或调控神经功能退化相关复杂性状的机制机理。 

本研究方向重点以灵长类动物为模型，建立系统的精神神经类疾病（抑郁症、老年痴呆等）发生和发展相关的肠道微生态研究技术体系，目标是从肠道微生物视角出发开发保护和促进脑功能的新策略。 

Zhang Zhigang^(#),Dongming Xu, Li Wang, Junjun Hao, JinFeng Wang, Xin Zhou, Weiwei Wang, Qiang Qiu, Xiaodan Huang, Jianwei Zhou, Ruijun Long^(*), Fangqing Zhao^(*), Peng Shi^(*).Convergent evolution of rumen microbiomes in high-altitude mammals.Current Biology, 2016,26(14):1873-1879.(^#Firstauthor) 

Zhang Zhigang^(#), Geng J, Tang X, Fan H, Xu J, Wen X, Ma Z, Shi P. Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota.ISME J,2014,8(4): 881-893.(^#Firstauthor) 

Wu Tao^(#),ZhangZhigang^(#), Liu B, Hou D, Liang Y, Zhang J, Shi P. Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study.BMC Genomics, 2013,14(1): 669.(^#Co-firstauthor)(Highly Assessed) 

Yanhui Li, Cheng-Gang Zou, Yu Fu, Yanhong Li, Qin Zhou, Bo Liu,ZhangZhigang^(*), Juan Liu^(*).Oral microbial community typing of caries and pigment in primary dentition.BMC Genomics, 2016, 17(1):1-11.(*Co-correspondence author) 

Li ZhiPeng, Wright A-DG, Si H, Wang X, Qian W,ZhangZhigang^(*), Li G^(*). 2016. Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses.Environmental Microbiology Reports, 2016, 8(6):1016-1023.(*Co-correspondence author) 

 Li Jilian, J. E. Powell, J. Guo, J. D. Evans, J. Wu, P. Williams, Q. Lin, N. A. Moran^(*)andZhangZhigang^(*). Two gut community enterotypes recur in diverse bumblebee species.Current Biology, 2015,25(15): R652-R653.(^*Co-correspondence author) 

Li Zhipeng, Wright A-D, Liu H, Bao K, Zhang T, Wang K, Cui X, Yang F,ZhangZhigang^(*), Li G^(*).Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets.Microbial Ecology,2015, 69(2): 307-318.(^*Co-correspondence author) 

Li Zhipeng, A.-D. G. Wright, H. Liu, Z. Fan, F. Yang,ZhangZhigang^(*)and G. Li^(*). Response of the rumen microbiota of sika deer (Cervus nippon) fed different concentrations of tannin rich plants.PLoS ONE, 2015,10(5): e0123481.(^*Co-correspondence author) 

Zhu Lin, A.-H. Lei, H.-Y. Zheng, L.-B. Lyu,ZhangZhigang^(*)and Y.-T. Zheng^(*). Longitudinal analysis reveals characteristically high proportions of bacterial vaginosis-associated bacteria and temporal variability of vaginal microbiota in northern pig-tailed macaques (Macaca leonina).Zoological Research, 2015,36(5): 285-298. (^*Co-correspondence author) 

Geng Jiawei, Song Q, Tang X, Liang X, Fan H, Peng H, Guo Q^(*),ZhangZhigang^(*). Co-occurrence of driver and passenger bacteria in human colorectal cancer.Gut Pathogens, 2014, 6(1): 26. (^*Co-correspondence author) 

Li Zhipeng,ZhangZhigang^(*), Xu C, Zhao J, Liu H, Fan Z, Yang F, Wright A-DG, Li G^(*). Bacteria and methanogens differ along the gastrointestinal tract of chinese roe deer (Capreolus pygargus.PLoS ONE, 2014, 9(12): e114513.(^*Co-correspondence author) 

 Ma Lanqing, Zou T, Yuan Y, Lv J, Dong X, Yang G, Zhu Y, Luo J,ZhangZhigang^(*), Yang J^(*),Duodenal ferroportin is up-regulated in patients with chronic hepatitis C.PLoS ONE, 2014, 9(10): e110658. (*Co-correspondence author) 

Zou Tong, Zhang Zhigang (*), Zou Chenggang,ChenKeping,DaiYan,TongJiabin,YuXue,LiuJunpeng,ChenDongke,XuHongtao,ShiHaifeng,WangZhilei,WuSujuan,SunChen,CuiWen,ChenHao,YuJun,YangJiefu(*).Subclinical infections of cardiac implantable electronic devices: Insights into the host–bacteria dialog from blood and pocket tissue with pyrosequencing.International journal of cardiology, 2014, 174(3): 545-549.(^*Co-correspondence author) 

Zhang Zhigang^(*#), Zhai H, Geng J, Yu R, Ren H, Fan H^(*), Shi P^(*). Large-scale survey of gut microbiota associated with MHE via 16S rRNA-based pyrosequencing.Am J Gastroenterol, 2013, 108(10): 1601-1611.(^*Co-correspondence author) 

Geng Jiawei, Fan H, Tang X, Zhai H,Zhang Zhigang^(*).Diversified pattern of the human colorectal cancer microbiome.Gut Pathogens, 2013,5(1): 2. (^*Correspondence author)