In human, about 90% of cells in the body are bacteria. Most of them reside in the gut. The bacteria play a vital role in human health and physiology, which is sometimes referred to as our “forgotten organ”. Human bacteria are related to energy harvest and storage, diet metabolic process, host immune reaction. A large fraction of them cannot be cultured but cultureindependent high-throughput sequencing promotes largely the development of microbiome research. Due to ethical considerations and shared characters, animal models are usually used for many microbiota studies instead of human. Commonly, the stable microbial composition in a specific body site of healthy human plays a vital role in human health. Those factors shaping or changing microbial composition have recently attracted unprecedented attention along with the sequencing technology development and popularization. During my PhD, three studies were carried on to investigate the impacts of the factors including bacterial transmission, heavy metals, biocides and antibiotics on host microbiota. The three studies employed group-living captive baboons, mice, and pigs as a model, respectively. The first study analyzed the similarity of baboon microbial compositions in oral, pharynx, nose, lung, cervix, uterus, vagina and rectum, and speculated on the possible role of bacterial transmission in shaping those microbial compositions. The second study investigated the impact of arsenic and cadmium on mice gut microbiota and gut microbial metabolites linked to T2DM. The third study targeted the public available metagenomics data of 278 pigs gut microbiota from China, Denmark, and France, to investigate the impacts of the various extent of antibiotics, metals and biocides exposure on co-selection patterns and strength. Therefore, this PhD thesis consists of three manuscripts: Manuscript I similarity across multiple body sites> analyzed a total of 184 oral, oropharyngeal, cervical, uterine, vaginal, nasal, lungs and rectal samples from 16 hamadryas baboons via 16S rRNA gene sequencing. Our analyses show that cohabitants share similar microbial profiles not only in their gut but also in their oral cavity, oropharynx, cervix, uterus, vagina, nose and lungs. Furthermore, the profiles were also very similar between multiple body sites including uterus, cervix, vagina, lung, and rectum; indicating that transmission of microorganisms is common throughout the body, with social interactions (grooming and promiscuity) and shared environment being speculated to be the main modes of transfer. No significant differences within the maternity line and between maternity lines were detected, suggesting that the offspring inherited their gut microbiota primarily through bacterial transmission among cohabitants. Manuscript II microbiome and metabolites> described a murine intervention study using a heavy metal treatment that was carefully characterized by the untargeted microbiome and metabolomics techniques. The investigation was prompted by a sizable amount of epidemiological evidence that heavy metal exposure can lead to metabolic health issues such as type 2 diabetes and obesity. It has been suspected that this could be mediated by the gut microbiome through their impact on the fecal metabolome. This study provides evidence that microbial composition and fecal metabolites previously implicated in metabolic problems changed as a result of heavy metal High throughput sequencing applied to analyze microbial communities in different animal models with an erpreation in a human health perspectives exposure. Additionally, we attempted integrating these two techniques of observation to clarify the fine-scale contribution of the observed microbiome to the metabolome. Manuscript III resistance genes in pigs> described the distribution of mobile antibiotics resistance genes (ARGs), metal resistance genes (MRGs), biocides resistance genes (BRGs) and mobile genetic elements (MGEs) and the co-selection phenomena between ARGs and MRGs/BRGs/MGEs of 278 pigs gut microbiomes from China, Danmark and France. In Europe antibiotics for farming is strictly controlled while used more liberally in China. Metal and biocides are used everywhere. We pursue a two-pronged strategy of establishing evidence from both abundance correlations and contigs harboring several types of resistance. We found that the abundance resistance genes and co-selection frequency and patterns were the most in Chinese pigs, suggesting the unmonitored metals, biocides, and antibiotics use not only resulted in the enhanced abundances of resistance genes but also promoted the maintenance and persistence of ARGs via co-selection. Co-selection phenomena in various countries had both generalities and individualities, which were probably driven by individual selective pressure. Co-selection phenomena in Danish pigs gut was least which may be due to the least use of metal and biocides use in farm-stocking. But Danish pigs gut had abundant mobile ARGs and the possible reason need to be further elucidated. The possible mobility of a many ARGs BRGs, MRGs was mediated by only a couple of MGEs, indicating the co-resistance as a mechanism of co-selection was likely mediated by HGT. Due to its universal significance, the abundant co-selection pool between BRGs/MRGs and ARGs in Chinese pigs gut provide a reference resource for coselection research and a warning for antibiotics, metals and biocides use.