Fig. 2.

Experimental designs in animal microbiome research.(A)The microbial composition of the gut can be manipulated with antibiotics, probiotics, and prebiotics. (B) Germ-free mice are raised in sterile environments and possess no intrinsic microbes. (C) Microbes can be transferred from one animal to another, either via co-housing (i.e. sharing the same physical environment), or by transplantation of faecal matter. The arrows show that germ-free mice can be colonised with specific types of probiotics (monoassociation), with normal or atypical microbiomes from other conspecifics (via co-housing or faecal transplants), and with normal or atypical microbiomes from humans in order to evaluate the extent to which the microbiome can recapitulate donor phenotypes in the recipient.