Metabonomic Phenotyping for the Gut Microbiota and Mammal Interactions

All mammals consist of two distinct but integrated parts including hosts themselves and some symbiotic microorganisms ^[1–3]. Their symbiosis is established interactively through co-evolution and mutual selections ^[3–5]. Therefore, mammals are regarded as ‘superorganisms’ and their physiology and health in entirety have to be understood by taking into consideration hosts, symbiotic microbes and their interactions ^[1–4]. The symbiotic microorganisms are living mostly in the mammals’ gut and also known in different contexts as the gut microbiota, microparasites and microbiomes. It is now known that mammals harbor trillions of symbiotic microbes mainly in their gastrointestinal tract (GIT) with many different microbial species ^[2–7]. In normal adult human GIT, for instance, there is more than one kilogram of microbes with over ten times more cells than hosts and several thousands of species ^[2–7]. These symbiotic gut microbiota are co-developed with their hosts’ growth playing essential roles in many aspects of mammalian physiology and thus have profound effects on the hosts’ health ^[3–7]. For this reason, microbiomes are now considered collectively as an ‘essential organ’ or extended genomes, transcriptomes, proteomes and metabonomes ^{[4, 7, 8]} for their mammalian hosts. However, it is nontrivial at the moment to completely define the genomes of these microbiomes as has been done for human and rodent hosts. Neither can their composition, transcriptomes and proteomes be defined in detail, since many species cannot be cultured ex vivo.