Humans have evolved intimate symbiotic relationships with a consortium of gut microbes (microbiome) and individual variations in the microbiome influence host health, may be implicated in disease etiology, and affect drug metabolism, toxicity, and efficacy. However, the molecular basis of these microbe–host interactions and the roles of individual bacterial species are obscure. We now demonstrate a“transgenomic” approach to link gut microbiome and metabolic phenotype (metabotype) variation. We have used a combination of spectroscopic, microbiomic, and multivariate statistical tools to analyze fecal and urinary samples from seven Chinese individuals (sampled twice) and to model the microbial–host metabolic connectivities. At the species level, we found structural differences in the Chinese family gut microbiomes and those reported for American volunteers, which is consistent with population microbial cometabolic differences reported in epidemiological studies. We also introduce the concept of functional metagenomics, defined as “the characterization of key functional members of the microbiome that most influence host metabolism and hence health.” For example, Faecalibacterium prausnitzii population variation is associated with modulation of eight urinary metabolites of diverse structure, indicating that this species is a highly functionally active member of the microbiome, influencing numerous host pathways. Other species were identified showing different and varied metabolic interactions. Our approach for understanding the dynamic basis of host–microbiome symbiosis provides a foundation for the development of functional metagenomics as a probe of systemic effects of drugs and diet that are of relevance to personal and public health care solutions.

Symbiotic gut microorganisms (microbiome) interact closely with the mammalian host's metabolism and are important determinants of human health. Here, we decipher the complex metabolic effects of microbial manipulation, by comparing germfree mice colonized by a human baby flora (HBF) or a normal flora to conventional mice. We perform parallel microbiological profiling, metabolic profiling by 1H nuclear magnetic resonance of liver, plasma, urine and ileal flushes, and targeted profiling of bile acids by ultra performance liquid chromatography–mass spectrometry and short‐chain fatty acids in cecum by GC‐FID. Top‐down multivariate analysis of metabolic profiles reveals a significant association of specific metabotypes with the resident microbiome. We derive a transgenomic graph model showing that HBF flora has a remarkably simple microbiome/metabolome correlation network, impacting directly on the host's ability to metabolize lipids: HBF mice present higher ileal concentrations of tauro‐conjugated bile acids, reduced plasma levels of lipoproteins but higher hepatic triglyceride content associated with depletion of glutathione. These data indicate that the microbiome modulates absorption, storage and the energy harvest from the diet at the systems level. ### Synopsis The symbiotic gut microbiome acts as an extended genome ([Lederberg, 2000][1]) and has evolved to exert control on a number of important mammalian metabolic regulatory functions ([Backhed et al , 2004][2]; [Eckburg et al , 2005][3]; [Holmes and Nicholson, 2005][4]; [Nicholson et al , 2005][5]; [Martin et al , 2006][6]; [Nicholson, 2006][7]; [Turnbaugh et al , 2006][8]). Gut microbial composition is now known to vary significantly in obese animal ([Turnbaugh et al , 2006][8]) and human ([Ley et al , 2006][9]) populations, and recent studies have shown that the exact state of the gut microbial ecology and metabolic activities may be of fundamental importance in the control of calorific absorption ([Xu et al , 2003][10]; [Backhed et al , 2004][2]) and in the development of insulin resistance and non‐alcoholic fatty liver disease ([Dumas et al , 2006][11]). The integrated mammalian microbial co‐metabolism of the bile acid pool is a good example of the complex biochemical interactions between host and resident symbionts, as summarized in [Figure 1][12]. Bile acids are crucial for the absorption of dietary fats and lipid‐soluble vitamins in the intestine ([Staggers et al , 1982][13]) and might have an essential role in regulating obesity or type II diabetes ([Houten et al , 2006][14]; [Watanabe et al , 2006][15]). Many so‐called secondary bile acids (deoxycholic, lithocholic, hyodeoxycholic and ω‐muricholic acids) can be regarded as examples of mammalian–microbiotal co‐metabolism ([Nicholson et al , 2005][5]) and have different metabolic fates via enterohepatic recirculation ([Nicholson et al , 2004][16]). The aim of the study is to assess the effects of the induction of a non‐adapted microflora in a murine model (human baby flora (HBF)) on the host metabolism by comparison with animals colonized with a natural, conventional gut microflora, the result of a long period of co‐evolution. Here, we have integrated the effects of modulation of the microbiome in mouse models on the co‐metabolism of the major bile acids and the general metabolic profiles of the animals. We acquired parallel metabolic profiles of plasma, urine, liver, fecal extracts and ileal flushes using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to characterize a broad range of metabolites across these multiple compartments and 14 bile acids, which were also specifically measured in ileal flushes. The application of high‐resolution 1H NMR spectroscopy of biofluids and tissues coupled with multivariate statistical methods is a well‐established tool for differential metabolic pathway profiling ([Nicholson et al , 2002][17]; [Nicholson et al , 2005][5]; [Nicholson and Wilson, 1989][18]; [Wang et al , 2005][19]). Hyphenated chromatographic‐mass spectrometric methods such as ultra‐performance liquid chromatography–mass spectrometry (UPLC–MS)‐based profiling techniques have also been recently used effectively for functional genomic discrimination ([Plumb et al , 2005][20]; [Wilson et al , 2005][21]). We have now developed and enhanced bile acid analysis method using UPLC–MS, which gives superior chromatographic resolution and sensitivity ([Wilson et al , 2005][21]; [Plumb et al , 2006][22]). We show here a significant association of specific metabotypes obtained from urine, plasma, intact liver tissue and ileal flushes with changes of the gut microbiome in mice colonized naturally with a conventional microflora or with a defined population of microbes in a pathogen‐free environment, that is, exposing germ‐free mice to normal environment to be naturally re‐colonized by bacteria or fed with an HBF. Such exhaustive metabolic profiling revealed that re‐conventionalized mice, that is, those germ‐free mice allowed to equilibrate to a conventional flora, tend to converge metabolically and ecologically towards conventional mice and a healthy physiology. We also report that the re‐colonization of germ‐free mice with a non‐adapted microflora (HBF) modifies the physiology of the murine host towards a pre‐pathologic state (compared to conventional animals) and maintains the gut tract and the liver outside a sustainable mouse ecological equilibrium. Using a transgenomic bipartite graph model highlighting functional relationships between fecal bacteria profiles and bile acid profiles, we show that HBF flora has a remarkably simple microbiome/metabolome correlation network, impacting directly on the host's ability to metabolize fats. The metabolic consequences for the host...

Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation. Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader-Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.