Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

Abstract

The transgenomic metabolic effects of exposure to either Lactobacillus paracasei or Lactobacillus rhamnosus probiotics have been measured and mapped in humanized extended genome mice (germ‐free mice colonized with human baby flora). Statistical analysis of the compartmental fluctuations in diverse metabolic compartments, including biofluids, tissue and cecal short‐chain fatty acids (SCFAs) in relation to microbial population modulation generated a novel top‐down systems biology view of the host response to probiotic intervention. Probiotic exposure exerted microbiome modification and resulted in altered hepatic lipid metabolism coupled with lowered plasma lipoprotein levels and apparent stimulated glycolysis. Probiotic treatments also altered a diverse range of pathways outcomes, including amino‐acid metabolism, methylamines and SCFAs. The novel application of hierarchical‐principal component analysis allowed visualization of multicompartmental transgenomic metabolic interactions that could also be resolved at the compartment and pathway level. These integrated system investigations demonstrate the potential of metabolic profiling as a top‐down systems biology driver for investigating the mechanistic basis of probiotic action and the therapeutic surveillance of the gut microbial activity related to dietary supplementation of probiotics. ### Synopsis The gut microbiome–mammalian ‘Superorganism’ ([Lederberg, 2000][1]) represents the highest level of biological evolutionary development in which there is extensive ‘transgenomic’ modulation of metabolism and physiology, which is a characteristic of true symbiosis. By definition, superorganisms contain multiple cell types and the coevolved interacting genomes can only be effectively studied as an in vivo unit in situ using top‐down systems biology approaches ([Nicholson, 2006][2]; [Martin et al , 2007a][3]). Interest in the impact of gut microbial activity on human health is expanding rapidly and many mammalian–microbial associations, both positive and negative, have been reported ([Dunne, 2001][4]; [Verdu et al , 2004][5]; [Nicholson et al , 2005][6]; [Gill et al , 2006][7]; [Ley et al , 2006][8]). As the microbiome interacts strongly with the host to determine the metabolic phenotype ([Holmes and Nicholson, 2005][9]; [Gavaghan McKee et al , 2006][10]) and metabolic phenotype influences outcomes of drug interventions ([Nicholson et al , 2004][11]; [Clayton et al , 2006][12]) there is clearly an important role of understanding these interactions as part of personalized healthcare solutions ([Nicholson, 2006][2]). Probiotics, most commonly Lactobacillus and Bifidobacteria , is one of the current approaches used to modulate the balance of the intestinal microflora in a beneficial way ([Collins and Gibson, 1999][13]). However, the functional effects of probiotic interventions cannot be fully assessed without probing the biochemistry of the host at multiple compartmental levels and we propose that top‐down systems biology provides an ideal approach to further understanding in this field. The microbiota observed in human baby flora mice has a number of similarities with that found in formula‐fed neonates ([Mackie et al , 1999][14]) that makes it be a well‐adapted and simplified model to assess probiotics impact on gut microbial functional ecosystem (in particular on metabolism of Bifidobacteria and potential pathogens) and subsequent effects on host metabolism. Metabolic profiling using high‐density data generating spectroscopic techniques, in combination with multivariate mathematical modelling is a tool that is well suited to generating metabolic profiles that encapsulate the top‐down system response of an organism to a stressor or intervention ([Nicholson and Wilson, 2003][15]). Recently, metabolic profiling strategies have been successfully applied to investigating the effects of the gut microflora on mammalian metabolism ([Martin et al , 2007a][3]), including probiotic treatment on germ‐free mice ([Martin et al , 2007b][16]), modulation of Trichinella spiralis ‐induced gut disorders ([Martin et al , 2006][17]) and mechanisms of insulin‐resistance ([Dumas et al , 2006][18]). In the current study, both 1H nuclear magnetic resonance spectroscopy and ultra performance liquid chromatography‐mass spectrometry analysis have been applied to characterize the global metabolic responses of humanized microbiome mice subsequently exposed to placebo, Lactobacillus paracasei or Lactobacillus rhamnosus supplementation. Correlation of the response across multiple biofluids and tissue, using plasma, urine, fecal extracts, liver tissues and ileal flushes as the biological matrices for the detection of dietary intervention, generates a top‐down systems biology view of the response to probiotics intervention. Significant associations between host metabolic phenotypes and a nutritionally modified gut‐microbiota strongly supports the idea that changes across a whole range of metabolic pathways are the products of extended genome perturbations that can be oriented using probiotic supplementation, and which may play a role in host metabolic health. Here, we show that probiotics supplementation of humanized mice resulted in a decrease in the plasma concentrations of VLDL and low density lipoproteins (LDL), and increased triglyceride concentrations ([Figure 1][19]), through inducing changes in the enterohepatic recirculation of bile acids, which were shown to lower cholesterol and systemic levels of blood lipids ([Pereira and Gibson, 2002][20]). In particular, the Lactobacillus supplementation resulted in decreased fecal excretion of bile acids ([Figure 1C][19]), that may be caused by accumulation of bile acids in Lactobacillus probiotics ([Kurdi et al , 2000][21]). Moreover, probiotic‐specific modulation of the ileal...