Kwashiorkor, an enigmatic form of severe acute malnutrition, is the consequence of inadequate nutrient intake plus additional environmental insults. To investigate the role of the gut microbiome, we studied 317 Malawian twin pairs during the first 3 years of life. During this time, half of the twin pairs remained well nourished, whereas 43% became discordant, and 7% manifested concordance for acute malnutrition. Both children in twin pairs discordant for kwashiorkor were treated with a peanut-based, ready-to-use therapeutic food (RUTF). Time-series metagenomic studies revealed that RUTF produced a transient maturation of metabolic functions in kwashiorkor gut microbiomes that regressed when administration of RUTF was stopped. Previously frozen fecal communities from several discordant pairs were each transplanted into gnotobiotic mice. The combination of Malawian diet and kwashiorkor microbiome produced marked weight loss in recipient mice, accompanied by perturbations in amino acid, carbohydrate, and intermediary metabolism that were only transiently ameliorated with RUTF. These findings implicate the gut microbiome as a causal factor in kwashiorkor.

http://www.humeco.m.u-tokyo.ac.jp/individuals/umezaki/PDF_files/Meeting/Malawi_Gutmicrobiome_Kwashiorkor_Science2013.pdf

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor

Metabolomics aims to provide a global snapshot of all small-molecule metabolites in cells and biological fluids, free of observational biases inherent to more focused studies of metabolism. However, the staggeringly high information content of such global analyses introduces a challenge of its own; efficiently forming biologically relevant conclusions from any given metabolomics dataset indeed requires specialized forms of data analysis. One approach to finding meaning in metabolomics datasets involves multivariate analysis (MVA) methods such as principal component analysis (PCA) and partial least squares projection to latent structures (PLS), where spectral features contributing most to variation or separation are identified for further analysis. However, as with any mathematical treatment, these methods are not a panacea; this review discusses the use of multivariate analysis for metabolomics, as well as common pitfalls and misconceptions.

/pdf/multivariate-analysis-in-metabolomics-3qjszfszcn.pdf

Multivariate Analysis in Metabolomics.

Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in subjects from the same populations, where African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet, under close supervision. In comparison with their usual diets, the food changes resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis, and suppressed secondary bile acid synthesis in the African Americans.

/pdf/fat-fibre-and-cancer-risk-in-african-americans-and-rural-3fxiqyiz69.pdf

Fat, fibre and cancer risk in African Americans and rural Africans

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

Objective To highlight the contribution of the gut microbiota to the modulation of host metabolism by dietary inulin-type fructans (ITF prebiotics) in obese women. Methods A double blind, placebo controlled, intervention study was performed with 30 obese women treated with ITF prebiotics (inulin/oligofructose 50/50 mix; n=15) or placebo (maltodextrin; n=15) for 3 months (16 g/day). Blood, faeces and urine sampling, oral glucose tolerance test, homeostasis model assessment and impedancemetry were performed before and after treatment. The gut microbial composition in faeces was analysed by phylogenetic microarray and qPCR analysis of 16S rDNA. Plasma and urine metabolic profiles were analysed by 1 H-NMR spectroscopy. Results Treatment with ITF prebiotics, but not the placebo, led to an increase in Bifidobacterium and Faecalibacterium prausnitzii; both bacteria negatively correlated with serum lipopolysaccharide levels. ITF prebiotics also decreased Bacteroides intestinalis, Bacteroides vulgatus and Propionibacterium, an effect associated with a slight decrease in fat mass and with plasma lactate and phosphatidylcholine levels. No clear treatment clustering could be detected for gut microbial analysis or plasma and urine metabolomic profile analyses. However, ITF prebiotics led to subtle changes in the gut microbiota that may importantly impact on several key metabolites implicated in obesity and/or diabetes. Conclusions ITF prebiotics selectively changed the gut microbiota composition in obese women, leading to modest changes in host metabolism, as suggested by the correlation between some bacterial species and metabolic endotoxaemia or metabolomic signatures.

https://gut.bmj.com/content/gutjnl/62/8/1112.full.pdf

Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women

Chemical shift variation in small-molecule 1H NMR signals of biofluids complicates biomarker information recovery in metabonomic studies when using multivariate statistical and pattern recognition tools. Current peak realignment methods are generally time-consuming or align major peaks at the expense of minor peak shift accuracy. We present a novel recursive segment-wise peak alignment (RSPA) method to reduce variability in peak positions across the multiple 1H NMR spectra used in metabonomic studies. The method refines a segmentation of reference and test spectra in a top-down fashion, sequentially subdividing the initial larger segments, as required, to improve the local spectral alignment. We also describe a general procedure that allows robust comparison of realignment quality of various available methods for a range of peak intensities. The RSPA method is illustrated with respect to 140 1H NMR rat urine spectra from a caloric restriction study and is compared with several other widely used peak align...

Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery

Multicellular organisms maintain the stability of their internal environment using metabolic and physiological regulatory mechanisms that are disrupted during disease. The loss of homeostatic contr...

A metabolic entropy approach for measurements of systemic metabolic disruptions in patho-physiological States.

One- and two-dimensional 1 HNMR spectroscopy (500 MHz) was used to study the heteroassociation of caffeine (CAF), a hydrotropic agent, with flavin mononucleotide (FMN) in an aqueous solution in order to gain insights intothe molecular mechanism of solubilization in the FMN-CAF system. The equilibrium constants, induced proton chemical shifts and thermochemical parameters (AH and AS) for the heteroassociation of the molecules were determined from the concentration and temperature dependences of the proton chemical shifts for interacting CAF and FMN molecules. An analysis of the results obtained demonstrated that CAF-FMN heteroassociates are formed due to the stacking-interaction between the aromatic chromophores of these molecules. The most probable structure of the 1 : 1 CAF-FMN complex was determined from molecular dynamics simulations with the use of the X-PLOR program and an analysis of the induced proton chemical shifts for the molecules under study. Calculations of the relative content of homo- and heterocomplexes at various values of the ratio r of the concentrations CAF and FMN demonstrated that, at r > 10, the contribution from the CAF-FMN heterocomplexes is predominant in the equilibrium distribution of associates in aqueous solutions. It was concluded that the formation of stack-type intermolecular associates of hydrotropic agents (caffeine and nicotinamide) with bioactive compounds is the governing factor in the solubilization of such compounds.

A 1H NMR study of the association of caffeine with flavin mononucleotide in aqueous solutions

The molecular basis of the marked structure-activity relationship for a homologous series of DNA-binding phenoxazone drugs (ActII-ActIV) has been investigated by NMR spectroscopy and molecular mechanics The spatial structures of the complexes between the drugs and a model deoxytetranucleotide, 5′-d(TpGpCpA), have been determined by molecular mechanics methods using homonuclear 1H-1H 2D-NOESY and heteronuclear 1H-31P (HMBC) NMR spectroscopic data Observed intermolecular NOE contacts and equilibrium binding studies confirm that the binding affinity of the synthetic phenoxazone derivatives with d(TGCA) decreases with an increase in the number of CH2 groups in the dimethylami- noalkyl side chains, ie, ActII > ActIII > ActIV, in agreement with the observed biological activity of these compounds Molecular mechanics calculations of the spatial structures of the intercalated complexes of ActII-ActIV with d(TGCA) indicate that the different binding constants of the phenoxazone derivatives with the DN

D. B. Davies

Papers

Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery

A metabolic entropy approach for measurements of systemic metabolic disruptions in patho-physiological States.

A 1H NMR study of the association of caffeine with flavin mononucleotide in aqueous solutions

Structural basis for the binding affinity of a homologous series of synthetic phenoxazone drugs with DNA: NMR and molecular mechanics analysis.