Journal ArticleDOI
Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery
Kirill Veselkov,John C. Lindon,Timothy M. D. Ebbels,Derek J. Crockford,Vladimir V. Volynkin,Elaine Holmes,D. B. Davies,Jeremy Nicholson +7 more
TLDR
A novel recursive segment-wise peak alignment (RSPA) method to reduce variability in peak positions across the multiple NMR spectra used in metabonomic studies and its capacity to enhance interpretability and robustness of multivariate statistical tools is demonstrated.Abstract:
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...read more
Citations
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Journal ArticleDOI
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor
Michelle I. Smith,Tanya Yatsunenko,Mark J. Manary,Mark J. Manary,Mark J. Manary,Indi Trehan,Indi Trehan,Rajhab S. Mkakosya,Jiye Cheng,Andrew L. Kau,Stephen S. Rich,Patrick Concannon,Josyf C. Mychaleckyj,Jie Liu,Eric R. Houpt,Jia V. Li,Elaine Holmes,Jeremy K. Nicholson,Dan Knights,Luke K. Ursell,Rob Knight,Jeffrey I. Gordon +21 more
TL;DR: The authors investigated the role of the gut microbiome in kwashiorkor, an enigmatic form of severe acute malnutrition that is the consequence of inadequate nutrient intake plus additional environmental insults, and found that RUTF produced a transient maturation of metabolic functions that regressed when administration of RUTF was stopped.
Journal ArticleDOI
Multivariate Analysis in Metabolomics.
Bradley Worley,Robert Powers +1 more
TL;DR: The use of multivariate analysis for metabolomics is discussed, as well as common pitfalls and misconceptions, and spectral features contributing most to variation or separation are identified for further analysis.
Journal ArticleDOI
Fat, fibre and cancer risk in African Americans and rural Africans
Stephen J. O'Keefe,Jia V. Li,Leo Lahti,Junhai Ou,Franck Carbonero,Khaled Mohammed,Joram M. Posma,James Kinross,Elaine Wahl,Elizabeth H. Ruder,Kishore Vipperla,Vasudevan G. Naidoo,Lungile Mtshali,Sebastian Tims,Philippe G. B. Puylaert,James P. DeLany,Alyssa M. Krasinskas,Ann C. Benefiel,Hatem Kaseb,Keith Newton,Jeremy K. Nicholson,Willem M. de Vos,H. Rex Gaskins,Erwin G. Zoetendal +23 more
TL;DR: The food changes performed in subjects from the same populations 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.
Journal ArticleDOI
icoshift: A versatile tool for the rapid alignment of 1D NMR spectra
TL;DR: The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis and is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning.
Journal ArticleDOI
Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women
Evelyne M. Dewulf,Patrice D. Cani,Sandrine P. Claus,Susana Fuentes,Philippe G. B. Puylaert,Audrey M. Neyrinck,Laure B. Bindels,Willem M. de Vos,Glenn R. Gibson,Jean-Paul Thissen,Nathalie M. Delzenne +10 more
TL;DR: 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.
References
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Journal ArticleDOI
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Olaf Beckonert,Hector C. Keun,Timothy M. D. Ebbels,Jacob G. Bundy,Elaine Holmes,John C. Lindon,Jeremy K. Nicholson +6 more
TL;DR: The main NMR spectroscopic applications in modern metabolic research are summarized, and detailed protocols for biofluid and tissue sample collection and preparation are provided, including the extraction of polar and lipophilic metabolites from tissues.