Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

EBioMedicine - Tập 2 - Trang 968-984 - 2015
Chenhong Zhang1, Aihua Yin2, Hongde Li3, Ruirui Wang1, Guojun Wu1, Jian Shen1, Menghui Zhang1, Linghua Wang1, Yaping Hou2, Haimei Ouyang2, Yan Zhang2, Yinan Zheng2, Jicheng Wang2, Xiaofei Lv2, Yulan Wang3, Feng Zhang1, Benhua Zeng4, Wenxia Li4, Feiyan Yan1, Yufeng Zhao1
1State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
2Medical Genetic Centre and Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
3CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
4Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China

Tài liệu tham khảo

Abubucker, 2012, Metabolic reconstruction for metagenomic data and its application to the human microbiome, PLoS Comput. Biol., 8, e1002358, 10.1371/journal.pcbi.1002358 Askree, 2011, Allelic dropout can cause false-positive results for Prader–Willi and Angelman syndrome testing, J. Mol. Diagn., 13, 108, 10.1016/j.jmoldx.2010.11.006 Backhed, 2004, The gut microbiota as an environmental factor that regulates fat storage, Proc. Natl. Acad. Sci. U. S. A., 101, 15718, 10.1073/pnas.0407076101 Backhed, 2007, Mechanisms underlying the resistance to diet-induced obesity in germ-free mice, Proc. Natl. Acad. Sci. U. S. A., 104, 979, 10.1073/pnas.0605374104 Barreto, 2009, Serum indoxyl sulfate is associated with vascular disease and mortality in chronic kidney disease patients, Clin. J. Am. Soc. Nephrol., 4, 1551, 10.2215/CJN.03980609 Bonfig, 2009, A special, strict, fat-reduced, and carbohydrate-modified diet leads to marked weight reduction even in overweight adolescents with Prader–Willi syndrome (PWS), TheScientificWorldJOURNAL, 9, 934, 10.1100/tsw.2009.105 Butler, 2011, Prader–Willi syndrome: obesity due to genomic imprinting, Curr. Genomics, 12, 204, 10.2174/138920211795677877 Cani, 2008, Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice, Diabetes, 57, 1470, 10.2337/db07-1403 Cantarel, 2012, Complex carbohydrate utilization by the healthy human microbiome, PLoS One, 7, e28742, 10.1371/journal.pone.0028742 Claesson, 2012, Gut microbiota composition correlates with diet and health in the elderly, Nature, 488, 178, 10.1038/nature11319 Cloarec, 2005, Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets, Anal. Chem., 77, 1282, 10.1021/ac048630x Cotillard, 2013, Dietary intervention impact on gut microbial gene richness, Nature, 500, 585, 10.1038/nature12480 Craciun, 2012, Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme, Proc. Natl. Acad. Sci. U. S. A., 109, 21307, 10.1073/pnas.1215689109 David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820 Deeley, 1982, Transcription initiation at the tryptophanase promoter of Escherichia coli K-12, J. Bacteriol., 151, 942, 10.1128/JB.151.2.942-951.1982 Dodt, 2012, FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms, Biology, 1, 895, 10.3390/biology1030895 Dumas, 2006, Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice, Proc. Natl. Acad. Sci. U. S. A., 103, 12511, 10.1073/pnas.0601056103 Dykens, 2007, Assessment of hyperphagia in Prader–Willi syndrome, Obesity (Silver Spring), 15, 1816, 10.1038/oby.2007.216 Ellison, 2005, Loss of foundation species: consequences for the structure and dynamics of forested ecosystems, Front. Ecol. Environ., 3, 479, 10.1890/1540-9295(2005)003[0479:LOFSCF]2.0.CO;2 Eriksson, 2008, CV-ANOVA for significance testing of PLS and OPLS (R) models, J. Chemom., 22, 594, 10.1002/cem.1187 Fagan, 2007, A multivariate analysis approach to the integration of proteomic and gene expression data, Proteomics, 7, 2162, 10.1002/pmic.200600898 Fei, 2013, An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice, ISME J., 7, 880, 10.1038/ismej.2012.153 Finn, 2011, HMMER web server: interactive sequence similarity searching, Nucleic Acids Res., 39, W29, 10.1093/nar/gkr367 Flint, 2012, Microbial degradation of complex carbohydrates in the gut, Gut Microbes, 3, 289, 10.4161/gmic.19897 Gibson, 1994, Regulatory effects of bifidobacteria on the growth of other colonic bacteria, J. Appl. Bacteriol., 77, 412, 10.1111/j.1365-2672.1994.tb03443.x Godon, 1997, Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis, Appl. Environ. Microbiol., 63, 2802, 10.1128/AEM.63.7.2802-2813.1997 Jiang, 2012, Eliminating the dication-induced intersample chemical-shift variations for NMR-based biofluid metabonomic analysis, Analyst, 137, 4209, 10.1039/c2an35392j Kanehisa, 2012, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res., 40, D109, 10.1093/nar/gkr988 Kubota, 1997, Methylation-specific PCR simplifies imprinting analysis, Nat. Genet., 16, 16, 10.1038/ng0597-16 Kurtz, 2004, Versatile and open software for comparing large genomes, Genome Biol., 5, R12, 10.1186/gb-2004-5-2-r12 Labruna, 2011, High leptin/adiponectin ratio and serum triglycerides are associated with an “at-risk” phenotype in young severely obese patients, Obesity, 19, 1492, 10.1038/oby.2010.309 Lacroix, 2014, Metabolic and adipose-tissue signatures in adults with Prader–Willi syndrome, a model of extreme adiposity, J. Clin. Endocrinol. Metab., jc20143127 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Le Chatelier, 2013, Richness of human gut microbiome correlates with metabolic markers, Nature, 500, 541, 10.1038/nature12506 Ley, 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. U. S. A., 102, 11070, 10.1073/pnas.0504978102 Li, 2006, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158 Li, 2008, Symbiotic gut microbes modulate human metabolic phenotypes, Proc. Natl. Acad. Sci. U. S. A., 105, 2117, 10.1073/pnas.0712038105 Li, 2009, SOAP2: an improved ultrafast tool for short read alignment, Bioinformatics, 25, 1966, 10.1093/bioinformatics/btp336 Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Mende, 2013, Accurate and universal delineation of prokaryotic species, Nat. Methods, 10, 881, 10.1038/nmeth.2575 Miller, 2013, A reduced-energy intake, well-balanced diet improves weight control in children with Prader–Willi syndrome, J. Hum. Nutr. Diet., 26, 2, 10.1111/j.1365-277X.2012.01275.x Nielsen, 2014, Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes, Nat. Biotechnol., 32, 822, 10.1038/nbt.2939 Overbeek, 2014, The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST), Nucleic Acids Res., 42, D206, 10.1093/nar/gkt1226 Papavramidis, 2006, Prader–Willi syndrome-associated obesity treated by biliopancreatic diversion with duodenal switch. Case report and literature review, J. Pediatr. Surg., 41, 1153, 10.1016/j.jpedsurg.2006.01.065 Peng, 2012, IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420, 10.1093/bioinformatics/bts174 Pokusaeva, 2011, Carbohydrate metabolism in Bifidobacteria, Genes Nutr., 6, 285, 10.1007/s12263-010-0206-6 Prevey, 2010, Loss of foundation species increases population growth of exotic forbs in sagebrush steppe, Ecol. Appl., 20, 1890, 10.1890/09-0750.1 Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 Ridaura, 2013, Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, 341, 1241214, 10.1126/science.1241214 Russell, 2011, High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health, Am. J. Clin. Nutr., 93, 1062, 10.3945/ajcn.110.002188 Scott, 2013, The influence of diet on the gut microbiota, Pharmacol. Res., 69, 52, 10.1016/j.phrs.2012.10.020 Segata, 2011, Metagenomic biomarker discovery and explanation, Genome Biol., 12, R60, 10.1186/gb-2011-12-6-r60 Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414 Turnbaugh, 2008, Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome, Cell Host Microbe, 3, 213, 10.1016/j.chom.2008.02.015 Vijay-Kumar, 2010, Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5, Science, 328, 228, 10.1126/science.1179721 Vrieze, 2012, Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome, Gastroenterology, 143, 913, 10.1053/j.gastro.2012.06.031 Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, 472, 57, 10.1038/nature09922 Wang, 2014, Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide, Eur. Heart J., 35, 904, 10.1093/eurheartj/ehu002 Wu, 2010, An optimised sample preparation method for NMR-based faecal metabonomic analysis, Analyst, 135, 1023, 10.1039/b927543f Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344 Xiao, 2009, An optimized buffer system for NMR-based urinary metabonomics with effective pH control, chemical shift consistency and dilution minimization, Analyst, 134, 916, 10.1039/b818802e Xiao, 2014, A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome, FEMS Microbiol. Ecol., 87, 357, 10.1111/1574-6941.12228 Xu, 2009, CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes, Nucleic Acids Res., 37, W174, 10.1093/nar/gkp278 Yang, 2002 Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res., 18, 821, 10.1101/gr.074492.107 Zhang, 2010, Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice, ISME J., 4, 232, 10.1038/ismej.2009.112 Zhang, 2012, Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations, ISME J., 6, 1848, 10.1038/ismej.2012.27 Zhao, 2013, The gut microbiota and obesity: from correlation to causality, Nat. Rev. Microbiol., 11, 639, 10.1038/nrmicro3089 Zhou, 2013, Biogeography of the ecosystems of the healthy human body, Genome Biol., 14, R1, 10.1186/gb-2013-14-1-r1 Zhu, 2010, Ab initio gene identification in metagenomic sequences, Nucleic Acids Res., 38, e132, 10.1093/nar/gkq275 Zweigner, 2006, The role of lipopolysaccharide-binding protein in modulating the innate immune response, Microb. Inf./Instit. Pasteur, 8, 946, 10.1016/j.micinf.2005.10.006