Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007;56:1761–72.
Article
CAS
PubMed
Google Scholar
Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3:213–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 2009;137:1716–24.
Article
CAS
PubMed
Google Scholar
Murphy EF, Cotter PD, Healy S, Marques TM, O’Sullivan O, Fouhy F, et al. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut. 2010;59:1635–42.
Article
CAS
PubMed
Google Scholar
Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature. 2012;487:104–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F. Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling. Cell Metab. 2015;22:658–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim K-A, Gu W, Lee I-A, Joh E-H, Kim D-H. High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One. 2012;7:e47713.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam YY, Ha CWY, Hoffmann JMA, Oscarsson J, Dinudom A, Mather TJ, et al. Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice. Obesity. 2015;23:1429–39.
Article
CAS
PubMed
Google Scholar
Ghosh S, DeCoffe D, Brown K, Rajendiran E, Estaki M, Dai C, et al. Fish oil attenuates Omega-6 polyunsaturated fatty acid-induced Dysbiosis and infectious colitis but impairs LPS Dephosphorylation activity causing sepsis. PLoS One. 2013;8:e55468.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang EY, Leone VA, Devkota S, Wang Y, Brady MJ, Chang EB. Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. JPEN J Parenter Enteral Nutr. 2013;37:746–54.
Article
CAS
PubMed
Google Scholar
Kaliannan K, Wang B, Li X-Y, Kim K-J, Kang JX. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci Rep. 2015;5:11276.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patterson E O’ Doherty RM, Murphy EF, Wall R O’ Sullivan O, Nilaweera K, et al. Impact of dietary fatty acids on metabolic activity and host intestinal microbiota composition in C57BL/6J mice. Br. J. Nutr 2014;111:1–13.
Google Scholar
Shen W, Gaskins HR, McIntosh MK. Influence of dietary fat on intestinal microbes, inflammation, barrier function and metabolic outcomes. J. Nutr. Biochem. 2014;25:270–80.
Article
CAS
PubMed
Google Scholar
Marten B, Pfeuffer M, Schrezenmeir J. Medium-chain triglycerides. Int. Dairy J. 2006;16:1374–82.
Article
CAS
Google Scholar
Deol P, Evans JR, Dhahbi J, Chellappa K, Han DS, Spindler S, et al. Soybean oil is more obesogenic and diabetogenic than coconut oil and fructose in mouse: potential role for the liver. PLoS One. 2015;10:e0132672.
Article
PubMed
PubMed Central
Google Scholar
Deol P, Fahrmann J, Yang J, Evans JR, Rizo A, Grapov D, et al. Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice. Sci Rep. 2017;7:12488.
Patrone V, Ferrari S, Lizier M, Lucchini F, Minuti A, Tondelli B, et al. Short-term modifications in the distal gut microbiota of weaning mice induced by a high-fat diet. Microbiology. 2012;158:983–92.
Article
CAS
PubMed
Google Scholar
De Wit N, Derrien M, Bosch-Vermeulen H, Oosterink E, Duval C, Kleerebezem M, et al. Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine. AJP Gastrointest Liver Physiol. 2012;303:G589–99.
Article
Google Scholar
De Weirdt R, Coenen E, Vlaeminck B, Fievez V, Van den Abbeele P, Van de Wiele T. A simulated mucus layer protects lactobacillus reuteri from the inhibitory effects of linoleic acid. Benef Microbes. 2013;4:299–312.
Shin N-R, Whon TW, Bae J-W. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33:496–503.
Article
CAS
PubMed
Google Scholar
Everard A, Lazarevic V, Gaïa N, Johansson M, Ståhlman M, Backhed F, et al. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. ISME J. 2014;8:2116–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martinez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, et al. Diet-Induced Metabolic Improvements in a Hamster Model of Hypercholesterolemia Are Strongly Linked to Alterations of the Gut Microbiota. Appl Environ Microbiol. 2009;75:4175–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brinig MM, Lepp PW, Ouverney CC, Armitage GC, Relman DA. Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl Environ Microbiol. 2003;69:1687–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuehbacher T, Rehman A, Lepage P, Hellmig S, Fölsch UR, Schreiber S, et al. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J Med Microbiol. 2008;57:1569–76.
Article
CAS
PubMed
Google Scholar
Zhang C, Li S, Yang L, Huang P, Li W, Wang S, et al. Structural modulation of gut microbiota in life-long calorie-restricted mice. Nat Commun. 2013;4:2163.
Article
PubMed
Google Scholar
Flynn CR, Albaugh VL, Cai S, Cheung-Flynn J, Williams PE, Brucker RM, et al. Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery. Nat Commun. 2015;6:7715.
Article
CAS
PubMed
Google Scholar
Lin H, An Y, Hao F, Wang Y, Tang H. Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State. Sci Rep. 2016;6:21618.
Daniel H, Gholami AM, Berry D, Desmarchelier C, Hahne H, Loh G, et al. High-fat diet alters gut microbiota physiology in mice. ISME J. 2014;8:295–308.
Article
CAS
PubMed
Google Scholar
Xiao Y, Cui J, Shi YH, Sun J, Wang ZP, Le GW. Effects of duodenal redox status on calcium absorption and related genes expression in high-fat diet-fed mice. Nutrition. 2010;26:1188–94.
Article
CAS
PubMed
Google Scholar
Qiao Y, Sun J, Ding Y, Le G, Shi Y. Alterations of the gut microbiota in high-fat diet mice is strongly linked to oxidative stress. Appl Microbiol Biotechnol. 2013;97:1689–97.
Article
CAS
PubMed
Google Scholar
Ozdal T, Sela DA, Xiao J, Boyacioglu D, Chen F, Capanoglu E. The reciprocal interactions between polyphenols and gut microbiota and effects on bioaccessibility. Nutrients. 2016;8:78.
Article
PubMed
PubMed Central
Google Scholar
Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, et al. Complete genome sequence of lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A. 2003;100:1990–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marco ML, Peters THF, Bongers RS, Molenaar D, Van Hemert S, Sonnenburg JL, et al. Lifestyle of lactobacillus plantarum in the mouse caecum. Environ Microbiol. 2009;11:2747–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwarzer M, Makki K, Storelli G, Machuca-Gayet I, Srutkova D, Hermanova P, et al. Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition. Science. 2016;351:854–7.
Article
CAS
PubMed
Google Scholar
Ahima RS, Flier JS. Leptin. Annu Rev Physiol. 2000;62:413–37.
Article
CAS
PubMed
Google Scholar
Cha MC, Jones PJ. Dietary fat type and energy restriction interactively influence plasma leptin concentration in rats. J Lipid Res. 1998;39:1655–60.
CAS
PubMed
Google Scholar
Kratz M, von Eckardstein A, Fobker M, Buyken A, Posny N, Schulte H, et al. The impact of dietary fat composition on serum leptin concentrations in healthy nonobese men and women. J Clin Endocrinol Metab. 2002;87:5008–14.
Article
CAS
PubMed
Google Scholar
Tovar AR, Díaz-Villaseñor A, Cruz-Salazar N, Ordáz G, Granados O, Palacios-González B, et al. Dietary type and amount of fat modulate lipid metabolism gene expression in liver and in adipose tissue in high-fat diet-fed rats. Arch Med Res. 2011;42:540–53.
Article
CAS
PubMed
Google Scholar
Hamilton BS, Paglia D, Kwan AY, Deitel M. Increased obese mRNA expression in omental fat cells from massively obese humans. Nat Med. 1995;1:953–6.
Article
CAS
PubMed
Google Scholar
Clavel T, Lippman R, Gavini F, Doré J, Blaut M. Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. Syst. Appl. Microbiol. 2007;30:16–26.
Article
CAS
PubMed
Google Scholar
Woting A, Pfeiffer N, Loh G, Klaus S, Blaut M. Clostridium ramosum promotes high-fat diet-induced obesity in Gnotobiotic mouse models. MBio. 2014;5:e01530–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shiratori H, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, et al. Lutispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming bacterium isolated from a thermophilic methanogenic bioreactor digesting municipal solid wastes. Int. J. Syst. Evol. Microbiol. 2008;58:964–9.
Article
PubMed
Google Scholar
Ouchi N, Parker JL, Lugus JJ, Walsh K. Adipokines in inflammation and metabolic disease. Nat Rev Immunol. 2011;11:85–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qiao L, Lee B, Kinney B, Yoo HS, Shao J. Energy intake and adiponectin gene expression. Am J Physiol Endocrinol Metab. 2011;300:E809–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lecomte V, Kaakoush NO, Maloney CA, Raipuria M, Huinao KD, Mitchell HM, et al. Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters. PLoS One. 2015;10:e0126931.
Article
PubMed
PubMed Central
Google Scholar
Nishina PM, Lowe S, Verstuyft J, Naggert JK, Kuypers FA, Paigen B. Effects of dietary fats from animal and plant sources on diet-induced fatty streak lesions in C57BL/6J mice. J Lipid Res. 1993;34:1413–22.
CAS
PubMed
Google Scholar
Nishimoto T, Pellizzon MA, Aihara M, Stylianou IM, Billheimer JT, Rothblat G, et al. Fish oil promotes macrophage reverse cholesterol transport in mice. Arterioscler Thromb Vasc Biol. 2009;29:1502–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lahti L, Salonen A, Kekkonen RA, Salojärvi J, Jalanka-Tuovinen J, Palva A, et al. Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ. 2013;1:e32.
Article
PubMed
PubMed Central
Google Scholar
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to cyanobacteria. elife. 2013;2:e01102.
Article
PubMed
PubMed Central
Google Scholar
Zeng B, Han S, Wang P, Wen B, Jian W, Guo W, et al. The bacterial communities associated with fecal types and body weight of rex rabbits. Sci Rep. 2015;5:9342.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bueno AA, Oyama LM, de Oliveira C, Pisani LP, Ribeiro EB, Silveira VLF, et al. Effects of different fatty acids and dietary lipids on adiponectin gene expression in 3T3-L1 cells and C57BL/6J mice adipose tissue. Pflugers Arch. 2008;455:701–9.
Article
CAS
PubMed
Google Scholar
Duivenvoorde LPM, van Schothorst EM, Swarts HM, Kuda O, Steenbergh E, Termeulen S, et al. A Difference in Fatty Acid Composition of Isocaloric High-Fat Diets Alters Metabolic Flexibility in Male C57BL/6JOlaHsd Mice. Alemany M, editor. PLoS One. Public Libr Sci. 2015;10:e0128515.
Google Scholar
Kalliomäki M, Collado MC, Salminen S, Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr. 2008;87:534–8.
Article
PubMed
Google Scholar
Collado MC, Isolauri E, Laitinen K, Salminen S. Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr. 2008;88:894–9.
Article
CAS
PubMed
Google Scholar
Hamilton MK, Boudry G, Lemay DG, Raybould HE. Changes in intestinal barrier function and gut microbiota in high-fat diet-fed rats are dynamic and region dependent. Am J Physiol Gastrointest Liver Physiol. 2015;308:G840–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castro-Mejía J, Jakesevic M, Krych Ł, Nielsen DS, Hansen LH, Sondergaard BC, et al. Treatment with a monoclonal anti-IL-12p40 antibody induces substantial gut microbiota changes in an experimental colitis model. Gastroenterol Res Pract. 2016;2016:4953120.
Article
PubMed
PubMed Central
Google Scholar
Sousa DZ, Smidt H, Alves MM, AJM S. Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids. FEMS Microbiol. Ecol; 2009. p. 257–72.
Google Scholar
Mann A, Thompson A, Robbins N, Blomkalns AL. Localization, Identification, and Excision of Murine Adipose Depots. J. Vis. Exp; 2014.
Google Scholar
Lizier M, Bomba L, Minuti A, Chegdani F, Capraro J, Tondelli B, et al. The nutrigenomic investigation of C57BL/6N mice fed a short-term high-fat diet highlights early changes in clock genes expression. Genes Nutr. 2013;8:465–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162:156–9.
Article
CAS
PubMed
Google Scholar
Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang X, Spandidos A, Wang H, Seed B. PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Res. 2012;40:D1144–9.
Article
CAS
PubMed
Google Scholar
Calamari L, Ferrari A, Minuti A, Trevisi E. Assessment of the main plasma parameters included in a metabolic profile of dairy cow based on Fourier Transform mid-infrared spectroscopy: preliminary results. BMC Vet. Res. BioMed Central. 2016;12:4.
Article
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ Prepr. 2016;4:e2409v1.
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Article
CAS
PubMed
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Torriani S, Clementi F, Vancanneyt M, Hoste B, Dellaglio F, Kersters K. Differentiation of lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP. Syst. Appl. Microbiol. 2001;24:554–60.
Article
CAS
PubMed
Google Scholar
Collado MC, Derrien M, Isolauri E, De Vos WM, Salminen S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007;73:7767–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
R Core team. R Core Team. R A Lang. Environ. Stat. Comput. R Found. Stat. Comput. , Vienna, Austria. ISBN 3–900051–07-0, URL http//www.R-project.org/. 2015. p. 275–86.
Oksanen J. Multivariate analysis of ecological communities in R: vegan tutorial. R Doc. 2015;43:11–2.
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
Langille M, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes J, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123–4.
Article
CAS
PubMed
PubMed Central
Google Scholar