Mulders RJ, de Git KCG, Schéle E, Dickson SL, Sanz Y, Adan RAH. Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems. Obes Rev. 2018;19:435–51.
Nyberg ST, Batty GD, Pentti J, Virtanen M, Alfredsson L, Fransson EI, et al. Obesity and loss of disease-free years O6 wing to major non-communicable diseases: a multigroup study. Lancet Public Health. 2018;3:e490–7.
Ng M, Fleming T, Robinson M, Thomson B, Graetz N, Margono C, et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the global burden of disease study 2013. Lancet. 2014;384:766–81.
Batsis JA, Villareal DT. Sarcopenic obesity in older adults: aetiology, epidemiology and treatment strategies. Nat Rev Endocrinol. 2018;14:513–37.
Ford ES, Mokdad AH, Giles WH, Galuska DA, Serdula MK. Geographic variation in the prevalence of obesity, diabetes, and obesity-related behaviors. Obes Res. 2005;13:118–22.
Wan Y, Wang FL, Yuan JH, Li J, Jiang DD, Zhang JJ, et al. Effects of macronutrient distribution on eight and related cardiometabolic profile in healthy non-obese chinese: a 6-month, randomized controlled-feeding trial. EBioMedicine. 2017;22:200–7.
Seconda L, Egnell M, Julia C, Touvier M, Hercberg S, Pointereau P, et al. Association between sustainable dietary patterns and body weight, overweight, and obesity risk in the nutriNet-Santé prospective cohort. Am J Clin Nutr. 2019;00:1–12.
Rankin W, Wittert G. Anti-obesity drugs. Curr Opin Lipidol. 2015;26:536–43.
Kang JG, Park CY. Anti-obesity drugs: a review about their effects and safety. Diabetes Metab J. 2012;36:13–25.
Spittal MJ, Frühbeck G. Bariatric surgery: many benefits, but emerging risks. Lancet Diabetes Endo. 2018;6(3):P161–3.
van Neerven RJJ, Savelkoul H. Nutrition and allergic diseases. Nutrients. 2017;9:1–8.
Li Q, Liu F, Liu J, Liao S, Zou Y. Mulberry leaf polyphenols and fiber induce synergistic antiobesity and display a modulation effect on gut microbiota and metabolites. Nutrients. 2019;11(5):1017.
Imamura F, Fretts A, Marklund M, Ardisson Korat AV, Yang WS, et al. Fatty acid biomarkers of dairy fat consumption and incidence of type 2 diabetes: a pooled analysis of prospective group studies. Plos Med. 2018;15:1–18.
Yoneshiro T, Wang Q, Tajima K, Matsushita M, Maki H, Igarashi K, et al. BCAA catabolism in brown fat controls energy homeostasis through SLC25A44. Nature. 2019;572:614–9.
O’Grady J, O’Connor EM, Shanahan F. Dietary fibre in the era of microbiome science. Aliment Pharm Ther. 2019;49:506–15.
Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, De los Reyes-Gavilán CG, Salazar N. Intestinal short chain fatty acids and their link with diet and human health. Front Microbiol. 2016;7:1–9.
Li Z, Yi CX, Katiraei S, Kooijman S, Zhou EC, Chung CK, et al. Butyrate reduces appetite and activates brown adipose tissue via the gut-brain neural circuit. Gut. 2017;67:1269–79.
Gao RY, Zhu CL, Li H, Yin MM, Pan C, Huang LS, et al. Dysbiosis signatures of gut microbiota along the sequence from healthy, young patients to those with overweight and obesity. Obesity. 2017;26:351–61.
Takahashi M, Mccartney E, Knox A, Francesch M, Oka K, Wada K, et al. Effects of the butyric acid-producing strain Clostridium butyricum MIYAIRI 588 on broiler and piglet zootechnical performance and prevention of necrotic enteritis. Anim Sci J. 2018;89:895–905.
Miquel S, Martı R, Chatel JM, Rossi O, Bermu LG, Sokol H, et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol. 2013;16:255–61.
Chen ZY, Guo LL, Zhang Y, Rosemary LW, Julie SP, Richard LP, et al. Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. J Clin Invest. 2014;124:3391–406.
Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol. 2018;36:857–64.
He YY, Mao CX, Wen H, Chen ZY, Lai T, Li LG, et al. Influence of Ad libitum feeding of piglets with Bacillus subtilis fermented liquid feed on gut flora, luminal contents and health. Sci Rep. 2017;7:44553.
Ozdemir T, Fedorec AJH, Danino T, Barnes CP. Synthetic biology and engineered live biotherapeutics: toward increasing system complexity. Cell Syst. 2018;7:5–16.
Hansen NL, Miettinen K, Zhao Y, Ignea C, Andreadelli A, Raadam MH, et al. Integrating pathway elucidation with yeast engineering to produce polpunonic acid the precursor of the anti-obesity agent celastrol. Microb Cell Fact. 2020;19:5.
Zhang XZ, Zhang YHP. Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis. Microb Biotechnol. 2011;4:98–105.
Bashir S, Sadaf S, Ahmad S, Akhtar MW. Enhanced and secretory expression of human granulocyte colony stimulating factor by Bacillus subtilis SCK6. Biomed Res Int. 2015;3:1–9.
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997;390:249–56.
Louis P, Duncan SH, McCrae SI, Millar J, Jackson MS, Flint HJ. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol. 2004;186:2099–106.
Liu WT, Yang YL, Xu YQ, Lamsa A, Haste NM, Yang JY, et al. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. PNAS. 2010;107:16286–90.
De Paepe K, Verspreet J, Verbeke K, Raes J, Courtin CM, Van de Wiele T. Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community. Environ Microbiol. 2018;20:3406–26.
Di T, Chen GJ, Sun Y, Ou SY, Zeng XX, Hong Y. In vitro digestion by saliva, simulated gastric and small intestinal juices and fermentation by human fecal microbiota of sulfated polysaccharides from gracilaria rubra. J Funct Foods. 2018;40:18–27.
Merklein K, Fong SS, Deng Y. Production of butyric acid by a cellulolytic actinobacterium thermobifida fusca on cellulose. Biochem Eng J. 2014;90:239–44.
Muller NT, Zhang MY, Juraschek SP, Miller ER, Appel LJ. Effects of high-fiber diets enriched with carbohydrate, protein, or unsaturated fat on circulating short chain fatty acids: results from the omniHert randomized trial. Am J Clin Nutr. 2020;11:545–54.
Hyde PN, Sapper TN, Crabtree CD, LaFountain RA, Bowling ML, Buga A, et al. Dietary carbohydrate restriction improves metabolic syndrome independent of weight loss. JCI Insight. 2019;4:e128308.
Liang YJ, Lin CL, Zhang YP, Deng YJ, Liu C, Yang Q. Probiotic mixture of Lactobacillus and Bifidobacterium alleviates systemic adiposity and inflammation in non-alcoholic fatty liver disease rats through Gpr109a and the commensal metabolite butyrate. Inflammopharmacology. 2018;26:1051–5.
Koh A, De Vadder F, Kovatcheva-Datchary P. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165:P1332–45.
Saltiel AR. New therapeutic approaches for the treatment of obesity. Sci Transl Med. 2016;8:323rv2.
Fang QY, Hu JL, Nie QX, Nie SP. Effects of polysaccharides on glycometabolism based on gut microbiota alteration. Trends Food Sci Tech. 2019;92:65–70.
Whitt J, Woo V, Lee P, Moncivaiz J, Haberman Y, Tso P, et al. Disruption of epithelial HDAC3 in intestine prevents diet-induced obesity in mice. Gastroenterology. 2018;155:501–13.
Cirulli ET, Guo LL, Swisher CL, Shah N, Huang L, Napier LA, et al. Profound perturbation of the metabolome in obesity is associated with health risk. Cell Metab. 2019;29:488–500.
Kuriz CB, Millet YA, Puurunen MK, Perreault M, Charbonneau MR, Isabell VM. An engineered E. coli nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans. Sci Transl Med. 2019;11:eaau7975.
Wang L, Zeng B, Liu Z, Liao Z, Zhong Q, Gu L, et al. Green tea polyphenols modulate colonic microbiota diversity and lipid metabolism in high-fat diet treated HFA mice. J Food Sci. 2018;83:864–73.
Orgeron ML, Stone KP, Wanders D, Cortez CC, Van NT, Gettys TW. The impact of dietary methionine restriction on biomarkers of metabolic health. Pron Mol Biol Trans Sci. 2014;121:351–76.
Mudumba S, Menezes A, Fries D, Blankenship J. Differentiation of PC12 cells induced by N8-acetylspermidine and by N8-acetylspermidine deacetylase inhibition. Biochem Pharmacol. 2002;63:2011–8.
Qi S, Xu D, Li Q, Xie N, Xia J, Huo Q, et al. Metabonomics screening of serum identifies pyroglutamate as a diagnostic biomarker for nonalcoholic steatohepatitis. Clin Chim Acta. 2017;473:89–95.
Guimarães J, Matos E, Rosas MJ, Vieira-Coelho A, Borges N, Correia F, et al. Modulation of nutritional state in parkinsonian patients with bilateral subthalamic nucleus stimulation. J Neurol. 2009;256:2072–8.
Nguyen VB, Nguyen AD, Wang SL. Utilization of fishery processing by-product squid pens for α-glucosidase inhibitors production by Paenibacillus sp. Mar Drugs. 2017;15:1–11.
Kim DJ, Yoon S, Ji SC, Yang J, Kim YK, Lee SH, et al. Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction. Sci Rep. 2018;8:1–11.
Lin A, An Y, Tang H, Wang Y. Alterations of bile acids and gut microbiota in obesity induced by high fat diet in rat model. J Agr Food Chem. 2019;67:3624–32.
Zhou J, Tang LL, Shen CW, Wang J. Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female sprague-dawley rats. J Nutr Biochem. 2018;61:68–81.
Yang X, Zhao Y, Sun Q, Yang Y, Gao Y, Ge W, et al. Adenine nucleotiede-mediated regulation of hepatic PTP1B activity in mouse models of type 2 diabetes. Diabetologia. 2019;62:2106–17.
Zhang X, Chen Y, Zhu J, Zhang M, Ho CT, Huang Q, et al. Metagenomics analysis of gut microbiota in a high fat diet-induced obesity mouse model fed with (−)-epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3). Mol Nutr Food Res. 2018;62:1–35.
Xiao Y, Li X, Zeng X, Wang H, Mai Q, Cheng Y, et al. A low ω-6/ω-3 ratio high-fat diet improves rat metabolism via purine and tryptophan metabolism in the intestinal tract, while reversed by inulin. J Agric Food Chem. 2019;67:7315–24.
Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-cas9 system. Appl Environ Microb. 2015;81:2506–14.
Zhang K, Duan X, Wu J. Multigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/cas9 system. Sci Rep. 2016;6:27943.
Sprouffske K, Wagner A. Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves. BMC Bioinf. 2016;17:17–20.