Obesity is a complex disease that increases the risk of other pathologies. Its prevention and long-term weight loss maintenance are problematic. Gut microbiome is considered a potential obesity modulator. The objective of the present study was to summarize recent findings regarding the relationships between obesity, gut microbiota, and diet (vegetable/animal proteins, high-fat diets, restriction of carbohydrates), with an emphasis on dietary fiber and resistant starch. The composition of the human gut microbiome and the methods of its quantification are described. Products of the gut microbiome metabolism, such as short-chain fatty acids and secondary bile acids, and their effects on the gut microbiota, intestinal barrier function and immune homeostasis are discussed in the context of obesity. The importance of dietary fiber and resistant starch is emphasized as far as effects of the host diet on the composition and function of the gut microbiome are concerned. The complex relationships between human gut microbiome and obesity are finally summarized.

Department of Food Technology Mendel University in Brno 61300 Brno Czech Republic

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Haslam D.W., James W.T.P. Obesity. Lancet. 2005;366:1197–1209. doi: 10.1016/S0140-6736(05)67483-1. PubMed DOI

Schwartz M.W., Seeley R.J., Zeltser L.M., Drewnowski A., Ravussin E., Redman L.M., Leibel R.L. Obesity Pathogenesis: An Endocrine Society Scientific Statement. Endocr. Rev. 2017;38:267–296. doi: 10.1210/er.2017-00111. PubMed DOI PMC

Blüher M. Obesity: Global Epidemiology and Pathogenesis. Nat. Rev. Endocrinol. 2019;15:288–298. doi: 10.1038/s41574-019-0176-8. PubMed DOI

Strohacker K., Carpenter K.C., McFarlin B.K. Consequences of Weight Cycling: An Increase in Disease Risk? Int. J. Exerc. Sci. 2009;2:191–201. doi: 10.70252/ASAQ8961. PubMed DOI PMC

Dombrowski S.U., Knittle K., Avenell A., Araujo-Soares V., Sniehotta F.F. Long Term Maintenance of Weight Loss with Non-Surgical Interventions in Obese Adults: Systematic Review and Meta-Analyses of Randomised Controlled Trials. BMJ. 2014;348:g2646. doi: 10.1136/bmj.g2646. PubMed DOI PMC

Lim Y.Y., Lee Y.S., Ooi D.S.Q. Engineering the Gut Microbiome for Treatment of Obesity: A Review of Current Understanding and Progress. Biotechnol. J. 2020;15:e2000013. doi: 10.1002/biot.202000013. PubMed DOI

Breton J., Galmiche M., Déchelotte P. Dysbiotic Gut Bacteria in Obesity: An Overview of the Metabolic Mechanisms and Therapeutic Perspectives of Next-Generation Probiotics. Microorganisms. 2022;10:452. doi: 10.3390/microorganisms10020452. PubMed DOI PMC

Moser B., Milligan M.A., Dao M.C. The Microbiota-Gut-Brain Axis: Clinical Applications in Obesity and Type 2 Diabetes. Rev. Investig. Clin. 2022;74:302–313. doi: 10.24875/RIC.22000197. PubMed DOI

Liébana-García R., Olivares M., Bullich-Vilarrubias C., López-Almela I., Romaní-Pérez M., Sanz Y. The Gut Microbiota as a Versatile Immunomodulator in Obesity and Associated Metabolic Disorders. Best Pract. Res. Clin. Endoc. Metab. 2021;35:101542. doi: 10.1016/j.beem.2021.101542. PubMed DOI

Pedroza Matute S., Iyavoo S. Exploring the Gut Microbiota: Lifestyle Choices, Disease Associations, and Personal Genomics. Front. Nutr. 2023;10:1225120. doi: 10.3389/fnut.2023.1225120. PubMed DOI PMC

Hodgkinson K., El Abbar F., Dobranowski P., Manoogian J., Butcher J., Figeys D., Mack D., Stintzi A. Butyrate’s Role in Human Health and the Current Progress Towards Its Clinical Application to Treat Gastrointestinal Disease. Clin. Nutr. 2023;42:61–75. doi: 10.1016/j.clnu.2022.10.024. PubMed DOI

Portincasa P., Bonfrate L., Vacca M., De Angelis M., Farella I., Lanza E., Khalil M., Wang D.Q.-H., Sperandio M., Di Ciaula A. Gut Microbiota and Short Chain Fatty Acids: Implications in Glucose Homeostasis. Int. J. Mol. Sci. 2022;23:1105. doi: 10.3390/ijms23031105. PubMed DOI PMC

Fusco W., Lorenzo M.B., Cintoni M., Porcari S., Rinninella E., Kaitsas F., Lener E., Mele M.C., Gasbarrini A., Collado M.C., et al. Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota. Nutrients. 2023;15:2211. doi: 10.3390/nu15092211. PubMed DOI PMC

Li R., Andreu-Sánchez S., Kuipers F., Fu J. Gut Microbiome and Bile Acids in Obesity-Related Diseases. Best Pract. Res. Clin. Endoc. Metab. 2021;35:101493. doi: 10.1016/j.beem.2021.101493. PubMed DOI

Larabi A.B., Masson H.L.P., Bäumler A.J. Bile Acids as Modulators of Gut Microbiota Composition and Function. Gut Microbes. 2023;15:2172671. doi: 10.1080/19490976.2023.2172671. PubMed DOI PMC

Singh J., Metrani R., Shivanagoudra S.R., Jayaprakasha G.K., Patil B.S. Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds. J. Agric. Food Chem. 2019;67:9124–9138. doi: 10.1021/acs.jafc.8b07306. PubMed DOI

Beane K.E., Redding M.C., Wang X., Pan J.H., Le B., Cicalo C., Jeon S., Kim Y.J., Lee J.H., Shin E.-C., et al. Effects of Dietary Fibers, Micronutrients, and Phytonutrients on Gut Microbiome: A Review. Appl. Biol. Chem. 2021;64:36. doi: 10.1186/s13765-021-00605-6. DOI

Kok C.R., Rose D., Hutkins R. Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health. Annu. Rev. Food Sci. Technol. 2023;14:157–182. doi: 10.1146/annurev-food-060721-015516. PubMed DOI

Chen Z., Liang N., Zhang H., Li H., Guo J., Zhang Y., Chen Y., Wang Y., Shi N. Resistant Starch and the Gut Microbiome: Exploring Beneficial Interactions and Dietary Impacts. Food Chem. X. 2024;21:101118. doi: 10.1016/j.fochx.2024.101118. PubMed DOI PMC

Frolova M.S., Suvorova I.A., Iablokov S.N., Petrov S.N., Rodionov D.A. Genomic Reconstruction of Short-Chain Fatty Acid Production by the Human Gut Microbiota. Front. Mol. Biosci. 2022;9:949563. doi: 10.3389/fmolb.2022.949563. PubMed DOI PMC

Canfora E.E., Jocken J.W., Blaak E.E. Short-Chain Fatty Acids in Control of Body Weight and Insulin Sensitivity. Nat. Rev. Endocrinol. 2015;11:577–591. doi: 10.1038/nrendo.2015.128. PubMed DOI

Rinninella E., Raoul P., Cintoni M., Franceschi F., Miggiano G.A.D., Gasbarrini A., Mele M.C. What Is the Healthy Gut Microbiota Composition? A Changing Ecosystem Across Age, Environment, Diet, and Diseases. Microorganisms. 2019;7:14. doi: 10.3390/microorganisms7010014. PubMed DOI PMC

Gomes A.C., Hoffmann C., Mota J.F. The Human Gut Microbiota: Metabolism and Perspective in Obesity. Gut Microbes. 2018;9:308–325. doi: 10.1080/19490976.2018.1465157. PubMed DOI PMC

Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., Fernandes G.R., Tap J., Bruls T., Batto J.-M., et al. Enterotypes of the Human Gut Microbiome. Nature. 2011;473:174–180. doi: 10.1038/nature09944. PubMed DOI PMC

Putignani L., Del Chierico F., Petrucca A., Vernocchi P., Dallapiccola B. The Human Gut Microbiota: A Dynamic Interplay with the Host from Birth to Senescence Settled During Childhood. Pediatr. Res. 2014;76:2–10. doi: 10.1038/pr.2014.49. PubMed DOI

Pannaraj P.S., Li F., Cerini C., Bender J.M., Yang S., Rollie A., Adisetiyo H., Zabih S., Lincez P.J., Bittinger K., et al. Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. JAMA Pediatr. 2017;171:647–654. doi: 10.1001/jamapediatrics.2017.0378. PubMed DOI PMC

Zhang P. Influence of Foods and Nutrition on the Gut Microbiome and Implications for Intestinal Health. Int. J. Mol. Sci. 2022;23:9588. doi: 10.3390/ijms23179588. PubMed DOI PMC

David L.A., Materna A.C., Friedman J., Campos-Baptista M.I., Blackburn M.C., Perrotta A., Erdman S.E., Alm E.J. Host Lifestyle Affects Human Microbiota on Daily Timescales. Genome Biol. 2014;15:550. doi: 10.1186/gb-2014-15-7-r89. PubMed DOI PMC

Yatsunenko T., Rey F.E., Manary M.J., Trehan I., Dominguez-Bello M.G., Contreras M., Magris M., Hidalgo G., Baldassano R.N., Anokhin A.P., et al. Human Gut Microbiome Viewed Across Age and Geography. Nature. 2012;486:222–227. doi: 10.1038/nature11053. PubMed DOI PMC

Bajinka O., Tan Y., Abdelhalim K.A., Özdemir G., Qiu X. Extrinsic Factors Influencing Gut Microbes, the Immediate Consequences and Restoring Eubiosis. AMB Express. 2020;10:130. doi: 10.1186/s13568-020-01066-8. PubMed DOI PMC

Rothschild D., Weissbrod O., Barkan E., Kurilshikov A., Korem T., Zeevi D., Costea P.I., Godneva A., Kalka I.N., Bar N., et al. Environment Dominates Over Host Genetics in Shaping Human Gut Microbiota. Nature. 2018;555:210–215. doi: 10.1038/nature25973. PubMed DOI

Jeffery I.B., Claesson M.J., O’Toole P.W., Shanahan F. Categorization of the Gut Microbiota: Enterotypes or Gradients? Nat. Rev. Microbiol. 2012;10:591–592. doi: 10.1038/nrmicro2859. PubMed DOI

Knights D., Ward T.L., McKinlay C.E., Miller H., Gonzalez A., McDonald D., Knight R. Rethinking “Enterotypes”. Cell Host Microbe. 2014;16:433–437. doi: 10.1016/j.chom.2014.09.013. PubMed DOI PMC

Stewart E.J. Growing Unculturable Bacteria. J. Bacteriol. 2012;194:4151–4160. doi: 10.1128/JB.00345-12. PubMed DOI PMC

Sanschagrin S., Yergeau E. Next-Generation Sequencing of 16S Ribosomal Rna Gene Amplicons. J. Vis. Exp. 2014;90:51709. doi: 10.3791/51709-v. PubMed DOI PMC

Byrd D.A., Sinha R., Hoffman K.L., Chen J., Hua X., Shi J., Chia N., Petrosino J., Vogtmann E., Rao K. Comparison of Methods to Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. mSphere. 2020;5:e00827-19. doi: 10.1128/mSphere.00827-19. PubMed DOI PMC

Tessler M., Neumann J.S., Afshinnekoo E., Pineda M., Hersch R., Velho L.F.M., Segovia B.T., Lansac-Toha F.A., Lemke M., DeSalle R., et al. Large-Scale Differences in Microbial Biodiversity Discovery Between 16S Amplicon and Shotgun Sequencing. Sci. Rep. 2017;7:6589. doi: 10.1038/s41598-017-06665-3. PubMed DOI PMC

Souche E., Beltran S., Brosens E., Belmont J.W., Fossum M., Riess O., Gilissen C., Ardeshirdavani A., Houge G., van Gijn M., et al. Recommendations for Whole Genome Sequencing in Diagnostics for Rare Diseases. Eur. J. Hum. Genet. 2022;30:1017–1021. doi: 10.1038/s41431-022-01113-x. PubMed DOI PMC

Song Z., Cai Y., Lao X., Wang X., Lin X., Cui Y., Kalavagunta P.K., Liao J., Jin L., Shang J., et al. Taxonomic Profiling and Populational Patterns of Bacterial Bile Salt Hydrolase (Bsh) Genes Based on Worldwide Human Gut Microbiome. Microbiome. 2019;7:9. doi: 10.1186/s40168-019-0628-3. PubMed DOI PMC

Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. a Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing. Nature. 2010;464:59–65. doi: 10.1038/nature08821. PubMed DOI PMC

Postler T.S., Ghosh S. Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System. Cell Metab. 2017;26:110–130. doi: 10.1016/j.cmet.2017.05.008. PubMed DOI PMC

Zhang K., Zhang Q., Qiu H., Ma Y., Hou N., Zhang J., Kan C., Han F., Sun X., Shi J. The Complex Link Between the Gut Microbiome and Obesity-Associated Metabolic Disorders: Mechanisms and Therapeutic Opportunities. Heliyon. 2024;10:e37609. doi: 10.1016/j.heliyon.2024.e37609. PubMed DOI PMC

Wu J., Wang K., Wang X., Pang Y., Jiang C. The Role of the Gut Microbiome and Its Metabolites in Metabolic Diseases. Protein Cell. 2021;12:360–373. doi: 10.1007/s13238-020-00814-7. PubMed DOI PMC

Sonnenburg E.D., Sonnenburg J.L. Starving Our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates. Cell Metab. 2014;20:779–786. doi: 10.1016/j.cmet.2014.07.003. PubMed DOI PMC

Ayakdaş G., Ağagündüz D. Microbiota-Accessible Carbohydrates (Macs) as Novel Gut Microbiome Modulators in Noncommunicable Diseases. Heliyon. 2023;9:e19888. doi: 10.1016/j.heliyon.2023.e19888. PubMed DOI PMC

Topping D.L., Clifton P.M. Short-Chain Fatty Acids and Human Colonic Function: Roles of Resistant Starch and Nonstarch Polysaccharides. Physiol. Rev. 2001;81:1031–1064. doi: 10.1152/physrev.2001.81.3.1031. PubMed DOI

Tabat M.W., Marques T.M., Markgren M., Löfvendahl L., Brummer R.J., Wall R. Acute Effects of Butyrate on Induced Hyperpermeability and Tight Junction Protein Expression in Human Colonic Tissues. Biomolecules. 2020;10:766. doi: 10.3390/biom10050766. PubMed DOI PMC

Liang L., Liu L., Zhou W., Yang C., Mai G., Li H., Chen Y. Gut Microbiota-Derived Butyrate Regulates Gut Mucus Barrier Repair by Activating the Macrophage/Wnt/Erk Signaling Pathway. Clin. Sci. 2022;136:291–307. doi: 10.1042/CS20210778. PubMed DOI

Donohoe D.R., Garge N., Zhang X., Sun W., O’Connell T.M., Bunger M.K., Bultman S.J. The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon. Cell Metab. 2011;13:517–526. doi: 10.1016/j.cmet.2011.02.018. PubMed DOI PMC

Frost G., Sleeth M.L., Sahuri-Arisoylu M., Lizarbe B., Cerdan S., Brody L., Anastasovska J., Ghourab S., Hankir M., Zhang S., et al. The Short-Chain Fatty Acid Acetate Reduces Appetite Via a Central Homeostatic Mechanism. Nat. Commun. 2014;5:3611. doi: 10.1038/ncomms4611. PubMed DOI PMC

González Hernández M.A., Canfora E.E., Jocken J.W.E., Blaak E.E. The Short-Chain Fatty Acid Acetate in Body Weight Control and Insulin Sensitivity. Nutrients. 2019;11:1943. doi: 10.3390/nu11081943. PubMed DOI PMC

Yoshida H., Ishii M., Akagawa M. Propionate Suppresses Hepatic Gluconeogenesis Via Gpr43/Ampk Signaling Pathway. Arch. Biochem. Biophys. 2019;672:108057. doi: 10.1016/j.abb.2019.07.022. PubMed DOI

den Besten G., Bleeker A., Gerding A., van Eunen K., Havinga R., van Dijk T.H., Oosterveer M.H., Jonker J.W., Groen A.K., Reijngoud D.-J., et al. Short-Chain Fatty Acids Protect Against High-Fat Diet–Induced Obesity Via a Pparγ-Dependent Switch from Lipogenesis to Fat Oxidation. Diabetes. 2015;64:2398–2408. doi: 10.2337/db14-1213. PubMed DOI

Xiong Y., Miyamoto N., Shibata K., Valasek M.A., Motoike T., Kedzierski R.M., Yanagisawa M. Short-Chain Fatty Acids Stimulate Leptin Production in adipocytes Through the G Protein-Coupled Receptor Gpr41. Proc. Natl. Acad. Sci. USA. 2004;101:1045–1050. doi: 10.1073/pnas.2637002100. PubMed DOI PMC

Maslowski K.M., Vieira A.T., Ng A., Kranich J., Sierro F., Di Y., Schilter H.C., Rolph M.S., Mackay F., Artis D., et al. Regulation of Inflammatory Responses by Gut Microbiota and Chemoattractant Receptor Gpr43. Nature. 2009;461:1282–1286. doi: 10.1038/nature08530. PubMed DOI PMC

Zapolska-Downar D., Naruszewicz M. Propionate reduces the cytokine-induced VCAM-1 and ICAM-1 expression by inhibiting nuclear factor-kappa B (NF-kappaB) activation. J. Physiol. Pharmacol. 2009;60:123–131. PubMed

Cox M.A., Jackson J., Stanton M., Rojas-Triana A., Bober L., Laverty M., Yang X., Zhu F., Liu J., Wang S., et al. Short-Chain Fatty Acids Act as Antiinflammatory Mediatorsby Regulating Prostaglandin E2 and Cytokines. World J. Gastroenterol. 2009;15:5549–5557. doi: 10.3748/wjg.15.5549. PubMed DOI PMC

Silva Y.P., Bernardi A., Frozza R.L. The Role of Short-Chain Fatty Acids from Gut Microbiota in Gut-Brain Communication. Front. Endocrinol. 2020;11:25. doi: 10.3389/fendo.2020.00025. PubMed DOI PMC

Herrmann E., Young W., Reichert-Grimm V., Weis S., Riedel C., Rosendale D., Stoklosinski H., Hunt M., Egert M. in Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using Rna-Based Stable Isotope Probing—A Proof-Of-Principle Study. Nutrients. 2018;10:179. doi: 10.3390/nu10020179. PubMed DOI PMC

Sela D.A., Mills D.A. Nursing Our Microbiota: Molecular Linkages Between Bifidobacteria and Milk Oligosaccharides. Trends Microbiol. 2010;18:298–307. doi: 10.1016/j.tim.2010.03.008. PubMed DOI PMC

Conlon M., Bird A. The Impact of Diet and Lifestyle on Gut Microbiota and Human Health. Nutrients. 2015;7:17–44. doi: 10.3390/nu7010017. PubMed DOI PMC

Reichardt N., Duncan S.H., Young P., Belenguer A., McWilliam Leitch C., Scott K.P., Flint H.J., Louis P. Phylogenetic Distribution of Three Pathways for Propionate Production Within the Human Gut Microbiota. ISME J. 2014;8:1323–1335. doi: 10.1038/ismej.2014.14. PubMed DOI PMC

Anand S., Kaur H., Mande S.S. Comparative in Silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens. Front. Microbiol. 2016;7:1945. doi: 10.3389/fmicb.2016.01945. PubMed DOI PMC

Singh V., Lee G.D., Son H.W., Koh H., Kim E.S., Unno T., Shin J.-H. Butyrate Producers, “the Sentinel of Gut”: Their Intestinal Significance with and Beyond Butyrate, and Prospective Use as Microbial Therapeutics. Front. Microbiol. 2023;13:1103836. doi: 10.3389/fmicb.2022.1103836. PubMed DOI PMC

Vacca M., Celano G., Calabrese F.M., Portincasa P., Gobbetti M., De Angelis M. The Controversial Role of Human Gut Lachnospiraceae. Microorganisms. 2020;8:573. doi: 10.3390/microorganisms8040573. PubMed DOI PMC

Martín R., Bermúdez-Humarán L.G., Langella P. Searching for the Bacterial Effector: The Example of the Multi-Skilled Commensal Bacterium Faecalibacterium Prausnitzii. Front. Microbiol. 2018;9:346. doi: 10.3389/fmicb.2018.00346. PubMed DOI PMC

Miquel S., Martín R., Rossi O., Bermúdez-Humarán L.G., Chatel J.M., Sokol H., Thomas M., Wells J.M., Langella P. Faecalibacterium Prausnitzii and Human Intestinal Health. Curr. Opin. Microbiol. 2013;16:255–261. doi: 10.1016/j.mib.2013.06.003. PubMed DOI

Rivière A., Selak M., Lantin D., Leroy F., De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front. Microbiol. 2016;7:979. doi: 10.3389/fmicb.2016.00979. PubMed DOI PMC

Litvak Y., Byndloss M.X., Bäumler A.J. Colonocyte Metabolism Shapes the Gut Microbiota. Science. 2018;362:eaat9076. doi: 10.1126/science.aat9076. PubMed DOI PMC

Rivera-Chávez F., Zhang L.F., Faber F., Lopez C.A., Byndloss M.X., Olsan E.E., Xu G., Velazquez E.M., Lebrilla C.B., Winter S.E., et al. Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella. Cell Host Microbe. 2016;19:443–454. doi: 10.1016/j.chom.2016.03.004. PubMed DOI PMC

Blottiere H.M., Buecher B., Galmiche J.-P., Cherbut C. Molecular Analysis of the Effect of Short-Chain Fatty Acids on Intestinal Cell Proliferation. Proc. Nutr. Soc. 2003;62:101–106. doi: 10.1079/PNS2002215. PubMed DOI

Hamer H.M., Jonkers D., Venema K., Vanhoutvin S., Troost F.J., Brummer R.-J. Review Article: The Role of Butyrate on Colonic Function. Aliment. Pharmacol. Ther. 2008;27:104–119. doi: 10.1111/j.1365-2036.2007.03562.x. PubMed DOI

Kim K.N., Yao Y., Ju S.Y. Short Chain Fatty Acids and Fecal Microbiota Abundance in Humans with Obesity: A Systematic Review and Meta-Analysis. Nutrients. 2019;11:2512. doi: 10.3390/nu11102512. PubMed DOI PMC

Lange O., Proczko-Stepaniak M., Mika A. Short-Chain Fatty Acids—A Product of the Microbiome and Its Participation in Two-Way Communication on the Microbiome-Host Mammal Line. Curr. Obes. Rep. 2023;12:108–126. doi: 10.1007/s13679-023-00503-6. PubMed DOI PMC

Schwiertz A., Taras D., Schäfer K., Beijer S., Bos N.A., Donus C., Hardt P.D. Microbiota and Scfa in Lean and Overweight Healthy Subjects. Obesity. 2010;18:190–195. doi: 10.1038/oby.2009.167. PubMed DOI

De la Cuesta-Zuluaga J., Mueller N., Álvarez-Quintero R., Velásquez-Mejía E., Sierra J., Corrales-Agudelo V., Carmona J., Abad J., Escobar J. Higher Fecal Short-Chain Fatty Acid Levels Are Associated with Gut Microbiome Dysbiosis, Obesity, Hypertension and Cardiometabolic Disease Risk Factors. Nutrients. 2019;11:51. doi: 10.3390/nu11010051. PubMed DOI PMC

Wang Y., Wang H., Howard A.G., Meyer K.A., Tsilimigras M.C.B., Avery C.L., Sha W., Sun S., Zhang J., Su C., et al. Circulating Short-Chain Fatty Acids Are Positively Associated with adiposity Measures in Chinese Adults. Nutrients. 2020;12:2127. doi: 10.3390/nu12072127. PubMed DOI PMC

Monte M.J., Marin J.J.G., Antelo A., Vazquez-Tato J. Bile Acids: Chemistry, Physiology, and Pathophysiology. World J. Gastroenterol. 2009;15:804–816. doi: 10.3748/wjg.15.804. PubMed DOI PMC

Di Ciaula A., Garruti G., Lunardi Baccetto R., Molina-Molina E., Bonfrate L., Wang D.Q.-H., Portincasa P. Bile Acid Physiology. Ann. Hepatol. 2017;16:S4–S14. doi: 10.5604/01.3001.0010.5493. PubMed DOI

Grüner N., Mattner J. Bile Acids and Microbiota: Multifaceted and Versatile Regulators of the Liver–Gut Axis. Int. J. Mol. Sci. 2021;22:1397. doi: 10.3390/ijms22031397. PubMed DOI PMC

Hofmann A.F. The Enterohepatic Circulation of Bile Acids in Mammals: Form and Functions. Front. Biosci. 2009;14:2584–2598. doi: 10.2741/3399. PubMed DOI

Dawson P.A., Karpen S.J. Intestinal Transport and Metabolism of Bile Acids. J. Lipid Res. 2015;56:1085–1099. doi: 10.1194/jlr.R054114. PubMed DOI PMC

Kliewer S.A., Mangelsdorf D.J. Bile Acids as Hormones: The Fxr-Fgf15/19 Pathway. Dig. Dis. 2015;33:327–331. doi: 10.1159/000371670. PubMed DOI PMC

Fiorucci S., Carino A., Baldoni M., Santucci L., Costanzi E., Graziosi L., Distrutti E., Biagioli M. Bile Acid Signaling in Inflammatory Bowel Diseases. Dig. Dis. Sci. 2021;66:674–693. doi: 10.1007/s10620-020-06715-3. PubMed DOI PMC

Friedman E.S., Li Y., Shen T.-C.D., Jiang J., Chau L., Adorini L., Babakhani F., Edwards J., Shapiro D., Zhao C., et al. Fxr-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid. Gastroenterology. 2018;155:1741–1752.e5. doi: 10.1053/j.gastro.2018.08.022. PubMed DOI PMC

Ginos B.N.R., Navarro S.L., Schwarz Y., Gu H., Wang D., Randolph T.W., Shojaie A., Hullar M.A.J., Lampe P.D., Kratz M., et al. Circulating Bile Acids in Healthy Adults Respond Differently to a Dietary Pattern Characterized by Whole Grains, Legumes and Fruits and Vegetables Compared to a Diet High in Refined Grains and Added Sugars: A Randomized, Controlled, Crossover Feeding Study. Metabolism. 2018;83:197–204. doi: 10.1016/j.metabol.2018.02.006. PubMed DOI PMC

Vaz F.M., Ferdinandusse S. Bile Acid Analysis in Human Disorders of Bile Acid Biosynthesis. Mol. Asp. Med. 2017;56:10–24. doi: 10.1016/j.mam.2017.03.003. PubMed DOI

Makki K., Deehan E.C., Walter J., Bäckhed F. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018;23:705–715. doi: 10.1016/j.chom.2018.05.012. PubMed DOI

Jones B.V., Begley M., Hill C., Gahan C.G.M., Marchesi J.R. Functional and Comparative Metagenomic Analysis of Bile Salt Hydrolase Activity in the Human Gut Microbiome. Proc. Natl. Acad. Sci. USA. 2008;105:13580–13585. doi: 10.1073/pnas.0804437105. PubMed DOI PMC

Guzior D.V., Quinn R.A. Review: Microbial Transformations of Human Bile Acids. Microbiome. 2021;9:140. doi: 10.1186/s40168-021-01101-1. PubMed DOI PMC

Joyce S.A., Gahan C.G.M. Disease-Associated Changes in Bile Acid Profiles and Links to altered Gut Microbiota. Dig. Dis. 2017;35:169–177. doi: 10.1159/000450907. PubMed DOI

Doden H.L., Ridlon J.M. Microbial Hydroxysteroid Dehydrogenases: From alpha to Omega. Microorganisms. 2021;9:469. doi: 10.3390/microorganisms9030469. PubMed DOI PMC

Funabashi M., Grove T.L., Wang M., Varma Y., McFadden M.E., Brown L.C., Guo C., Higginbottom S., Almo S.C., Fischbach M.A. a Metabolic Pathway for Bile Acid Dehydroxylation by the Gut Microbiome. Nature. 2020;582:566–570. doi: 10.1038/s41586-020-2396-4. PubMed DOI PMC

Urdaneta V., Casadesús J. Interactions Between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts. Front. Med. 2017;4:163. doi: 10.3389/fmed.2017.00163. PubMed DOI PMC

Sannasiddappa T.H., Lund P.A., Clarke S.R. in Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus Aureus. Front. Microbiol. 2017;8:1581. doi: 10.3389/fmicb.2017.01581. PubMed DOI PMC

Kurdi P., Kawanishi K., Mizutani K., Yokota A. Mechanism of Growth Inhibition by Free Bile Acids in Lactobacilli and Bifidobacteria. J. Bacteriol. 2006;188:1979–1986. doi: 10.1128/JB.188.5.1979-1986.2006. PubMed DOI PMC

Bustos A.Y., Font de Valdez G., Fadda S., Taranto M.P. New Insights into Bacterial Bile Resistance Mechanisms: The Role of Bile Salt Hydrolase and Its Impact on Human Health. Food Res. Int. 2018;112:250–262. doi: 10.1016/j.foodres.2018.06.035. PubMed DOI

Levy M., Blacher E., Elinav E. Microbiome, Metabolites and Host Immunity. Curr. Opin. Microbiol. 2017;35:8–15. doi: 10.1016/j.mib.2016.10.003. PubMed DOI

Jia B., Park D., Chun B.H., Hahn Y., Jeon C.O. Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome. Int. J. Mol. Sci. 2021;22:3652. doi: 10.3390/ijms22073652. PubMed DOI PMC

Ridlon J.M., Harris S.C., Bhowmik S., Kang D.-J., Hylemon P.B. Consequences of Bile Salt Biotransformations by Intestinal Bacteria. Gut Microbes. 2016;7:22–39. doi: 10.1080/19490976.2015.1127483. PubMed DOI PMC

Wise J.L., Cummings B.P. The 7-A-Dehydroxylation Pathway: An Integral Component of Gut Bacterial Bile Acid Metabolism and Potential Therapeutic Target. Front. Microbiol. 2023;13:1093420. doi: 10.3389/fmicb.2022.1093420. PubMed DOI PMC

Gérard P. Metabolism of Cholesterol and Bile Acids by the Gut Microbiota. Pathogens. 2014;3:14–24. doi: 10.3390/pathogens3010014. PubMed DOI PMC

de Diego-Cabero N., Mereu A., Menoyo D., Holst J.J., Ipharraguerre I.R. Bile Acid Mediated Effects on Gut Integrity and Performance of Early-Weaned Piglets. BMC Vet. Res. 2015;11:111. doi: 10.1186/s12917-015-0425-6. PubMed DOI PMC

Verbeke L., Farre R., Verbinnen B., Covens K., Vanuytsel T., Verhaegen J., Komuta M., Roskams T., Chatterjee S., Annaert P., et al. The Fxr Agonist Obeticholic Acid Prevents Gut Barrier Dysfunction and Bacterial Translocation in Cholestatic Rats. Am. J. Pathol. 2015;185:409–419. doi: 10.1016/j.ajpath.2014.10.009. PubMed DOI

Xu M., Cen M., Shen Y., Zhu Y., Cheng F., Tang L., Hu W., Dai N. Deoxycholic Acid-Induced Gut Dysbiosis Disrupts Bile Acid Enterohepatic Circulation and Promotes Intestinal Inflammation. Dig. Dis. Sci. 2021;66:568–576. doi: 10.1007/s10620-020-06208-3. PubMed DOI

Lajczak N.K., Saint-Criq V., O’Dwyer A.M., Perino A., Adorini L., Schoonjans K., Keely S.J. Bile Acids Deoxycholic Acid and Ursodeoxycholic Acid Differentially Regulate Human Β-Defensin-1 and -2 Secretion by Colonic Epithelial Cells. Faseb J. 2017;31:3848–3857. doi: 10.1096/fj.201601365R. PubMed DOI

Cipriani S., Mencarelli A., Chini M.G., Distrutti E., Renga B., Bifulco G., Baldelli F., Donini A., Fiorucci S., Ryffel B. The Bile Acid Receptor Gpbar-1 (Tgr5) Modulates Integrity of Intestinal Barrier and Immune Response to Experimental Colitis. PLoS ONE. 2011;6:e25637. doi: 10.1371/journal.pone.0025637. PubMed DOI PMC

Ichikawa R., Takayama T., Yoneno K., Kamada N., Kitazume M.T., Higuchi H., Matsuoka K., Watanabe M., Itoh H., Kanai T., et al. Bile Acids Induce Monocyte Differentiation Toward Interleukin-12 Hypo-Producing Dendritic Cells Via a Tgr5-Dependent Pathway. Immunology. 2012;136:153–162. doi: 10.1111/j.1365-2567.2012.03554.x. PubMed DOI PMC

Vavassori P., Mencarelli A., Renga B., Distrutti E., Fiorucci S. The Bile Acid Receptor Fxr Is a Modulator of Intestinal Innate Immunity. J. Immunol. 2009;183:6251–6261. doi: 10.4049/jimmunol.0803978. PubMed DOI

Biagioli M., Carino A., Cipriani S., Francisci D., Marchianò S., Scarpelli P., Sorcini D., Zampella A., Fiorucci S. The Bile Acid Receptor Gpbar1 Regulates the M1/M2 Phenotype of Intestinal Macrophages and Activation of Gpbar1 Rescues Mice from Murine Colitis. J. Immunol. 2017;199:718–733. doi: 10.4049/jimmunol.1700183. PubMed DOI

Haselow K., Bode J.G., Wammers M., Ehlting C., Keitel V., Kleinebrecht L., Schupp A.-K., Häussinger D., Graf D. Bile Acids Pka-Dependently Induce a Switch of the Il-10/Il-12 Ratio and Reduce Proinflammatory Capability of Human Macrophages. J. Leukoc. Biol. 2013;94:1253–1264. doi: 10.1189/jlb.0812396. PubMed DOI

Zhao X., Liu Z., Sun F., Yao L., Yang G., Wang K. Bile Acid Detection Techniques and Bile Acid-Related Diseases. Front. Physiol. 2022;13:826740. doi: 10.3389/fphys.2022.826740. PubMed DOI PMC

Teodoro J.S., Varela A.T., Rolo A.P., Palmeira C.M. High-Fat and Obesogenic Diets: Current and Future Strategies to Fight Obesity and Diabetes. Genes Nutr. 2014;9:406. doi: 10.1007/s12263-014-0406-6. PubMed DOI PMC

Ludwig D.S., Apovian C.M., Aronne L.J., Astrup A., Cantley L.C., Ebbeling C.B., Heymsfield S.B., Johnson J.D., King J.C., Krauss R.M., et al. Competing Paradigms of Obesity Pathogenesis: Energy Balance Versus Carbohydrate-Insulin Models. Eur. J. Clin. Nutr. 2022;76:1209–1221. doi: 10.1038/s41430-022-01179-2. PubMed DOI PMC

Hall K.D., Farooqi I.S., Friedman J.M., Klein S., Loos R.J.F., Mangelsdorf D.J., O’Rahilly S., Ravussin E., Redman L.M., Ryan D.H., et al. The Energy Balance Model of Obesity: Beyond Calories In, Calories Out. Am. J. Clin. Nutr. 2022;115:1243–1254. doi: 10.1093/ajcn/nqac031. PubMed DOI PMC

Dicken S.J., Batterham R.L. Ultra-Processed Food and Obesity: What Is the Evidence? Curr. Nutr. Rep. 2024;13:23–38. doi: 10.1007/s13668-024-00517-z. PubMed DOI PMC

Monda A., de Stefano M.I., Villano I., Allocca S., Casillo M., Messina A., Monda V., Moscatelli F., Dipace A., Limone P., et al. Ultra-Processed Food Intake and Increased Risk of Obesity: A Narrative Review. Foods. 2024;13:2627. doi: 10.3390/foods13162627. PubMed DOI PMC

Magkos F., Sørensen T.I.A., Raubenheimer D., Dhurandhar N.V., Loos R.J.F., Bosy-Westphal A., Clemmensen C., Hjorth M.F., Allison D.B., Taubes G., et al. on the Pathogenesis of Obesity: Causal Models and Missing Pieces of the Puzzle. Nat. Metab. 2024;6:1856–1865. doi: 10.1038/s42255-024-01106-8. PubMed DOI

Heindel J.J., Lustig R.H., Howard S., Corkey B.E. Obesogens: A Unifying Theory for the Global Rise in Obesity. Int. J. Obes. 2024;48:449–460. doi: 10.1038/s41366-024-01460-3. PubMed DOI PMC

Flier J.S. Moderating “the Great Debate”: The Carbohydrate-Insulin Vs. The Energy Balance Models of Obesity. Cell Metab. 2023;35:737–741. doi: 10.1016/j.cmet.2023.03.020. PubMed DOI

Valicente V.M., Peng C.-H., Pacheco K.N., Lin L., Kielb E.I., Dawoodani E., Abdollahi A., Mattes R.D. Ultraprocessed Foods and Obesity Risk: A Critical Review of Reported Mechanisms. Adv. Nutr. 2023;14:718–738. doi: 10.1016/j.advnut.2023.04.006. PubMed DOI PMC

Poti J.M., Braga B., Qin B. Ultra-Processed Food Intake and Obesity: What Really Matters for Health—Processing or Nutrient Content? Curr. Obes. Rep. 2017;6:420–431. doi: 10.1007/s13679-017-0285-4. PubMed DOI PMC

Johnston B.C., Kanters S., Bandayrel K., Wu P., Naji F., Siemieniuk R.A., Ball G.D.C., Busse J.W., Thorlund K., Guyatt G., et al. Comparison of Weight Loss Among Named Diet Programs in Overweight and Obese Adults. JAMA. 2014;312:923–933. doi: 10.1001/jama.2014.10397. PubMed DOI

Ge L., Sadeghirad B., Ball G.D.C., da Costa B.R., Hitchcock C.L., Svendrovski A., Kiflen R., Quadri K., Kwon H.Y., Karamouzian M., et al. Comparison of Dietary Macronutrient Patterns of 14 Popular Named Dietary Programmes for Weight and Cardiovascular Risk Factor Reduction in adults: Systematic Review and Network Meta-Analysis of Randomised Trials. BMJ. 2020;369:m696. doi: 10.1136/bmj.m696. PubMed DOI PMC

Kim J.Y. Optimal Diet Strategies for Weight Loss and Weight Loss Maintenance. J. Obes. Metab. Syndr. 2021;30:20–31. doi: 10.7570/jomes20065. PubMed DOI PMC

Fappi A., Mittendorfer B. Dietary Protein Intake and Obesity-Associated Cardiometabolic Function. Curr. Opin. Clin. Nutr. Metab. Care. 2020;23:380–386. doi: 10.1097/MCO.0000000000000689. PubMed DOI PMC

Deehan E.C., Mocanu V., Madsen K.L. Effects of Dietary Fibre on Metabolic Health and Obesity. Nat. Rev. Gastroenterol. Hepatol. 2024;21:301–318. doi: 10.1038/s41575-023-00891-z. PubMed DOI

Sacks F.M., Bray G.A., Carey V.J., Smith S.R., Ryan D.H., Anton S.D., McManus K., Champagne C.M., Bishop L.M., Laranjo N., et al. Comparison of Weight-Loss Diets with Different Compositions of Fat, Protein, and Carbohydrates. N. Engl. J. Med. 2009;360:859–873. doi: 10.1056/NEJMoa0804748. PubMed DOI PMC

Botchlett R., Wu C. Diet Composition for the Management of Obesity and Obesity-Related Disorders. J. Diabetes Mellit Metab. Syndr. 2018;3:10–25. doi: 10.28967/jdmms.2018.01.18002. PubMed DOI PMC

Leeming E.R., Johnson A.J., Spector T.D., Le Roy C.I. Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration. Nutrients. 2019;11:2862. doi: 10.3390/nu11122862. PubMed DOI PMC

David L.A., Maurice C.F., Carmody R.N., Gootenberg D.B., Button J.E., Wolfe B.E., Ling A.V., Devlin A.S., Varma Y., Fischbach M.A., et al. Diet Rapidly and Reproducibly Alters the Human Gut Microbiome. Nature. 2014;505:559–563. doi: 10.1038/nature12820. PubMed DOI PMC

Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.-Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R., et al. Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes. Science. 2011;334:105–108. doi: 10.1126/science.1208344. PubMed DOI PMC

Xu Z., Knight R. Dietary Effects on Human Gut Microbiome Diversity. Br. J. Nutr. 2015;113:S1–S5. doi: 10.1017/S0007114514004127. PubMed DOI PMC

Senghor B., Sokhna C., Ruimy R., Lagier J.-C. Gut Microbiota Diversity According to Dietary Habits and Geographical Provenance. Hum. Microbiome J. 2018;7–8:1–9. doi: 10.1016/j.humic.2018.01.001. DOI

Parizadeh M., Arrieta M.-C. The Global Human Gut Microbiome: Genes, Lifestyles, and Diet. Trends Mol. Med. 2023;29:789–801. doi: 10.1016/j.molmed.2023.07.002. PubMed DOI

Brinkworth G.D., Noakes M., Clifton P.M., Bird A.R. Comparative Effects of Very Low-Carbohydrate, High-Fat and High-Carbohydrate, Low-Fat Weight-Loss Diets on Bowel Habit and Faecal Short-Chain Fatty Acids and Bacterial Populations. Br. J. Nutr. 2009;101:1493–1502. doi: 10.1017/S0007114508094658. PubMed DOI

Duncan S.H., Belenguer A., Holtrop G., Johnstone A.M., Flint H.J., Lobley G.E. Reduced Dietary Intake of Carbohydrates by Obese Subjects Results in Decreased Concentrations of Butyrate and Butyrate-Producing Bacteria in Feces. Appl. Environ. Microbiol. 2007;73:1073–1078. doi: 10.1128/AEM.02340-06. PubMed DOI PMC

Walker A.W., Ince J., Duncan S.H., Webster L.M., Holtrop G., Ze X., Brown D., Stares M.D., Scott P., Bergerat A., et al. Dominant and Diet-Responsive Groups of Bacteria Within the Human Colonic Microbiota. ISME J. 2011;5:220–230. doi: 10.1038/ismej.2010.118. PubMed DOI PMC

De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., Collini S., Pieraccini G., Lionetti P. Impact of Diet in Shaping Gut Microbiota Revealed by a Comparative Study in Children from Europe and Rural Africa. Proc. Natl. Acad. Sci. USA. 2010;107:14691–14696. doi: 10.1073/pnas.1005963107. PubMed DOI PMC

Zimmer J., Lange B., Frick J.-S., Sauer H., Zimmermann K., Schwiertz A., Rusch K., Klosterhalfen S., Enck P. a Vegan or Vegetarian Diet Substantially Alters the Human Colonic Faecal Microbiota. Eur. J. Clin. Nutr. 2012;66:53–60. doi: 10.1038/ejcn.2011.141. PubMed DOI

Sidhu S.R.K., Kok C.W., Kunasegaran T., Ramadas A. Effect of Plant-Based Diets on Gut Microbiota: A Systematic Review of Interventional Studies. Nutrients. 2023;15:1510. doi: 10.3390/nu15061510. PubMed DOI PMC

Singh R.K., Chang H.-W., Yan D., Lee K.M., Ucmak D., Wong K., Abrouk M., Farahnik B., Nakamura M., Zhu T.H., et al. Influence of Diet on the Gut Microbiome and Implications for Human Health. J. Transl. Med. 2017;15:73. doi: 10.1186/s12967-017-1175-y. PubMed DOI PMC

Kase B.E., Liese A.D., Zhang J., Murphy E.A., Zhao L., Steck S.E. The Development and Evaluation of a Literature-Based Dietary Index for Gut Microbiota. Nutrients. 2024;16:1045. doi: 10.3390/nu16071045. PubMed DOI PMC

Schoonakker M.P., van Peet P.G., van den Burg E.L., Numans M.E., Ducarmon Q.R., Pijl H., Wiese M. Impact of Dietary Carbohydrate, Fat or Protein Restriction on the Human Gut Microbiome: A Systematic Review. Nutr. Res. Rev. 2024:1–18. doi: 10.1017/S0954422424000131. PubMed DOI

Dai Z.-L. Amino Acid Metabolism in Intestinal Bacteria: Links Between Gut Ecology and Host Health. Front. Biosci. 2011;16:1768–1786. doi: 10.2741/3820. PubMed DOI

Bartlett A., Kleiner M. Dietary Protein and the Intestinal Microbiota: An Understudied Relationship. iScience. 2022;25:105313. doi: 10.1016/j.isci.2022.105313. PubMed DOI PMC

Wan Y., Wang F., Yuan J., Li J., Jiang D., Zhang J., Li H., Wang R., Tang J., Huang T., et al. Effects of Dietary Fat on Gut Microbiota and Faecal Metabolites, and Their Relationship with Cardiometabolic Risk Factors: A 6-Month Randomised Controlled-Feeding Trial. Gut. 2019;68:1417–1429. doi: 10.1136/gutjnl-2018-317609. PubMed DOI

Clemente-Suárez V.J., Beltrán-Velasco A.I., Redondo-Flórez L., Martín-Rodríguez A., Tornero-Aguilera J.F. Global Impacts of Western Diet and Its Effects on Metabolism and Health: A Narrative Review. Nutrients. 2023;15:2749. doi: 10.3390/nu15122749. PubMed DOI PMC

Piernas C., Gao M., Jebb S.A. Dietary Patterns Derived by Reduced Rank Regression and Non-Communicable Disease Risk. Proc. Nutr. Soc. 2022:1–8. doi: 10.1017/S0029665122001094. PubMed DOI

Beam A., Clinger E., Hao L. Effect of Diet and Dietary Components on the Composition of the Gut Microbiota. Nutrients. 2021;13:2795. doi: 10.3390/nu13082795. PubMed DOI PMC

Muscogiuri G., Cantone E., Cassarano S., Tuccinardi D., Barrea L., Savastano S., Colao A. Gut Microbiota: A New Path to Treat Obesity. Int. J. Obes. Suppl. 2019;9:10–19. doi: 10.1038/s41367-019-0011-7. PubMed DOI PMC

Borrego-Ruiz A., Borrego J.J. Human Gut Microbiome, Diet, and Mental Disorders. Int. Microbiol. 2024 doi: 10.1007/s10123-024-00518-6. PubMed DOI

Nagpal R., Neth B.J., Wang S., Craft S., Yadav H. Modified Mediterranean-Ketogenic Diet Modulates Gut Microbiome and Short-Chain Fatty Acids in association with alzheimer’s Disease Markers in Subjects with Mild Cognitive Impairment. EBioMedicine. 2019;47:529–542. doi: 10.1016/j.ebiom.2019.08.032. PubMed DOI PMC

Estruch R., Ros E., Salas-Salvadó J., Covas M.-I., Corella D., Arós F., Gómez-Gracia E., Ruiz-Gutiérrez V., Fiol M., Lapetra J., et al. Primary Prevention of Cardiovascular Disease with a Mediterranean Diet Supplemented with Extra-Virgin Olive Oil or Nuts. N. Engl. J. Med. 2018;378:e34. doi: 10.1056/NEJMoa1800389. PubMed DOI

De Filippis F., Pellegrini N., Vannini L., Jeffery I.B., La Storia A., Laghi L., Serrazanetti D.I., Di Cagno R., Ferrocino I., Lazzi C., et al. High-Level Adherence to a Mediterranean Diet Beneficially Impacts the Gut Microbiota and Associated Metabolome. Gut. 2016;65:1812–1821. doi: 10.1136/gutjnl-2015-309957. PubMed DOI

Garcia-Mantrana I., Selma-Royo M., Alcantara C., Collado M.C. Shifts on Gut Microbiota Associated to Mediterranean Diet Adherence and Specific Dietary Intakes on General Adult Population. Front. Microbiol. 2018;9:890. doi: 10.3389/fmicb.2018.00890. PubMed DOI PMC

Pagliai G., Russo E., Niccolai E., Dinu M., Di Pilato V., Magrini A., Bartolucci G., Baldi S., Menicatti M., Giusti B., et al. Influence of a 3-Month Low-Calorie Mediterranean Diet Compared to the Vegetarian Diet on Human Gut Microbiota and Scfa: The Cardiveg Study. Eur. J. Nutr. 2020;59:2011–2024. doi: 10.1007/s00394-019-02050-0. PubMed DOI

Wang Y., Wymond B., Tandon H., Belobrajdic D.P. Swapping White for High-Fibre Bread Increases Faecal Abundance of Short-Chain Fatty Acid-Producing Bacteria and Microbiome Diversity: A Randomized, Controlled, Decentralized Trial. Nutrients. 2024;16:989. doi: 10.3390/nu16070989. PubMed DOI PMC

Holscher H.D. Dietary Fiber and Prebiotics and the Gastrointestinal Microbiota. Gut Microbes. 2017;8:172–184. doi: 10.1080/19490976.2017.1290756. PubMed DOI PMC

Kaoutari A.E., Armougom F., Gordon J.I., Raoult D., Henrissat B. The Abundance and Variety of Carbohydrate-Active Enzymes in the Human Gut Microbiota. Nat. Rev. Microbiol. 2013;11:497–504. doi: 10.1038/nrmicro3050. PubMed DOI

Gibson G.R., Roberfroid M.B. Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics. J. Nutr. 1995;125:1401–1412. doi: 10.1093/jn/125.6.1401. PubMed DOI

Roberfroid M. Prebiotics: The Concept Revisited1. J. Nutr. 2007;137:830S–837S. doi: 10.1093/jn/137.3.830S. PubMed DOI

Deehan E.C., Duar R.M., Armet A.M., Perez-Muñoz M.E., Jin M., Walter J., Britton R.A., Cani P.D. Modulation of the Gastrointestinal Microbiome with Nondigestible Fermentable Carbohydrates to Improve Human Health. Microbiol. Spectr. 2017;5:10-1128. doi: 10.1128/microbiolspec.BAD-0019-2017. PubMed DOI

Delcour J.A., Aman P., Courtin C.M., Hamaker B.R., Verbeke K. Prebiotics, Fermentable Dietary Fiber, and Health Claims. Adv. Nutr. 2016;7:1–4. doi: 10.3945/an.115.010546. PubMed DOI PMC

Guzman J.R., Conlin V.S., Jobin C. Diet, Microbiome, and the Intestinal Epithelium: An Essential Triumvirate? Biomed Res. Int. 2013;2013:1–12. doi: 10.1155/2013/425146. PubMed DOI PMC

Mogensen T.H. Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses. Clin. Microbiol. Rev. 2009;22:240–273. doi: 10.1128/CMR.00046-08. PubMed DOI PMC

Lozupone C.A., Knight R. Species Divergence and the Measurement of Microbial Diversity. Fems Microbiol. Rev. 2008;32:557–578. doi: 10.1111/j.1574-6976.2008.00111.x. PubMed DOI PMC

Cadotte M.W., Jonathan Davies T., Regetz J., Kembel S.W., Cleland E., Oakley T.H. Phylogenetic Diversity Metrics for Ecological Communities: Integrating Species Richness, Abundance and Evolutionary History. Ecol. Lett. 2010;13:96–105. doi: 10.1111/j.1461-0248.2009.01405.x. PubMed DOI

Flint H.J., Duncan S.H., Scott K.P., Louis P. Links Between Diet, Gut Microbiota Composition and Gut Metabolism. Proc. Nutr. Soc. 2015;74:13–22. doi: 10.1017/S0029665114001463. PubMed DOI

So D., Whelan K., Rossi M., Morrison M., Holtmann G., Kelly J.T., Shanahan E.R., Staudacher H.M., Campbell K.L. Dietary Fiber Intervention on Gut Microbiota Composition in Healthy Adults: A Systematic Review and Meta-Analysis. Am. J. Clin. Nutr. 2018;107:965–983. doi: 10.1093/ajcn/nqy041. PubMed DOI

Zhang C., Yin A., Li H., Wang R., Wu G., Shen J., Zhang M., Wang L., Hou Y., Ouyang H., et al. Dietary Modulation of Gut Microbiota Contributes to alleviation of Both Genetic and Simple Obesity in Children. EBioMedicine. 2015;2:968–984. doi: 10.1016/j.ebiom.2015.07.007. PubMed DOI PMC

Simpson H.L., Campbell B.J. Review Article: Dietary Fibre-Microbiota Interactions. Aliment. Pharmacol. Ther. 2015;42:158–179. doi: 10.1111/apt.13248. PubMed DOI PMC

Vandeputte D., Falony G., Vieira-Silva S., Wang J., Sailer M., Theis S., Verbeke K., Raes J. Prebiotic Inulin-Type Fructans Induce Specific Changes in the Human Gut Microbiota. Gut. 2017;66:1968–1974. doi: 10.1136/gutjnl-2016-313271. PubMed DOI PMC

Liu F., Li P., Chen M., Luo Y., Prabhakar M., Zheng H., He Y., Qi Q., Long H., Zhang Y., et al. Fructooligosaccharide (Fos) and Galactooligosaccharide (Gos) Increase Bifidobacterium But Reduce Butyrate Producing Bacteria with adverse Glycemic Metabolism in Healthy Young Population. Sci. Rep. 2017;7:11789. doi: 10.1038/s41598-017-10722-2. PubMed DOI PMC

Hamaker B.R., Tuncil Y.E. a Perspective on the Complexity of Dietary Fiber Structures and Their Potential Effect on the Gut Microbiota. J. Mol. Biol. 2014;426:3838–3850. doi: 10.1016/j.jmb.2014.07.028. PubMed DOI

Tuncil Y.E., Thakkar R.D., Arioglu-Tuncil S., Hamaker B.R., Lindemann S.R., Young V.B. Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of Gut Microbiota. mSphere. 2020;5:e00180-20. doi: 10.1128/mSphere.00180-20. PubMed DOI PMC

Cantu-Jungles T.M., Hamaker B.R. Tuning Expectations to Reality: Don’t Expect Increased Gut Microbiota Diversity with Dietary Fiber. J. Nutr. 2023;153:3156–3163. doi: 10.1016/j.tjnut.2023.09.001. PubMed DOI

Bai J., Li Y., Li T., Zhang W., Fan M., Zhang K., Qian H., Zhang H., Qi X., Wang L. Comparison of Different Soluble Dietary Fibers During the in Vitro Fermentation Process. J. Agric. Food Chem. 2021;69:7446–7457. doi: 10.1021/acs.jafc.1c00237. PubMed DOI

Flint H.J., Scott K.P., Duncan S.H., Louis P., Forano E. Microbial Degradation of Complex Carbohydrates in the Gut. Gut Microbes. 2014;3:289–306. doi: 10.4161/gmic.19897. PubMed DOI PMC

Lombard V., Golaconda Ramulu H., Drula E., Coutinho P.M., Henrissat B. The Carbohydrate-Active Enzymes Database (Cazy) in 2013. Nucleic Acids Res. 2013;42:D490–D495. doi: 10.1093/nar/gkt1178. PubMed DOI PMC

Cecchini D.A., Laville E., Laguerre S., Robe P., Leclerc M., Doré J., Henrissat B., Remaud-Siméon M., Monsan P., Potocki-Véronèse G., et al. Functional Metagenomics Reveals Novel Pathways of Prebiotic Breakdown by Human Gut Bacteria. PLoS ONE. 2013;8:e72766. doi: 10.1371/journal.pone.0072766. PubMed DOI PMC

Saito Y., Shigehisa A., Watanabe Y., Tsukuda N., Moriyama-Ohara K., Hara T., Matsumoto S., Tsuji H., Matsuki T., Zhou N.-Y. Multiple Transporters and Glycoside Hydrolases Are Involved in arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium Pseudocatenulatum. Appl. Environ. Microbiol. 2020;86:e01782-20. doi: 10.1128/AEM.01782-20. PubMed DOI PMC

Kim C.C., Healey G.R., Kelly W.J., Patchett M.L., Jordens Z., Tannock G.W., Sims I.M., Bell T.J., Hedderley D., Henrissat B., et al. Genomic Insights from Monoglobus Pectinilyticus: A Pectin-Degrading Specialist Bacterium in the Human Colon. ISME J. 2019;13:1437–1456. doi: 10.1038/s41396-019-0363-6. PubMed DOI PMC

Boger M.C.L., Lammerts van Bueren A., Dijkhuizen L., McBain A.J. Cross-Feeding Among Probiotic Bacterial Strains on Prebiotic Inulin Involves the Extracellular Exo-Inulinase of Lactobacillus Paracasei Strain W20. Appl. Environ. Microbiol. 2018;84:e01539-18. doi: 10.1128/AEM.01539-18. PubMed DOI PMC

Delannoy-Bruno O., Desai C., Raman A.S., Chen R.Y., Hibberd M.C., Cheng J., Han N., Castillo J.J., Couture G., Lebrilla C.B., et al. Evaluating Microbiome-Directed Fibre Snacks in Gnotobiotic Mice and Humans. Nature. 2021;595:91–95. doi: 10.1038/s41586-021-03671-4. PubMed DOI PMC

Koropatkin N.M., Cameron E.A., Martens E.C. How Glycan Metabolism Shapes the Human Gut Microbiota. Nat. Rev. Microbiol. 2012;10:323–335. doi: 10.1038/nrmicro2746. PubMed DOI PMC

Sheridan P.O., Martin J.C., Lawley T.D., Browne H.P., Harris H.M.B., Bernalier-Donadille A., Duncan S.H., O’Toole P.W., Scott K.P., Flint H.J. Polysaccharide Utilization Loci and Nutritional Specialization in a Dominant Group of Butyrate-Producing Human Colonic Firmicutes. Microb. Genom. 2016;2:e000043. doi: 10.1099/mgen.0.000043. PubMed DOI PMC

Rodriguez J., Hiel S., Neyrinck A.M., Le Roy T., Pötgens S.A., Leyrolle Q., Pachikian B.D., Gianfrancesco M.A., Cani P.D., Paquot N., et al. Discovery of the Gut Microbial Signature Driving the Efficacy of Prebiotic Intervention in Obese Patients. Gut. 2020;69:1975–1987. doi: 10.1136/gutjnl-2019-319726. PubMed DOI PMC

Chen T., Long W., Zhang C., Liu S., Zhao L., Hamaker B.R. Fiber-Utilizing Capacity Varies in Prevotella- Versus Bacteroides-Dominated Gut Microbiota. Sci. Rep. 2017;7:2594. doi: 10.1038/s41598-017-02995-4. PubMed DOI PMC

Christensen L., Roager H.M., Astrup A., Hjorth M.F. Microbial Enterotypes in Personalized Nutrition and Obesity Management. Am. J. Clin. Nutr. 2018;108:645–651. doi: 10.1093/ajcn/nqy175. PubMed DOI

Van den Abbeele P., Duysburgh C., Ghyselinck J., Goltz S., Berezhnaya Y., Boileau T., De Blaiser A., Marzorati M. Fructans with Varying Degree of Polymerization Enhance the Selective Growth of Bifidobacterium Animalis Subsp. Lactis Bb-12 in the Human Gut Microbiome in Vitro. Appl. Sci. 2021;11:598. doi: 10.3390/app11020598. DOI

Klimenko N.S., Tyakht A.V., Popenko A.S., Vasiliev A.S., Altukhov I.A., Ischenko D.S., Shashkova T.I., Efimova D.A., Nikogosov D.A., Osipenko D.A., et al. Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project. Nutrients. 2018;10:576. doi: 10.3390/nu10050576. PubMed DOI PMC

Magne F., Gotteland M., Gauthier L., Zazueta A., Pesoa S., Navarrete P., Balamurugan R. The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? Nutrients. 2020;12:1474. doi: 10.3390/nu12051474. PubMed DOI PMC

Mobeen F., Sharma V., Prakash T. Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions. Bioinformation. 2018;14:560–573. doi: 10.6026/97320630014560. PubMed DOI PMC

Healey G., Murphy R., Butts C., Brough L., Whelan K., Coad J. Habitual Dietary Fibre Intake Influences Gut Microbiota Response to an Inulin-Type Fructan Prebiotic: A Randomised, Double-Blind, Placebo-Controlled, Cross-Over, Human Intervention Study. Br. J. Nutr. 2018;119:176–189. doi: 10.1017/S0007114517003440. PubMed DOI

Smith A.M. The Biosynthesis of Starch Granules. Biomacromolecules. 2001;2:335–341. doi: 10.1021/bm000133c. PubMed DOI

Sim L., Willemsma C., Mohan S., Naim H.Y., Pinto B.M., Rose D.R. Structural Basis for Substrate Selectivity in Human Maltase-Glucoamylase and Sucrase-Isomaltase N-Terminal Domains. J. Biol. Chem. 2010;285:17763–17770. doi: 10.1074/jbc.M109.078980. PubMed DOI PMC

Birt D.F., Boylston T., Hendrich S., Jane J.-L., Hollis J., Li L., McClelland J., Moore S., Phillips G.J., Rowling M., et al. Resistant Starch: Promise for Improving Human Health. Adv. Nutr. 2013;4:587–601. doi: 10.3945/an.113.004325. PubMed DOI PMC

Jane J.L. Starch. Elsevier; Amsterdam, The Netherlands: 2009. Structural Features of Starch Granules II; pp. 193–236. DOI

Sajilata M.G., Singhal R.S., Kulkarni P.R. Resistant Starch–a Review. Compr. Rev. Food. Sci. Food Saf. 2006;5:1–17. doi: 10.1111/j.1541-4337.2006.tb00076.x. PubMed DOI

McCleary B.V., Monaghan D.A. Measurement of Resistant Starch. J. AOAC Int. 2002;85:665–675. doi: 10.1093/jaoac/85.3.665. PubMed DOI

Englyst H.N., Hudson G.J. The classification and measurement of dietary carbohydrates. Food Chem. 1996;57:15–21. doi: 10.1016/0308-8146(96)00056-8. DOI

Raigond P., Ezekiel R., Raigond B. Resistant Starch in Food: A Review. J. Sci. Food Agric. 2015;95:1968–1978. doi: 10.1002/jsfa.6966. PubMed DOI

Macfarlane S., Macfarlane G.T. Regulation of short-chain fatty acid production. Proc. Nutr. Soc. 2003;62:67–72. doi: 10.1079/PNS2002207. PubMed DOI

Louis P., Flint H.J. Formation of Propionate and Butyrate by the Human Colonic Microbiota. Environ. Microbiol. 2017;19:29–41. doi: 10.1111/1462-2920.13589. PubMed DOI

Morrison D.J., Preston T. Formation of Short Chain Fatty Acids by the Gut Microbiota and Their Impact on Human Metabolism. Gut Microbes. 2016;7:189–200. doi: 10.1080/19490976.2015.1134082. PubMed DOI PMC

Turroni F., Peano C., Pass D.A., Foroni E., Severgnini M., Claesson M.J., Kerr C., Hourihane J., Murray D., Fuligni F., et al. Diversity of Bifidobacteria Within the Infant Gut Microbiota. PLoS ONE. 2012;7:e36957. doi: 10.1371/journal.pone.0036957. PubMed DOI PMC

Suzuki T. Regulation of Intestinal Epithelial Permeability by Tight Junctions. Cell. Mol. Life Sci. 2013;70:631–659. doi: 10.1007/s00018-012-1070-x. PubMed DOI PMC

Segain J.-P. Butyrate Inhibits Inflammatory Responses Through Nfkappa B Inhibition: Implications for Crohn’s Disease. Gut. 2000;47:397–403. doi: 10.1136/gut.47.3.397. PubMed DOI PMC

Furusawa Y., Obata Y., Fukuda S., Endo T.A., Nakato G., Takahashi D., Nakanishi Y., Uetake C., Kato K., Kato T., et al. Commensal Microbe-Derived Butyrate Induces the Differentiation of Colonic Regulatory T Cells. Nature. 2013;504:446–450. doi: 10.1038/nature12721. PubMed DOI

Krishnan V., Awana M., Samota M.K., Warwate S.I., Kulshreshtha A., Ray M., Bollinedi H., Singh A.K., Thandapilly S.J., Praveen S., et al. Pullulanase Activity: A Novel Indicator of Inherent Resistant Starch in Rice (Oryza sativa L) Int. J. Biol. Macromol. 2020;152:1213–1223. doi: 10.1016/j.ijbiomac.2019.10.218. PubMed DOI

Barros F., Awika J., Rooney L.W. Effect of Molecular Weight Profile of Sorghum Proanthocyanidins on Resistant Starch Formation. J. Sci. Food Agric. 2014;94:1212–1217. doi: 10.1002/jsfa.6400. PubMed DOI

Cao R., Liu X., Liu Y., Zhai X., Cao T., Wang A., Qiu J. Applications of Nuclear Magnetic Resonance Spectroscopy to the Evaluation of Complex Food Constituents. Food Chem. 2021;342:128258. doi: 10.1016/j.foodchem.2020.128258. PubMed DOI

Cuevas-Sierra A., Ramos-Lopez O., Riezu-Boj J.I., Milagro F.I., Martinez J.A. Diet, Gut Microbiota, and Obesity: Links with Host Genetics and Epigenetics and Potential Applications. Adv. Nutr. 2019;10:S17–S30. doi: 10.1093/advances/nmy078. PubMed DOI PMC

Bien J., Palagani V., Bozko P. The Intestinal Microbiota Dysbiosis and Clostridium Difficile Infection: Is There a Relationship with Inflammatory Bowel Disease? Ther. Adv. Gastroenterol. 2013;6:53–68. doi: 10.1177/1756283X12454590. PubMed DOI PMC

Shanahan F. The Colonic Microbiota in Health and Disease. Curr. Opin. Gastroenterol. 2013;29:49–54. doi: 10.1097/MOG.0b013e32835a3493. PubMed DOI

Peterson C.T., Sharma V., Elmén L., Peterson S.N. Immune Homeostasis, Dysbiosis and Therapeutic Modulation of the Gut Microbiota. Clin. Exp. Immunol. 2015;179:363–377. doi: 10.1111/cei.12474. PubMed DOI PMC

DeGruttola A.K., Low D., Mizoguchi A., Mizoguchi E. Current Understanding of Dysbiosis in Disease in Human and Animal Models. Inflamm. Bowel Dis. 2016;22:1137–1150. doi: 10.1097/MIB.0000000000000750. PubMed DOI PMC

Liu B.-N., Liu X.-T., Liang Z.-H., Wang J.-H. Gut Microbiota in Obesity. World J. Gastroenterol. 2021;27:3837–3850. doi: 10.3748/wjg.v27.i25.3837. PubMed DOI PMC

Ciobârcă D., Cătoi A.F., Copăescu C., Miere D., Crișan G. Bariatric Surgery in Obesity: Effects on Gut Microbiota and Micronutrient Status. Nutrients. 2020;12:235. doi: 10.3390/nu12010235. PubMed DOI PMC

Heiss C.N., Olofsson L.E. Gut Microbiota-Dependent Modulation of Energy Metabolism. J. Innate Immun. 2018;10:163–171. doi: 10.1159/000481519. PubMed DOI PMC

Verdam F.J., Fuentes S., de Jonge C., Zoetendal E.G., Erbil R., Greve J.W., Buurman W.A., de Vos W.M., Rensen S.S. Human Intestinal Microbiota Composition Is Associated with Local and Systemic Inflammation in Obesity. Obesity. 2013;21:E607–E615. doi: 10.1002/oby.20466. PubMed DOI

Kasai C., Sugimoto K., Moritani I., Tanaka J., Oya Y., Inoue H., Tameda M., Shiraki K., Ito M., Takei Y., et al. Comparison of the Gut Microbiota Composition Between Obese and Non-Obese Individuals in a Japanese Population, as Analyzed by Terminal Restriction Fragment Length Polymorphism and Next-Generation Sequencing. BMC Gastroenterol. 2015;15:100. doi: 10.1186/s12876-015-0330-2. PubMed DOI PMC

Koliada A., Syzenko G., Moseiko V., Budovska L., Puchkov K., Perederiy V., Gavalko Y., Dorofeyev A., Romanenko M., Tkach S., et al. Association Between Body Mass Index and Firmicutes/Bacteroidetes Ratio in an Adult Ukrainian Population. BMC Microbiol. 2017;17:120. doi: 10.1186/s12866-017-1027-1. PubMed DOI PMC

Ley R.E., Bäckhed F., Turnbaugh P., Lozupone C.A., Knight R.D., Gordon J.I. Obesity Alters Gut Microbial Ecology. Proc. Natl. Acad. Sci. USA. 2005;102:11070–11075. doi: 10.1073/pnas.0504978102. PubMed DOI PMC

Stojanov S., Berlec A., Štrukelj B. The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel Disease. Microorganisms. 2020;8:1715. doi: 10.3390/microorganisms8111715. PubMed DOI PMC

Cani P.D., Moens de Hase E., Van Hul M. Gut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention. Microorganisms. 2021;9:1302. doi: 10.3390/microorganisms9061302. PubMed DOI PMC

Peters B.A., Shapiro J.A., Church T.R., Miller G., Trinh-Shevrin C., Yuen E., Friedlander C., Hayes R.B., Ahn J. a Taxonomic Signature of Obesity in a Large Study of American Adults. Sci Rep. 2018;8:9749. doi: 10.1038/s41598-018-28126-1. PubMed DOI PMC

Hu H.-J., Park S.-G., Jang H.B., Choi M.-G., Park K.-H., Kang J.H., Park S.I., Lee H.-J., Cho S.-H., Zoetendal E.G. Obesity Alters the Microbial Community Profile in Korean Adolescents. PLoS ONE. 2015;10:e0134333. doi: 10.1371/journal.pone.0134333. PubMed DOI PMC

Duncan S.H., Lobley G.E., Holtrop G., Ince J., Johnstone A.M., Louis P., Flint H.J. Human Colonic Microbiota Associated with Diet, Obesity and Weight Loss. Int. J. Obes. 2008;32:1720–1724. doi: 10.1038/ijo.2008.155. PubMed DOI

Méndez-Salazar E.O., Ortiz-López M.G., Granados-Silvestre M.D.L., Palacios-González B., Menjivar M. Altered Gut Microbiota and Compositional Changes in Firmicutes and Proteobacteria in Mexican Undernourished and Obese Children. Front. Microbiol. 2018;9:2494. doi: 10.3389/fmicb.2018.02494. PubMed DOI PMC

Million M., Maraninchi M., Henry M., Armougom F., Richet H., Carrieri P., Valero R., Raccah D., Vialettes B., Raoult D. Retracted Article: Obesity-Associated Gut Microbiota Is Enriched in Lactobacillus Reuteri and Depleted in Bifidobacterium Animalis and Methanobrevibacter Smithii. Int. J. Obes. 2012;36:817–825. doi: 10.1038/ijo.2011.153. PubMed DOI PMC

Le Chatelier E., Nielsen T., Qin J., Prifti E., Hildebrand F., Falony G., Almeida M., Arumugam M., Batto J.-M., Kennedy S., et al. Richness of Human Gut Microbiome Correlates with Metabolic Markers. Nature. 2013;500:541–546. doi: 10.1038/nature12506. PubMed DOI

Mariat D., Firmesse O., Levenez F., Guimarăes V.D., Sokol H., Doré J., Corthier G., Furet J.-P. The Firmicutes/Bacteroidetes Ratio of the Human Microbiota Changes with age. BMC Microbiol. 2009;9:123. doi: 10.1186/1471-2180-9-123. PubMed DOI PMC

Larraufie P., Martin-Gallausiaux C., Lapaque N., Dore J., Gribble F.M., Reimann F., Blottiere H.M. Scfas Strongly Stimulate Pyy Production in Human Enteroendocrine Cells. Sci Rep. 2018;8:74. doi: 10.1038/s41598-017-18259-0. PubMed DOI PMC

Psichas A., Sleeth M.L., Murphy K.G., Brooks L., Bewick G.A., Hanyaloglu A.C., Ghatei M.A., Bloom S.R., Frost G. The Short Chain Fatty Acid Propionate Stimulates Glp-1 and Pyy Secretion Via Free Fatty Acid Receptor 2 in Rodents. Int. J. Obes. 2015;39:424–429. doi: 10.1038/ijo.2014.153. PubMed DOI PMC

Mraz M., Haluzik M. The Role of Adipose Tissue Immune Cells in Obesity and Low-Grade Inflammation. J. Endocrinol. 2014;222:R113–R127. doi: 10.1530/JOE-14-0283. PubMed DOI

Cani P.D., Bibiloni R., Knauf C., Waget A., Neyrinck A.M., Delzenne N.M., Burcelin R. Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice. Diabetes. 2008;57:1470–1481. doi: 10.2337/db07-1403. PubMed DOI

Trøseid M., Nestvold T.K., Rudi K., Thoresen H., Nielsen E.W., Lappegård K.T. Plasma Lipopolysaccharide Is Closely Associated with Glycemic Control and Abdominal Obesity. Diabetes Care. 2013;36:3627–3632. doi: 10.2337/dc13-0451. PubMed DOI PMC

Cani P.D., Neyrinck A.M., Fava F., Knauf C., Burcelin R.G., Tuohy K.M., Gibson G.R., Delzenne N.M. Selective Increases of Bifidobacteria in Gut Microflora Improve High-Fat-Diet-Induced Diabetes in Mice Through a Mechanism Associated with Endotoxaemia. Diabetologia. 2007;50:2374–2383. doi: 10.1007/s00125-007-0791-0. PubMed DOI

Cani P.D., Possemiers S., Van de Wiele T., Guiot Y., Everard A., Rottier O., Geurts L., Naslain D., Neyrinck A., Lambert D.M., et al. Changes in Gut Microbiota Control Inflammation in Obese Mice Through a Mechanism Involving Glp-2-Driven Improvement of Gut Permeability. Gut. 2009;58:1091–1103. doi: 10.1136/gut.2008.165886. PubMed DOI PMC

Bevins C.L., Salzman N.H. Paneth Cells, Antimicrobial Peptides and Maintenance of Intestinal Homeostasis. Nat. Rev. Microbiol. 2011;9:356–368. doi: 10.1038/nrmicro2546. PubMed DOI

Everard A., Lazarevic V., Gaïa N., Johansson M., Ståhlman M., Backhed F., Delzenne N.M., Schrenzel J., François P., Cani P.D. Microbiome of Prebiotic-Treated Mice Reveals Novel Targets Involved in Host Response During Obesity. ISME J. 2014;8:2116–2130. doi: 10.1038/ismej.2014.45. PubMed DOI PMC

Tan T.G., Sefik E., Geva-Zatorsky N., Kua L., Naskar D., Teng F., Pasman L., Ortiz-Lopez A., Jupp R., Wu H.-J.J., et al. Identifying Species of Symbiont Bacteria from the Human Gut That, Alone, Can Induce Intestinal Th17 Cells in Mice. Proc. Natl. Acad. Sci. USA. 2016;113:E8150. doi: 10.1073/pnas.1617460113. PubMed DOI PMC

Luck H., Khan S., Kim J.H., Copeland J.K., Revelo X.S., Tsai S., Chakraborty M., Cheng K., Tao Chan Y., Nøhr M.K., et al. Gut-Associated Iga+ Immune Cells Regulate Obesity-Related Insulin Resistance. Nat. Commun. 2019;10:3650. doi: 10.1038/s41467-019-11370-y. PubMed DOI PMC

Petersen C., Bell R., Klag K.A., Lee S.-H., Soto R., Ghazaryan A., Buhrke K., Ekiz H.A., Ost K.S., Boudina S., et al. T Cell–Mediated Regulation of the Microbiota Protects Against Obesity. Science. 2019;365:eaat9351. doi: 10.1126/science.aat9351. PubMed DOI PMC

Cani P.D., Amar J., Iglesias M.A., Poggi M., Knauf C., Bastelica D., Neyrinck A.M., Fava F., Tuohy K.M., Chabo C., et al. Metabolic Endotoxemia Initiates Obesity and Insulin Resistance. Diabetes. 2007;56:1761–1772. doi: 10.2337/db06-1491. PubMed DOI

Tran H.Q., Ley R.E., Gewirtz A.T., Chassaing B. Flagellin-Elicited Adaptive Immunity Suppresses Flagellated Microbiota and Vaccinates Against Chronic Inflammatory Diseases. Nat. Commun. 2019;10:5650. doi: 10.1038/s41467-019-13538-y. PubMed DOI PMC

Cavallari J.F., Fullerton M.D., Duggan B.M., Foley K.P., Denou E., Smith B.K., Desjardins E.M., Henriksbo B.D., Kim K.J., Tuinema B.R., et al. Muramyl Dipeptide-Based Postbiotics Mitigate Obesity-Induced Insulin Resistance Via Irf4. Cell Metab. 2017;25:1063–1074.e3. doi: 10.1016/j.cmet.2017.03.021. PubMed DOI

Mazmanian S.K., Round J.L., Kasper D.L. a Microbial Symbiosis Factor Prevents Intestinal Inflammatory Disease. Nature. 2008;453:620–625. doi: 10.1038/nature07008. PubMed DOI

Plovier H., Everard A., Druart C., Depommier C., Van Hul M., Geurts L., Chilloux J., Ottman N., Duparc T., Lichtenstein L., et al. a Purified Membrane Protein from akkermansia Muciniphila or the Pasteurized Bacterium Improves Metabolism in Obese and Diabetic Mice. Nat. Med. 2017;23:107–113. doi: 10.1038/nm.4236. PubMed DOI

Koh A., Molinaro A., Ståhlman M., Khan M.T., Schmidt C., Mannerås-Holm L., Wu H., Carreras A., Jeong H., Olofsson L.E., et al. Microbially Produced Imidazole Propionate Impairs Insulin Signaling Through Mtorc1. Cell. 2018;175:947–961.e17. doi: 10.1016/j.cell.2018.09.055. PubMed DOI

Roager H.M., Licht T.R. Microbial Tryptophan Catabolites in Health and Disease. Nat. Commun. 2018;9:3294. doi: 10.1038/s41467-018-05470-4. PubMed DOI PMC

Natividad J.M., Agus A., Planchais J., Lamas B., Jarry A.C., Martin R., Michel M.-L., Chong-Nguyen C., Roussel R., Straube M., et al. Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome. Cell Metab. 2018;28:737–749.e4. doi: 10.1016/j.cmet.2018.07.001. PubMed DOI

Laurans L., Venteclef N., Haddad Y., Chajadine M., Alzaid F., Metghalchi S., Sovran B., Denis R.G.P., Dairou J., Cardellini M., et al. Genetic Deficiency of Indoleamine 2,3-Dioxygenase Promotes Gut Microbiota-Mediated Metabolic Health. Nat. Med. 2018;24:1113–1120. doi: 10.1038/s41591-018-0060-4. PubMed DOI

Tassoni D.S., Macedo R.C.O., Delpino F.M., Santos H.O. Gut Microbiota and Obesity: The Chicken or the Egg? Obesities. 2023;3:296–321. doi: 10.3390/obesities3040024. DOI

Rinninella E., Tohumcu E., Raoul P., Fiorani M., Cintoni M., Mele M.C., Cammarota G., Gasbarrini A., Ianiro G. The Role of Diet in Shaping Human Gut Microbiota. Best Pract. Res. Clin. Gastroenterol. 2023;62–63:101828. doi: 10.1016/j.bpg.2023.101828. PubMed DOI

Zsálig D., Berta A., Tóth V., Szabó Z., Simon K., Figler M., Pusztafalvi H., Polyák É. A Review of the Relationship Between Gut Microbiome and Obesity. Appl. Sci. 2023;13:610. doi: 10.3390/app13010610. DOI

Li Z., Liu D., Gu R., Qiao Y., Jin Q., Zhang Y., Ran S., Liu X., Yi W., Ni M., et al. Fecal Microbiota Transplantation in Obesity Metabolism: A Meta Analysis and Systematic Review. Diabetes Res. Clin. Prac. 2023;202:110803. doi: 10.1016/j.diabres.2023.110803. PubMed DOI

Bui T.P.N. The Human Microbiome as a Therapeutic Target for Metabolic Diseases. Nutrients. 2024;16:2322. doi: 10.3390/nu16142322. PubMed DOI PMC