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Dietary interventions and the gut microbiota: a systematic literature review of 80 controlled clinical trials

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Aslam, Hajara, Trakman, Gina, Dissanayake, Thusharika, Todd, Emma, Harrison, Phelia, Alby, Clemence, Jabeen, Tabinda, Gamage, Elizabeth +11 more·2026·Journal of Translational Medicine
DOI 10.1186/s12967-025-07428-9PMC PMC12781466
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Abstract

BACKGROUND: The gut microbiota are increasingly recognised as key mediators of diet-related health outcomes. This systematic review primarily aimed to comprehensively evaluate associations between dietary interventions and gut microbiota in healthy and clinical adult populations, utilising controlled trials. Secondary outcomes included biological markers measured in blood, faecal, and urine samples. METHODS: A systematic literature search was conducted following the PRISMA guidelines, using the electronic databases PubMed, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL), CINAHL (via EBSCOhost), and Scopus to gather controlled trials of dietary interventions that reported within-group changes from baseline for gut microbiota and biomarkers. Study screening, data extraction, and risk-of-bias assessment were conducted by two independent reviewers. RESULTS: Eighty studies met the eligibility criteria, trialling 13 distinct dietary interventions: Mediterranean, Western, Korean, Japanese, Nordic, low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP), ketogenic, gluten-free, calorie-restricted, macronutrient altered, animal- and plant-based, as well as diets high in functional nutrients and bioactive compounds. Dietary interventions were associated with within-group changes in taxonomy and particular biological markers; however, they were not consistently associated with changes in the alpha or beta diversity of the gut microbiota. The Mediterranean, Japanese, Korean, calorie-restricted, high-polyphenol, high-fibre, plant-based, low-fat, and low-protein diets were all associated with increased abundances of either short chain fatty acids (SCFA)- or lactic acid-producing bacteria or reduced abundance of opportunistic pathogenic bacteria. Some of these diets were also associated with reduced levels of inflammatory markers. In contrast, Western, animal-based, low FODMAP, ketogenic, and gluten-free diets were associated with a reduced abundance of SCFA-producing bacteria. There was substantial heterogeneity across studies in methodology and reporting. CONCLUSION: This systematic review identifies differential associations between a wide range of dietary interventions and gut microbiota and inflammatory outcomes, both beneficial and adverse.

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  • Lifestyle behaviors such as dietary habits, physical activity, and exposure to natural environments modulate the adult microbiome and thereby influence mental well-being.

    “In parallel, lifestyle behaviors such as dietary habits (Aslam et al., 2026), physical activity (Min et al., 2024), and exposure to natural environments (Zhang et al., 2024) act as powerful modulators of the adult microbiome, thereby influencing mental well-being.”

    From Psychobiotics in mental health: insights from human clinical trials via the gut-brain axis (2026) · cites this paper as Aslam et al., 2026

    The Introduction describes diet as a highly modifiable influence on gut microbiota, and the Discussion reports microbiota changes associated with dietary interventions. The paper notes links between gut microbiota and psychiatric disorders, but the cited passages do not establish that diet-induced microbiota changes thereby improve mental well-being. The other lifestyle behaviors have separate citations and are not assessed here. (LLM, conf=0.84)

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  1. [1]Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19(1):55–71. 32887946 · DOI · Paper page
  2. [2]Wagenaar CA, van de Put M, Bisschops M, Walrabenstein W, de Jonge CS, Herrema H, et al. The effect of dietary interventions on chronic inflammatory diseases in relation to the microbiome: a systematic review. Nutrients. 2021;13(9):3208. 34579085 PMC8464906 · DOI
  3. [3]Nance CL, Deniskin R, Diaz VC, Paul M, Anvari S, Anagnostou A. The role of the microbiome in food allergy: a review. Children. 2020;7(6):50. 32466620 PMC7346163 · DOI
  4. [4]Cryan JF, Kj O, Sandhu K, Peterson V, Dinan TG. The gut microbiome in neurological disorders. The Lancet Neurol. 2020;19(2):179–94. 31753762 · DOI · Paper page
  5. [7]Ghosh TS, Rampelli S, Jeffery IB, Santoro A, Neto M, Capri M, et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut. 2020;69(7):1218–28. 32066625 PMC7306987 · DOI · Paper page
  6. [8]Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Feiqiao BY, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137–53. e14. 34256014 PMC9020749 · DOI · Paper page
  7. [9]Caputo M, Pigni S, Antoniotti V, Agosti E, Caramaschi A, Antonioli A, et al. Targeting microbiota in dietary obesity management: a systematic review on randomized control trials in adults. Crit Rev Food Sci Nutr. 2023;63(33):11449–81. 35708057 · DOI
  8. [10]Kimble R, Gouinguenet P, Ashor A, Stewart C, Deighton K, Matu J, et al. Effects of a mediterranean diet on the gut microbiota and microbial metabolites: a systematic review of randomized controlled trials and observational studies. Crit Rev Food Sci Nutr. 2023;63(27):8698–719. 35361035 · DOI
  9. [12]Duncanson K, Williams G, Hoedt EC, Collins CE, Keely S, Talley NJ. Diet-microbiota associations in gastrointestinal research: a systematic review. Gut Microbes. 2024;16(1):2350785. 38725230 PMC11093048 · DOI
  10. [15]Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163(5):1079–94. 26590418 · DOI · Paper page
  11. [16]Nagpal R, Neth BJ, 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;47:529–42. 31477562 PMC6796564 · DOI · Paper page
  12. [17]Pagliai G, Russo E, Niccolai E, Dinu M, Di Pilato V, Magrini A, 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;59:2011–24. 31292752 · DOI
  13. [21]Lee D-C, Dissanayaka T, Burton E, Meyer C, Hunter SW, Suttanon P, et al. Effectiveness of gait aid prescription for improving spatiotemporal gait parameters and associated outcomes in community-dwelling older people: a systematic review. Disability And Rehabil. 2022;44(21):6139–54. 34375545 · DOI
  14. [22]Prasad M. Introduction to the grade tool for rating certainty in evidence and recommendations. Clin Epidemiol and Global Health. 2024;25:101484. · DOI · Paper page
  15. [23]Barber C, Mego M, Sabater C, Vallejo F, Bendezu RA, Masihy M, et al. Differential effects of western and mediterranean-type diets on gut microbiota: a metagenomics and metabolomics approach. Nutrients. 2021;13(8):2638. 34444797 PMC8400818 · DOI
  16. [24]Galié S, García-Gavilán J, Camacho-Barcía L, Atzeni A, Muralidharan J, Papandreou C, et al. Effects of the mediterranean diet or nut consumption on gut microbiota composition and fecal metabolites and their relationship with cardiometabolic risk factors. Mol Nutr Food Res. 2021;65(19):2000982. 34331403 · DOI
  17. [25]Ismael S, Silvestre MP, Vasques M, Araújo JR, Morais J, Duarte MI, et al. A pilot study on the metabolic impact of Mediterranean diet in type 2 diabetes: is gut microbiota the key? Nutrients. 2021;13(4):1228. 33917736 PMC8068165 · DOI
  18. [27]Michalsen A, Riegert M, Lüdtke R, Bäcker M, Langhorst J, Schwickert M, et al. Mediterranean diet or extended fasting’s influence on changing the intestinal microflora, immunoglobulin a secretion and clinical outcome in patients with rheumatoid arthritis and fibromyalgia: an observational study. BMC Complementary And Alternative Med. 2005;5:1–9. PMC1352378 16372904 · DOI
  19. [28]Muralidharan J, Moreno-Indias I, Bulló M, Lopez JV, Corella D, Castañer O, et al. Effect on gut microbiota of a 1-y lifestyle intervention with Mediterranean diet compared with energy-reduced Mediterranean diet and physical activity promotion: PREDIMED-Plus study. The Am J Clin Nutr. 2021;114(3):1148–58. 34020445 PMC8408861 · DOI
  20. [29]Pastor-Ibáñez R, Blanco-Heredia J, Etcheverry F, Sánchez-Palomino S, Díez-Fuertes F, Casas R, et al. Adherence to a supplemented mediterranean diet drives changes in the gut microbiota of HIV-1-infected individuals. Nutrients. 2021;13(4):1141. 33808476 PMC8067262 · DOI
  21. [30]Pisanu S, Palmas V, Madau V, Casula E, Deledda A, Cusano R, et al. Impact of a moderately hypocaloric Mediterranean diet on the gut microbiota composition of Italian obese patients. Nutrients. 2020;12(9):2707. 32899756 PMC7551852 · DOI
  22. [32]Tagliamonte S, Laiola M, Ferracane R, Vitale M, Gallo MA, Meslier V, et al. Mediterranean diet consumption affects the endocannabinoid system in overweight and obese subjects: possible links with gut microbiome, insulin resistance and inflammation. Eur J Nutr. 2021;60:3703–16. 33763720 PMC8437855 · DOI
  23. [33]Vitale M, Giacco R, Laiola M, Della Pepa G, Luongo D, Mangione A, et al. Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: can SCFAs play a role? Clin Nutr. 2021;40(2):428–37. 32698959 · DOI
  24. [34]Haro C, Montes-Borrego M, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, et al. Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population. The J Clin Endocrinol. 2016;101(1):233–42. 26505825 · DOI
  25. [35]Di Iorio BR, Rocchetti MT, De Angelis M, Cosola C, Marzocco S, Di Micco L, et al. Nutritional therapy modulates intestinal microbiota and reduces serum levels of total and free indoxyl sulfate and p-cresyl sulfate in chronic kidney disease (medika study). J Clin Med. 2019;8(9):1424. 31510015 PMC6780815 · DOI
  26. [36]Avelar-Barragan J, Mendez Luque LF, Nguyen J, Nguyen H, Odegaard AO, Fleischman AG, et al. Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention. Mbio. 2023;14(6):e02308–23. 37877698 PMC10746218 · DOI
  27. [37]Choo JM, Murphy KJ, Wade AT, Wang Y, Bracci EL, Davis CR, et al. Interactions between mediterranean diet supplemented with dairy foods and the gut microbiota influence cardiovascular health in an Australian population. Nutrients. 2023;15(16):3645. 37630835 PMC10459086 · DOI
  28. [38]Deledda A, Palmas V, Heidrich V, Fosci M, Lombardo M, Cambarau G, et al. Dynamics of gut microbiota and clinical variables after ketogenic and Mediterranean diets in drug-naïve patients with type 2 diabetes mellitus and obesity. Metabolites. 2022;12(11):1092. 36355175 PMC9693465 · DOI
  29. [39]Haskey N, Estaki M, Ye J, Shim RK, Singh S, Dieleman LA, et al. A Mediterranean diet pattern improves intestinal inflammation concomitant with reshaping of the bacteriome in ulcerative colitis: a randomised controlled trial. J Crohn’s And Colitis. 2023;17(10):1569–78. 37095601 PMC10637046 · DOI
  30. [40]Shoer S, Shilo S, Godneva A, Ben-Yacov O, Rein M, Wolf BC, et al. Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines. Nat Commun. 2023;14(1):5384. 37666816 PMC10477304 · DOI
  31. [41]Staudacher HM, Mahoney S, Canale K, Opie RS, Loughman A, So D, et al. Clinical trial: a Mediterranean diet is feasible and improves gastrointestinal and psychological symptoms in irritable bowel syndrome. Alimentary Pharmacol Ther. 2024;59(4):492–503. 37969059 · DOI
  32. [42]Shin J-H, Jung S, Kim S-A, Kang M-S, Kim M-S, Joung H, et al. Differential effects of typical Korean versus American-style diets on gut microbial composition and metabolic profile in healthy overweight koreans: a randomized crossover trial. Nutrients. 2019;11(10):2450. 31615057 PMC6835328 · DOI
  33. [43]Kushida M, Sugawara S, Asano M, Yamamoto K, Fukuda S, Tsuduki T. Effects of the 1975 Japanese diet on the gut microbiota in younger adults. The J Nutritional Biochem. 2019;64:121–27. 30502656 · DOI
  34. [44]Roager HM, Licht TR, Poulsen SK, Larsen TM, Bahl MI. Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet. Appl Environ Microbiol. 2014;80(3):1142–49. 24296500 PMC3911217 · DOI · Paper page
  35. [45]Bennet SM, Böhn L, Störsrud S, Liljebo T, Collin L, Lindfors P, et al. Multivariate modelling of faecal bacterial profiles of patients with ibs predicts responsiveness to a diet low in FODMAPs. Gut. 2018;67(5):872–81. 28416515 · DOI · Paper page
  36. [46]Cox SR, Lindsay JO, Fromentin S, Stagg AJ, McCarthy NE, Galleron N, et al. Effects of low FODMAP diet on symptoms, fecal microbiome, and markers of inflammation in patients with quiescent inflammatory bowel disease in a randomized trial. Gastroenterology. 2020;158(1):176–88. e7. 31586453 · DOI
  37. [49]Hustoft T, Hausken T, Ystad S, Valeur J, Brokstad K, Hatlebakk J, et al. Effects of varying dietary content of fermentable short-chain carbohydrates on symptoms, fecal microenvironment, and cytokine profiles in patients with irritable bowel syndrome. Neurogastroenterology Motil. 2017;29(4):e12969. 27747984 · DOI
  38. [50]McIntosh K, Reed DE, Schneider T, Dang F, Keshteli AH, De Palma G, et al. FODMAPs alter symptoms and the metabolome of patients with ibs: a randomised controlled trial. Gut. 2016;gutjnl-2015–311339. 26976734
  39. [51]Naseri K, Dabiri H, Rostami-Nejad M, Yadegar A, Houri H, Olfatifar M, et al. Influence of low FODMAP-gluten free diet on gut microbiota alterations and symptom severity in Iranian patients with irritable bowel syndrome. BMC Gastroenterol. 2021;21:1–14. 34261437 PMC8278734 · DOI
  40. [52]Staudacher HM, Lomer MC, Anderson JL, Barrett JS, Muir JG, Irving PM, et al. Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. The J Nutr. 2012;142(8):1510–18. 22739368 · DOI · Paper page
  41. [53]Valdez-Palomares F, Nambo-Venegas R, Uribe-García J, Mendoza-Vargas A, Granados-Portillo O, Meraz-Cruz N, et al. Intestinal microbiota fingerprint in subjects with irritable bowel syndrome responders to a low FODMAP diet. Food Function. 2021;12(7):3206–18. 33877245 · DOI
  42. [54]Valeur J, Småstuen MC, Knudsen T, Lied GA, Røseth AG. Exploring gut microbiota composition as an indicator of clinical response to dietary FODMAP restriction in patients with irritable bowel syndrome. Digestive Dis And Sci. 2018;63:429–36. 29302878 · DOI
  43. [55]Zhang Y, Feng L, Wang X, Fox M, Luo L, Du L, et al. Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet compared with traditional dietary advice for diarrhea-predominant irritable bowel syndrome: a parallel-group, randomized controlled trial with analysis of clinical and microbiological factors associated with patient outcomes. The Am J Clin Nutr. 2021;113(6):1531–45. 33740048 · DOI
  44. [56]Liu Y, Jin D, He T, Liao X, Shao L, Shi L, et al. Effect of the combined intervention of low-FODMAPs diet and probiotics on ibs symptoms in Western China: a randomized controlled trial. Food Sciamp; Nutr. 2024. PMC11167163 38873474
  45. [57]Tunali V, Arslan N, Ermiş BH, Derviş Hakim G, Gündoğdu A, Hora M, et al. A multicenter randomized controlled trial of microbiome-based artificial intelligence-assisted personalized diet vs low-fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet: a novel approach for the management of irritable bowel syndrome. Am J Gastroenterol. 2024;119(9):1901–12. 38717025 PMC11365594 · DOI
  46. [58]Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, et al. Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells. Cell. 2020;181(6):1263–75. e16. 32437658 PMC7293577 · DOI
  47. [59]Gutiérrez-Repiso C, Hernández-García C, García-Almeida JM, Bellido D, Martín-Núñez GM, Sánchez-Alcoholado L, et al. Effect of synbiotic supplementation in a Very-Low-Calorie ketogenic diet on weight loss achievement and gut microbiota: a randomized controlled pilot study. Mol Nutr Food Res. 2019;63(19):1900167. 31298466 · DOI · Paper page
  48. [60]Yuan W, Lu W, Wang H, Wu W, Zhou Q, Chen Y, et al. A multiphase dietetic protocol incorporating an improved ketogenic diet enhances weight loss and alters the gut microbiome of obese people. Int J Food Sci And Nutr. 2022;73(2):238–50. 34353205 · DOI
  49. [61]Hengist A, Davies RG, Walhin J-P, Buniam J, Merrell LH, Rogers L, et al. Ketogenic diet but not free-sugar restriction alters glucose tolerance, lipid metabolism, peripheral tissue phenotype, and gut microbiome: rct. Cell Rep Med. 2024;5(8). PMC11384946 39106867
  50. [62]Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med. 2016;8:1–11. 27102333 PMC4841035 · DOI
  51. [64]Brinkworth GD, Noakes M, Clifton PM, Bird AR. 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(10):1493–502. 19224658 · DOI · Paper page
  52. [65]Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD. Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. The Am J Clin Nutr. 2020;111(6):1127–36. 32186326 PMC7266695 · DOI · Paper page
  53. [66]Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K, Duncan SH, et al. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. The ISME J. 2014;8(11):2218–30. 24763370 PMC4992075 · DOI · Paper page
  54. [68]Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME J. 2011;5(2):220–30. 20686513 PMC3105703 · DOI · Paper page
  55. [69]Johnstone AM, Kelly J, Ryan S, Romero-Gonzalez R, McKinnon H, Fyfe C, et al. Nondigestible carbohydrates affect metabolic health and gut microbiota in overweight adults after weight loss. The J Nutr. 2020;150(7):1859–70. 32510158 · DOI
  56. [70]Dong TS, Luu K, Lagishetty V, Sedighian F, Woo S-L, Dreskin BW, et al. A high protein calorie restriction diet alters the gut microbiome in obesity. Nutrients. 2020;12(10):3221. 33096810 PMC7590138 · DOI
  57. [71]Cuevas-Sierra A, Romo-Hualde A, Aranaz P, Goni L, Cuervo M, Martínez JA, et al. Diet-and sex-related changes of gut microbiota composition and functional profiles after 4 months of weight loss intervention. Eur J Nutr. 2021;60:3279–301. 33591390
  58. [72]Ghanavati M, Nasrollahzadeh J. A calorie-restricted diet enriched with tree nuts and peanuts reduces the expression of CX3CR1 in peripheral blood mononuclear cells in patients with coronary artery disease. Int J Vitamin Nutr Res. 2021. 34794330
  59. [73]Henning SM, Yang J, Woo SL, Lee R-P, Huang J, Rasmusen A, et al. Hass avocado inclusion in a weight-loss diet supported weight loss and altered gut microbiota: a 12-week randomized, parallel-controlled trial. Curr Developments In Nutr. 2019;3(8):nzz068. PMC6658913 31367691 · DOI
  60. [74]Ma Y, Sun Y, Sun L, Liu X, Zeng R, Lin X, et al. Effects of gut microbiota and fatty acid metabolism on dyslipidemia following weight-loss diets in women: results from a randomized controlled trial. Clin Nutr. 2021;40(11):5511–20. 34656033 · DOI
  61. [75]Karbalaiee M, Chiti H, Mousavi SN, Afshar D. Low-carbohydrate hypo calorie diet has a beneficial effect on gut phyla and metabolic markers in healthy women with obesity: a randomized crossover study. Obes Med. 2022;35:100461. · DOI
  62. [76]Li L, Li R, Tian Q, Luo Y, Li R, Lin X, et al. Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: feeding rct. Cell Rep Med. 2024;5(11). PMC11604488 39454570
  63. [77]Diao Z, Molludi J, Latef Fateh H, Moradi S. Comparison of the low-calorie dash diet and a low-calorie diet on serum TMAO concentrations and gut microbiota composition of adults with overweight/obesity: a randomized control trial. Int J Food Sci Nutr. 2024;75(2):207–20. 38149315 · DOI
  64. [78]Fava F, Gitau R, Griffin BA, Gibson G, Tuohy K, Lovegrove J. The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’population. Int J Obes. 2013;37(2):216–23. 22410962 · DOI
  65. [79]Ren M, Zhang H, Qi J, Hu A, Jiang Q, Hou Y, et al. An almond-based low carbohydrate diet improves depression and glycometabolism in patients with type 2 diabetes through modulating gut microbiota and GLP-1: a randomized controlled trial. Nutrients. 2020;12(10):3036. 33022991 PMC7601479 · DOI
  66. [81]Lai S, Molfino A, Testorio M, Perrotta AM, Currado A, Pintus G, et al. Effect of low-protein diet and inulin on microbiota and clinical parameters in patients with chronic kidney disease. Nutrients. 2019;11(12):3006. 31818021 PMC6950025 · DOI
  67. [82]Kelder T, Stroeve J, Bijlsma S, Radonjic M, Roeselers G. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health. nutr & Diabetes. 2014;4(6):e122–e. PMC4079927 24979151 · DOI
  68. [83]Qian L, Huang J, Qin H. Probiotics and dietary intervention modulate the colonic mucosa-associated microbiota in high-fat diet populations. The Turk J Gastroenterol. 2020;31(4):295. 32412900 PMC7236651 · DOI
  69. [84]Fritsch J, Garces L, Quintero MA, Pignac-Kobinger J, Santander AM, Fernández I, et al. Low-fat, high-fiber diet reduces markers of inflammation and dysbiosis and improves quality of life in patients with ulcerative colitis. Clin Gastroenterol And Hepatol. 2021;19(6):1189–99. e30. 32445952 · DOI
  70. [85]Li J, Morrow C, McLain A, Womack ED, Yarar-Fisher C. Effects of a low-carbohydrate, high-protein diet on gut microbiome composition in insulin-resistant individuals with chronic spinal cord injury: preliminary results from a randomized controlled trial. Archiv Phys Med And Rehabil. 2022;103(7):1269–78. 35417758 · DOI
  71. [86]Ferraz-Bannitz R, Beraldo RA, Peluso AA, Dall M, Babaei P, Foglietti RC, et al. Dietary protein restriction improves metabolic dysfunction in patients with metabolic syndrome in a randomized, controlled trial. Nutrients. 2022;14(13):2670. 35807851 PMC9268415 · DOI
  72. [87]Wan Y, Wang F, Yuan J, Li J, Jiang D, Zhang J, 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(8):1417–29. 30782617 · DOI · Paper page
  73. [88]David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63. 24336217 PMC3957428 · DOI · Paper page
  74. [89]Kohnert E, Kreutz C, Binder N, Hannibal L, Gorkiewicz G, Müller A, et al. Changes in gut microbiota after a four-week intervention with vegan vs. meat-rich diets in healthy participants: a randomized controlled trial. Microorganisms. 2021;9(4):727. 33807447 PMC8066554 · DOI
  75. [90]Kahleova H, Rembert E, Alwarith J, Yonas WN, Tura A, Holubkov R, et al. Effects of a low-fat vegan diet on gut microbiota in overweight individuals and relationships with body weight, body composition, and insulin sensitivity. A randomized clinical trial. Nutrients. 2020;12(10):2917. 32987642 PMC7598634 · DOI
  76. [91]Kim MS, Hwang SS, Park EJ, Bae JW. Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation. Environ Microbiol Rep. 2013;5(5):765–75. 24115628 · DOI · Paper page
  77. [92]Zhang C, Björkman A, Cai K, Liu G, Wang C, Li Y, et al. Impact of a 3-months vegetarian diet on the gut microbiota and immune repertoire. Front Immunol. 2018;9:908. 29755475 PMC5934425 · DOI · Paper page
  78. [93]Wang Y, Lindemann SR, Cross T-W, Tang M, Clark CM, Campbell WW. Effects of adding lean red meat to a US-style healthy vegetarian dietary pattern on gut microbiota and cardiovascular risk factors in young adults: a crossover randomized controlled trial. The J Nutr. 2023;153(5):1439–52. 36921804 · DOI
  79. [94]Berding K, Bastiaanssen TF, Moloney GM, Boscaini S, Strain CR, Anesi A, et al. Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population. Mol Psychiatry. 2023;28(2):601–10. 36289300 PMC9908549 · DOI · Paper page
  80. [95]Bo C D, Bernardi S, Cherubini A, Porrini M, Gargari G, Hidalgo-Liberona N, et al. A polyphenol-rich dietary pattern improves intestinal permeability, evaluated as serum zonulin levels, in older subjects: the MaPLE randomised controlled trial. Clin Nutr. 2021;40(5):3006–18. 33388204 · DOI · Paper page
  81. [96]Cai X, Wang L, Wang X, Liu S. Effect of high dietary fiber low glycemic index diet on intestinal flora, blood glucose and inflammatory response in T2DM patients. Biomed Res. 2017;28:9371–75.
  82. [97]Lin Z, Zhang X, Wu M, Ming Y, Wang X, Li H, et al. High-fiber diet and rope-skipping benefit cardiometabolic health and modulate gut microbiota in young adults: a randomized controlled trial. Food Res Int. 2023;173:113421. 37803759 · DOI
  83. [98]Ryu Y-K, Chang D-H, Park H-Y, Go J, Maeng S-Y, Hwang DY, et al. Agathobaculum butyriciproducens shows neuroprotective effects in a 6-OHDA-induced mouse model of Parkinson’s disease. J Microbiol And Biotechnol. 2022;32(9):1168. 36168204 PMC9628974 · DOI
  84. [99]Go J, Chang D-H, Ryu Y-K, Park H-Y, Lee I-B, Noh J-R, et al. Human gut microbiota agathobaculum butyriciproducens improves cognitive impairment in LPS-induced and APP/PS1 mouse models of Alzheimer’s disease. nutr Res. 2021;86:96–108. 33551257 · DOI
  85. [100]Tian B, Yao J-H, Lin X, Lv W-Q, Jiang L-D, Wang Z-Q, et al. Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women. Front Microbiol. 2022;13:957885. 36051762 PMC9425034 · DOI
  86. [101]Lenoir M, Martín R, Torres-Maravilla E, Chadi S, González-Dávila P, Sokol H, et al. Butyrate mediates anti-inflammatory effects of faecalibacterium prausnitzii in intestinal epithelial cells through Dact3. Gut Microbes. 2020;12(1):1826748. 33054518 PMC7567499 · DOI · Paper page
  87. [102]Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. The ISME J. 2017;11(4):841–52. 28045459 PMC5364359 · DOI
  88. [103]Dillon S, Lee E, Kotter C, Austin G, Gianella S, Siewe B, et al. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection. Mucosal Immunol. 2016;9(1):24–37. 25921339 PMC4626441 · DOI
  89. [104]Rodrigues VF, Elias-Oliveira J, Pereira ÍS, Pereira JA, Barbosa SC, Machado MSG, et al. Akkermansia muciniphila and gut immune system: a good friendship that attenuates inflammatory bowel disease, obesity, and diabetes. Front Immunol. 2022;13:934695. 35874661 PMC9300896 · DOI
  90. [105]Xu Y, Duan J, Wang D, Liu J, Chen X, Qin X-Y, et al. Akkermansia muciniphila alleviates persistent inflammation, immunosuppression, and catabolism syndrome in mice. Metabolites. 2023;13(2):194. 36837813 PMC9961567 · DOI
  91. [107]Wang K, Liao M, Zhou N, Bao L, Ma K, Zheng Z, et al. Parabacteroides distasonis alleviates obesity and metabolic dysfunctions via production of succinate and secondary bile acids. Cell Rep. 2019;26(1):222–35. e5. 30605678 · DOI
  92. [108]Feng Z, Long W, Hao B, Ding D, Ma X, Zhao L, et al. A human stool-derived bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice. Gut Pathog. 2017;9:1–10. 29090023 PMC5657053 · DOI
  93. [109]Natividad JM, Lamas B, Pham HP, Michel M-L, Rainteau D, Bridonneau C, et al. Bilophila wadsworthia aggravates high fat diet induced metabolic dysfunctions in mice. Nat Commun. 2018;9(1):2802. 30022049 PMC6052103 · DOI
  94. [111]Suarez G, Liu B, Herzog J, Sartor R. Pro-inflammatory molecular and inflammatory mechanisms of sulfur metabolism in IBD-relevant clostridia species. Gastroenterology. 2021;160(3):S41. · DOI
  95. [112]Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, et al. Ethanol-producing enterocloster bolteae is enriched in chronic hepatitis B-associated gut dysbiosis: a case–control culturomics study. Microorganisms. 2023;11(10):2437. 37894093 PMC10608849 · DOI
  96. [113]Kleessen B, Kroesen A, Buhr H, Blaut M. Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand J Gastroenterol. 2002;37(9):1034–41. 12374228 · DOI
  97. [114]Hakansson A, Molin G. Gut microbiota and inflammation. Nutrients. 2011;3(6):637–82. 22254115 PMC3257638 · DOI
  98. [115]Abarca J, Awada B, Itkin B, Milupi M. Poly-microbial Clostridium cadaveris bacteremia in an immune-compromised patient. Oxford Med Case Rep. 2023;2023(1):omac146. PMC9853932 36694598 · DOI
  99. [116]Hu C, Niu X, Chen S, Wen J, Bao M, Mohyuddin SG, et al. A comprehensive analysis of the colonic flora diversity, short chain fatty acid metabolism, transcripts, and biochemical indexes in heat-stressed pigs. Front Immunol. 2021;12:717723. 34745096 PMC8567839 · DOI
  100. [117]Guo P, Zhang K, Ma X, He P. Clostridium species as probiotics: potentials and challenges. J Anim Sci Biotechnol. 2020;11:1–10. 32099648 PMC7031906 · DOI
  101. [118]Soman R, Eashwernath R. Bacteremia due to streptococcus gallolyticus: a name with an ominous significance? Indian J Crit Care Med: Peer-Reviewed, Off Publ Of Indian Soc Of Crit Care Med. 2020;24(10):901. PMC7689113 33281311 · DOI
  102. [119]Roux E, Nicolas A, Valence F, Siekaniec G, Chuat V, Nicolas J, et al. The genomic basis of the streptococcus thermophilus health-promoting properties. BMC Genomics. 2022;23(1):210. 35291951 PMC8925076 · DOI
  103. [120]Raabe VN, Shane AL. Group B streptococcus (streptococcus agalactiae). Microbiol Spectr. 2019;7(2):gpp3–0007–2018. 10.1128/microbiolspec. PMC6432937 30900541 · DOI
  104. [121]Schaus SR, Periera GV, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, et al. Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by bacteroides thetaiotaomicron. bioRxiv. 2024. PMC11323728 38975756
  105. [122]Wiredu Ocansey DK, Hang S, Yuan X, Qian H, Zhou M, Valerie Olovo C, et al. The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease. Gut Microbes. 2023;15(1):2176118. 36794838 PMC9980661 · DOI
  106. [124]Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Proceedings of the National Academy of Sciences. 2019:12672–77;116(26). PMC6601261 31182571
  107. [125]Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. The ISME J. 2012;6(8):1535–43. 22343308 PMC3400402 · DOI · Paper page
  108. [126]Tb VDH, Van LJ, Kappen JH, Van Hagen PM, De Zoete MR, Van Muijlwijk GH, et al. Behcet’s disease under microbiotic surveillance? A combined analysis of two cohorts of Behcet’s disease patients. Front Immunol. 2020;11:1192. 32595645 PMC7303268 · DOI
  109. [127]Park J, Lee J, Yeom Z, Heo D, Lim Y-H. Neuroprotective effect of ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals. Sci Rep. 2017;7(1):14520. 29109537 PMC5674049 · DOI
  110. [128]Wegmann U, Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ. Complete genome of a new F irmicutes species belonging to the dominant human colonic microbiota (‘R uminococcus bicirculans’) reveals two chromosomes and a selective capacity to utilize plant glucans. Environ Microbiol. 2014;16(9):2879–90. 23919528 · DOI
  111. [129]Du X, Li Q, Tang Z, Yan L, Zhang L, Zheng Q, et al. Alterations of the gut microbiome and fecal metabolome in colorectal cancer: implication of intestinal metabolism for tumorigenesis. Front Physiol. 2022;13:854545. 35600308 PMC9116530 · DOI
  112. [130]Upadhyaya B, McCormack L, Fardin-Kia AR, Juenemann R, Nichenametla S, Clapper J, et al. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions. Sci Rep. 2016;6(1):28797. 27356770 PMC4928084 · DOI
  113. [131]Dan Z, Mao X, Liu Q, Guo M, Zhuang Y, Liu Z, et al. Altered gut microbial profile is associated with abnormal metabolism activity of autism spectrum disorder. Gut Microbes. 2020;11(5):1246–67. 32312186 PMC7524265 · DOI · Paper page
  114. [132]Zhang X, Zhang D, Jia H, Feng Q, Wang D, Liang D, et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat Med. 2015;21(8):895–905. 26214836 · DOI · Paper page
  115. [133]Akhtar M, Chen Y, Ma Z, Zhang X, Shi D, Khan JA, et al. Gut microbiota-derived short chain fatty acids are potential mediators in gut inflammation. Anim nutr. 2022;8:350–60. 35510031 PMC9040132 · DOI
  116. [134]Yang R, Shan S, Shi J, Li H, An N, Li S, et al. Coprococcus eutactus, a potent probiotic, alleviates colitis via acetate-mediated IgA response and microbiota restoration. J Agric And Food Chem. 2023;71(7):3273–84. 36786768 · DOI
  117. [135]Ogita T, Yamamoto Y, Mikami A, Shigemori S, Sato T, Shimosato T. Oral administration of flavonifractor plautii strongly suppresses Th2 immune responses in mice. Front Immunol. 2020;11:379. 32184789 PMC7058663 · DOI
  118. [136]Mikami A, Ogita T, Namai F, Shigemori S, Sato T, Shimosato T. Oral administration of flavonifractor plautii, a bacteria increased with green tea consumption, promotes recovery from acute colitis in mice via suppression of IL-17. Front Nutr. 2021;7:610946. 33614691 PMC7890079 · DOI
  119. [137]Luo S, Zhao Y, Zhu S, Liu L, Cheng K, Ye B, et al. Flavonifractor plautii protects against elevated arterial stiffness. Circ Res. 2023;132(2):167–81. 36575982 · DOI
  120. [138]Naicker M, Dessai F, Singh R, Mitchev N, Tinarwo P, Abbai NS. ‘Mycoplasma hominis does not share common risk factors with other genital pathogens’: findings from a South African pregnant cohort. South Afr J Infect Dis. 2021;36(1). PMC8377787 34485492
  121. [139]Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and their health-promoting effects. Bugs As Drugs: Ther Microbes For The Prev And Treat Of Disease. 2018;73–98. PMC11687494 28643627
  122. [140]Yao S, Zhao Z, Wang W, Liu X. Bifidobacterium longum: protection against inflammatory bowel disease. J Immunol Res. 2021; 2021. PMC8324359 34337079
  123. [141]T-B B, Wen J, Y-C Z, S-J T, X-Y Z, D-H W. Bifidobacterium pseudolongum reduces triglycerides by modulating gut microbiota in mice fed high-fat food. The J Steroid Biochem And Mol Biol. 2020;198:105602. 31987886 · DOI
  124. [142]Guo W, Mao B, Cui S, Tang X, Zhang Q, Zhao J, et al. Protective effects of a novel probiotic bifidobacterium pseudolongum on the intestinal barrier of colitis mice via modulating the Pparγ/STAT3 pathway and intestinal microbiota. Foods. 2022;11(11):1551. 35681301 PMC9180506 · DOI
  125. [143]Percival SL, Williams DW. Chapter Six - Escherichia coli. In: Percival S, Yates M, Williams D, Chalmers R, Gray N, editors. Microbiology of waterborne diseases. Second. London: Academic Press; 2014. p. 89–117.
  126. [145]Choi SI, Kim N, Nam RH, Jang JY, Kim EH, Ha S, et al. The protective effect of Roseburia faecis against repeated water avoidance stress-induced irritable bowel syndrome in a wister rat Model. J Cancer Prev. 2023;28(3):93. 37830115 PMC10564633 · DOI
  127. [146]La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, et al. The human gut firmicute roseburia intestinalis is a primary degrader of dietary β-mannans. Nat Commun. 2019;10(1):905. 30796211 PMC6385246 · DOI
  128. [147]Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol. 2018;11:1–10. 29285689 · DOI
  129. [149]Ariefdjohan MW, Dilk A, Brown-Esters ON, Savaiano DA. Chapter 37 - intestinal microbiota and Diet in health. In: Coulston A, Boushey C, Ferruzzi M, Delahanty L, editors. Nutrition in the prevention and treatment of disease. Fourth. Academic Press; 2017. p. 811–34.
  130. [150]Fernández-Veledo S, Vendrell J. Gut microbiota-derived succinate: friend or foe in human metabolic diseases? Rev In Endocr And Metabolic Disord. 2019;20(4):439–47. PMC6938788 31654259 · DOI
  131. [151]Ijaz UZ, Quince C, Hanske L, Loman N, Calus ST, Bertz M, et al. The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred. PLoS One. 2017;12(2):e0172605. 28222161 PMC5319678 · DOI
  132. [152]Shkoporov AN, Chaplin AV, Shcherbakova VA, Suzina NE, Kafarskaia LI, Bozhenko VK, et al. Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces. Int J Systematic And Evol Microbiol. 2016;66(8):3041–49. 27154556 · DOI
  133. [153]Zhou X, Baumann R, Gao X, Mendoza M, Singh S, Sand IK, et al. Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course. Cell. 2022;185(19):3467–86. e16. 36113426 PMC10143502 · DOI
  134. [154]Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, et al. Analysis of 1321 eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol. 2020;21:1–27. PMC7278147 32513234 · DOI · Paper page
  135. [155]Purohit A, Kandiyal B, Kumar S, Pragasam AK, Kamboj P, Talukdar D, et al. Collinsella aerofaciens linked with increased ethanol production and liver inflammation contribute to the pathophysiology of NAFLD. Iscience. 2024;27(2). PMC10837629 38313048
  136. [156]Zhao T, Wei Y, Zhu Y, Xie Z, Hai Q, Li Z, et al. Gut microbiota and rheumatoid arthritis: from pathogenesis to novel therapeutic opportunities. Front Immunol. 2022;13:1007165. 36159786 PMC9499173 · DOI
  137. [157]Forman-Ankjær B, Hvid-Jensen F, Kobel CM, Greve T. First case of bacteraemia caused by Dielma fastidiosa in a patient hospitalized with diverticulitis. APMIS. 2024;132(2):130–33. 38095319 · DOI
  138. [158]Miyake S, Ding Y, Soh M, Low A, Seedorf H. Cultivation and description of duncaniella dubosii sp. nov., duncaniella freteri sp. nov. And emended description of the species duncaniella muris. Int J Systematic And Evol Microbiol. 2020;70(5):3105–10. 32250242 · DOI
  139. [159]Parker BJ, Wearsch PA, Veloo AC, Rodriguez-Palacios A. The genus alistipes: gut bacteria with emerging implications to inflammation, cancer, and mental health. Front Immunol. 2020;11:906. 32582143 PMC7296073 · DOI
  140. [160]Verbarg S, Rheims H, Emus S, Frühling A, Kroppenstedt RM, Stackebrandt E, et al. Erysipelothrix inopinata sp. nov., isolated in the course of sterile filtration of vegetable peptone broth, and description of erysipelotrichaceae fam. nov. Int J Systematic and Evol Microbiol. 2004;54(1):221–25. 14742484 · DOI
  141. [161]Wang H-T, Hsu J-T. Optimal protease production condition for prevotella ruminicola 23 and characterization of its extracellular crude protease. Anaerobe. 2005;11(3):155–62. 16701546 · DOI
  142. [162]Zhou B, Dong C, Zhao B, Lin K, Tian Y, Zhang R, et al. Bacteroides fragilis participates in the therapeutic effect of methotrexate on arthritis through metabolite regulation. Front Microbiol. 2022;13:1015130. 36590441 PMC9798205 · DOI
  143. [164]Yan Y, Lei Y, Qu Y, Fan Z, Zhang T, Xu Y, et al. Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments. Npj Biofilms And Microbiomes. 2023;9(1):56. 37580334 PMC10425470 · DOI
  144. [165]Dai W, Zhang J, Chen L, Yu J, Zhang J, Yin H, et al. Discovery of bacteroides uniformis F18-22 as a safe and novel Probiotic bacterium for the treatment of ulcerative colitis from the healthy human colon. Int J Mol Sci. 2023;24(19):14669. 37834117 PMC10572632 · DOI
  145. [166]Asgharian M, Gholizadeh P, Kafil HS, Ghojazadeh M, Samadi A, Soleymani J, et al. Correlation of inflammatory biomarkers with the diversity of bacteroidaceae, bifidobacteriaceae, prevotellaceae and lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease. Adv Med Sci. 2022;67(2):304–10. 35994929 · DOI
  146. [167]Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev. 2007;20(4):593–621. 17934076 PMC2176045 · DOI
  147. [168]Niu Y, Hu X, Song Y, Wang C, Luo P, Ni S, et al. Blautia coccoides is a newly identified bacterium increased by leucine deprivation and has a novel function in improving metabolic disorders. Advanced science. 2024;2309255. PMC11095201 38429906
  148. [169]Rais A, Chand P, Malik M, Prasad T. Chapter 5 - human microbiota: role in cancer progression and therapy. In: Das A, editor. Microbial crosstalk with immune system. Academic Press; 2022. p. 145–75.
  149. [170]Lee C, Koh SJ, Hong HT, Park H, Im JP, Kim JS. P926 blautia obeum aggravates colitis in a murine Model [Abstract]. J Crohn’s And Colitis. 2023;17(Supplement_1):i1035–i. · DOI
  150. [171]Hosomi K, Saito M, Park J, Murakami H, Shibata N, Ando M, et al. Oral administration of blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota. Nat Commun. 2022;13(1):4477. 35982037 PMC9388534 · DOI
  151. [172]Arasu MV, Na A-D, Ilavenil S, Choi KC, Srigopalram S. In vitro importance of probiotic lactobacillus plantarum related to medical field. Saudi J Biol Sci. 2016;23(1):S6–10. 26858567 PMC4705246 · DOI
  152. [173]Schaffer JN, Pearson MM. Proteus mirabilis and urinary tract infections. Urinary tract infections. Mol Pathogen And Clin Manag. 2017;383–433.
  153. [174]Companys J, Gosalbes MJ, Pla-Pagà L, Calderón-Pérez L, Llauradó E, Pedret A, et al. Gut microbiota profile and its association with clinical variables and dietary intake in overweight/obese and lean subjects: a cross-sectional study. Nutrients. 2021;13(6):2032. 34199239 PMC8231825 · DOI
  154. [175]Liu W, Zheng C, Li Q, Xu T, Cao W, Shi M, et al. Preoperative oral probiotics relieve insulin resistance and gut dysbacteriosis in patients with gastric cancer after gastrectomy. J Funct Foods. 2023;101:105426. · DOI
  155. [176]Ramirez Garcia A, Greppi A, Constancias F, Ruscheweyh H-J, Gasser J, Hurley K, et al. Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota. Front Microbiomes. 2023;2:1194516. PMC12993610 41853383 · DOI
  156. [177]Cobo F, Pérez-Carrasco V, García-Salcedo JA, Navarro-Marí JM. Bacteremia caused by Veillonella dispar in an oncological patient. Anaerobe. 2020;66:102285. 33075505 PMC7563575 · DOI
  157. [178]Abdelsalam NA, Hegazy SM, Aziz RK. The curious case of prevotella copri. Gut Microbes. 2023;15(2):2249152. 37655441 PMC10478744 · DOI
  158. [179]Higuchi R, Goto T, Hirotsu Y, Otake S, Oyama T, Amemiya K, et al. Streptococcus australis and ralstonia pickettii as Major microbiota in Mesotheliomas. J Personalized Med. 2021;11(4):297. PMC8070724 33919754 · DOI
  159. [180]Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus eubacterium and their various contributions to gut health. Gut Microbes. 2020;12(1):1802866. 32835590 PMC7524325 · DOI
  160. [181]Toya T, Corban MT, Marrietta E, Horwath IE, Lerman LO, Murray JA, et al. Coronary artery disease is associated with an altered gut microbiome composition. PLoS One. 2020;15(1):e0227147. 31995569 PMC6988937 · DOI
  161. [182]Delday M, Mulder I, Logan ET, Grant G. Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s disease. Inflamm Bowel Dis. 2019;25(1):85–96. 30215718 PMC6290787 · DOI · Paper page
  162. [183]Jiang S, Shi D, Bai L, Niu T, Kang R, Liu Y. Inhibition of interleukin-6 trans-signaling improves survival and prevents cognitive impairment in a mouse model of sepsis. Int Immunopharmacol. 2023;119:110169. 37058750 · DOI
  163. [184]Xu X, Luo A, Lu X, Liu M, Wang H, Song H, et al. P-hydroxybenzoic acid alleviates inflammatory responses and intestinal mucosal damage in DSS-induced colitis by activating ERβ signaling. J Funct Foods. 2021;87:104835. · DOI
  164. [185]Sieber M, Hegel J. Azelaic acid: properties and mode of action. Skin Pharmacol And Physiol. 2013;27(Suppl. 1):9–17. 24280644 · DOI
  165. [186]Branco ACCC, Yoshikawa FSY, Pietrobon AJ, Sato MN. Role of histamine in modulating the immune response and inflammation. Mediators Of Inflammation. 2018; 2018. PMC6129797 30224900
  166. [187]Summerton CB, Longlands MG, Wiener K, Shreeve DR. Faecal calprotectin: a marker of inflammation throughout the intestinal tract. Eur J Gastroenterol Hepatol. 2002;14(8):841–45. 12172403 · DOI
  167. [188]Moriki D, Koumpagioti D, Francino MP, Rufián-Henares JÁ, Kalogiannis M, Priftis KN, et al. How different are the influences of Mediterranean and Japanese diets on the gut microbiome? Endocr, Metabolic & Immune Disord-Drug Targets. 2024;24(15):1733–45. 38243975 · DOI
  168. [189]Dy K. Diet in Korea. In: Meiselman H, editor. Handbook of eating and drinking: interdisciplinary perspectives. Cham: Springer International Publishing; 2020. p. 1–32.
  169. [190]Gill P, Van Zelm M, Muir J, Gibson P. Short chain fatty acids as potential therapeutic agents in human gastrointestinal and inflammatory disorders. Alimentary Pharmacol Ther. 2018;48(1):15–34. 29722430 · DOI · Paper page
  170. [192]Rahman MN, Barua N, Tin MC, Dharmaratne P, Wong SH, Ip M. The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes. Gut Microbes. 2024;16(1):2356279. 38778521 PMC11123511 · DOI
  171. [193]Kim SH, Kim MS, Lee MS, Park YS, Lee HJ, S-A K, et al. Korean diet: characteristics and historical background. J Ethnic Foods. 2016;3(1):26–31. · DOI
  172. [194]Murooka Y, Yamshita M. Traditional healthful fermented products of Japan. J Ind Microbiol and Biotechnol. 2008;35(8):791. 18461373 · DOI
  173. [195]Shah SH, Svetkey LP, Newgard CB. Branching out for detection of type 2 diabetes. Cell Metab. 2011;13(5):491–92. 21531330 · DOI
  174. [196]Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, et al. Origins and evolution of the Western diet: health implications for the 21st century1, 2. The Am J Clin Nutr. 2005;81(2):341–54. 15699220 · DOI · Paper page
  175. [197]Nishitani S, Fukuhara A, Tomita I, Kume S, Shin J, Okuno Y, et al. Ketone body 3-hydroxybutyrate enhances adipocyte function. Sci Rep. 2022;12(1):10080. 35710581 PMC9203800 · DOI
  176. [198]Qin F, Li J, Mao T, Feng S, Li J, Lai M. 2 hydroxybutyric acid-producing bacteria in gut microbiome and fusobacterium nucleatum regulates 2 hydroxybutyric acid level in vivo. Metabolites. 2023;13(3):451. 36984891 PMC10059959 · DOI
  177. [199]Kim DH, Gim J-A, Yoon D, Kim S, Kim H-S. Metabolomics and mitochondrial dysfunction in Alzheimer’s disease. Genes Genomics. 2017;39:295–300. · DOI
  178. [201]Liu J, Chey WD, Haller E, Eswaran S. Low-FODMAP diet for irritable bowel syndrome: what we know and what we have yet to learn. Annu Rev Med. 2020;71(1):303–14. 31986083 · DOI
  179. [202]Sultan N, Varney JE, Halmos EP, Biesiekierski JR, Yao CK, Muir JG, et al. How to implement the 3-phase FODMAP diet into gastroenterological practice. J Neurogastroenterology And Motil. 2022;28(3):343. PMC9274476 35799231 · DOI
  180. [203]Paoli A, Rubini A, Volek J, Grimaldi K. Beyond weight loss: a review of the therapeutic uses of very-low-carbohydrate (ketogenic) diets. Eur J Clin Nutr. 2013;67(8):789–96. 23801097 PMC3826507 · DOI · Paper page
  181. [204]Staudacher HM, Gibson PR. How healthy is a gluten-free diet? Br J Nutr. 2015;114(10):1539–41. 26370139 · DOI
  182. [205]O’leary C, Wieneke P, Buckley S, O’regan P, Cronin CC, Quigley EM, et al. Celiac disease and irritable bowel-type symptoms. Off J Am Coll Gastroenterol| ACG. 2002;97(6):1463–67. 12094866 · DOI
  183. [206]Ng QX, Soh AYS, Loke W, Lim DY, Yeo W-S. The role of inflammation in irritable bowel syndrome (ibs). J Inflammation Res. 2018;345–49. PMC6159811 30288077
  184. [207]Sowah SA, Riedl L, Damms-Machado A, Johnson TS, Schübel R, Graf M, et al. Effects of weight-loss interventions on short-chain fatty acid concentrations in blood and feces of adults: a systematic review. Adv Nutr. 2019;10(4):673–84. 31075175 PMC6628843 · DOI
  185. [208]Heimann E, Nyman M, Pålbrink A-K, Lindkvist-Petersson K, Degerman E. Branched short-chain fatty acids modulate glucose and lipid metabolism in primary adipocytes. Adipocyte. 2016;5(4):359–68. 27994949 PMC5160390 · DOI
  186. [209]Liu Z, Que S, Xu J, Peng T. Alanine aminotransferase-old biomarker and new concept: a review. Int J Med Sci. 2014;11(9):925. 25013373 PMC4081315 · DOI
  187. [211]McCoin CS, Knotts TA, Adams SH. Acylcarnitines—old actors auditioning for new roles in metabolic physiology. Nat Rev Endocrinol. 2015;11(10):617–25. 26303601 PMC4966159 · DOI
  188. [212]Hu Y, Zhang L, Wen R, Chen Q, Kong B. Role of lactic acid bacteria in flavor development in traditional Chinese fermented foods: a review. Crit Rev Food Sci Nutr. 2022;62(10):2741–55. 33377402 · DOI
  189. [213]Hahn D, Hodson EM, Fouque D. Low protein diets for non-diabetic adults with chronic kidney disease. Cochrane Database Of Systematic Rev. 2018(10). PMC6517211 30284724
  190. [214]Lin X, Liang W, Li L, Xiong Q, He S, Zhao J, et al. The accumulation of gut microbiome–derived indoxyl sulfate and P-Cresyl sulfate in patients with end-stage renal disease. J Renal Nutr. 2022;32(5):578–86. 34736844 · DOI
  191. [215]Xuan W, Ou Y, Chen W, Huang L, Wen C, Huang G, et al. Faecalibacterium prausnitzii improves lipid metabolism disorder and insulin Resistance in type 2 diabetic mice. Br J Biomed Sci. 2023;80:10794. 37025162 PMC10070466 · DOI
  192. [216]Facchin S, Bertin L, Bonazzi E, Lorenzon G, De Barba C, Barberio B, et al. Short-chain fatty acids and human health: from metabolic pathways to current therapeutic implications. Life. 2024;14(5):559. 38792581 PMC11122327 · DOI
  193. [217]Den Besten G, Van Eunen K, Groen AK, Venema K, Reijngoud D-J, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54(9):2325–40. 23821742 PMC3735932 · DOI · Paper page
  194. [218]Lyons TJ, Basu A. Biomarkers in diabetes: hemoglobin A1c, vascular and tissue markers. Transl Res. 2012;159(4):303–12. 22424433 PMC3339236 · DOI
  195. [219]Neufingerl N, Eilander A. Nutrient intake and status in adults consuming plant-based diets compared to meat-eaters: a systematic review. Nutrients. 2021;14(1):29. 35010904 PMC8746448 · DOI
  196. [220]Goff HD, Repin N, Fabek H, El Khoury D, Gidley MJ. Dietary fibre for glycaemia control: towards a mechanistic understanding. Bioactive carbohydrates and dietary fibre. 2018;14:39–53.
  197. [221]Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, et al. Expert consensus document: the International Scientific association for Probiotics and prebiotics (isapp) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491–502. 28611480 · DOI · Paper page
  198. [222]Stone TW. Kynurenic acid antagonists and kynurenine pathway inhibitors. Expert Opin On Investigational Drugs. 2001;10(4):633–45. 11281814 · DOI · Paper page
  199. [223]Qi Y, Goel R, Kim S, Richards EM, Carter CS, Pepine CJ, et al. Intestinal permeability biomarker zonulin is elevated in healthy aging. J Am Med Directors Assoc. 2017;18(9):. e810. 1–. 4. PMC5581307 28676292 · DOI · Paper page
  200. [224]Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, et al. Association of dietary fibre intake and gut microbiota in adults. Br J nutr. 2018;120(9):1014–22. 30355393 PMC8451428 · DOI · Paper page

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Authors
Aslam, H., Trakman, G., Dissanayake, T., Todd, E., Harrison, P., Alby, C., Jabeen, T., Gamage, E., Travica, N., Marshall, S., Ruusunen, A., Rocks, T., Marx, W., Berk, M., O’Neil, A., McGuinness, A. J., Jennings, L., Jacka, F. N., & Dawson, S. L.
Affiliations
  • Barwon Health (AU)
  • La Trobe University (AU)
  • Deakin University (AU)
Corresponding author
Dawson, Samantha L.
ORCID
Venue
Journal of Translational Medicine
Publisher
Springer Science and Business Media LLC
Published
2026-01-07
Volume
24
Issue
1
Pages
39-39
ISSN
1479-5876 (ISSN-L)
DOI
10.1186/s12967-025-07428-9
PMC
PMC12781466
OpenAlex
W7118544044
Cited by
30
References
23
Citations by year
2026: 30
FWCI
20.10
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Translational Medicine (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • UEF eRepo (University of Eastern Finland) (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Deakin University (1194982)
  • Western Alliance Health Research
  • National Health and Medical Research Council (1194982, 2008971)
  • Medical Research Future Fund (2025947)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Keywords
gut microbiota, dietary intervention, Mediterranean diet, Western diet, FODMAP diet, ketogenic diet, gluten-free diet, caloric restriction, plant-based diet, short-chain fatty acids, lactic acid bacteria, inflammatory markers, gut microbiota diversity, dietary fiber, polyphenols, animal-based diet
MeSH terms
Gastrointestinal Microbiome, Clinical Trials as Topic, Diet, Humans, Biomarkers

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