{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T23:56:36Z","timestamp":1787874996075,"version":"build-2784847793"},"reference-count":59,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,3,21]],"date-time":"2025-03-21T00:00:00Z","timestamp":1742515200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Neurosci."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Gastrointestinal problems including vomiting, reflux, flatulence, diarrhea, constipation and colic are common comorbidities in fragile X syndrome. There is accumulating evidence suggesting that leaky gut syndrome causes neurological phenotypes. Although fragile X messenger ribonucleoprotein is ubiquitously expressed, there is a dearth of knowledge regarding its role outside of the brain including effects on gut dysfunction in fragile X. The aim of this study was to generate novel data on gastrointestinal barrier function and the gut microbiome in response to <jats:italic>Fmr1<\/jats:italic> genotype, sex and diet in mice.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p><jats:italic>Fmr1<jats:sup>KO<\/jats:sup><\/jats:italic> male mice and littermate controls in an FVB background were maintained on two purified ingredient diets (AIN-93G with casein protein versus soy protein isolate) versus two standard chows (Teklad 2019 with wheat, corn and yeast protein versus Purina 5015 with wheat, soy, corn, yeast and whey protein sources). Gut permeability was quantified by FITC-dextran levels in blood plasma. The cecal microbiome was identified by 16S rRNA sequencing. In addition, gut permeability was tested in <jats:italic>Fmr1<jats:sup>KO<\/jats:sup><\/jats:italic> mice in the C57BL\/6\u202fJ background maintained on casein- and soy protein isolate-based AIN-93G versus Teklad 2019.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Knockout of the <jats:italic>Fmr1<\/jats:italic> gene in FVB mice did not affect gut permeability. Soy protein isolate-based AIN-93G increased gut permeability. Beta-diversity of the cecal microbiome was significantly altered as a function of the four test diets. <jats:italic>Akkermansia_muciniphila<\/jats:italic> was increased in <jats:italic>Fmr1<jats:sup>KO<\/jats:sup><\/jats:italic> mice fed AIN-93G while unnamed species within the genus <jats:italic>Anaerovorax<\/jats:italic> and family Ruminococcaceae were increased and the order Clostridales decreased in <jats:italic>Fmr1<jats:sup>KO<\/jats:sup><\/jats:italic> mice fed AIN-93G\/soy. <jats:italic>Fmr1<jats:sup>KO<\/jats:sup><\/jats:italic> mice in the C57BL\/6\u202fJ background exhibited increased gut permeability in response to soy protein.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>These findings regarding the effects of diet on gut permeability and the microbiome have important implications for experimental design. Single-source diets are ubiquitously used to maintain laboratory animals for medical research and feed details are frequently not reported in publications. Diet\/phenotype interactions could have a large impact on inter-laboratory replicability in premedical research. For infants with fragile X, early-life diet could impact the severity of disease outcomes.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fnmol.2025.1520211","type":"journal-article","created":{"date-parts":[[2025,3,21]],"date-time":"2025-03-21T09:58:02Z","timestamp":1742551082000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Soy-based purified ingredient diet affects mouse gut permeability and the microbiome in fragile X mice"],"prefix":"10.3389","volume":"18","author":[{"given":"Cara J.","family":"Westmark","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,3,21]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1016\/j.cgh.2018.09.017","article-title":"Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians","volume":"17","author":"Allaband","year":"2019","journal-title":"Clin. 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J."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/s40168-021-01162-2","article-title":"Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome","volume":"9","author":"Barlow","year":"2021","journal-title":"Microbiome"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1016\/j.tins.2004.04.009","article-title":"The mGluR theory of fragile X mental retardation","volume":"27","author":"Bear","year":"2004","journal-title":"Trends Neurosci."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. 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Nutr."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/j.tig.2017.07.008","article-title":"Multifarious functions of the fragile X mental retardation protein","volume":"33","author":"Davis","year":"2017","journal-title":"Trends Genet."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"254","DOI":"10.4161\/gmic.1.4.12778","article-title":"Mucin-bacterial interactions in the human oral cavity and digestive tract","volume":"1","author":"Derrien","year":"2010","journal-title":"Gut Microbes"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1099\/ijs.0.02873-0","article-title":"Akkermansia muciniphila gen. Nov., sp. nov., a human intestinal mucin-degrading bacterium","volume":"54","author":"Derrien","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref14","first-page":"411","article-title":"Influence of casein and soy flour proteins on aminoacid content in the liver of experimental animals","volume":"41","author":"Dud\u00e1sov\u00e1","year":"1992","journal-title":"Physiol. Res."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"4500","DOI":"10.3748\/wjg.v23.i25.4500","article-title":"Localization and role of metabotropic glutamate receptors subtype 5 in the gastrointestinal tract","volume":"23","author":"Ferrigno","year":"2017","journal-title":"World J. Gastroenterol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"118497","DOI":"10.1016\/j.lfs.2020.118497","article-title":"The effect of fecal microbiota transplantation on autistic-like behaviors in Fmr1 KO mice","volume":"262","author":"Goo","year":"2020","journal-title":"Life Sci."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"582320","DOI":"10.3389\/fcell.2020.58","article-title":"Microbiome profiling reveals gut dysbiosis in the metabotropic glutamate receptor 5 knockout mouse model of schizophrenia","volume":"8","author":"Gubert","year":"2020","journal-title":"Front. Cell Dev. Biol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.bbi.2023.02.019","article-title":"Dietary fish oil improves autistic behaviors and gut homeostasis by altering the gut microbial composition in a mouse model of fragile X syndrome","volume":"110","author":"Guo","year":"2023","journal-title":"Brain Behav. Immun."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1001\/archpedi.1987.04460020074031","article-title":"Recurrent otitis media in the fragile X syndrome","volume":"141","author":"Hagerman","year":"1987","journal-title":"Am. J. Dis. Child."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/2040-2392-1-12","article-title":"Fragile X and autism: intertwined at the molecular level leading to targeted treatments","volume":"1","author":"Hagerman","year":"2010","journal-title":"Mol. Autism"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"G799","DOI":"10.1152\/ajpgi.00081.2010","article-title":"Orally administered soymorphins, soy-derived opioid peptides, suppress feeding and intestinal transit via gut mu(1)-receptor coupled to 5-HT(1A), D(2), and GABA(B) systems","volume":"299","author":"Kaneko","year":"2010","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2257","DOI":"10.1038\/oby.2012.110","article-title":"The microbiota of the gut in preschool children with normal and excessive body weight","volume":"20","author":"Karlsson","year":"2012","journal-title":"Obesity (Silver Spring)"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"104539","DOI":"10.1016\/j.dci.2022.104539","article-title":"Prediction of intestinal stem cell regulatory genes from Drosophila gut damage model created using multiple inducers: differential gene expression-based protein-protein interaction network analysis","volume":"138","author":"Lee","year":"2023","journal-title":"Dev. Comp. Immunol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"120","DOI":"10.3389\/fncel.2017.00120","article-title":"The gut microbiota and autism Spectrum disorders","volume":"11","author":"Li","year":"2017","journal-title":"Front. Cell. 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Sci."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1016\/0092-8674(91)90397-H","article-title":"Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome","volume":"65","author":"Verkerk","year":"1991","journal-title":"Cell"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41387-022-00230-2","article-title":"The intestinal permeability marker FITC-dextran 4kDa should be dosed according to lean body mass in obese mice","volume":"13","author":"Voetmann","year":"2023","journal-title":"Nutr. Diabetes"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"6718","DOI":"10.1128\/AEM.05212-11","article-title":"Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism","volume":"77","author":"Wang","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"6500","DOI":"10.3390\/molecules28186500","article-title":"Soybean antigen protein-induced intestinal barrier damage by trigging endoplasmic reticulum stress and disordering gut microbiota in weaned piglets","volume":"28","author":"Wang","year":"2023","journal-title":"Molecules"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"153","DOI":"10.2147\/PHMT.S85717","article-title":"Gastrointestinal symptoms and autism spectrum disorder: links and risks - a possible new overlap syndrome","volume":"6","author":"Wasilewska","year":"2015","journal-title":"Pediatric Health Med. Ther."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1016\/S0140-6736(89)92669-X","article-title":"Soy-based infant milk formulas and passive intestinal permeability","volume":"1","author":"Weaver","year":"1989","journal-title":"Lancet"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"20727","DOI":"10.4172\/2165-7890.1000120","article-title":"Soy infant formula may be associated with autistic behaviors","volume":"3","author":"Westmark","year":"2013","journal-title":"Autism Open Access"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"169","DOI":"10.3389\/fneur.2014.00169","article-title":"A hypothesis regarding the molecular mechanism underlying dietary soy-induced effects on seizure propensity","volume":"5","author":"Westmark","year":"","journal-title":"Front. 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Neurobiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"3448","DOI":"10.3390\/ani12243448","article-title":"Improving reproducibility to enhance scientific rigor through consideration of mouse diet","volume":"12","author":"Westmark","year":"","journal-title":"Animals (Basel)"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.3390\/cells11081350","article-title":"Effects of soy-based infant formula on weight gain and neurodevelopment in an autism mouse model","volume":"11","author":"Westmark","year":"","journal-title":"Cells"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"3136","DOI":"10.3390\/nu12103136","article-title":"Soy-based infant formula is associated with an increased prevalence of comorbidities in fragile X syndrome","volume":"12","author":"Westmark","year":"2020","journal-title":"Nutrients"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"284","DOI":"10.3390\/nu16020284","article-title":"Effects of soy protein isolate on fragile X phenotypes in mice","volume":"16","author":"Westmark","year":"2024","journal-title":"Nutrients"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"797","DOI":"10.3233\/JAD-2012-121426","article-title":"Soy-based diet exacerbates seizures in mouse models of neurological disease","volume":"33","author":"Westmark","year":"2013","journal-title":"J. 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