Both inorganic and organic fluoride compounds affect the gut microbiota and may promote dysbiosis.
Fluoride
Bibi S, Kerbiriou C, Uzma, Mckirdy S, Kostrytsia A, Rasheed H, Eqani SAMAS, Gerasimidis K, Nurulain SM, Ijaz UZ - "Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan" Ecotoxicol Environ Saf 284:116959 (2024). doi: 10.1016/j.ecoenv.2024.116959
https://www.sciencedirect.com/science/a ... 1324010352
Cao Q, Li R, Fu R, Zhang X, Yue B, Wang J, Sun Z, Niu R - "Intestinal fungal dysbiosis in mice induced by fluoride" Chemosphere 245:125617 (2020)
https://pubmed.ncbi.nlm.nih.gov/31855763/
Chen G, Hu P, Xu Z, Peng C, Wang Y, Wan X, Cai H - "The beneficial or detrimental fluoride to gut microbiota depends on its dosages" Ecotoxicol Environ Saf 209:111732 (2021)
https://pubmed.ncbi.nlm.nih.gov/33373928/
Chen J, Xu M, Li L, Lu Y, Luo Y, Cao J - "Chronic fluoride induces neurotoxicity in zebrafish through the gut-brain axis" Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 292:110157 (2025)
https://doi.org/10.1016/j.cbpc.2025.110157
Dionizio A, Uyghurturk DA, Melo CGS, Sabino-Arias IT, Araujo TT, Ventura TMS, Perles JVCM, Zanoni JN, Den Besten P, Buzalaf MAR - "Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses" Chemosphere 273:129607 (2021)
https://www.sciencedirect.com/science/a ... 3521000771
Fu R, Niu R, Zhao F, Wang J, Cao Q, Yu Y, Liu C, Zhang D, Sun Z - "Exercise alleviated intestinal damage and microbial disturbances in mice exposed to fluoride" Chemosphere 132658 (2021)
https://www.sciencedirect.com/science/a ... 3521031301
Fu R, Niu R, Li R, Yue B, Zhang X, Cao Q, Wang J, Sun Z - "Fluoride-Induced Alteration in the Diversity and Composition of Bacterial Microbiota in Mice Colon" Biol Trace Elem Res 196(2):537-544 (2020)
https://pubmed.ncbi.nlm.nih.gov/31741202/
Li A, Wang Y, He Y, Liu B, Iqbal M, Mehmood K, Jamil T, Chang YF, Hu L, Li Y, Guo J, Pan J, Tang Z, Zhang H - "Environmental fluoride exposure disrupts the intestinal structure and gut microbial composition in ducks" Chemosphere 277:130222 (2021)
https://pubmed.ncbi.nlm.nih.gov/33794430/
Li G, Zheng X, Zhu Y, Long Y, Xia X - "In-depth insights into the disruption of the microbiota-gut-blood barrier of model organism (Bombyx mori) by fluoride" Sci Total Environ 838(Pt 2):156220(2022) doi: 10.1016/j.scitotenv.2022.156220
https://pubmed.ncbi.nlm.nih.gov/35623528/
Li G, Wu M, Yang X, Song Y, Zhao T, Zeng Z - "Disruption of the core intestinal microbiota contributes to fluoride-induced neurotoxicity in the host organisms" Comp Biochem Physiol C Toxicol Pharmacol 306:110547 (2026)
https://doi.org/10.1016/j.cbpc.2026.110547
Liu P, Li R, Tian X, Zhao Y, Li M, Wang M, Ying X, Yuan J, Xie J, Yan X, Lyu Y, Wei C, Qiu Y, Tian F, Zhao Q, Yan X - "Co-exposure to fluoride and arsenic disrupts intestinal flora balance and induces testicular autophagy in offspring rats" Ecotoxicol Environ Saf 222:112506 (2021)
https://pubmed.ncbi.nlm.nih.gov/34265531/
Liu J, Wang HW, Lin L, Miao CY, Zhang Y, Zhou BH - "Intestinal barrier damage involved in intestinal microflora changes in fluoride-induced mice" Chemosphere 234:409-418 (2019)
https://www.sciencedirect.com/science/a ... 3519313049
Luo Q, Cui H, Peng X, Fang J, Zuo Z, Deng J, Liu J, Deng Y - "Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens" Biol Trace Elem Res 173(2):483-91 (2016)
https://pubmed.ncbi.nlm.nih.gov/26997344/
Miao L, Gong Y, Li H, Xie C, Xu Q, Dong X, Elwan HAM, Zou X - "Alterations in cecal microbiota and intestinal barrier function of laying hens fed on fluoride supplemented diets" Ecotoxicol Environ Saf 193:110372 (2020)
https://www.sciencedirect.com/science/a ... 1320302116
Meenakshi S, Amrutha TV, Abubakar M, Prakash V, Kumar N, Murti K - "Fluoride-induced gut dysbiosis in metabolic disorders: Mechanisms and public health implications." Journal of Trace Elements in Medicine and Biology 93:127806 (2026)
https://doi.org/10.1016/j.jtemb.2025.127806
Mo Z, Wang J, Meng X, Li A, Li Z, Que W, Wang T, Tarnue KF, Ma X, Liu Y, Yan S, Wu L, Zhang R, Pei J, Wang X - "The Dose-Response Effect of Fluoride Exposure on the Gut Microbiome and Its Functional Pathways in Rats" Metabolites 13(11):1159 (2023) doi: 10.3390/metabo13111159.
https://www.mdpi.com/2218-1989/13/11/1159
Ommati MM, Zuo Q, Sabouri S, Retana-Marquez S, Nategh Ahmadi H, Gholami A, Eftekhari A, Shojaei S, Lijuan L, Heidari R, Wang HW - "Fluoride-Induced Autophagy and Apoptosis in the Mouse Ovary: Genomic Insights into IL-17 Signaling and Gut Microbiota Dysbiosis" J Agric Food Chem (2025) doi: 10.1021/acs.jafc.4c10165
https://pubmed.ncbi.nlm.nih.gov/39791957/
Qiu Y, Chen X, Yan X, Wang J, Yu G, Ma W, Xiao B, Quinones S, Tian X, Ren X - "Gut microbiota perturbations and neurodevelopmental impacts in offspring rats concurrently exposure to inorganic arsenic and fluoride" Environ Int 140:105763 (2020)
https://www.sciencedirect.com/science/a ... 2019341832
Rawat N, Sivanesan S, Kanade GS, Bafana A - "Interaction of environmental fluoride exposure and gut microbes: Potential implication in the development of fluorosis in human subjects" Food Chem Toxicol 200:115388 (2025) doi: 10.1016/j.fct.2025.115388
https://www.sciencedirect.com/science/a ... 1525001553
Sun N, Ni X, Wang H, Xin J, Zhao Y, Pan K, Jing B, Zeng D - "Probiotic Lactobacillus johnsonii BS15 Prevents Memory Dysfunction Induced by Chronic High-Fluorine Intake through Modulating Intestinal Environment and Improving Gut Development" Probiotics Antimicrob Proteins 12(4):1420-1438 (2020)
https://link.springer.com/article/10.10 ... 20-09644-9
Tian X, Yan X, Chen X, Liu P, Sun Z, Niu R - "Identifying Serum Metabolites and Gut Bacterial Species Associated with Nephrotoxicity Caused by Arsenic and Fluoride Exposure" Biol Trace Elem Res (2023) doi: 10.1007/s12011-023-03568-5
https://link.springer.com/article/10.10 ... 23-03568-5
Wang HW, Miao CY, Liu J, Zhang Y, Zhu SQ, Zhou BH - "Fluoride-induced rectal barrier damage and microflora disorder in mice" Environ Sci Pollut Res Int 27(7):7596-7607 (2020)
https://pubmed.ncbi.nlm.nih.gov/31885060/
Wang J, Yu C, Zhang J, Liu R, Xiao J - "Aberrant gut microbiota and fecal metabolites in patients with coal-burning endemic fluorosis in Guizhou, China" Environ Sci Pollut Res Int 30(27):69913-69926 (2023) doi: 10.1007/s11356-023-27051-9
https://link.springer.com/article/10.10 ... 23-27051-9
Wang D, Xin J, Lai C, Sun N, Yang Y, He Y, Duan L, Luo J, He Y, Zhang Y, Zhang Y, Wang H, Zeng D, Bai Y, Ni X - "High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling" Ecotoxicol Environ Saf (2026) 312:119898. doi: 10.1016/j.ecoenv.2026.119898
https://www.sciencedirect.com/science/a ... 1326002277
NOTE: RhoA/ROCK signaling pathway operates downstream of Gq/11 signaling.
Wei J, Chen X, Chen G, Qin Q, Chen H, Liang W, Zhang W, Xue S, Wang W, Wang Y - "Gut microbiota-derived indole-3-Acetic Acid attenuates skeletal fluorosis via AHR-mediated suppression of Wnt/β-Catenin signaling." Ecotoxicology and Environmental Safety 309:119520 (2025)
https://doi.org/10.1016/j.ecoenv.2025.119520
Xin J, Wang H, Sun N, Bughio S, Zeng D, Li L, Wang Y, Khalique A, Zeng Y, Pan K, Jing B, Ma H, Bai Y, Ni X - "Probiotic alleviate fluoride-induced memory impairment by reconstructing gut microbiota in mice" Ecotoxicol Environ Saf 215:112108 (2021)
https://pubmed.ncbi.nlm.nih.gov/33799132/
Yan X, Chen X, Tian X, Qiu Y, Wang J, Yu G, Dong N, Feng J, Xie J, Nalesnik M, Niu R, Xiao B, Song G, Quinones S, Ren X - "Co-exposure to inorganic arsenic and fluoride prominently disrupts gut microbiota equilibrium and induces adverse cardiovascular effects in offspring rats" Sci Total Environ. 767:144924 (2021)
https://www.sciencedirect.com/science/a ... 9720384576
Zhang XL, Yu SN, Qu RD, Zhao QY, Pan WZ, Chen XS, Zhang Q, Liu Y, Li J, Gao Y, Lyu Y, Yan XY, Li B, Ren XF, Qiu YL - "Mechanism of Learning and Memory Impairment in Rats Exposed to Arsenic and/or Fluoride Based on Microbiome and Metabolome" Biomed Environ Sci 36(3):253-268 (2023) doi: 10.3967/bes2023.028
https://www.besjournal.com/en/article/d ... es2023.028
Zhang Z, Zhong S, Zhang R, Zeng Q, Lei P, Qiu W, Chen W, Wang D, Wei X, Huang Q, Hu T, Luo P - "Rosa roxburghii Tratt juice ameliorates fluoride exposure-induced bone metabolism disorders by modulating gut microbiota and serum metabolites" Food Res Int 221(Pt 3):117359 (2025)
https://doi.org/10.1016/j.foodres.2025.117359
Zhang JR, Li YW, Chen HX, Luo Y, Liu RM, Wang JB, Liu NN, Xiao JH - "Chronic Excessive Exposure to Fluoride Impairs the Intestinal Mucosal Barrier to Cause Inflammatory Response and Microbiome Dysbiosis in Rats" Biological Trace Element Research (2026)
DOI: https://doi.org/10.1007/s12011-026-05050-4
Zhao T, Lv J, Peng M, Mi J, Zhang S, Liu J, Chen T, Sun Z, Niu R - "Fecal microbiota transplantation and short-chain fatty acids improve learning and memory in fluorosis mice by BDNF-PI3K/AKT pathway" Chem Biol Interact 110786 (2023) doi: 10.1016/j.cbi.2023.110786
https://www.sciencedirect.com/science/a ... 9723004532
Zhao WP, Zhu SQ, Yin ZH, Ommati MM, Zhang YW, Zhao J, Zhou BH, Wang HW - "Short-chain fatty acids alleviated fluoride-induced neuroinflammation via the gut-brain axis in rats" Environ Pollut (Online ahead of print):127503 (2025)
https://doi.org/10.1016/j.envpol.2025.127503
Fluoride-induced dysbiosis, barrier breakdown and TLR4/NF-κB neuroinflammation are reversed by SCFA supplementation in rats.
Zhong N, Ma Y, Meng X, Sowanou A, Wu L, Huang W, Gao Y, Pei J - "Effect of Fluoride in Drinking Water on Fecal Microbial Community in Rats" Biol Trace Elem Res (2021)
https://link.springer.com/article/10.10 ... 21-02617-1
Zhu SQ, Liu J, Han B, Zhao WP, Zhou BH, Zhao J, Wang HW - "Fluoride exposure cause colon microbiota dysbiosis by destroyed microenvironment and disturbed antimicrobial peptides expression in colon" Environ Pollut 292(Pt B):118381 (2021)
https://pubmed.ncbi.nlm.nih.gov/34673156/
PFAS
Lamichhane S, Härkönen T, Vatanen T, Hyötyläinen T, Knip M, Orešič M - "Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads" Environ Int 176:107965 (2023). doi: 10.1016/j.envint.2023.107965
https://www.sciencedirect.com/science/a ... 2023002386
Lin H, Wu H, Liu F, Yang H, Shen L, Chen J, Zhang X, Zhong Y, Zhang H, Liu Z - "Assessing the hepatotoxicity of PFOA, PFOS, and 6:2 Cl-PFESA in black-spotted frogs (Rana nigromaculata) and elucidating potential association with gut microbiota" Environ Pollut 312:120029 (2022) doi: 10.1016/j.envpol.2022.120029
https://www.sciencedirect.com/science/a ... 912201243X
Liu S, Zhan Z, Zhang X, Chen X, Xu J, Wang Q, Zhang M, Liu Y -"Per- and polyfluoroalkyl substance (PFAS) mixtures induce gut microbiota dysbiosis and metabolic disruption in silkworm (Bombyx mori L.)" Sci Total Environ 914:169782 (2024). doi: 10.1016/j.scitotenv.2023.169782
https://www.sciencedirect.com/science/a ... 9723084127
Pan Z, Yuan X, Tu W, Fu Z, Jin Y - "Subchronic exposure of environmentally relevant concentrations of F-53B in mice resulted in gut barrier dysfunction and colonic inflammation in a sex-independent manner" Environ Pollut 253:268-277 (2019). doi: 10.1016/j.envpol.2019.07.021
https://linkinghub.elsevier.com/retriev ... 19)32730-7
Zhao Y, Wang M, Chu W – “Neurotoxicity and intestinal microbiota dysbiosis induced by per- and polyfluoroalkyl substances in crucian carp (Carassius auratus)” Journal of Hazardous Materials 478:135611 (2024)
https://doi.org/10.1016/j.jhazmat.2024.135611
Zhou Y, Zhang L, Li Q, Wang P, Wang H, Shi H, Lu W, Zhang Y - "Prenatal PFAS exposure, gut microbiota dysbiosis, and neurobehavioral development in childhood" Journal of Hazardous Materials 133920 (2024) doi.org/10.1016/j.jhazmat.2024.133920
https://www.sciencedirect.com/science/a ... 9424004990
- SEE also: PFAS effects on liver - gut dysbiosis
Ma S, Sun Y, Zheng X, Yang Y - "Gastrodin attenuates perfluorooctanoic acid-induced liver injury by regulating gut microbiota composition in mice" Bioengineered 12(2):11546-11556 (2021). doi: 10.1080/21655979.2021.2009966
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810172/
Shi L, Pan R, Lin G, Liang X, Zhao J, Zhang H, Chen W, Wang G - "Lactic acid bacteria alleviate liver damage caused by perfluorooctanoic acid exposure via antioxidant capacity, biosorption capacity and gut microbiota regulation" Ecotoxicol Environ Saf 222:112515 (2021) doi: 10.1016/j.ecoenv.2021.112515
https://www.sciencedirect.com/science/a ... 1321006278
Wang G, Pan R, Liang X, Wu X, Wu Y, Zhang H, Zhao J, Chen W - "Perfluorooctanoic acid-induced liver injury is potentially associated with gut microbiota dysbiosis" Chemosphere 266:129004 (2021) doi: 10.1016/j.chemosphere.2020.129004
https://www.sciencedirect.com/science/a ... 352033201X
Yang W, Zou P, He S, Cui H, Yang Z, An H, Chen Q, Huang W, Guo H, Liu J, Ling X, Cao J, Ao L - "Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism" J Adv Res S2090-1232(25)00446-1 (2025) doi: 10.1016/j.jare.2025.06.037
https://www.sciencedirect.com/science/a ... 3225004461
- PFAS & Gut Dysbiosis - Kidney
Hampson HE, Li S, Walker DI, Wang H, Jia Q, Rock S, Costello E, Bjornstad P, Pyle L, Nelson J, Gilliland FD, Chen Z, Aung M, Chatzi L, Conti DV, Alderete TL, Goodrich JA - "The potential mediating role of the gut microbiome and metabolites in the association between PFAS and kidney function in young adults: A proof-of-concept study" Sci Total Environ 176519 (2024). doi: 10.1016/j.scitotenv.2024.176519. Epub ahead of print
https://www.sciencedirect.com/science/a ... 9724066750
Gut Dysbiosis - Thyroid Dysfunction
There are hundreds of studies exploring the association between gut dysbiosis and thyroid hormone metabolism. Listed below are just a few examples to demonstrate the breadth of this research.
Aydın BK, Yildiz M, Akgün A, Topal N, Adal E, Önal H - "Children with Hashimoto's thyroiditis have increased intestinal permeability, results of a pilot study" J Clin Res Pediatr Endocrinol 12(3):303-307 (2020)
https://pmc.ncbi.nlm.nih.gov/articles/PMC7499128/
Cao J, Wang N, Luo Y, Ma C, Chen Z, Chenzhao C, Zhang F, Qi X, Xiong W - "A cause-effect relationship between Graves' disease and the gut microbiome contributes to the thyroid-gut axis: A bidirectional two-sample Mendelian randomization study" Front Immunol 14:977587 (2023). doi: 10.3389/fimmu.2023.977587
https://www.frontiersin.org/articles/10 ... 77587/full
Cayres LCF, de Salis LVV, Rodrigues GSP, Lengert AVH, Biondi APC, Sargentini LDB, Brisotti JL, Gomes E, de Oliveira GLV - "Detection of Alterations in the Gut Microbiota and Intestinal Permeability in Patients With Hashimoto Thyroiditis" Frontiers in Immunology 12:579140 (2021)
https://doi.org/10.3389/fimmu.2021.579140
Patients with Hashimoto thyroiditis have distinct gut dysbiosis and increased intestinal permeability compared with controls, supporting a gut–thyroid axis in autoimmunity.
Chao H, Shan J, Che LQ, Cheng Y, Li HJ, Qian XY - "Correlations between serum cytokines and gut microbiota in patients with Graves' disease: A case-control study" Medicine (Baltimore) 104(25):e43000 (2025)
https://doi.org/10.1097/MD.0000000000043000
"Our findings identify that GD gut ecosystem demonstrates profound microbial dysbiosis characterized by depleted commensal symbionts and expansion of immunomodulatory pathobionts. Specific bacterial taxa correlate with both cytokine and clinical thyroid dysfunction markers."
Covelli D, Ludgate M - "The thyroid, the eyes and the gut: a possible connection" J Endocrinol Invest 40(6):567-576 (2017)
https://pubmed.ncbi.nlm.nih.gov/28063079/
Ejtahed HS, Angoorani P, Soroush AR, Siadat SD, Shirzad N, Hasani-Ranjbar S, Larijani B - "Our Little Friends with Big Roles: Alterations of the Gut Microbiota in Thyroid Disorders" Endocr Metab Immune Disord Drug Targets 20(3):344-350 (2020)
https://pubmed.ncbi.nlm.nih.gov/31566142/
El-Zawawy HT, Ahmed SM, El-Attar EA, Ahmed AA, Roshdy YS, Header DA - "Study of gut microbiome in Egyptian patients with autoimmune thyroid diseases" Int J Clin Pract 75(5):e14038 (2021)
https://pubmed.ncbi.nlm.nih.gov/33482041/
Fröhlich E, Wahl R - "Microbiota and Thyroid Interaction in Health and Disease" Trends Endocrinol Metab 30(8):479-490 (2019)
https://pubmed.ncbi.nlm.nih.gov/31257166/
Gomes RGO - "Major influences of the gut microbiota on thyroid metabolism, a concise systematic review" Int J Nutrology 16(2):e23203 (2023)
https://doi.org/10.54448/ijn23203
Gong B, Wang C, Meng F, Wang H, Song B, Yang Y, Shan Z - "Association between gut microbiota and autoimmune thyroid disease, a systematic review and meta-analysis" Front Endocrinol 12:774362 (2021)
https://doi.org/10.3389/fendo.2021.774362
Hu L, Xu Y, Li J, Zhang M, Sun Z, Ban Y, Tian X, Liu D, Hu L - "Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic" Front Cell Infect Microbiol 14:1369192 (2024). doi: 10.3389/fcimb.2024.1369192.
https://www.frontiersin.org/journals/ce ... 69192/full
Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou YJ, Ma C, Naseem Z, Wu X, Shi P, Xu J - "Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients" Biomed Pharmacother 95:865-874 (2017)
https://pubmed.ncbi.nlm.nih.gov/28903182/
Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P, Xu J - "Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients" Int J Biol Sci 14(11):1558-1570 (2018)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158725/
Jiang W, Yu X, Kosik RO, Song Y, Qiao T, Tong J, Liu S, Fan S, Luo Q, Chai L, Lv Z, Li D - "Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease" Thyroid 31(5):810-820 (2021)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158725/
Jiang W, Lu G, Gao D, Lv Z, Li D - "The relationships between the gut microbiota and its metabolites with thyroid diseases" Front Endocrinol 13:943408 (2022)
https://doi.org/10.3389/fendo.2022.943408
Knezevic J, Starchl C, Tmava Berisha A, Amrein K - "Thyroid-Gut-Axis: How Does the Microbiota Influence Thyroid Function?" Nutrients 12(6):1769 (2020)
https://pubmed.ncbi.nlm.nih.gov/32545596/
Li M, Chen K, Chen Y, Zhang L, Cui Y, Xiao F, Liu Z, Zhang W, Jiang J, Zhou Q, Yan J, Sun Y, Guan F - "Integrative analysis of gut microbiome and host transcriptome reveal novel molecular signatures in Hashimoto's thyroiditis" Journal of Translational Medicine 22(1):1045 (2024)
https://doi.org/10.1186/s12967-024-05876-3
Li J, Ju J, Xu Q, Han X, Ju H - "Profiling gut microbiome dynamics in subacute thyroiditis: Implications for pathogenesis, diagnosis, and treatment" Open Medicine 20(1):20251291 (2025)
https://doi.org/10.1515/med-2025-1291
Liu X, Liu J, Zhang T, Wang Q, Zhang - "Complex relationship between gut microbiota and thyroid dysfunction: a bidirectional two-sample Mendelian randomization study" Front Endocrinol (Lausanne) 14:126738 (2023) doi: 10.3389/fendo.2023.1267383
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10667917/
Masetti G, Moshkelgosha S, Köhling HL, Covelli D, Banga JP, Berchner-Pfannschmidt U, Horstmann M, Diaz-Cano S, Goertz GE, Plummer S, Eckstein A, Ludgate M, Biscarini F, Marchesi JR; INDIGO consortium - "Gut microbiota in experimental murine model of Graves' orbitopathy established in different environments may modulate clinical presentation of disease" Microbiome 6(1):97 (2018)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970527/
Meng X, Hao R, Liu K, Zhang P, An C, Zhang Y, Li H, Wu B, Li M, Yu X, Tong X - "The trilateral nexus of autoimmune thyroiditis: integrating immunological triggers, endocrine disruption, and gut microbiome alterations for treatment strategies" Autoimmunity 59(1):2601015 (2026)
https://doi.org/10.1080/08916934.2025.2601015
Silva IB, Puig-Domingo M - "The impact of thyroid disorders on the gut microbiome: emerging mechanisms and clinical relevance" Archives of Endocrinology and Metabolism 70(Spe1):e250075 (2025)
https://doi.org/10.20945/2359-4292-2025-0075
Su X, Yin X, Liu Y, Yan X, Zhang S, Wang X, Lin Z, Zhou X, Gao J, Wang Z, Zhang Q - "Gut Dysbiosis Contributes to the Imbalance of Treg and Th17 Cells in Graves' Disease Patients by Propionic Acid" J Clin Endocrinol Metab 105(11):dgaa511 (2020)
https://pubmed.ncbi.nlm.nih.gov/32785703/
Su X, Zhao Y, Li Y, Ma S, Wang Z - "Gut dysbiosis is associated with primary hypothyroidism with interaction on gut-thyroid axis" Clin Sci (Lond) 134(12):1521-1535 (2020) doi: 10.1042/CS20200475
https://portlandpress.com/clinsci/artic ... th-primary
"Our study suggests that primary hypothyroidism causes changes in gut microbiome...The short chain fatty acid producing ability of the primary hypothyroidism patients' gut was significantly decreased, which resulted in the increased serum lipopolysaccharide (LPS) levels."
Talebi S, Karimifar M, Heidari Z, Mohammadi H, Askari G - " The effects of synbiotic supplementation on thyroid function and inflammation in hypothyroid patients: A randomized, double‑blind, placebo‑controlled trial" Complement Ther Med 48:102234 (2020)
https://pubmed.ncbi.nlm.nih.gov/31987229/
Tavassol ZH, Farsi F, Ettehad-Marvasti F, Ejtahed HS, Hasani-Ranjbar S - "Gut Microbiota Alterations in Hypothyroidism: A Pilot Study Revealing Increased Abundance of Specific Bacterial Genera" Journal of Nutrition and Metabolism 2026:9988966 (2026)
https://doi.org/10.1155/jnme/9988966
Virili C, Stramazzo I, Centanni M - "Gut microbiome and thyroid autoimmunity" Best Pract Res Clin Endocrinol Metab 35(3):101506 (2021). doi: 10.1016/j.beem.2021.101506
https://www.sciencedirect.com/science/a ... 0X21000233
Wang B, Xu Y, Hou X, Li J, Cai Y, Hao Y, Ouyang Q, Wu B, Sun Z, Zhang M, Ban Y - "Small Intestinal Bacterial Overgrowth in Subclinical Hypothyroidism of Pregnant Women" Front Endocrinol (Lausanne) 12:604070 (2021)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8181748/
Wang R, Yu X, Cai H, Lu G, Gao D, Zhang M, Chai L, Yi W, Lv Z - "Gut microbiota alteration was related to subclinical hypothyroidism and dyslipidemia in mice" FASEB J 39(5):e70445 (2025)
https://doi.org/10.1096/fj.202402289RR
Wu M, Chi C, Yang Y, Guo S, Li T, Gu M, Zhang T, Gao H, Liu R, Yin C - "Dynamics of gut microbiota during pregnancy in women with TPOAb-positive subclinical hypothyroidism: a prospective cohort study" BMC Pregnancy and Childbirth 22(1):592 (2022)
https://doi.org/10.1186/s12884-022-04923-5
"Our results indicated that low dynamics of gut microbiota composition and high dynamics of its metabolic function from T2 to T3 were associated with TPOAb+ SCH. We concluded that gut microbiota could be new targets for treatment of TPOAb+ SCH during pregnancy."
Xu Q, Ju J, Han X, Gu Y, Li J, Ju H - "Changes in gut microbiota before and after treatment in patients with primary hypothyroidism" Open Life Sci 21(1):20251307 (2026)
https://doi.org/10.1515/biol-2025-1307
"Spearman correlation analysis showed that Streptococcus was positively correlated with TT3, TT4, and FT4, and negatively correlated with AST; R. torques was negatively correlated with TT4 and FT4; Koalarothia was positively correlated with TgAb and TC; Blautia was positively correlated with TPOAb. Patients with primary hypothyroidism exhibit gut microbiota dysbiosis, with a decrease in the abundance of certain short-chain fatty acid-producing bacteria, which increases after treatment. There is a certain correlation between specific gut microbiota and thyroid function as well as lipid metabolism indicators."
Yadav A, Wankhede N, Sangamwar S, Taksande B, Aglawe M, Rahangdale S, Umekar M, Kale M - "Maternal thyroid-gut dynamics during pregnancy and cognitive trajectories in children" Front Neuroendocrinol 101254 (2026)
https://doi.org/10.1016/j.yfrne.2026.101254
"Dysbiosis may alter deiodinase activity, weaken intestinal barrier integrity, and promote inflammation, worsening thyroid dysfunction and increasing fetal vulnerability. Evidence suggests a feedback loop where microbiota affects thyroid homeostasis and thyroid hormones shape gut ecology."
Yan K, Sun X, Fan C, Wang X, Yu H - "Unveiling the Role of Gut Microbiota and Metabolites in Autoimmune Thyroid Diseases: Emerging Perspectives" International Journal of Molecular Sciences 25(20):10918 (2024)
https://doi.org/10.3390/ijms252010918
Yao Z, Zhao M, Gong Y, Chen W, Wang Q, Fu Y, Guo T, Zhao J, Gao L, Bo T - "Relation of Gut Microbes and L-Thyroxine Through Altered Thyroxine Metabolism in Subclinical Hypothyroidism Subjects" Front Cell Infect Microbiol. 10:495 (2020)
https://pubmed.ncbi.nlm.nih.gov/33072620/
Zheng D, Liao H, Chen S, Liu X, Mao C, Zhang C, Meng M, Wang Z, Wang Y, Jiang Q, Xue Y, Zhou L, Chen Y - "Elevated levels of circulating biomarkers related to leaky gut syndrome and bacterial translocation are associated with Graves' disease" Front Endocrinol 12:796212 (2021)
https://doi.org/10.3389/fendo.2021.796212
Zhao F, Feng J, Li J, Zhao L, Liu Y, Chen H, Jin Y, Zhu B, Wei Y - "Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients" Thyroid 28(2):175-186 (2018)
https://doi.org/10.1089/thy.2017.0395
Zhou L, Li X, Ahmed A, Wu D, Liu L, Qiu J, Yan Y, Jin M, Xin Y - "Gut microbe analysis between hyperthyroid and healthy individuals" Curr Microbiol 69(5):675-80 (2014)
https://pubmed.ncbi.nlm.nih.gov/24969306/
Iodine
Gong B, Meng F, Wang X, Han Y, Yang W, Wang C, Shan Z - "Effects of iodine intake on gut microbiota and gut metabolites in Hashimoto thyroiditis-diseased humans and mice" Commun Biol 7(1):136 (2024). doi: 10.1038/s42003-024-05813-6
https://pmc.ncbi.nlm.nih.gov/articles/PMC10824742/
"Gut dysbiosis, driven by excessive iodine intake, disrupts TH17/Treg balance by reducing butyric acid. In summary, iodine intake alters intestinal microbiota composition and metabolic changes influencing the microbiota-gut-thyroid axis."
SEE ALSO: IBD
Follin-Arbelet B, Moum B - "Fluoride: a risk factor for inflammatory bowel disease?" Scand J Gastroenterol 51(9):1019-24 (2016)
https://www.tandfonline.com/doi/abs/10. ... ode=igas20
Han N, Pan Z, Liu G, Yang R, Yujing B - "Hypoxia: The 'Invisible Pusher' of Gut Microbiota" Front Microbiol 12:690600 (2021)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8339470/
Sugar & Microbiome
Kearns CE, Apollonio D, Glantz SA - "Sugar industry sponsorship of germ-free rodent studies linking sucrose to hyperlipidemia and cancer: An historical analysis of internal documents" PLoS Biol 15(11):e2003460 (2017)
https://journals.plos.org/plosbiology/a ... io.2003460
Vitamin D & Gut Dysbiosis
Singh P, Rawat A, Alwakeel M, Sharif E, Al Khodor S - "The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals" Sci Rep 10(1):21641 (2020)
https://www.ncbi.nlm.nih.gov/labs/pmc/a ... MC7729960/
Other Fluorine Compounds:
NOTE: As all fluoride compounds - inorganic or organic - can affect thyroid hormone metabolism, they also may affect the gut microbiota.
Florfenicol
Ma Z, Gao X, Yang X, Lin L, Wei X, Wang S, Li Y, Peng X, Zhao C, Chen J, Xiao H, Yuan Y, Dai J - "Low-dose florfenicol and copper combined exposure during early life induced health risks by affecting gut microbiota and metabolome in SD rats" Ecotoxicol Environ Saf 245:114120 (2022)
https://doi.org/10.1016/j.ecoenv.2022.114120
Mei X, Ma B, Zhai X, Zhang A, Lei C, Zuo L, Yang X, Zhou C, Wang H - "Florfenicol Enhances Colonization of a Salmonella enterica Serovar Enteritidis floR Mutant with Major Alterations to the Intestinal Microbiota and Metabolome in Neonatal Chickens" Appl Environ Microbiol 87(24):e0168121 (2021)
https://doi.org/10.1128/AEM.01681-21
Sevoflurane
Han S, Bian R, Chen Y, Liang J, Zhao P, Gu Y, Zhang D - "Dysregulation of the gut microbiota contributes to sevoflurane-induced cognitive dysfunction in aged mice by activating the NLRP3 inflammasome" Molecular Neurobiology 61(12):10500-10516 (2024) doi: 10.1007/s12035-024-04229-x
https://link.springer.com/article/10.10 ... 24-04229-x
NOTE: NLRP3 is regulated by Gq/11
"Compared to those in the control group, sevoflurane significantly increased the expression of NLRP3 inflammasome-associated proteins in the gut and brain in the sevoflurane-exposed group, thus causing neuroinflammation and synaptic damage, which probiotics can mitigate (con vs. sev, P < 0.01; p+sev vs. sev, P < 0.05). "
Zhao Y, Ma S, Liang L, Cao S, Fan Z, He D, Shi X, Zhang Y, Liu B, Zhai M, Wu S, Kuang F, Zhang H - "Gut Microbiota-Metabolite-Brain Axis Reconstitution Reverses Sevoflurane-Induced Social and Synaptic Deficits in Neonatal Mice" Research (Wash D C) 7:0482 (2024) doi: 10.34133/research.0482
https://pmc.ncbi.nlm.nih.gov/articles/PMC11411162/
"The gut microbiota-metabolite-brain axis underlies social dysfunction caused by sevoflurane exposure in early age, and bile acid regulation may be a promising intervention to this impairment."
Ceprofloxacin
Dethlefsen L, Huse S, Sogin ML, Relman DA – "The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing" PLoS Biology 6(11):e280 (2008)
https://doi.org/10.1371/journal.pbio.0060280
Short ciprofloxacin courses in healthy adults caused large drops in richness and major taxonomic shifts, with only partial recovery after treatment, classic antibiotic-induced dysbiosis.
Dethlefsen L, Relman DA – "Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation" Proceedings of the National Academy of Sciences of the United States of America 108(Suppl 1):4554-4561 (2011)
https://doi.org/10.1073/pnas.1000087107
Repeated ciprofloxacin produced long lasting, subject specific alterations in microbiota composition, with some taxa failing to return to baseline.
Prozac/Paxil
Desorcy-Scherer K, Fricke HP, Hernandez LL - "Selective serotonin reuptake inhibitors during pregnancy and lactation: A scoping review of effects on the maternal and infant gut microbiome" Dev Psychobiol 66(1):e22441 doi: 10.1002/dev.22441 (2024)
https://pmc.ncbi.nlm.nih.gov/articles/PMC11017378/
"Results suggest that fluoxetine (SSRI) exposure may affect maternal gut microbiome dynamics during pregnancy and lactation."
Desorcy-Scherer K, Zuniga-Chaves I, Reisner MA, Suen G, Hernandez LL - "Investigating the influence of perinatal fluoxetine exposure on murine gut microbial communities during pregnancy and lactation" Sci Rep 14(1):13762 (2024) doi: 10.1038/s41598-024-62224-7
https://pmc.ncbi.nlm.nih.gov/articles/PMC11178873/
Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW – "Paroxetine administration affects microbiota and bile acid levels in mice" Frontiers in Psychiatry 11:518 (2020)
https://doi.org/10.3389/fpsyt.2020.00518
Paroxetine treatment changed microbiota diversity, specific taxa and bile acid profiles, linking a fluorinated SSRI to gut microbial and metabolic disruption.
Lyte M, Daniels KM, Schmitz-Esser S – "Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology based mechanism of action responsible for fluoxetine-induced side effects" PeerJ 7:e6199 (2019)
https://doi.org/10.7717/peerj.6199
Fluoxetine significantly altered community structure, reduced certain Firmicutes and shifted predicted metabolic functions, linking SSRI exposure to microbiota-mediated side effects.
Ramsteijn AS, Jasarevic E, Houwing DJ, Bale TL, Olivier JD – "Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression" Gut Microbes 11(4):735-753 (2020)
https://doi.org/10.1080/19490976.2019.1705728
Perinatal fluoxetine altered maternal and offspring microbial composition and fecal metabolites, with sex specific effects on bacterial community structure.
Favipiravir
Mukherjee I, Vasantharekha R, Seetharaman B - "Gut dysbiosis, anxiety and depression and the neurotoxic effects of formulated favipiravir and the restorative impact of vitamin D supplementation in adult zebrafish" J Food Sci Technol (2025)
https://doi.org/10.1007/s13197-025-06255-6
"Favipiravir (60.45 mg/L) showed reduced BDNF gene expression, serotonin levels, and AChE activity. There was an upregulation of CRH and TSHβ gene and an increase in whole body cortisol levels. Exposure to favipiravir induces gut dysbiosis, leading to an increase in abundance of Proteobacteria and a decrease in Fusobacteriota, altering the gut-brain axis."