Metabolic impact of persistent organic pollutants on gut microbiota

References

• Lim J-E, Nam C, Yang J, Rha KH, Lim K-M, Jee SH. Serum persistent organic pollutants (POPs) and prostate cancer risk: A case-cohort study. International Journal of Hygiene and Environmental Health. 2017;220(5):849–856. doi:10.1016/j.ijheh.2017.03.014.
   PubMed Web of Science ®Google Scholar
• Koual M, German CS, Anne SB, Celine T, Yael KA, Nathalie DH, Charlotte N, Helene B, Myriam D, Fabrice L, et al. Associations between persistent organic pollutants and risk of breast cancer metastasis. Environ Int. 2019;132:105028. doi:10.1016/j.envint.2019.105028.
   PubMed Web of Science ®Google Scholar
• Vafeiadi M, Vrijheid M, Fthenou E, Chalkiadaki G, Rantakokko P, Kiviranta H, Kyrtopoulos SA, Chatzi L, Kogevinas M. Persistent organic pollutants exposure during pregnancy, maternal gestational Weight gain, and birth outcomes in the mother-child cohort in Crete, Greece (RHEA study). Environ Int. 2014;64:116–123. doi:10.1016/j.envint.2013.12.015.
   PubMed Web of Science ®Google Scholar
• Ren AG, Qiu XH, Jin L, Ma J, Li ZW, Zhang L, Zhu HP, Finnell RH, Zhu T. Association of selected persistent organic pollutants in the placenta with the risk of neural tube defects. Proc Natl Acad Sci U S A. 2011;108:12770–12775. doi:10.1073/pnas.1105209108.
   PubMed Web of Science ®Google Scholar
• Gascon M, Morales E, Sunyer J, Vrijheid M. Effects of persistent organic pollutants on the developing respiratory and immune systems: A systematic review. Environ Int. 2013;52:51–65. doi:10.1016/j.envint.2012.11.005.
   PubMed Web of Science ®Google Scholar
• Damstra T. Potential effects of certain persistent organic pollutants and endocrine disrupting chemicals on the health of children. J Toxicol Clin Toxicol. 2002;40:457–465. doi:10.1081/clt-120006748.
   PubMed Web of Science ®Google Scholar
• Vested A, Giwercman A, Bonde JP, Toft G. Persistent organic pollutants and male reproductive health. Asian J Androl. 2014;16:71–80. doi:10.4103/1008-682x.122345.
   PubMed Web of Science ®Google Scholar
• Magliano DJ, Loh VHY, Harding JL, Botton J, Shaw JE. Persistent organic pollutants and diabetes: A review of the epidemiological evidence. Diabetes Metab. 2014;40:1–14. doi:10.1016/j.diabet.2013.09.006.
   PubMed Web of Science ®Google Scholar
• Lee DH, Porta M, Jacobs DR, Vandenberg LN. Chlorinated persistent organic pollutants, obesity, and type 2 diabetes. Endocr Rev. 2014;35:557–601. doi:10.1210/er.2013-1084.
   PubMed Web of Science ®Google Scholar
• Jin YX, Wu SS, Zeng ZY, Fu ZW. Effects of environmental pollutants on gut microbiota. Environmental Pollution. 2017;222:1–9. doi:10.1016/j.envpol.2016.11.045.
   PubMed Web of Science ®Google Scholar
• National academies of sciences, E. & Medicine. Environmental chemicals, the human microbiome, and health risk: a research strategy. The National Academies Press; 2018. https://doi.org/10.17226/24960
   Google Scholar
• Claus SP, Guillou H, Ellero-Simatos S. The gut microbiota: a major player in the toxicity of environmental pollutants? NPJ Biofilms Microbi. 2016;2:17001. doi:10.1038/npjbiofilms.2016.3.
   Web of Science ®Google Scholar
• Zhang LM, Nichols RG, Correll J, Murray IA, Tanaka N, Smith PB, Hubbard TD, Sebastian A, Albert I, Hatzakis E, et al. Persistent organic pollutants modify gut microbiota-host metabolic homeostasis in mice through aryl hydrocarbon receptor activation. Environ Health Perspect. 2015;123:679–688. doi:10.1289/ehp.1409055.
   PubMed Web of Science ®Google Scholar
• Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16:341–352. doi:10.1038/nri.2016.42.
   PubMed Web of Science ®Google Scholar
• Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121–141. doi:10.1016/j.cell.2014.03.011.
   PubMed Web of Science ®Google Scholar
• Tilg H, Moschen AR. Microbiota and diabetes: an evolving relationship. Gut. 2014;63:1513–1521. doi:10.1136/gutjnl-2014-306928.
   PubMed Web of Science ®Google Scholar
• Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. Host-gut microbiota metabolic interactions. Sci. 2012;336:1262–1267. doi:10.1126/science.1223813.
   PubMed Web of Science ®Google Scholar
• Snedeker SM, Hay AG. Do interactions between gut ecology and environmental chemicals contribute to obesity and diabetes?. Environ Health Perspect. 2012;120:332–339. doi:10.1289/ehp.1104204.
   PubMed Web of Science ®Google Scholar
• Zhang LM, Hatzakis E, Nichols RG, Hao RX, Correll J, Smith PB, Chiaro CR, Perdew GH, Patterson AD. Metabolomics reveals that aryl hydrocarbon receptor activation by environmental chemicals induces systemic metabolic dysfunction in mice. Environ Sci. 2015;49:8067–8077. doi:10.1021/acs.est.5b01389.
   Google Scholar
• Nichols RG, Zhang JT, Cai JW, Murray IA, Koo I, Smith PB, Perdew GH, Patterson AD. Metatranscriptomic analysis of the mouse gut microbiome response to the persistent organic pollutant 2,3,7,8-tetrachlorodibenzofuran. Metabolites. 2020;10:1. doi:10.3390/metabo10010001.
   Web of Science ®Google Scholar
• Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. Mbio. 2014;5:e00889. doi:10.1128/mBio.00889-14.
   PubMed Web of Science ®Google Scholar
• Sprusansky O, Stirrett K, Skinner D, Denoya C, Westpheling J. The bkdR gene of Streptomyces coelicolor is required for morphogenesis and antibiotic production and encodes a transcriptional regulator of a branched-chain amino acid dehydrogenase complex. J Bacteriol. 2005;187:664–671. doi:10.1128/jb.187.2.664-671.2005.
   PubMed Web of Science ®Google Scholar
• Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE. The rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol. 2010;192:4089–4102. doi:10.1128/jb.00201-10.
   PubMed Web of Science ®Google Scholar
• Setlow B, Sun DX, Setlow P. Interaction between DNA and alpha/beta-type small, acid-soluble spore protein - A new class of DNA-binding protein. J Bacteriol. 1992;174:2312–2322. doi:10.1128/jb.174.7.2312-2322.1992.
   PubMed Web of Science ®Google Scholar
• Miller SI. Antibiotic resistance and regulation of the gram-negative bacterial outer membrane barrier by host innate immune molecules. Mbio. 2016;7:e01541. doi:10.1128/mBio.01541-16.
   PubMed Web of Science ®Google Scholar
• Silhavy TJ, Kahne D, Walker S. The bacterial cell envelope. Cold Spring Harb Perspect Biol. 2010:2. doi:10.1101/cshperspect.a000414.
   PubMed Web of Science ®Google Scholar
• Sun LL, Xie C, Wang G, Wu Y, Wu Q, Wang XM, Liu J, Deng YY, Xia JL, Chen B, et al. Gut microbiota and intestinal FXR mediate the clinical benefits of metformin. Nat Med. 2018;24:1919–1929. doi:10.1038/s41591-018-0222-4.
   PubMed Web of Science ®Google Scholar
• Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623–628. doi:10.1038/nature25979.
   PubMed Web of Science ®Google Scholar
• Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M. Exercise attenuates PCB-induced changes in the mouse gut microbiome. Environ Health Perspect. 2013;121:725–730. doi:10.1289/ehp.1306534.
   PubMed Web of Science ®Google Scholar
• Mimura J, Fujii-Kuriyama Y. Functional role of AhR in the expression of toxic effects by TCDD. BBA-Gen Subj. 2003;1619:263–268. doi:10.1016/s0304-4165(02)00485-3.
   PubMed Web of Science ®Google Scholar
• Ovando BJ, Ellison CA, Vezina CM, Olson JR. Toxicogenomic analysis of exposure to TCDD, PCB126 and PCB153: identification of genomic biomarkers of exposure to AhR ligands. Bmc Genomics. 2010;11:583. doi:10.1186/1471-2164-11-583.
   PubMed Web of Science ®Google Scholar
• Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013;152:39–50. doi:10.1016/j.cell.2012.10.052.
   PubMed Web of Science ®Google Scholar
• Tian Y, Cai JW, Gui W, Nichols RG, Koo I, Zhang JT, Anitha M, Patterson AD. Berberine directly affects the gut microbiota to promote intestinal farnesoid X receptor activation. Drug Metab Dispos. 2019;47:86–93. doi:10.1124/dmd.118.083691.
   PubMed Web of Science ®Google Scholar
• Murínová S, Dercová K. Response mechanisms of bacterial degraders to environmental contaminants on the level of cell walls and cytoplasmic membrane. Int J Microbiol. 2014;2014:873081. doi:10.1155/2014/873081.
   PubMedGoogle Scholar
• Denich TJ, Beaudette LA, Lee H, Trevors JT. Effect of selected environmental and physico-chemical factors on bacterial cytoplasmic membranes. J Microbiol Methods. 2003;52:149–182. doi:10.1016/s0167-7012(02)00155-0.
   PubMed Web of Science ®Google Scholar
• Hoffman JB, Flythe MD, Hennig B. Environmental pollutant-mediated disruption of gut microbial metabolism of the prebiotic inulin. Anaerobe. 2019;55:96–102. doi:10.1016/j.anaerobe.2018.11.008.
   PubMed Web of Science ®Google Scholar
• Venegas DP, De la Fuente MK, Landskron G, Gonzalez MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019:10. doi:10.3389/fimmu.2019.00277.
   Web of Science ®Google Scholar
• Pugsley AP, Schwartz M. Export and secretion of proteins by bacteria. Fems Microbiol Lett. 1985;32:3–38. doi:10.1016/0378-1097(85)90024-2.
   Web of Science ®Google Scholar
• Kostakioti M, Newman CL, Thanassi DG, Stathopoulos C. Mechanisms of protein export across the bacterial outer membrane. J Bacteriol. 2005;187:4306–4314. doi:10.1128/jb.187.13.4306-4314.2005.
   PubMed Web of Science ®Google Scholar
• Freudl R. Leaving home ain’t easy: protein export systems in gram-positive bacteria. Res Microbiol. 2013;164:664–674. doi:10.1016/j.resmic.2013.03.014.
   PubMed Web of Science ®Google Scholar
• Parsons JB, Rock CO. Is bacterial fatty acid synthesis a valid target for antibacterial drug discovery? Curr Opin Microbiol. 2011;14:544–549. doi:10.1016/j.mib.2011.07.029.
   PubMed Web of Science ®Google Scholar
• Nilsen H, Krokan HE. Base excision repair in a network of defence and tolerance. Carcinogenesis. 2001;22:987–998. doi:10.1093/carcin/22.7.987.
   PubMed Web of Science ®Google Scholar
• Zhang WS, Sargis RM, Volden PA, Carmean CM, Sun XJ, Brady MJ. PCB 126 and other dioxin-like PCBs specifically suppress hepatic PEPCK expression via the Aryl hydrocarbon receptor. Plos One. 2012;7:e37103. doi:10.1371/journal.pone.0037103.
   PubMed Web of Science ®Google Scholar
• Gadupudi GS, Klaren WD, Olivier AK, Klingelhutz AJ, Robertson LW. PCB126-induced disruption in gluconeogenesis and fatty acid oxidation precedes fatty liver in male rats. Toxicol Sci. 2016;149:98–110. doi:10.1093/toxsci/kfv215.
   PubMed Web of Science ®Google Scholar
• Fischer LJ, Seegal RF, Ganey PE, Pessah IN, Kodavanti PRS. Symposium overview: toxicity of non-coplanar PCBs. Toxicol Sci. 1998;41:49–61.
   PubMed Web of Science ®Google Scholar
• Totland C, Nerdal W, Steinkopf S. Effects and location of coplanar and noncoplanar PCB in a lipid bilayer: a solid-state NMR study. Environ Sci Technol. 2016;50:8290–8295. doi:10.1021/acs.est.6b01723.
   PubMed Web of Science ®Google Scholar
• Tan YS, Chen CH, Lawrence D, Carpenter DO. Ortho-substituted PCBs kill cells by altering membrane structure. Toxicol Sci. 2004;80:54–59. doi:10.1093/toxsci/kfh119.
   PubMed Web of Science ®Google Scholar
• Wojcik A, Bieniasz A, Wydro P, Broniatowski M. The effect of chlorination degree and substitution pattern on the interactions of polychlorinated biphenyls with model bacterial membranes. BBA-Biomembranes. 2019;1861:1057–1068. doi:10.1016/j.bbamem.2019.03.009.
   PubMed Web of Science ®Google Scholar
• Cai JW, Nichols RG, Koo I, Kalikow ZA, Zhang LM, Tian Y, Zhang JT, Smith PB, Patterson AD. Multiplatform physiologic and metabolic phenotyping reveals microbial toxicity. Msystems. 2018;3:e00123. doi:10.1128/mSystems.00123-18.
   PubMed Web of Science ®Google Scholar
• Xu WX, Wu JF, An YP, Xiao CN, Hao FH, Liu HB, Wang YL, Tang HR. Streptozotocin-Induced dynamic metabonomic changes in rat biofluids. J Proteome Res. 2012;11:3423–3435. doi:10.1021/pr300280t.
   PubMed Web of Science ®Google Scholar
• Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGhenst J, Fiehn O, Arita M, et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015;12:523–526. doi:10.1038/nmeth.3393.
   PubMed Web of Science ®Google Scholar
• Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O. MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinform. 2012;13:99. doi:10.1186/1471-2105-13-99.
   PubMed Web of Science ®Google Scholar
• Allman EL, Painter HJ, Samra J, Carrasquilla M, Llinas M. Metabolomic profiling of the malaria box reveals antimalarial target pathways. Antimicrob Agents Chemother. 2016;60:6635–6649. doi:10.1128/aac.01224-16.
   PubMed Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–12.
   Google Scholar
• Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–3217. doi:10.1093/bioinformatics/bts611.
   PubMed Web of Science ®Google Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596. doi:10.1093/nar/gks1219.
   PubMed Web of Science ®Google Scholar
• Kim JW, Kim MS, Koh AY, Xie Y, Zhan XW. FMAP: functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. BMC Bioinform. 2016;17:420. doi:10.1186/s12859-016-1278-0.
   PubMed Web of Science ®Google Scholar
• Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60. doi:10.1038/nmeth.3176.
   PubMed Web of Science ®Google Scholar
• Chong J, Liu P, Zhou GY, Xia JG. Using MICROBIOMEANALYST for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat Protoc. 2020;15:799–821. doi:10.1038/s41596-019-0264-1.
   PubMed Web of Science ®Google Scholar
• Helmecke J, Schomburg D, Neumann-Schaal M. MetaboMAPS: pathway sharing and multi-omics data visualization in metabolic context. F1000Research 2020;9:288.
   Google Scholar
• Tian Y, Gui W, Koo I, Smith PB, Allman EL, Nichols RG, Rimal B, Cai JW, Liu Q, Patterson AD. The microbiome modulating activity of bile acids. Gut Microbes. 2020;11. doi:10.1080/19490976.2020.1732268.
   Web of Science ®Google Scholar
• Tian Y, Nichols RG, Roy P, Gui W, Smith PB, Zhang JT, Lin YD, Weaver V, Cai JW, Patterson AD, et al. Prebiotic effects of white button mushroom (Agaricus bisporus) feeding on succinate and intestinal gluconeogenesis in C57BL/6 mice. J Funct Foods. 2018;45:223–232. doi:10.1016/j.jff.2018.04.008.
   Web of Science ®Google Scholar
• Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–5120. doi:10.1128/aem.01043-13.
   PubMed Web of Science ®Google Scholar