Abstract
The risk of methylmercury (MeHg) toxicity following ingestion of contaminated foodstuffs (e.g., fish) is directly related to the kinetics of MeHg elimination among individuals. Yet, the factors driving the wide range of inter-individual variability in MeHg elimination within a population are poorly understood. Here, we investigated the relationship between MeHg elimination, gut microbiome demethylation activity, and gut microbiome composition using a coordinated human clinical trial and gnotobiotic mouse modeling approach together with metagenomic sequence analysis. We first observed MeHg elimination half-lives (t1/2) ranging from 28 to 90 days across 27 volunteers. Subsequently, we found that ingestion of a prebiotic induced changes in the gut microbiome and mixed effects (increased, decrease, and no effect) on elimination in these same individuals. Nonetheless, elimination rates were found to correlate with MeHg demethylation activity in cultured stool samples. In mice, attempts to remove the microbiome via generation of germ-free (GF) animals or through antibiotic (Abx) treatment both diminished MeHg demethylation to a similar extent. While both conditions substantially slowed elimination, Abx treatment resulted in significantly slower elimination than the GF condition, indicating an additional role for host-derived factors in supporting elimination. Human fecal microbiomes transplanted to GF mice restored elimination rates to that seen in control mice. Metagenomic sequence analysis of human fecal DNA did not identify genes encoding proteins typically involved in demethylation (e.g., merB, organomercury lyase). However, the abundance of several anaerobic taxa, notably Alistipes onderdonkii, were positively correlated with MeHg elimination. Surprisingly, mono-colonization of GF free mice with A. onderdonkii did not restore MeHg elimination to control levels. Collectively, our findings indicate the human gut microbiome uses a non-conventional pathway of demethylation to increase MeHg elimination that relies on yet to be resolved functions encoded by the gut microbes and the host
Clinical Trial NCT04060212, prospectively registered 10/1/2019.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The datasets generated are available in the NCBI SRA repository, bioproject: PRJNA954827 (web link pending).
References
Aaberg B, Ekman L, Falk R, Greitz U, Persson G, Snihs JO (1969) Metabolism of methyl mercury (203Hg) compounds in man. Arch Environ Health 19(4):478–484
Ali Aldroobi KS, Shukri A, Bauk S, Abdel Munem E, Abuarra AMA (2013) Determination of arsenic and mercury level in scalp hair from a selected population in Penang, Malaysia using XRF technique. Radiat Phys Chem 91:9–14
Baldi F, Pepi M, Filippelli M (1993) Methylmercury resistance in desulfovibrio desulfuricans strains in relation to methylmercury degradation. Appl Environ Microbiol 59(8):2479–2485
Ballatori N, Clarkson TW (1983) Biliary transport of glutathione and methylmercury. Am J Physiol 244(4):G435–G441
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
Barkay T, Gu B (2022) Demethylation—the other side of the mercury methylation coin: a critical review. ACS Environ Au 2:77–97
Barkay T, Miller SM, Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27(2–3):355–384
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B57:289–300
Boyd ES, Barkay T (2012) The mercury resistance operon: from an origin in a geothermal environment to an efficient detoxification machine. Front Microbiol. https://doi.org/10.3389/fmicb.2012.00349
Caito SW, Jackson BP, Punshon T et al (2018) Variation in methylmercury metabolism and elimination status in humans following fish consumption. Toxicol Sci 161:443–453. https://doi.org/10.1093/toxsci/kfx226
Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinform 10:421. https://doi.org/10.1186/1471-2105-10-421
Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ (2012) Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12:302. https://doi.org/10.1186/1471-2180-12-302
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH (2019) GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36(6):1925–1927. https://doi.org/10.1093/bioinformatics/btz848
Christakis CA, Barkay T, Boyd ES (2021) Expanded diversity and phylogeny of mer genes broadens mercury resistance paradigms and reveals an origin for MerA among thermophilic archaea. Front Microbiol 12:682605. https://doi.org/10.3389/fmicb.2021.682605
Colman DR, Amenabar MJ, Fernandes-MArtin MC, Boyd ES (2022) Subsurface Archaea associated with rapid geobiological change in a model Yellowstone hot spring. Nat Commun Earth Environ. https://doi.org/10.1038/s43247-022-00542-2
Davidson PW, Myer GJ, Shamlaye C et al (1999) Association between prenatal exposure to methylmercury and developmental outcomes in Seychellois children: effect modification by social and environmental factors. Neurotoxicology 20(5):833–841
Davidson PW, Myers GJ, Cox C et al (2006) Methylmercury and neurodevelopment: longitudinal analysis of the Seychelles child development cohort. Neurotoxicol Teratol 28(5):529–535. https://doi.org/10.1016/j.ntt.2006.06.002
Davidson PW, Strain JJ, Myers GJ et al (2008) Neurodevelopmental effects of maternal nutritional status and exposure to methylmercury from eating fish during pregnancy. Neurotoxicology 29(5):767–775
Debes F, Budtz-Jorgensen E, Weihe P, White RF, Grandjean P (2006) Impact of prenatal methylmercury exposure on neurobehavioral function at age 14 years. Neurotoxicol Teratol 28(5):536–547
Dietl B, Henares D, Boix-Palop L, Munoz-Almagro C, Garau J, Calbo E (2021) Related factors to streptococcus pneumoniae invasive infection and clinical manifestations: the potential role of nasopharyngeal microbiome. Front Med (lausanne) 8:650271. https://doi.org/10.3389/fmed.2021.650271
Driscoll CT, Mason RP, Chan HM, Jacob DJ, Pirrone N (2013) Mercury as a global pollutant: sources, pathways, and effects. Environ Sci Technol 47(10):4967–4983. https://doi.org/10.1021/es305071v
Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Cons 61:1–10. https://doi.org/10.1016/0006-3207(92)91201-3
Falony G, Joossens M, Vieira-Silva S et al (2016) Population-level analysis of gut microbiome variation. Science 352(6285):560–564. https://doi.org/10.1126/science.aad3503
FDA (1991–2010) Mercury levels in commercial fish and shellfish. http://www.fda.gov/Food/FoodborneIllnessContaminants/Metals/ucm115644.htm
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152. https://doi.org/10.1093/bioinformatics/bts565
Gilmour CC, Elias DA, Kucken AM et al (2011) Sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation. Appl Environ Microbiol 77(12):3938–3951. https://doi.org/10.1128/AEM.02993-10
Gilmour CC, Podar M, Bullock AL, Graham AM, Brown SD, Somenahally AC, Johs A, Hurt RA Jr, Bailey KL, Elias DA (2013) Mercury methylation by novel microorganisms from new environments. Environ Sci Technol 47(20):11810–11820. https://doi.org/10.1021/es403075t
Graham AM, Bullock AL, Maizel AC, Elias DA, Gilmour CC (2012) Detailed assessment of the kinetics of Hg-cell association, Hg methylation, and methylmercury degradation in several Desulfovibrio species. Appl Environ Microbiol 78(20):7337–7346. https://doi.org/10.1128/AEM.01792-12
Grandjean P, Weihe P, White RF et al (1997) Cognitive deficit in 7-year-old children with prenatal exposure to methylmercury. Neurotoxicol Teratol 19(6):417–428
Guo G, Yumvihoze E, Poulain AJ, Man Chan H (2018) Monomethylmercury degradation by the human gut microbiota is stimulated by protein amendments. J Toxicol Sci 43(12):717–725. https://doi.org/10.2131/jts.43.717
Han J, Yang X, Chen X et al (2017) Hydrogen sulfide may attenuate methylmercury-induced neurotoxicity via mitochondrial preservation. Chem Biol Interact 263:66–73. https://doi.org/10.1016/j.cbi.2016.12.020
Harkey MR (1993) Anatomy and physiology of hair. Forensic Sci Int 63(1–3):9–18
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35(2):518–522. https://doi.org/10.1093/molbev/msx281
Holscher HD, Bauer LL, Gourineni V, Pelkman CL, Fahey GC Jr, Swanson KS (2015) Agave inulin supplementation affects the fecal microbiota of healthy adults participating in a randomized, double-blind, placebo-controlled, crossover. Trial J Nutr 145(9):2025–2032. https://doi.org/10.3945/jn.115.217331
Ishihara N (2000) Excretion of methyl mercury in human feces. Arch Environ Health 55(1):44–47. https://doi.org/10.1080/00039890009603384
Iwata H, Masukawa T, Kito H, Hayashi M (1982) Degradation of methylmercury by selenium. Life Sci 31(9):859–866. https://doi.org/10.1016/0024-3205(82)90541-0
Jacobson JL (2001) Contending with contradictory data in a risk assessment context: the case of methylmercury. Neurotoxicology 22(5):667–675
Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1):5114. https://doi.org/10.1038/s41467-018-07641-9
Kembel SW, Cowan PD, Helmus MR et al (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26(11):1463–1464. https://doi.org/10.1093/bioinformatics/btq166
Khan MA, Wang F (2010) Chemical demethylation of methylmercury by selenoamino acids. Chem Res Toxicol 23(7):1202–1206. https://doi.org/10.1021/tx100080s
Kozak S, Forsberg CW (1979) Transformation of mercuric chloride and methylmercury by the rumen microflora. Appl Environ Microbiol 38(4):626–636
Kreuger F (2023) Trim Galore 0.6.5. https://github.com/FelixKrueger/TrimGalore Accessed June 2022
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923
Legrand M, Lam R, Passos CJ, Mergler D, Salin ED, Chan HM (2007) Analysis of mercury in sequential micrometer segments of single hair strands of fish-eaters. Environ Sci Technol 41(2):593–598
Li YF, Chen C, Li B et al (2008) Scalp hair as a biomarker in environmental and occupational mercury exposed populations: suitable or not? Environ Res 107(1):39–44. https://doi.org/10.1016/j.envres.2007.07.003
Liebert CA, Wireman J, Smith T, Summers AO (1997) Phylogeny of mercury resistance (mer) operons of gram-negative bacteria isolated from the fecal flora of primates. Appl Environ Microbiol 63(3):1066–1076
Menni C, Zierer J, Pallister T et al (2017) Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women. Sci Rep 7(1):11079. https://doi.org/10.1038/s41598-017-10382-2
Myers RJ, Hamilton JB (1951) Regeneration and rate of growth of hairs in man. Ann N Y Acad Sci 53(3):562–568
Narukawa T, Iwai T, Chiba K, Feldmann J (2018) A method for methylmercury and inorganic mercury in biological samples using high performance liquid chromatography-inductively coupled plasma mass spectrometry. Anal Sci 34(11):1329–1334. https://doi.org/10.2116/analsci.18P255
Norseth T (1973) Biliary excretion and intestinal reabsorption of mercury in the rat after injection of methyl mercuric cloride. Acta Pharmacol Toxicol (copenh) 33(4):280–288
Norseth T, Clarkson TW (1970) Studies on the biotransformation of 203Hg-labeled methyl mercury chloride in rats. Arch Environ Health 21(6):717–727
NRC (2000) toxicological effects of methylmercury. National Academies Press, Washington
Oken E, Bellinger DC (2008) Fish consumption, methylmercury and child neurodevelopment. Curr Opin Pediatr 20(2):178–183
Pan-Hou HS, Imura N (1981) Role of hydrogen sulfide in mercury resistance determined by plasmid of Clostridium cochlearium T-2. Arch Microbiol 129(1):49–52. https://doi.org/10.1007/BF00417179
Perez-Valdespino A, Celestino-Mancera M, Villegas-Rodriguez VL, Curiel-Quesada E (2013) Characterization of mercury-resistant clinical Aeromonas species. Braz J Microbiol 44(4):1279–1283
Podar M, Gilmour CC, Brandt CC et al (2015) Global prevalence and distribution of genes and microorganisms involved in mercury methylation. Sci Adv 1(9):e1500675. https://doi.org/10.1126/sciadv.1500675
Rand MD (2014) A method of permeabilization of Drosophila embryos for assays of small molecule activity. J Visual Exp JoVE. https://doi.org/10.3791/51634
Rand MD, Caito SW (2019) Variation in the biological half-life of methylmercury in humans: methods, measurements and meaning. Biochim Biophys Acta Gen Subj. https://doi.org/10.1016/j.bbagen.2019.02.003
Rand MD, Montgomery SL, Prince L, Vorojeikina D (2014) Developmental toxicity assays using the Drosophila model. Curr Protoc Toxicol 59:1 12 1-1 12 20. https://doi.org/10.1002/0471140856.tx0112s59
Rand MD, Vorojeikina D, van Wijngaarden E et al (2016) Methods for individualized determination of methylmercury elimination rate and de-methylation status in humans following fish consumption. Toxicol Sci 149(2):385–395. https://doi.org/10.1093/toxsci/kfv241
Rothenberg SE, Keiser S, Ajami NJ et al (2016) The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study. Toxicol Lett 242:60–67. https://doi.org/10.1016/j.toxlet.2015.11.022
Rowland IR (1988) Interactions of the gut microflora and the host in toxicology. Toxicol Pathol 16(2):147–153. https://doi.org/10.1177/019262338801600207
Rowland IR, Davies MJ, Grasso P (1975) The methylation of mercury by the gastro-intestinal contents of the rat. Biochem Soc Trans 3(4):502–504
Rowland IR, Davies MJ, Grasso P (1977) The effect of elimination of the gastrointestinal flora on the accumulation of methylmercuric chloride by the rat. Biochem Soc Trans 5(2):423–425
Rowland IR, Davies MJ, Grasso P (1978) Metabolism of methylmercuric chloride by the gastro-intestinal flora of the rat. Xenobiotica Fate Foreign Compd Biol Syst 8(1):37–43
Rowland IR, Robinson RD, Doherty RA (1984) Effects of diet on mercury metabolism and excretion in mice given methylmercury: role of gut flora. Arch Environ Health 39(6):401–408
Salazar N, Dewulf EM, Neyrinck AM et al (2015) Inulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women. Clin Nutr 34(3):501–507. https://doi.org/10.1016/j.clnu.2014.06.001
Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M, Blum P (2004) Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption. J Bacteriol 186(2):427–437. https://doi.org/10.1128/JB.186.2.427-437.2004
Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541. https://doi.org/10.1128/AEM.01541-09
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153
Shannon PT, Grimes M, Kutlu B, Bot JJ, Galas DJ (2013) RCytoscape: tools for exploratory network analysis. BMC Bioinform 14:217. https://doi.org/10.1186/1471-2105-14-217
Sherlock J, Hislop J, Newton D, Topping G, Whittle K (1984) Elevation of mercury in human blood from controlled chronic ingestion of methylmercury in fish. Hum Toxicol 3(2):117–131
Sievers F, Higgins DG (2021) The clustal omega multiple alignment package. Methods Mol Biol 2231:3–16. https://doi.org/10.1007/978-1-0716-1036-7_1
Smith JC, Allen PV, Turner MD, Most B, Fisher HL, Hall LL (1994) The kinetics of intravenously administered methyl mercury in man. Toxicol Appl Pharmacol 128(2):251–256. https://doi.org/10.1006/taap.1994.1204
Stanisich VA, Bennett PM, Richmond MH (1977) Characterization of a translocation unit encoding resistance to mercuric ions that occurs on a nonconjugative plasmid in Pseudomonas aeruginosa. J Bacteriol 129(3):1227–1233. https://doi.org/10.1128/jb.129.3.1227-1233.1977
Stringary J, Nunes AKC, Franco JL, Bohrer D, Garcia SC, Dafre AL, Milatovie D, Souza DO, Rocha JBT, Aschner M, Farina M (2008) Prenatal methylmercury exposure hampers glutathione antioxidant system ontogenesis and causes long-lasting oxidative stress in the mouse brain. Toxicol Appl Pharmacol 227:147–154
Team RC (2020) R: a language and environment for statisical computing. R Foundation for Statistical Computing, Vienna
Uritskiy GV, DiRuggiero J, Taylor J (2018) MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6(1):158. https://doi.org/10.1186/s40168-018-0541-1
Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15(3):R46. https://doi.org/10.1186/gb-2014-15-3-r46
Xiao J, Cao H, Chen J (2017) False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing. Bioinformatics 33(18):2873–2881. https://doi.org/10.1093/bioinformatics/btx311
Yaginuma-Sakurai K, Murata K, Iwai-Shimada M et al (2012) Hair-to-blood ratio and biological half-life of mercury: experimental study of methylmercury exposure through fish consumption in humans. J Toxicol Sci 37(1):123–130
Yamashita Y, Yabu T, Yamashita M (2010) Discovery of the strong antioxidant selenoneine in tuna and selenium redox metabolism. World J Biol Chem 1(5):144–150. https://doi.org/10.4331/wjbc.v1.i5.144
Yang XF, Yang SC, Wen FL et al (2022) Impacts of mercury exposure levels and sources on the demethylation of methylmercury through human gut microbiota. Bull Environ Contam Toxicol 109(3):534–541. https://doi.org/10.1007/s00128-022-03569-5
Zhernakova A, Kurilshikov A, Bonder MJ et al (2016) Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352(6285):565–569. https://doi.org/10.1126/science.aad3369
Zhuang P, Zhang Y, Shou Q et al (2020) Eicosapentaenoic and docosahexaenoic acids differentially alter gut microbiome and reverse high-fat diet-induced insulin resistance. Mol Nutr Food Res 64(10):e1900946. https://doi.org/10.1002/mnfr.201900946
Funding
Supported by NIEHS R01 ES030940, P30 ES001247, T32 207026.
Author information
Authors and Affiliations
Contributions
GLC: Germ-free and gnotobiotic mouse models, Alistipes onderdonkii experiments, mouse model sample processing and MeHg elimination data acquisition, interpretation, materials and methods, results, figures, and editing. INK: Human Trials, human sample processing and MeHg elimination data acquisition, in vitro human fecal cultures, mouse model sample processing and MeHg elimination data acquisition, interpretation, materials and methods, results, figures, and editing. MM-E: Metagenomic sequence analysis, bioinformatics, interpretation, materials and methods, results, figures, and editing. CRB: Human Trials, human MeHg elimination data acquisition, materials and methods, and results. DV: Human Trials and human sample processing. DRC: Bioinformatics and materials and methods. EJB: Co-advisor, experimental design, interpretation, results, introduction, discussion, and editing. STW: Co-advisor, experimental design, interpretation, results, introduction, discussion, and editing. MDR: Co-advisor, experimental design, human Trials, human sample processing interpretation, results, introduction, discussion, and editing.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare there are no conflicts of interest.
Ethical standards
All the procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. All human and animal studies included in this study have been reviewed and approved by the appropriate Institutional Review Boards (IRBs) of the respective institutions where the studies were conducted (Human Clinical Trials reviewed by the University of Rochester IRB and registered (NCT04060212) and mouse studies reviewed by the Montana State University IRB). All human volunteers participating in this study have given their informed consent prior to enrolling in the study.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Coe, G.L., Krout, I.N., Munro-Ehrlich, M. et al. Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice. Arch Toxicol 97, 2399–2418 (2023). https://doi.org/10.1007/s00204-023-03548-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00204-023-03548-7