Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/870105

Shotgun metagenomics and metabolomics reveal glyphosate alters the gut microbiome of Sprague-Dawley rats by inhibiting the shikimate pathway

Mesnage, R.·Teixeira, M.·Mandrioli, D.·Falcioni, L.·Ducarmon, Q. R.·Zwittink, R. D.·Amiel, C.·Panoff, J.-M.·Belpoggi, F.·Antoniou, M.
View original source ↗Export metadata ↓

Abstract

There is intense debate as to whether glyphosate can interfere with aromatic amino acid biosynthesis in microorganisms inhabiting the gastrointestinal tract, which could potentially lead to negative health outcomes. We have addressed this major gap in glyphosate toxicology by using a multi-omics strategy combining shotgun metagenomics and metabolomics. We tested whether glyphosate (0.5, 50, 175 mg/kg bw/day), or its representative EU commercial herbicide formulation MON 52276 at the same glyphosate equivalent doses, has an effect on the rat gut microbiome in a 90-day subchronic toxicity test. Clinical biochemistry measurements in blood and histopathological evaluations showed that MON 52276 but not glyphosate was associated with statistically significant increase in hepatic steatosis and necrosis. Similar lesions were also present in the liver of glyphosate-treated groups but not in the control group. Caecum metabolomics revealed that glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase in the shikimate pathway as evidenced by an accumulation of shikimic acid and 3-dehydroshikimic acid. Levels of caecal microbiome dipeptides involved in the regulation of redox balance ({gamma}-glutamylglutamine, cysteinylglycine, valylglycine) had their levels significantly increased. Shotgun metagenomics showed that glyphosate affected caecum microbial community structure and increased levels of Eggerthella spp. and Homeothermacea spp.. MON 52276, but not glyphosate, increased the relative abundance of Shinella zoogleoides. Since Shinella spp. are known to degrade alkaloids, its increased abundance may explain the decrease in solanidine levels measured with MON 52776 but not glyphosate. Other glyphosate formulations may have different effects since Roundup(R) GT Plus inhibited bacterial growth in vitro at concentrations at which MON 52276 did not present any visible effect. Our study highlights the power of a multiomics approach to investigate effects of pesticides on the gut microbiome. This revealed the first biomarker of glyphosate effects on rat gut microbiome. Although more studies will be needed to ascertain if there are health implications arising from glyphosate inhibition of the shikimate pathway in the gut microbiome, our findings can be used in environmental epidemiological studies to understand if glyphosate can have biological effects in human populations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/870105v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@66578corg.highwire.dtl.DTLVardef@fddcd9org.highwire.dtl.DTLVardef@ae4ffforg.highwire.dtl.DTLVardef@5f7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

Source connections

Explore related subjects

pharmacology and toxicologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mesnage, R., Teixeira, M., Mandrioli, D., Falcioni, L., Ducarmon, Q. R., Zwittink, R. D., Amiel, C., Panoff, J.-M., Belpoggi, F., Antoniou, M.. 2019-12-11. Shotgun metagenomics and metabolomics reveal glyphosate alters the gut microbiome of Sprague-Dawley rats by inhibiting the shikimate pathway. https://doi.org/10.1101/870105

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Mathematical model of phenotypic plasticity predicts interconversion is a drug target for neuroblastoma.

Neuroblastoma is a paediatric cancer arising from the sympathetic nervous system as neural crest cells, made up of noradrenergic (NOR/ADRN/N), mesenchymal like (MES/S), and intermediate (I-type/I) cell types. These cells can interconvert between types, contributing to treatment resistance and relapse. We developed a mathematical model to investigate how interconversion patterns affect the efficacy of phenotype-specific inhibitors. We used three ordinary differential equations to describe the dynamics of the three populations, including logistic growth, interconversion, and drug-induced death. Of the 64 possible interconversion patterns, five reduced the target population: two for N cells and three for S cells. N targeting patterns were more effective with higher interconversion rates, while mesenchymal targeting patterns were more effective with lower interconversion rates. Stability analysis revealed that natural tumour growth was always unstable, but during treatment, N-suppressing patterns combined with an S inhibitor gave the most consistently stable origin. Testing multi-stage and cyclic treatment schedules revealed that N-suppressing patterns with an S inhibitor, followed by an S-suppressing pattern with an N inhibitor, achieved more reliable remission. Three of the five patterns of interest correspond to reported biological plausibility, and known compounds exist to induce most of the required transitions, supporting the clinical relevance of these strategies for improving neuroblastoma treatment outcomes.

pharmacology and toxicology↗
bioRxiv2026

Organism-dependent ecotoxicological effects of transition metal-containing layered double hydroxides

Due to low environmental stability of certain molecule classes, such as phytohormones and RNA interference, layered double hydroxides (LDHs) have been investigated as nanocarriers capable of protecting and transporting molecules of interest in natural systems. Herein, the ecotoxicological effects of LDH nanoparticles composed by different transition metals (Al-Ni, Al-Co, and Al-Cu) were evaluated in maize (Zea mays), tomato (Lycopersicum esculentum), and the nematode Caenorhabditis elegans, two important crops and one soil organism found in agricultural systems. Plants were exposed to the nanoparticles through foliar spraying (5, 50, and 500 ug/mL), and physiological parameters were evaluated. In C. elegans, lethality, locomotion, larval development, and body length were analyzed. The nanoparticles exhibited high colloidal stability and characteristic lamellar morphology. The results demonstrated low phytotoxicity for all formulations, without significant changes in photochemical activity, effective quantum yield of photosystem II (psi-PSII), stomatal conductance (gs), and chlorophyll index (Chl a+b; ICF) in plants. In contrast, C. elegans exhibited greater sensitivity, showing reduced motility, developmental delay, and decreased body length, although mortality remained below 12% under all evaluated conditions. Toxicity was dependent on the metallic composition, following the order Al-Cu > Al-Ni > Al-Co. Collectively, the results indicate that LDHs exhibit high compatibility with those two crops but may cause sublethal effects in soil organisms. These findings highlight the importance of multispecies ecotoxicological assessments for the safe development of nanocarriers intended for agricultural applications.

pharmacology and toxicology↗
bioRxiv2026

Aging, HIV Status, and Sex Differentially Influence Antiretroviral Therapy Disposition Pathways in Rectosigmoid Tissue and Peripheral Blood Mononuclear Cells

People living with human immunodeficiency virus (HIV) are increasingly surviving into older age due to the effectiveness of antiretroviral (ARV) therapy (ART), creating a growing population in whom age-related changes may influence treatment outcomes. Although aging is known to affect drug disposition, the molecular mechanisms by which aging alters ARV pharmacology remain incompletely understood, particularly within tissue compartments, including the rectosigmoid region of the colon, that serve as sites of HIV transmission and persistence. To address this knowledge gap, we used proteomics by liquid chromatography-mass spectrometry (LC-MS) to evaluate the impact of age and HIV status on proteins and pathways relevant to ARV disposition in peripheral blood mononuclear cells (PBMC) and rectosigmoid colon tissue obtained from young (18-50) HIV-seronegative adults, older (65-80) HIV-seronegative adults, and older virally suppressed people living with HIV. We found that aging and HIV infection differentially influenced proteins predominantly within nucleos(t)ide reverse transcriptase inhibitor (NRTI) pathways, in rectosigmoid tissue and PBMC. HIV-associated effects to the proteome were more prominent in PBMC, whereas aging produced broader alterations in ARV disposition-related proteins in rectosigmoid tissue, including proteins involved in drug transport, intracellular drug activation, dephosphorylation, and nucleotide homeostasis. Several age-associated changes were further influenced by biologic sex, suggesting that aging may not affect ARV disposition uniformly across populations. To place these findings within a broader context, pathway analyses were performed that identified extensive tissue-specific remodeling associated with aging and HIV infection involving drug disposition, immune regulation, cellular metabolism, and disease-related pathways. Notably, aging was associated with alterations in pathways relevant to nucleotide metabolism and gastrointestinal tissue function, suggesting that processes beyond traditional drug transport and metabolism pathways may contribute to variability in ARV disposition with advancing age. Together, these findings identify aging as an important modifier of pathways that regulate ARV disposition within compartments relevant to HIV transmission and persistence. While the clinical consequences of our findings are unknown, these data provide a mechanistic foundation for future studies investigating whether age-associated changes influence the effectiveness of ART and HIV pre-exposure prophylaxis in older adults.

pharmacology and toxicology↗