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

Robin Mesnage, Maxime Teixeira, Daniele Mandrioli, Laura Falcioni, Quinten
Raymond Ducarmon, Romy Daniëlle Zwittink , Caroline Amiel, Jean-Michel Panoff,
Fiorella Belpoggi , Michael N Antoniou


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 (γ-
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® 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 multi-
omics 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.