Glyphosate Exposure Found To Modulate Gut Microbiome Composition

Glyphosate-based herbicides have been extensively used in agriculture, mainly due to the prevalence of genetically modified, glyphosate-resistant food crops. 


However, the widespread use of glyphosate has led to its detection and prevalence in water, soils, food crops, and even human urine, raising flags about its potential effects on human health. Recent studies have linked glyphosate exposure to various diseases, including cancer. 


The gut microbiota has emerged as a potential mediator of glyphosate’s adverse health effects, as it plays a crucial role in maintaining human health and interacts with multiple systems for host homeostasis.


In this article, we’ll take a closer look at this research, alongside how the CosmosID-HUB was used to investigate the effects of glyphosate on gut microbiome composition.


Glyphosate kills weeds by inhibiting the 5-enolpyruvylshikimate-3 phosphate synthase (EPSPS) enzyme, which is a key step in the shikimate pathway responsible for the biosynthesis of essential aromatic amino acids in plants and some microorganisms. 


Mammals lack a shikimate pathway, but glyphosate exposure can impact the gut microbiota by inhibiting gut bacteria that utilize this pathway. 


Past research has demonstrated the sensitivity of many gut resident microbes, including beneficial bacteria like Lactobacillus and Bifidobacterium, to glyphosate. However, the biological link between glyphosate-induced gut dysbiosis and its effects on host physiology remains to be elucidated. 


The widespread use of glyphosate-based herbicides, when combined with their detection in various environmental and human samples, elicits concern about its impact on human health. While glyphosate was initially considered safe for mammals, emerging evidence suggests a potential link between glyphosate exposure and gut dysbiosis. 


To disentangle glyphosate exposure in the human gut microbiome, Lehman et al. (2023) collected fecal samples from glyphosate-exposed mice. The mice were exposed to glyphosate at 0 µg/ml (control), 1 µg/ml, 10 µg/ml. Fecal samples from mice were collected at days 30, 60 and 90. 


The DNA was extracted from the fecal material of experimental mice and sequenced on the Illumina MiSeq platform. Bioinformatics analysis was done by the CosmosID-HUB. The bioinformatics analysis illustrated that increasing glyphosate concentrations crippled Firmicutes and elevated Bacteroidetes relative abundance by day 90. 


Differential abundance analysis of the fecal microbial communities of 10 µg/ml cohort at day 90 identified Clostridia and Lachnospiraceae as the distinguishing taxa, but Actinobacteria and Bifidobacterium were enriched in the control cohort. 


The functional analysis of data by comparing sequence reads against MetaCyc metabolic pathways database showed a clear distinction between the control and 10 µg/ml cohort. The intestinal metabolisms including “pyruvate fermentation to acetate and lactate II”, “acetylene degradation”, and “super pathway of glucose and xylose degradation” were enriched in the control cohort. 


Analyzing pro-inflammatory markers that may have followed microbiome dysbiosis illustrated that increased proinflammatory CD4+IL17A+ T cells and Lipocalin-2, a known marker of intestinal inflammation, were linked with microbial dysbiotic interactions. 


The study discussed here provides valuable insights into the effects of glyphosate on gut microbiota composition and highlights the potential mechanisms through which glyphosate exposure can influence host physiology. 


Further research is needed to fully understand the long-term consequences of glyphosate-induced gut dysbiosis and its implications for human health. Comparing fecal microbiome compositions of humans working in farms where glyphosate is regulated may illustrate how glyphosate exposure within similar environments may affect human health.

How did CosmosID enable this research?

The CosmosID-HUB played a crucial role in enabling this research study. It was the platform of choice for the bioinformatics analysis of microbial community composition and function in response to glyphosate exposure.


It provided a comprehensive suite of tools including differential abundance analysis, taxonomic and functional annotation, core microbiome comparison, gene-family analysis, etc., which enabled the research team to identify and quantify changes in the gut microbiome composition and its functions.


The highly scalable, cloud-based platform allowed the team to analyze large datasets quickly and accurately with ease. Furthermore, CosmosID’s automated sample tracking system enabled efficient data management of samples from multiple locations. 

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Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.