1.Introduction

Glyphosate, chemically N-(phosphonomethyl) glycine, has become a defining feature of modern agriculture. Since its introduction under the trade name Roundup in the 1970s, it has earned global prominence as the most widely applied herbicide, shaping landscapes from vast croplands to urban gardens (Duke & Powles, 2008; Benbrook, 2016). Its appeal lies in remarkable attributes: broad-spectrum weed control, cost-effectiveness, and compatibility with genetically modified glyphosate-resistant crops. By targeting a central metabolic pathway absent in humans and other animals, glyphosate was initially regarded as environmentally safe and biologically selective (Funke et al., 2006; Giesy et al., 2000). Yet, decades of research are revealing a more nuanced story—glyphosate’s reach extends far beyond plants, subtly influencing the microbial communities that underpin ecosystem health and human well-being (Kremer & Means, 2009; Krüger et al., 2013; Shehata et al., 2013).

At the heart of glyphosate’s herbicidal action is the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), a pivotal enzyme in the shikimate pathway that produces aromatic amino acids in plants and numerous microorganisms (Funke et al., 2006; Duke & Powles, 2008). Because mammals lack this pathway, glyphosate was long assumed to pose minimal risk to human and animal health (Samsel & Seneff, 2013). However, this assumption overlooks a crucial dimension: the shikimate pathway is essential in soil microbes, fungi, and bacteria, making these microbial communities vulnerable to glyphosate exposure (Claus et al., 2011; Flint et al., 2012). As global glyphosate use continues to rise, the potential for widespread microbial disruption raises urgent questions about ecological resilience and long-term sustainability (Battaglin et al., 2014; Benbrook, 2016).

Soil represents one of the most sensitive and consequential arenas of glyphosate impact. Beneath the surface, diverse microbial communities—nitrogen-fixing bacteria, mycorrhizal fungi, and other beneficial organisms—drive nutrient cycling, bolster plant growth, and maintain soil fertility (Zobiole et. al., 2011; Ratcliff et al., 2006). Evidence shows that glyphosate can suppress these beneficial microbes while creating ecological niches for pathogenic species such as Fusarium, compromising crop health and yield (Kremer & Means, 2009; Johal & Huber, 2009; Jezierska-Tys et al., 2021). These shifts threaten soil resilience, undermining the very ecological services upon which sustainable agriculture depends (Neves et al., 2019).

Beyond terrestrial soils, glyphosate’s influence extends to the human gut microbiome, a complex ecosystem integral to metabolism, immunity, and overall health. Studies indicate that glyphosate selectively inhibits beneficial bacteria such as Lactobacillus and Bifidobacterium while enabling the proliferation of resistant pathogens like Clostridium (Shehata et al., 2013; Motto et al., 2018; Balbuena et al., 2015). Such microbial imbalances, or dysbiosis, have been associated with metabolic disorders, inflammatory conditions, and immune dysfunctions (Mesnage, Defarge, Rocque, & de Vendômois, 2015; Cryan & Dinan, 2012). Given the central role of gut microbiota in human health, these findings signal an underappreciated public health dimension of glyphosate exposure (Mao et al., 2018).

Aquatic ecosystems, too, are not spared. Herbicide runoff introduces glyphosate into freshwater habitats, where it can diminish phytoplankton populations, disrupt microbial food webs, and promote eutrophication (Vera et al., 2010; Relyea, 2005; Pleasants & Oberhauser, 2013). Such disturbances ripple through aquatic food chains, threatening biodiversity, altering energy flow, and compromising water quality—demonstrating that glyphosate’s ecological footprint is both pervasive and profound (Giesy et al., 2000).

Despite its global ubiquity and decades of research, the full scope of glyphosate’s ecological and biological impacts remains a topic of intense debate. Much of the early literature emphasized direct plant toxicity and acute effects, leaving the more subtle yet consequential microbial interactions underexplored (Motto et al., 2018; Mesnage et al., 2015). Addressing this gap is critical for understanding glyphosate’s broader consequences for ecosystem function and human health.

This study aims to synthesize current knowledge on glyphosate’s ecological and biological effects, with a focus on soil, gut, and aquatic microbiomes. Specifically, we evaluate its mode of action in relation to the absence of the shikimate pathway in animals, investigate impacts on soil microbial diversity, nutrient cycling, and pathogen prevalence, and examine glyphosate-induced alterations in the human gut microbiome and freshwater microbial ecosystems (Zobiole et al., 2011; Neves et al., 2019). By integrating evidence across terrestrial, human, and aquatic systems, we aim to provide a holistic perspective on the hidden legacy of this ubiquitous herbicide.

2. Material and Method

2.1 Study Design

This study employed a systematic literature review approach to examine the ecological and biological impacts of glyphosate, with a focus on soil microbiota, human gut microbiota, and aquatic ecosystems. A review methodology was deemed appropriate as it allowed for the synthesis of diverse research findings published prior to 2018, facilitating a comprehensive evaluation of glyphosate’s indirect effects on microbial communities and associated ecological and health outcomes. The review followed general principles of systematic evidence synthesis, prioritizing transparency, reproducibility, and critical appraisal of existing studies.

2.2 Data Sources and Search Strategy

Relevant literature was retrieved from a range of electronic databases, including Web of Science, PubMed, Scopus, and Google Scholar. Searches were conducted using combinations of keywords and Boolean operators: “glyphosate” AND “microbiome”, “glyphosate” AND “soil microorganisms”, “glyphosate” AND “gut microbiota”, and “glyphosate” AND “aquatic ecosystems”. Filters were applied to restrict studies to those published up to December 2017, ensuring the review aligned with the aim of evaluating pre-2018 evidence. Additional articles were identified through reference list screening of key publications and relevant review papers.

2.3 Eligibility Criteria

To ensure rigor, the following inclusion criteria were applied:

• Study type: Peer-reviewed empirical studies, experimental research, or systematic reviews.
• Focus: Research addressing the impact of glyphosate or glyphosate-based herbicides on soil microbial communities, human gut microbiota, or aquatic ecosystems.

• Publication date: Studies published prior to January 2018.
• Language: Publications in English.
• Relevance: Studies explicitly assessing microbial changes, ecological outcomes, or health implications associated with glyphosate exposure.

Exclusion criteria included: non-peer-reviewed reports, conference abstracts without full papers, studies focusing exclusively on plant physiology without microbial assessment, and publications not available in English.

2.4 Data Extraction and Synthesis

Data extraction was carried out systematically using a structured template to ensure consistency across studies. Extracted information included:

• Author(s) and year of publication
• Study location and design (laboratory, field, or clinical)
• Microbial system assessed (soil, gut, or aquatic)
• Type and concentration of glyphosate exposure
• Main findings relating to microbial diversity, function, or ecological consequences

The synthesis process was narrative rather than meta-analytical, due to heterogeneity in study designs, exposure concentrations, and outcome measures. Findings were grouped thematically into three domains: (1) soil microbiota and agricultural sustainability, (2) gut microbiota and human health, and (3) aquatic ecosystems and biodiversity. This thematic organization aligned with the study objectives and facilitated comparison across ecological contexts.

2.5 Quality Assessment

Each included study was appraised for methodological rigor. Criteria included clarity of experimental design, appropriateness of controls, exposure relevance to real-world conditions, and statistical robustness. Studies with clear methodological weaknesses (e.g., absence of control groups or unrealistic glyphosate concentrations) were not excluded but were critically evaluated to contextualize the strength of their conclusions.

2.6 Limitations of Methodology

The methodology has several limitations. First, restricting the review to studies published before 2018 excludes more recent findings that may provide additional insights into glyphosate’s impacts. However, this was intentional to align with the study’s scope. Second, the narrative synthesis approach, while suitable for heterogeneous data, limits the ability to quantify effect sizes through meta-analysis. Third, language restrictions may have excluded non-English studies that could contribute valuable regional perspectives, particularly from areas with intensive glyphosate use. Despite these limitations, the systematic approach and use of multiple databases ensured a broad and comprehensive coverage of the literature.

3. The Expanding Evidence: Glyphosate’s Hidden Impacts on Microbial Life

3.1 Glyphosate: Mechanism of Action and Safety Assumptions

Glyphosate functions primarily as a non-selective herbicide by inhibiting the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) within the shikimate pathway, a critical metabolic route for synthesizing aromatic amino acids in plants and many microorganisms (Funke et al., 2006; Duke & Powles, 2008). Because animals and humans lack this pathway, glyphosate was initially considered non-toxic to higher organisms, a perception that contributed to its global dominance in agriculture, particularly with glyphosate-resistant genetically modified crops (Benbrook, 2016; Jezierska-Tys et al., 2021) (Table 1).

However, emerging evidence challenges this assumption of safety. Many microorganisms, including bacteria and fungi, rely on the shikimate pathway, making them vulnerable to glyphosate inhibition (Claus et al., 2011; Flint et al., 2012). These microbes are central to ecological processes in soil, water, and the human gut, suggesting that glyphosate’s widespread use may have cascading effects on ecosystem function and public health (Krüger et al., 2013; Shehata et al., 2013).

3.2 Impacts on Soil Microbiota

Soil is a dynamic ecosystem where microbial communities sustain fertility, regulate nutrient cycling, and support plant health (Zobiole, et al., 2011; Ratcliff et al., 2006). Glyphosate exposure disrupts these communities by suppressing beneficial organisms and facilitating the growth of pathogens. For instance, glyphosate reduces populations of nitrogen-fixing bacteria, such as Rhizobium, impairing plant nutrient uptake, and negatively affects mycorrhizal fungi, reducing soil productivity (Kremer & Means, 2009; Johal & Huber, 2009; Jezierska-Tys et al., 2021).

Pathogenic fungi, including Fusarium species, often proliferate under glyphosate exposure, increasing soilborne disease risk and threatening long-term crop sustainability (Neves et al., 2019). Glyphosate’s persistence in soil, amplified by repeated applications, intensifies these disruptions, ultimately undermining soil resilience and ecosystem services crucial for sustainable agriculture (Van Bruggen et al., 2018).

3.3 Effects on the Human Gut Microbiome

The human gut microbiome is essential for metabolism, immune regulation, and overall health (Cryan & Dinan, 2012). Glyphosate exposure has been shown to selectively inhibit beneficial bacteria, including Lactobacillus and Bifidobacterium, while allowing resistant pathogens such as Clostridium to persist (Shehata et al., 2013; Motto et al., 2018; Balbuena et al., 2015). This microbial imbalance, or dysbiosis, is associated with metabolic disorders, inflammatory diseases, and immune dysfunction (Mesnage et al., 2015; Cryan & Dinan, 2012).

Glyphosate residues have also been detected in food products and human urine, raising concerns about chronic low-dose exposure (Mao et al., 2018). Although regulatory agencies consider these levels below harmful thresholds, the cumulative impact on gut microbial diversity remains uncertain, particularly given that most studies prior to 2018 focused on acute toxicity rather than microbiome-specific outcomes.

3.4 Glyphosate in Aquatic Ecosystems

Aquatic ecosystems are highly susceptible to glyphosate contamination via agricultural runoff. Studies have documented reductions in phytoplankton populations, disruptions of microbial food webs, and the promotion of eutrophication in freshwater habitats (Vera et al., 2010; Relyea, 2005; Pleasants & Oberhauser, 2013). Reductions in photosynthetic microorganisms compromise oxygen production and nutrient cycling, while resistant cyanobacteria may proliferate, causing harmful algal blooms (Márquez et al., 2017).

Although glyphosate degrades faster in water than in soil, recurrent runoff ensures continuous exposure, posing ongoing risks to aquatic biodiversity and ecosystem stability (Annett etal., 2014). These ecological disruptions have downstream effects on human communities that rely on freshwater resources.

3.5 Ecological and Public Health Concerns

Collectively, glyphosate’s impacts on soil, gut, and aquatic microbiomes raise serious ecological and health concerns. Soil microbial disruption threatens crop resilience and food security; gut dysbiosis compromises metabolic and immune function; and aquatic disturbances reduce biodiversity and water quality (Mason et al., 2012; Benbrook, 2016). These effects are often subtle and cumulative, complicating regulatory assessments that emphasize acute toxicity rather than chronic ecological shifts.

Public health debates are further complicated by potential carcinogenicity. The International Agency for Research on Cancer (IARC) classified glyphosate as “probably carcinogenic to humans” in 2015, highlighting the need to integrate microbiome-focused evidence into risk assessments (Guyton et al., 2015).

3.6 Gaps in Literature and Research Directions

Research conducted prior to 2018 largely emphasized herbicidal properties and acute toxicity, overlooking glyphosate’s indirect effects on microbial systems (Mesnage & Antoniou, 2017). Many studies were short-term and conducted under controlled laboratory conditions, limiting their ecological relevance (Van Bruggen et al., 2018).

Future investigations should employ longitudinal, field-based studies to capture cumulative effects across ecosystems. Interdisciplinary approaches integrating soil science, microbiology, toxicology, and public health are essential for a holistic understanding of glyphosate’s impacts. Sustainable agricultural practices—such as crop diversification, reduced pesticide dependency, and non-chemical weed management—should also be explored to mitigate ecological and human health risks (Zobiole et al., 2011; Neves et al., 2019) (Table 2).

Table 1: Effects of Glyphosate on Microbial Communities

Table 2:  Research Gaps in Glyphosate Studies (Pre-2018 Literature)

4. Results

4.1 Glyphosate’s Mode of Action and Safety Assumptions

Glyphosate exerts its herbicidal effect primarily by inhibiting the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), a key component of the shikimate pathway necessary for the synthesis of aromatic amino acids in plants and many microorganisms (Funke et al., 2006; Duke & Powles, 2008). Because this pathway is absent in animals and humans, glyphosate was historically considered safe for higher organisms (Benbrook, 2016). However, microorganisms—including bacteria and fungi—possess this pathway, and emerging evidence suggests glyphosate can inadvertently disrupt microbial communities critical for ecosystem and human health (Mesnage et al., 2015; Motta et al., 2018). These non-target effects indicate that the initial safety assumptions may overlook broader ecological and biological risks.

4.2 Effects on Soil Microbial Communities

Glyphosate application has been shown to alter soil microbial composition, reducing populations of beneficial organisms such as nitrogen-fixing Rhizobium spp. and mycorrhizal fungi, which are essential for nutrient cycling, plant growth, and soil fertility (Zobiole et al., 2011; Van Bruggen et al., 2018). Simultaneously, pathogenic fungi, including Fusarium spp., often increase in abundance in treated soils, raising the risk of soilborne diseases and negatively impacting crop yields (Kremer & Means, 2009; Jezierska-Tys et al., 2021). The persistence of glyphosate in soil and repeated applications can exacerbate these microbial disruptions, cumulatively shifting microbial communities from mutualistic to pathogenic dominance and undermining agricultural resilience.

4.3 Impacts on the Human Gut Microbiome

Glyphosate’s influence extends to the human gut microbiome, where it selectively inhibits beneficial bacteria such as Lactobacillus and Bifidobacterium while allowing resistant taxa, including Clostridium, to persist or proliferate (Shehata et al., 2013; Motta et al., 2018). Such imbalances, or dysbiosis, have been associated with gastrointestinal disorders, metabolic dysfunctions, and immune dysregulation (Mesnage & Antoniou, 2017; Balbuena et al., 2015). Glyphosate residues have been detected in food products and human urine, indicating widespread exposure (Motta et al., 2018). Although acute toxicity is generally low, chronic low-dose intake may subtly but significantly affect gut microbial diversity, highlighting a potential gap in conventional risk assessments focused solely on direct toxicity.

4.4 Effects on Aquatic Microbial Ecosystems

Aquatic environments are particularly vulnerable to glyphosate runoff, which can reduce phytoplankton abundance, disrupt microbial food webs, and alter nutrient cycling (Vera et al., 2010; Annett et al., 2014). The decline of photosynthetic microorganisms reduces oxygen production, while resistant cyanobacteria may proliferate, contributing to harmful algal blooms (Márquez et al., 2017). These microbial imbalances promote eutrophication, compromise water quality, and threaten aquatic biodiversity, with cascading consequences for fisheries and human communities reliant on freshwater resources. Despite faster degradation in water relative to soil, recurring agricultural runoff ensures continuous exposure, maintaining ecological disruption.

4.5 Broader Ecological and Public Health Concerns

Across soil, gut, and aquatic systems, glyphosate’s effects extend beyond its intended herbicidal action. In soil, it reduces microbial diversity essential for agriculture; in humans, it destabilizes gut microbiota crucial for metabolic and immune health; and in aquatic systems, it disrupts ecological stability and biodiversity. These converging impacts suggest that glyphosate functions as a broad-spectrum microbial disruptor rather than a plant-selective herbicide (Mason et al., 2012). Moreover, glyphosate’s potential role in carcinogenesis adds complexity to risk evaluations. In 2015, the International Agency for Research on Cancer (IARC) classified glyphosate as “probably carcinogenic to humans,” intensifying debate over its safety (Guyton et al., 2015). Evidence of microbiome disruption provides additional indirect pathways through which glyphosate could influence human disease.

4.6 Gaps and Limitations in Existing Research

Prior to 2018, research largely emphasized glyphosate’s herbicidal properties and acute toxicity, often under controlled laboratory conditions (Mesnage & Antoniou, 2017). Long-term, cumulative effects on microbial communities in real-world agricultural and environmental contexts remain underexplored. Most studies focused on acute toxicity thresholds while neglecting sub-lethal impacts, such as shifts in community composition or functional disruption (Van Bruggen et al., 2018). These gaps underscore the need for longitudinal, interdisciplinary research integrating soil science, microbiology, toxicology, and public health to capture the full spectrum of glyphosate’s ecological and health effects. Such work is critical for informing sustainable agricultural practices and regulatory policies.

5. Discussion

The findings of this study underscore glyphosate’s far-reaching impacts on microbial ecosystems, challenging the long-standing narrative of its relative safety. While glyphosate was designed to target the shikimate pathway in plants, evidence indicates that its effects extend to microorganisms, which rely on the same pathway for survival. This disruption highlights a critical oversight in regulatory assumptions that considered glyphosate safe for humans and animals, since their cells lack this metabolic pathway (Funke et al., 2006; Mason et al., 2012). The discussion draws together evidence from soil, human gut, and aquatic systems to evaluate glyphosate’s broader ecological and health implications.

5.1 Soil Microbiome and Agricultural Sustainability

The reviewed literature demonstrates that glyphosate application consistently reduces populations of beneficial microorganisms, such as nitrogen-fixing bacteria and mycorrhizal fungi, while encouraging the proliferation of pathogenic fungi like Fusarium (Kremer & Means, 2009; Zobiole et al., 2011). This shift has significant implications for agricultural sustainability. Healthy soil microbial communities are essential for nutrient cycling, plant disease resistance, and long-term soil fertility. By undermining these processes, glyphosate indirectly contributes to declining crop resilience and increased dependency on chemical inputs. This aligns with the objective of evaluating glyphosate’s role in soil health and points to the risk of reduced agricultural sustainability over time (Van Bruggen et al., 2018).

5.2 Human Gut Microbiome and Public Health

A second objective of the study was to assess glyphosate’s effects on the human gut microbiome. Findings show that glyphosate selectively inhibits beneficial bacteria, including Lactobacillus and Bifidobacterium, while enabling resistant pathogens to thrive (Krüger, 2013). This microbial imbalance, or dysbiosis, is linked to immune dysfunction, inflammatory disorders, and metabolic diseases (Mesnage & Antoniou, 2017; Balbuena et al., 2015). Given that glyphosate residues are detectable in food and human urine, even at low levels of exposure (Motta et al., 2018), these findings suggest that glyphosate may act as a hidden driver of chronic disease. The results indicate that regulatory assessments focusing solely on toxicity thresholds may underestimate glyphosate’s indirect but significant role in shaping human health outcomes.

5.3 Aquatic Systems and Ecosystem Balance

The study’s third objective concerned glyphosate’s impact on aquatic microbial systems. Findings revealed that glyphosate runoff reduces phytoplankton populations while promoting cyanobacteria, leading to harmful algal blooms and eutrophication (Vera, et al., 2010; Márquez et al., 2017). These imbalances reduce oxygen production, degrade water quality, and threaten aquatic biodiversity. Such ecological consequences extend to human populations reliant on freshwater ecosystems for drinking water and fisheries. This illustrates that glyphosate’s environmental effects are not confined to agricultural soils but extend into interconnected ecosystems, exacerbating biodiversity loss and ecosystem instability (Annett et al., 2014).

5.4 Broader Implications and Theoretical Insights

Synthesizing across soil, gut, and aquatic systems, glyphosate emerges not as a plant-specific herbicide but as a broad-spectrum microbial disruptor. This insight expands the theoretical framing of herbicide risk: from narrow toxicological assessments of target organisms to a systems-level understanding of ecological and microbial networks. It highlights the need for environmental toxicology to incorporate microbiome science into risk assessments. The findings also align with ecological theories of resilience, which suggest that disturbances to keystone microbial populations can trigger cascading effects across ecosystems (Van Bruggen et al., 2018).

5.5 Practical Implications

From a practical perspective, the findings raise important questions for agricultural policy and practice. The overreliance on glyphosate-resistant crops and repeated herbicide application fosters ecological degradation, potentially leading to declining yields and food insecurity. Policymakers and practitioners should consider strategies such as crop diversification, integrated pest management, and the development of safer herbicide alternatives. For public health, stricter monitoring of glyphosate residues in food and water is necessary to reduce human exposure. These implications reinforce the urgency of reassessing glyphosate’s role in modern agriculture.

6. Conclusion

This study highlights that glyphosate, though widely regarded as an effective herbicide, poses significant risks by disrupting microbial systems vital to ecological and human health. Findings revealed that glyphosate reduces beneficial soil microorganisms while promoting pathogenic species, undermining nutrient cycling and agricultural sustainability. In humans, glyphosate selectively inhibits protective gut bacteria, contributing to dysbiosis and potential long-term health complications. Similarly, in aquatic environments, glyphosate runoff destabilizes microbial food webs, reduces phytoplankton populations, and fosters harmful algal blooms, threatening biodiversity and water quality. These outcomes challenge the long-standing assumption of glyphosate’s safety and emphasize its role as a broad-spectrum microbial disruptor rather than a plant-specific herbicide. The evidence underscores the urgent need for stricter regulation, continuous monitoring, and the development of sustainable agricultural alternatives. Ultimately, safeguarding soil, human, and aquatic microbiomes must be prioritized to balance food security with environmental and public health protection.

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