Biology subjects

Saikkonen, K.

Publications and source records attributed to Saikkonen, K..

5 recordsLinked to original sources

bioRxiv2026

Glyphosate as a driver of antimicrobial resistance evolution in bacteria

Glyphosate, the worlds most widely used herbicide, targets the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which is conserved across plants and many bacteria. While its environmental effects are increasingly recognized, its role on antimicrobial resistance (AMR) remains incompletely understood. In particular, the link between intrinsic glyphosate sensitivity and AMR gene content or evolutionary dynamics has not been systematically explored. We examined the relationship between bacterial sensitivity to glyphosate, AMR profiles, and the evolution of AMR genes. We analyzed genome datasets from the human gut microbiota and the Alignable Tight Genomic Clusters (ATGC). EPSPS sequences were identified via BLAST and annotations and classified based on the intrinsic sensitivity to glyphosate using the EPSPSClass webserver. AMR genes, including associated drug classes and resistance mechanisms, were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Across datasets, glyphosate-sensitive bacteria carried a greater diversity of AMR genes and mechanisms. In contrast, probabilistic modeling revealed that glyphosate-resistant bacteria accumulate AMR genes at significantly higher rates. Phylogenetic birth-and-death analyses and stochastic mapping further revealed elevated AMR gene gain, loss, expansion, and reduction in resistant strains. These results indicate a decoupling between AMR gene diversity and evolutionary dynamics: sensitive bacteria maintain more resistance genes, whereas resistant bacteria display accelerated AMR gene turnover. This suggests that glyphosate resistance is linked to increased genome dynamics, potentially enhancing bacterias adaptability under combined herbicide and antimicrobial pressures. Given glyphosates extensive agricultural use and potential human exposure, these findings highlight an underappreciated link between herbicide resistance and the evolution of AMR in bacterial populations.

microbiology↗

bioRxiv2025

Plastic-Degrading Clusters of Orthologous Groups in Prokaryotes

Micro- and nanoplastic pollution (MNPP) is an increasing environmental threat due to the persistence, dispersal, and potential toxicity of plastic particles. Although microbial biodegradation offers a sustainable mitigation strategy, a comprehensive understanding of plastic-degrading proteins across microbial taxa is lacking. Here, we present the Plastic-Degrading Clusters of Orthologous Groups (PDCOGs) database (https://phylobone.com/microworld/PDCOG), comprising 625,616 potential plastic-degrading proteins (PPDPs) from free-living prokaryotes organized into 51 orthologous groups. The database/PDCOGs enable systematic analysis of microbial plastic-degrading capacity across ecosystems and phylogenetic lineages. Notably, PPDPs constitute [~]3.5% of all prokaryotic proteins, with over 95% of the species having the potential to biodegrade at least one plastic polymer type. This resource provides a genomic tool/framework for exploring the ecological and evolutionary importance of plastic biodegradation and supports future efforts to mitigate the global MNPP crisis.

microbiology↗

bioRxiv2020

Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (EPSPS) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in autotrophs. Our results reveal that bacteria easily become resistant to glyphosate through changes in the EPSPS active site. This indicates the importance of examining how glyphosate affects microbe-mediated ecosystem functions and human microbiomes.

microbiology↗

bioRxiv2020

Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase)

Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from >90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.

bioinformatics↗

bioRxiv2019

Parental effects via glyphosate-based herbicides in a bird model?

Controversial glyphosate-based herbicides (GBHs) are the most frequently used herbicides across the globe. In an increasing number of studies, researchers have identified GBH residues in soil, water, crops, and food products exposing non-target organisms to health risks; these organisms include wildlife, livestock, and humans. However, GBH-related parental effects are poorly understood. In the case of birds, GBHs may be transferred directly from mother to developing offspring (i.e. direct effects) via eggs, or they may indirectly influence offspring performance by altered maternal condition or resource allocation to eggs, for example. We experimentally exposed a parental generation of Japanese quails (Coturnix japonica) to GBHs or respective controls, recorded egg quality and glyphosate residues in eggs, and studied embryonic development and oxidative biomarkers. Glyphosate accumulated in eggs (ca 0.76 kg/mg). Embryonic development tended to be lower in eggs of GBH-exposed parents compared to control parents. Embryonic brain tissue from GBH-exposed parents tended to express more lipid damage. Given that we detected no differences in egg quality (egg, yolk, or shell mass, or egg hormone concentration) across the treatment groups, our results suggest these are likely direct effects of GBHs on offspring rather than indirect effects via altered maternal allocation of resources or hormonal signals. CapsuleExperimental, long-term parental exposure to GBHs tends to hinder offspring embryonic development and increase embryonic oxidative damage to lipids in a bird model.

pharmacology and toxicology↗