Shigella infection, a clinical syndrome induced by the invasion of Shigella bacteria into the terminal ileum, colon, and rectal epithelium, manifests prominently with symptoms such as recurrent bloody stools, fever, diarrhea, weight loss, and abdominal spasms (Kotloff et al., 2018). Shigella, classified as Gram-negative short rods, currently comprises four species: Shigella dysenteriae, Shigella sonnei, Shigella boydii, and Shigella flexneri (Muzembo et al., 2023). This highly transmissible pathogen spreads through various means, including food, water, insect vectors, or direct fecal-oral transmission (Barry and Levine, 2019; Muzembo et al., 2023). Globally, low-income and middle-income countries witness an annual toll of over 200,000 deaths attributed to Shigella infection, with children under the age of five accounting for a staggering 30% (Khalil et al., 2018). In the United Kingdom, there has been an outbreak of multidrug-resistant Shigella sonnei among men who engage in sexual activities with other men (MSM). This outbreak has raised concerns due to the presence of extensively drug-resistant strains, highlighting the challenges posed by antimicrobial resistance in the field of public health. To better understand the genetic epidemiology of this outbreak, researchers conducted genomic analyses on isolates collected from various countries including the UK, Australia, Belgium, France, and the USA (Tansarli et al., 2023). The results of these analyses revealed a strain of Shigella sonnei that is not only multidrug-resistant but also shares a common resistance plasmid, indicating a potential international spread of this resistant strain (Mason et al., 2023; Thorley et al., 2023). Consequently, this underscores the urgent need for enhanced global surveillance and collaborative efforts in sharing genomic data to effectively combat the spread of antimicrobial resistance. In addition to the high incidence and mortality associated with Shigella infection, recurrent episodes contribute to prolonged distress for affected individuals, leading to complications such as delayed childhood development and cognitive impairments (Kotloff and Chisti, 2020). Given the incomplete understanding of therapeutic approaches for Shigella infection, exploring alternative effective treatments and identifying drug targets assumes paramount significance in the prevention and control of Shigella-related illnesses. Consequently, comprehensive research on treatment modalities for Shigella infection is imperative.

In recent years, the profound investigation into the gut microbiota has ushered in a maturation of strategies aimed at precision modulation for the prevention and treatment of various diseases (Cai et al., 2022). Throughout the pathogenic progression of Shigella infections, encompassing diverse pathogens, including Shigella dysenteriae, these organisms adeptly exploit various intestinal signals to augment their pathogenicity (Chowdhury et al., 2023). The competition among gut microbiota is crucial for the colonization of intestinal bacterial pathogens in the gut environment. Co-infection of Entamoeba histolytica and enteric pathogens leads to immune activation, epithelial cell damage, and increased virulence, possibly due to enhanced toxicity following bacterial engulfment by Entamoeba histolytica. Such co-infections have been reported in regions endemic for these pathogens, particularly among children with diarrheal diseases co-infected with Entamoeba histolytica and enteropathogenic Escherichia coli (EPEC) or Shigella dysenteriae (Bhagchandani et al., 2023; Jaswal et al., 2023). Concurrently, an array of studies underscores the antagonistic potential of the gut microbiota, a phenomenon capable of countering the colonization of exogenous pathogens, thereby presenting a novel avenue for Shigella infection management (Xerri and Payne, 2022). In certain animal experiments, the therapeutic efficacy and safety of mixed probiotics in treating Shigella dysenteriae infection in albino rats have shown promising results. Our study contributes to the enrichment of this therapeutic strategy (Ibejekwe et al., 2023). Nevertheless, the precise correlation between the onset of Shigella infections and the gut microbiota remains incompletely elucidated. The quest for microbial entities exerting antagonistic effects against Shigella encounters inherent complexities, thereby necessitating an urgent and comprehensive causal relationship analysis between Shigella infections and the gut microbiota.

Mendelian Randomization (MR), rooted in Mendel’s laws of inheritance and the principles of Instrumental Variables (IVs), stands as a robust statistical methodology. By employing genetic data as mediators, MR effectively unravels causal relationships between exposure risk factors and outcomes, thereby adeptly mitigating the interference of confounding factors (Davey Smith and Ebrahim, 2003). In this study, the application of MR analysis seeks to delve into the bidirectional causal relationships between the human gut microbiota and Shigella infections. When selecting Single Nucleotide Polymorphisms (SNPs) as IVs, certain criteria must be met: (a) the assumption of relevance, ensuring a strong correlation between each IV and the exposure factor; (b) the assumption of independence, asserting that each IV remains uncorrelated with other potential confounding factors; (c) the assumption of exclusivity, stipulating that each IV singularly influences the outcome through the exposure factor. These stringent conditions underpin the validity and integrity of the MR analysis, assuring a meticulous exploration of the intricate interplay between genetic determinants and the complex dynamics of the gut microbiota in relation to Shigella infections.

Through a rigorous series of quality control measures, we ultimately identified 2,818 SNPs associated with 211 bacterial species to serve as IVs. The F-statistics for the gut microbiota ranged from 14.58 to 88.42, with an average of 21.69, consistently surpassing the threshold of 10. This observation indicates a diminished likelihood of bias occurrence, affirming the robustness of our instrumental variable selection.

In our investigation, a bidirectional two-sample MR study was employed to elucidate the potential causal relationship between the gut microbiota and Shigella infection. Our findings unequivocally establish a reciprocal interaction between the gut microbiota and Shigella infection. Specifically, two microbial genera were identified as risk factors for Shigella infection, while six genera exhibited a protective role against the onset of Shigella infection. Importantly, in the outcomes of the reverse MR analysis, Shigella infection was shown to exert an impact on the composition of the gut microbiota, leading to alterations in four microbial genera.

Due to the predominant affliction site of Shigella infection within the gastrointestinal tract, coupled with the invasive nature of Shigella bacterial infiltration and resultant damage to intestinal epithelial cells, an indisputable and intricate correlation exists between Shigella infection and the gastrointestinal tract, as well as the gut microbiota (Baker and The, 2018). However, conventional research methodologies face formidable challenges in disentangling this relationship due to the myriad confounding factors. Consequently, we employed MR analysis, providing a robust framework to systematically investigate the causal relationship between Shigella infection and the gut microbiota.

In our investigation, we observed an inverse correlation between phylum Tenericutes, class Mollicutes, genus Intestinimonas, genus Gordonibacter, genus Butyrivibrio, and Shigella infection, while genus Sutterella and genus Alistipes exhibited a positive association with Shigella infection. Notably, phylum Tenericutes and class Mollicutes emerged as protective factors against Shigella infection, consistent with previous research indicating their negative correlation with inflammatory responses, particularly during the accumulation of C-reactive protein (CRP; Ren et al., 2023). CRP has been previously recognized as a marker of Shigella infection activity (Khan et al., 1995). Genus Sutterella, implicated in conditions such as autism, Down syndrome (Biagi et al., 2014), and inflammatory bowel disease (Lavelle et al., 2015), displayed a positive association with Shigella infection. In the human gastrointestinal tract, genus Sutterella exhibits varying abundance, with higher levels in the duodenum of healthy adults, decreasing toward the colon. Its correlation with the adhesion capacity of intestinal epithelial cells and intestinal permeability is highly significant, potentially fostering the occurrence of inflammatory reactions (Hiippala et al., 2016). Notably, the subtype Sutterella wadsworthensis, with strong adhesion capabilities to mucin and extracellular matrix proteins, induces the production of interleukin-8 by intestinal epithelial cells. Interleukin-8 and CRP serve as markers for bacterial infections (Franz et al., 1999), thereby establishing a close association with Shigella infection. Consequently, genus Sutterella may constitute a potential therapeutic target for Shigella infection. Genus Intestinimonas plays a pivotal role in promoting the metabolism of lysine into butyrate, a common anti-inflammatory short-chain fatty acid (Bui et al., 2020). On the other hand, genus Gordonibacter, associated with increased abundance in Crohn’s disease progression and closely linked to immune and inflammatory responses, aligns with our findings of an elevated correlation with Shigella infection and increased CRP levels (Salem et al., 2019). Similarly, the extensively studied butyrate-producing bacterium, genus Butyrivibrio, known to enhance intestinal mucosal barrier function and alleviate inflammation (Ye et al., 2021), exhibited a negative correlation with Shigella infection in our MR analysis. Conversely, genus Alistipes emerged as a risk factor in our study due to its close association with the activation pathway of interleukin-6, increasing the risk of inflammatory reactions in the host (Feng et al., 2015). In several animal experiments, it has also been clearly demonstrated that a decrease in the abundance of genus Alistipes occurs during the progression of infection with Shigella flexneri, which is consistent with the findings of our study analysis (Yang et al., 2020; Calvigioni et al., 2024). Consequently, these findings underscore the potential of these microbial taxa as biomarkers and therapeutic targets for Shigella infection, providing insights into the intricate interplay between the gut microbiota and the pathogenesis of Shigella-related disorders.

In the outcome of our reverse MR analysis, we infer that Shigella infection disrupts the equilibrium of the gut microbiota, leading to dysbiosis characterized by a decrease in the abundance of class Bacilli, genus RuminococcaceaeUCG002, and genus Senegalimassilia, coupled with a significant elevation in the abundance of order Lactobacillales, genus Roseburia, genus LachnospiraceaeUCG001, and genus Subdoligranulum. This observation aligns harmoniously with the findings from our forward MR analysis, thereby eliminating the possibility of reverse causation confounding our conclusions.

Ultimately, our research findings hold clear clinical significance. Whether it be Shigella dysenteriae, Shigella flexneri, Shigella boydii, or Shigella sonnei, their increasing infectiousness and the rampant misuse of antibiotics have contributed to a gradual surge in resistance, notably against frontline antibiotics such as cephalosporins (Matanza and Clements, 2023; Tsai et al., 2023). Given these circumstances, considering the protective role of gut microbiota, including bacteria like Genus Butyrivibrio, known for producing butyrate and reinforcing intestinal barriers, we regard them as potential interveners against the progression of the disease. Simultaneously, during the course of treating Shigella infections, intervening with collaborative pathogens such as genus Sutterella may yield significant therapeutic effects (Cai et al., 2022).

However, our study is not without limitations. Firstly, the data we utilized is derived from GWAS databases, and its availability is relatively constrained. Furthermore, the datasets pertaining to Shigella infection and gut microbiota predominantly originate from European populations. Secondly, our focus on the gut microbiota was primarily at the genus level, and we did not delve into specific bacterial species. Additionally, our examination of Shigella infection was comprehensive and did not involve subtyping, such as distinct analyses for Shigella dysenteriae, Shigella flexneri, Shigella sonnei, and Shigella boydii.

Our MR analysis has substantiated the bidirectional causal relationship between the gut microbiota and Shigella infection. This study not only opens novel avenues for the prevention and treatment of Shigella infections but also furnishes new insights into unraveling the pathogenic mechanisms by which the gut microbiota influences the onset of Shigella infection.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.

Our analysis does not entail the collection of raw data; instead, we leverage previously published studies or publicly available GWAS summary data. Therefore, ethical approval is not required for our study.

JP: Writing – original draft. KC: Writing – review & editing. GC: Formal analysis, Writing – review & editing, Data curation. LL: Data curation, Methodology, Writing – review & editing. LP: Conceptualization, Project administration, Writing – review & editing.