Gut Microbiota and Insecticide Resistance in the Mediterranean Fruit Fly (Ceratitis capitata)

Source: Charaabi, K., Hamdene, H., Djobbi, W. et al. Assessing gut microbiota diversity and functional potential in resistant and susceptible strains of the mediterranean fruit fly. Sci Rep15, 33456 (2025). https://doi.org/10.1038/s41598-025-01534-w
Dates: Received – 06 November 2024 | Accepted – 06 May 2025 | Published – 29 September 2025

Executive Summary

This briefing document synthesizes findings from a study investigating the link between gut microbiota and insecticide resistance in the Mediterranean fruit fly (Ceratitis capitata), a destructive agricultural pest. The research reveals a strong correlation between resistance to common insecticides (malathion, dimethoate, and spinosad) and significant alterations in the composition and functional potential of the fly’s gut bacterial community.

Resistant strains of the medfly, developed over 36 generations of insecticide exposure, exhibit significantly lower microbial diversity compared to their susceptible counterparts. This reduction in diversity is accompanied by a profound shift in the gut’s bacterial landscape. Specifically, the phylum Bacillota and the genera Enterococcus and Klebsiella are substantially enriched in resistant flies. Conversely, the dominant phylum Pseudomonadota and the genera Serratia and Buttiauxella are sharply reduced.

Functional analysis predicts that the gut microbiota of resistant flies possess enhanced metabolic capabilities for xenobiotic biodegradation. These enriched pathways are associated with the breakdown of various toxic environmental chemicals, suggesting a direct or indirect role in insecticide detoxification. The findings indicate that symbiont-mediated resistance is likely a key mechanism in the medfly, driven by the synergistic effect of multiple bacterial species rather than a single microbe. This research opens new avenues for pest management strategies that could target the gut microbiome to mitigate insecticide resistance.

Background and Research Objectives

The Mediterranean fruit fly (Ceratitis capitata), or medfly, is a highly polyphagous pest that infests over 300 plant species, causing billions of dollars in annual economic losses worldwide. These losses stem from reduced agricultural production, costly control measures, and restricted market access. While methods like the Sterile Insect Technique (SIT) are used, the predominant control practice remains the application of chemical insecticides.

The widespread and excessive use of insecticides has led to the development of significant resistance in medfly populations, undermining control efforts. While resistance is often linked to genetic traits in the insect, such as increased enzyme activity, recent evidence from other species suggests that symbiotic gut microorganisms can play a crucial role. These bacteria may contribute to resistance by directly metabolizing toxic substances or by modulating the host’s detoxification gene expression.

Despite extensive research on the medfly’s gut microbiota in relation to its fitness and SIT applications, the connection to insecticide resistance has remained largely unexplored. This study aimed to address this gap by investigating the potential association between the medfly gut microbiota and insecticide resistance. The primary objectives were to:

1. Characterize and compare the gut microbiota community structure between insecticide-susceptible (IS) and insecticide-resistant (IR) strains of the medfly.
2. Identify specific bacterial taxa that correlate with resistance phenotypes.
3. Predict the functional differences between the microbiomes of susceptible and resistant strains.

Experimental Design and Methodology

To achieve its objectives, the study employed a controlled laboratory selection process and advanced sequencing techniques.

• Strain Development: Three insecticide-resistant (IR) strains were developed from a susceptible parent strain (IS) originally from Egypt (Egypt II). For 36 successive generations, populations were exposed to increasing concentrations of one of three insecticides: malathion (ML-SEL strain), dimethoate (Dm-SEL strain), or spinosad (Sp-SEL strain). The selection pressure was calibrated to achieve 50-70% mortality in each generation.
• Resistance Confirmation: Toxicological bioassays were conducted on the 36th generation of each IR strain and the IS strain. The lethal concentration required to kill 50% of the population (LC50) was calculated to quantify the level of resistance. The results confirmed a significant increase in tolerance in the selected strains.

 | Strain | Insecticide | LC50 (ppm) | Resistance Ratio (RR) vs. IS Strain
 | IS | Malathion | 18.8 | –
| ML-SEL (G36) | Malathion | 1872.2 | 99.23-fold
| IS | Dimethoate | 0.85 | –
| Dm-SEL (G36) | Dimethoate | 215.79 | 252.68-fold
| IS | Spinosad | 0.55 | –
| Sp-SEL (G36) | Spinosad | 133.79 | 241.49-fold

• Microbiota Analysis: Gut tissues were dissected from adult flies of all four strains. Genomic DNA was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Bioinformatic analyses, including Principal Coordinate Analysis (PCoA), Non-metric Multidimensional Scaling (NMDS), and Linear discriminant analysis Effect Size (LEfSe), were used to analyze microbial diversity, structure, and to identify potential biomarkers. Functional potential was predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

Key Findings: Shifts in Gut Microbiota Composition

The study revealed dramatic and statistically significant differences between the gut microbiomes of insecticide-susceptible and resistant medflies.

Reduced Microbial Diversity in Resistant Strains

A primary finding was that all three IR strains exhibited significantly lower bacterial richness and diversity compared to the IS parent strain (p < 0.05). This suggests that insecticide exposure acts as a strong selective pressure, favoring the growth of a specialized subset of bacteria that can tolerate or metabolize the toxic compounds. This “selection-cumulation effect” leads to an enrichment of resistance-associated bacteria at the expense of overall diversity.

Altered Bacterial Abundance at Phylum and Genus Levels

The composition of the gut microbiota was fundamentally altered in the resistant strains.

• Phylum-Level Shifts: While the phylum Pseudomonadota was dominant in all strains, its relative abundance decreased significantly in the IR strains (from 91.03% in IS to 70.85-75.27% in IR). Conversely, the abundance of the phylum Bacillota increased dramatically (from 8.94% in IS to 24.70-28.90% in IR).
• Genus-Level Shifts: The most pronounced changes occurred at the genus level, pointing to specific bacteria potentially involved in resistance.

 | Bacterial Genus | Relative Abundance in IS Strain | Change in IR Strains | Specific Details
 | …