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PloS one2026; 21(2); e0339596; doi: 10.1371/journal.pone.0339596

Beyond the host: Unveiling the independent microbiome of equine gastrointestinal nematodes.

Abstract: Gastrointestinal nematode infections significantly impact equine health and welfare, with rising anthelmintic resistance demanding alternative control strategies. Emerging evidence suggests that parasitic nematodes harbour distinct microbiomes, potentially influencing host-parasite dynamics and parasite survival. This study aimed to characterize and compare the microbiomes of equine gastrointestinal nematodes and their hosts, focusing on differences in composition, diversity, and core microbiota structure across different intestinal sites, nematode subfamilies, and sexes. Faecal and nematode samples were collected from equids (Equus caballus and Equus asinus) at slaughterhouses. DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were amplified and sequenced using the Illumina iSeq 100 platform. Bioinformatic analyses were performed with QIIME2 and MicrobiomeAnalyst, and statistical comparisons employed PERMANOVA, LEfSe, and alpha and beta diversity metrics. Nematodes exhibited a distinct microbiome dominated by Firmicutes, Proteobacteria, Bacteroidota, Verrucomicrobiota, and Actinobacteriota, differing significantly from the faecal microbiota. Alpha diversity analyses revealed lower richness in nematodes, while beta diversity indicated distinct community structures (p = 0.007). Microbial composition varied by gastrointestinal site, nematode subfamily, and sex. Proteobacteria were consistently enriched in nematodes, particularly in the caecum. Core microbiome analysis identified exclusive nematode-associated taxa such as Fusobacterium, Mesorhizobium, and Mycoplasma. Equine gastrointestinal nematodes harbour independent and structured microbiomes, distinct from those of their hosts. These findings underscore the ecological specialization of nematodes and highlight the potential of targeting parasite-associated microbiota for novel control strategies.
Copyright: © 2026 Gentilini et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2026-02-10 PubMed ID: 41666179PubMed Central: PMC12890152DOI: 10.1371/journal.pone.0339596Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This research investigated the unique bacterial communities (microbiomes) that live inside equine gastrointestinal nematodes and how these differ from the microbiomes found in their host horses and donkeys.
  • The study revealed that these nematodes harbor distinct, specialized microbiomes independent of their host’s gut, which may influence parasite survival and could offer new avenues for parasite control.

Introduction and Research Context

  • Gastrointestinal nematodes are parasitic worms that infect horses and donkeys, causing significant health and welfare issues.
  • Anthelmintic resistance (resistance to worm-killing drugs) is increasing, making traditional control methods less effective.
  • There is emerging evidence that parasitic nematodes host their own unique microbiomes, which may impact how they survive and interact with their hosts.
  • This study aimed to explore the nature of these nematode microbiomes and how they differ from those of their host animals.

Methods

  • Samples were collected from the intestines and feces of horses (Equus caballus) and donkeys (Equus asinus) at slaughterhouses.
  • Nematodes were isolated from different areas of the gastrointestinal tract, accounting for differences by intestinal site, nematode subfamily, and sex of the parasites.
  • DNA was extracted from samples, and the bacterial 16S rRNA gene’s V3-V4 regions were amplified for sequencing, which helps identify bacterial species present.
  • Sequencing was performed using the Illumina iSeq 100 platform, a next-generation DNA sequencing technology.
  • Bioinformatics analyses were conducted using QIIME2 and MicrobiomeAnalyst software to process sequencing data and analyze microbial diversity and composition.
  • Statistical tools like PERMANOVA (to test community differences), LEfSe (to detect biomarkers), and alpha/beta diversity metrics (to measure microbial richness and differences) were used for comparisons.

Key Findings

  • The microbiomes found inside nematodes were distinctly different from those in the feces of their equine hosts.
  • Major bacterial groups dominating the nematode microbiome included Firmicutes, Proteobacteria, Bacteroidota, Verrucomicrobiota, and Actinobacteriota.
  • Alpha diversity (species richness) was lower inside nematodes compared to host fecal samples, indicating fewer types of bacteria internally.
  • Beta diversity, measuring differences between bacterial communities, showed that nematode microbiomes were significantly distinct (p = 0.007) from host microbiomes.
  • The specific bacterial makeup varied depending on the site of the intestine sampled, the nematode’s subfamily classification, and the parasite’s sex.
  • Proteobacteria were particularly abundant in nematodes from the caecum, an important part of the horse intestine.
  • Core microbiome analysis highlighted taxa unique to nematodes such as Fusobacterium, Mesorhizobium, and Mycoplasma, which were not found in host feces.

Conclusions and Implications

  • Equine gastrointestinal nematodes have an independent and structured microbiome, clearly separated from their host’s gut bacteria.
  • This finding supports the idea that the nematodes have co-evolved with their own specific bacterial communities, possibly aiding their survival and adaptation within the host environment.
  • The unique microbiome associated with nematodes could represent a target for new parasite control strategies that go beyond drug treatments, potentially exploiting the parasite’s bacterial partners to curb infections.
  • This study contributes to a deeper ecological understanding of host-parasite-microbiome interactions in equine health.

Cite This Article

APA
Gentilini F, Ogundipe TG, Turba ME, Romagnoli N, Lambertini C, Pollera C, Cremonesi P, Stancampiano L. (2026). Beyond the host: Unveiling the independent microbiome of equine gastrointestinal nematodes. PLoS One, 21(2), e0339596. https://doi.org/10.1371/journal.pone.0339596

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 21
Issue: 2
Pages: e0339596
PII: e0339596

Researcher Affiliations

Gentilini, Fabio
  • Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell´Emilia (Bo) Italy.
Ogundipe, Tolulope Grace
  • Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell´Emilia (Bo) Italy.
Turba, Maria Elena
  • Genefast srl, Forlì, Forlì-Cesena, Italy.
Romagnoli, Noemi
  • Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell´Emilia (Bo) Italy.
Lambertini, Carlotta
  • Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell´Emilia (Bo) Italy.
Pollera, Claudia
  • Department of Veterinary Medicine and Animal Sciences (DIVAS), University of Milan, Lodi, Italy.
Cremonesi, Paola
  • Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy.
Stancampiano, Laura
  • Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell´Emilia (Bo) Italy.

MeSH Terms

  • Animals
  • Horses / parasitology
  • Horses / microbiology
  • Nematoda / microbiology
  • Nematoda / genetics
  • Gastrointestinal Microbiome / genetics
  • Female
  • Male
  • RNA, Ribosomal, 16S / genetics
  • Nematode Infections / veterinary
  • Nematode Infections / parasitology
  • Feces / microbiology
  • Feces / parasitology
  • Horse Diseases / parasitology
  • Horse Diseases / microbiology
  • Host-Parasite Interactions
  • Bacteria / genetics
  • Bacteria / classification

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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