Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK, Hartmann S
Journal
Microbiome
Year
2022
BACKGROUND: Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. These pathogens live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. Knowledge of the bacterial host microbiome at the site of infection is limited, and data on the parasite microbiome is, to the best of our knowledge, non-existent. RESULTS: The intestinal microbiome of the natural parasite and zoonotic macropathogen, Ascaris suum was analyzed in contrast to the diversity and composition of the infected host gut. 16S sequencing of the parasite intestine and host intestinal compartments showed that the parasite gut has a significantly less diverse microbiome than its host, and the host gut exhibits a reduced microbiome diversity at the site of parasite infection in the jejunum. While the host's microbiome composition at the site of infection significantly determines the microbiome composition of its parasite, microbial signatures differentiate the nematodes from their hosts as the Ascaris intestine supports the growth of microbes that are otherwise under-represented in the host gut. CONCLUSION: Our data clearly indicate that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut. Video Abstract.
Experiment 1
Subjects
- Location of subjects
- Germany
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ascariasis Ascariasis,ascariasis,Ascariasis - roundworm,ascariasis - roundworm,Ascaris lumbricoides caused disease or disorder,Ascaris lumbricoides disease or disorder,Ascaris lumbricoides infection,Ascaris lumbricoides infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non infected Pigs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ascaris suum infected Pigs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- German Landrace pigs (Sus scrofa) from a conventional breeder, aged 6 weeks, which were orally infected with either two inoculums of 1000 embryonated Ascaris eggs (exp. 1) 2 days apart or a single inoculum of 4000 embryonated eggs (exp. 2)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 2
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 3
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 4
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 5
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Cecum mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 6
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non infected Pig Host Jejunum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ascaris suum Microbiome
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Microbiome of intestines harvested from Adult Ascaris worms that were harvested from host pig's gut
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infected Pig Host Jejunum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ascaris summ (Males)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ascaris suum (Females)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Microbiome of intestines harvested from Female Adult Ascaris worms that were harvested from host pig's gut
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 4D, Table S7
Description: Differentially abundant bacterial taxa between male and female worms (Ascaris suum) present in German Landrace pig gut.
Abundance in Group 1: increased abundance in Ascaris suum (Females)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. | ||
| Mitsuokella jalaludinii | ||
| Prevotella | ||
| Terrisporobacter |
Revision editor(s): Barrakat
Signature 2
Source: Figure 4D, Table S7
Description: Differentially abundant bacterial taxa between male and female worms (Ascaris suum) present in German Landrace pig gut.
Abundance in Group 1: decreased abundance in Ascaris suum (Females)
Revision editor(s): Barrakat
Experiment 9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Host (Ascaris suum infected Pigs) Microbiome
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parasite (Ascaris suum) Microbiome
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Microbiome of intestines harvested from Adult Ascaris worms that were harvested from host pig's gut
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 5A, Table S8
Description: Differentially abundant bacteria taxa between Host (Pig) and Parasite (Ascaris suum) Microbiome
Abundance in Group 1: increased abundance in Parasite (Ascaris suum) Microbiome
Revision editor(s): Barrakat
Signature 2
Source: Figure 5A, Table S8
Description: Differentially abundant bacteria taxa between Host (Pig) and Parasite (Ascaris suum) Microbiome
Abundance in Group 1: decreased abundance in Parasite (Ascaris suum) Microbiome
Revision editor(s): Barrakat
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