Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome
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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
Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P, Li RW
Journal
International journal for parasitology
Year
2019
Keywords:
16S rRNA gene, Ascaris suum, Infection, Microbiome, Network, Swine
The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. The infection significantly decreased various microbial diversity indices including Chao1 richness, but the effect on Chao1 in the colon luminal contents was worm burden-independent. The abundance of 49 genera present in colon contents, such as Prevotella and Faecalibacterium, and 179 operational taxonomic units was significantly changed as a result of infection. Notably, infection was also associated with a significant shift in the metabolic potential of the proximal colon microbiome, where the relative abundance of at least 30 metabolic pathways including carbohydrate metabolism and amino acid metabolism was reduced, while the abundance of 28 pathways was increased by infection. Furthermore, the microbial co-occurrence network in infected pigs was highly modular. Two of 52 modules or subnetworks were negatively correlated with fecal butyrate concentrations (r < -0.7; P < 0.05) while one module with 18 members was negatively correlated with fecal acetate, propionate and total short-chain fatty acids. A partial Mantel test identified a strong positive correlation between node connectivity of the operational taxonomic units assigned to β-Proteobacteria (especially the family Alcaligenaceae) and fecal acetate and propionate levels (r = 0.82 and 0.74, respectively), while that of the family Porphyromonadaceae was positively correlated with fecal egg counts. Overall, Ascaris infection was associated with a profound change in the gut microbiome, especially in the proximity of the initial site of larval infection, and should facilitate our understanding of the pathophysiological consequence of gastrointestinal nematode infections.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-14
Subjects
- Location of subjects
- Belgium
- 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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- 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
- Uninfected piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ascaris suum infected piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from ascariasis infected piglets
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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).
- relative abundances
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-14
Source: Figure 1A
Description: Differentially abundant microbial signatures in the colon of ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: decreased abundance in Ascaris suum infected piglets
Revision editor(s): JimFlashy, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Figure 1A
Description: Differentially abundant microbial signatures in the colon of ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: increased abundance in Ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Prevotella | ||
| Prevotellaceae |
Revision editor(s): JimFlashy, Scholastica
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-14
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Feces samples from ascariasis infected piglets
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-9
Source: Figure 1B
Description: Differentially abundant microbial signatures in the feces of ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: decreased abundance in Ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Citrobacter | ||
| Lachnospiraceae | ||
| Mycoplasma | ||
| Mycoplasmataceae | ||
| Mycoplasmatales | ||
| Roseburia |
Revision editor(s): JimFlashy, Scholastica
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-9
Source: Figure 1B
Description: Differentially abundant microbial signatures in the feces of ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: increased abundance in Ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus |
Revision editor(s): JimFlashy, Scholastica
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-14
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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low worm burden ascaris suum infected piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from low worm burden ascariasis infected piglets
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- LEfSe
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-14
Source: Table 2
Description: Differences in taxonomic units in the colon of low worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: decreased abundance in Low worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovibrio | ||
| Erysipelotrichaceae | ||
| Lachnospiraceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Prevotella | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Table 2
Description: Differences in taxonomic units in the colon of low worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: increased abundance in Low worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High worm burden ascaris suum infected piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from high worm burden ascariasis infected piglets
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Table 2
Description: Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: decreased abundance in High worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovibrio | ||
| Erysipelotrichaceae | ||
| Lachnospiraceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Prevotella | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-15
Source: Table 2
Description: Differences in taxonomic units in the colon of high worm burden ascaris suum infected piglets compared to uninfected piglets.
Abundance in Group 1: increased abundance in High worm burden ascaris suum infected piglets
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Segatella copri |
Revision editor(s): JimFlashy, Scholastica
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