Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host/Experiment 5

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Curated date: 2024/03/25

Curator: Caramel

Revision editor(s): Caramel, Barrakat

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

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

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

decreased