Reviewed Marked as Reviewed by Svetlana up on 2025-1-21

Curated date: 2024/04/22

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, KateRasheed, WikiWorks

Subjects

Location of subjects
Ireland
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
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Response to antibiotic Response to antibiotic,response to antibiotic
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Therapeutic zinc oxide (Zn) treatment + non-medicated control diet (Ct diet) - Faecal 7 days post weaning (7 dpw)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Antibiotic (Ab) treatment - Faecal 7 days post weaning (7 dpw)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Piglets treated with antibiotics at Faecal 7 days post weaning.

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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


Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-21

Curated date: 2024/04/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, KateRasheed, WikiWorks

Source: Fig 5C

Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data.

Abundance in Group 1: increased abundance in Antibiotic (Ab) treatment - Faecal 7 days post weaning (7 dpw)

NCBI Quality ControlLinks
Acetivibrio clariflavus
Acetivibrio saccincola
Acetobacterium woodii
Akkermansia muciniphila
Alkaliphilus oremlandii
Aminipila luticellarii
Christensenella massiliensis
Clostridium sp. BNL1100
Clostridium thermosuccinogenes
Dehalobacterium formicoaceticum
Dehalococcoides mccartyi
Desulfovibrio piger
Enterococcus faecium
Hungateiclostridiaceae bacterium KB18
Mahella australiensis
Mogibacterium diversum
Murdochiella vaginalis
Olsenella sp. oral taxon 807
Ruminococcus albus
Ruminococcus bicirculans (ex Liu et al. 2021)
Streptococcus suis
Acidilutibacter cellobiosedens
[Eubacterium] sulci

Revision editor(s): Fiddyhamma, KateRasheed, WikiWorks