Comparison of changes in fecal microbiota of calves with and without dam/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Bos grunniens
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
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Calves with dam on day 35
Group 1 name Corresponds to the case (exposed) group for case-control studies
Calves without dam on day 35
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Calves without dam on day 35 of the whole 95 days formal experimental period.
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
8
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
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.

Abundance in Group 1: increased abundance in Calves without dam on day 35

NCBI Quality ControlLinks
Actinomycetota
Myroides
Paraeggerthella
Peptostreptococcus

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.

Abundance in Group 1: decreased abundance in Calves without dam on day 35

NCBI Quality ControlLinks
Bacteroides
Escherichia/Shigella sp.
Parabacteroides

Revision editor(s): Folakunmi