Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19/Experiment 3

From BugSigDB


Needs review

Curated date: 2025/05/04

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects
France
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mesocricetus auratus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
SARS-CoV-2-related disease COVID-19-related disease,SARS-CoV-2-related disease,sARS-CoV-2-related disease
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Young and Aged D0 non-infected controls (Time effect)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Young and Aged D7 Infected (Time effect)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Young (2 months old) and Aged (22 months old) SARS-CoV-2-infected hamsters at Day 7 of infection with time of infection effect.

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
MaAsLin2
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

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Needs review

Curated date: 2025/05/04

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3C

Description: Differential abundance of taxa between Young and Aged D0 non-infected controls (Time effect) and Young and Aged D7 Infected (Time effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).

Abundance in Group 1: increased abundance in Young and Aged D7 Infected (Time effect)

NCBI Quality ControlLinks
Adlercreutzia
Bacteroides
Clostridium sp. CAG:273
Faecalibacterium sp. UBA7177
Firmicutes bacterium CAG:822
Limosilactobacillus
Parabacteroides
Phocaeicola
Ruthenibacterium
Thomasclavelia
UBA1820UBA1820
UBA2882UBA2882
UBA3789UBA3789
UBA1436UBA1436
CAG:776CAG:776
CAG:611 NOVCAG:611 NOV
UMGS995UMGS995
CAG:822 NOVCAG:822 NOV
UBA2730UBA2730
Christensenellales NOVChristensenellales NOV

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/04

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3C

Description: Differential abundance of taxa between Young and Aged D0 non-infected controls (Time effect) and Young and Aged D7 Infected (Time effect) hamsters analyzed with Maaslin2 (adjusted P-value < 0.05).

Abundance in Group 1: decreased abundance in Young and Aged D7 Infected (Time effect)

NCBI Quality ControlLinks
Acetobacter sp. CAG:267
Allobaculum
Angelakisella
Eubacterium sp. CAG:180
Frisingicoccus
Helicobacteraceae
Ileibacterium
Ligilactobacillus
Longicatena
Mucispirillum
Muribaculaceae
Prevotellamassilia
UBA7185UBA7185
Erysipelotrichaceae NOVErysipelotrichaceae NOV
Hungetella AHungetella A
UMGS1872UMGS1872
Butyricicoccaceae NOVButyricicoccaceae NOV
Eubacterium JEubacterium J
UBA1405UBA1405
Clostridium QClostridium Q
CAG:950CAG:950
Mycoplasmoidaceae NOVMycoplasmoidaceae NOV
Lachnospiraceae bacterium UBA7182

Revision editor(s): MyleeeA