Gastro-intestinal and oral microbiome signatures associated with healthy aging/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Age Age,age
Group 0 name Corresponds to the control (unexposed) group for case-control studies
healthy aging (HA)
Group 1 name Corresponds to the case (exposed) group for case-control studies
non-healthy aging (NHA)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.
Group 0 sample size Number of subjects in the control (unexposed) group
33
Group 1 sample size Number of subjects in the case (exposed) group
32
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 weeks

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V3
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).
centered log-ratio
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

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks, Claregrieve1

Source: Figure 2, Supplemental File S2

Description: Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts

Abundance in Group 1: increased abundance in non-healthy aging (NHA)

NCBI Quality ControlLinks
Rothia
Streptococcus
Veillonella
Lactobacillus
Bifidobacterium

Revision editor(s): WikiWorks, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks, Claregrieve1

Source: Figure 2, Supplemental File S2

Description: Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts

Abundance in Group 1: decreased abundance in non-healthy aging (NHA)

NCBI Quality ControlLinks
Capnocytophaga
Fusobacterium
Haemophilus
Neisseria
Tannerella
Treponema
Eikenella
Lautropia
Johnsonella
Cardiobacterium
Comamonas
Filifactor
Fusobacterium sp.
Propionibacterium
Haemophilus sp.
Corynebacterium
Porphyromonas
Peptoclostridium
candidate division SR1 bacterium

Revision editor(s): WikiWorks, Claregrieve1