Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients/Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
Netherlands
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
Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Oral mucositis inflammation of the mouth,oral cavity mucosal damage,oral mucosa irritation,oral mucosal damage,oral mucosal injury,oral mucosal lesions,stomatitis,Oral mucositis,oral mucositis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
one and two weeks after stem cell transplant
Group 1 name Corresponds to the case (exposed) group for case-control studies
pre- and three month after auto stem cell transplant
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patient developed uclerative oral mucositis
Group 0 sample size Number of subjects in the control (unexposed) group
31
Group 1 sample size Number of subjects in the case (exposed) group
20

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
RT-qPCR

Statistical Analysis

Statistical test
PERMANOVA
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group

Abundance in Group 1: increased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Streptococcus australis
Streptococcus parasanguinis
Veillonella atypica
Veillonella dispar
Actinomyces
Actinomyces graevenitzii
Gemella haemolysans
Gemella morbillorum
Gemella sanguinis

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group

Abundance in Group 1: decreased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Staphylococcus aureus
Staphylococcus caprae
Staphylococcus epidermidis
Staphylococcus warneri
Scardovia wiggsiae
Enterococcus faecalis

Revision editor(s): WikiWorks, Atrayees