Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis/Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-4

Curated date: 2025/03/31

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects

China

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

Pancreas Pancreas,pancreas

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

M1 distant metastasis stage M1 distant metastasis stage,m1 distant metastasis stage

Group 0 name Corresponds to the control (unexposed) group for case-control studies

M1 stage (Decreased)

Group 1 name Corresponds to the case (exposed) group for case-control studies

M1 stage (Increased)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The tumor stage was evaluated based on the TNM staging system. M1 Stage (Metastasis stage) is the Distant Metastasis stage where cancer has spread to other part of the body.

Group 0 sample size Number of subjects in the control (unexposed) group

3

Group 1 sample size Number of subjects in the case (exposed) group

3

Lab analysis

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

2b-RAD

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)

0.25

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment

body mass index, Confounders controlled for: "Metastasis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Metastasis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-4

Curated date: 2025/04/01

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 1

Description: Differential taxa at the species level identified by MaAsLin2 (*q < 0.25).

Abundance in Group 1: increased abundance in M1 stage (Increased)

NCBI	Quality Control	Links
Massilia timonae
Brevundimonas diminuta
Pseudomonas fulva
Dietzia maris

Revision editor(s): MyleeeA

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-4

Curated date: 2025/04/01

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 1

Description: Differential taxa at the species level identified by MaAsLin2 (*q < 0.25).

Abundance in Group 1: decreased abundance in M1 stage (Increased)

NCBI	Quality Control	Links
Pseudomonas sp.

Revision editor(s): MyleeeA