Tumor microbiome diversity influences papillary thyroid cancer invasion/Experiment 24

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2025/01/09

Curator: Aleru Divine

Revision editor(s): WikiWorks, Aleru Divine

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
Thyroid gland Glandula thyroidea,Thyroid,Thyroid gland,thyroid gland
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Papillary thyroid carcinoma papillary cancer of the thyroid,papillary cancer of the thyroid gland,papillary cancer of thyroid,papillary cancer of thyroid gland,papillary carcinoma of the thyroid,papillary carcinoma of the thyroid gland,papillary carcinoma of thyroid,papillary carcinoma of thyroid gland,papillary thyroid cancer,papillary thyroid carcinoma,papillary thyroid gland carcinoma,thyroid gland papillary cancer,thyroid gland papillary carcinoma,thyroid papillary carcinoma,Papillary thyroid carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Patients with PTC at clinical stage T1
Group 1 name Corresponds to the case (exposed) group for case-control studies
Patients with PTC at clinical stage T4
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Papillary thyroid cancer (PTC) at clinical stage T4.
Group 0 sample size Number of subjects in the control (unexposed) group
35
Group 1 sample size Number of subjects in the case (exposed) group
6

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-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
Kruskall-Wallis
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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2025/01/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine, WikiWorks

Source: Supplementary Data 4 (Sheet 2)

Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.

Abundance in Group 1: decreased abundance in Patients with PTC at clinical stage T4

NCBI Quality ControlLinks
Aliicoccus
Bradyrhizobium
Candidatus Izemoplasmatales
Candidatus Soleaferrea
Catonella
Chitinophagaceae
Johnsonella
Lachnoanaerobaculum
Mogibacterium
Oribacterium
Oscillibacter
Peptococcaceae
Pseudomonas
Rhodococcus
Shewanella
Solirubrobacter
Solobacterium
Sphingomonas
Stomatobaculum
Sulfuritalea
unclassified Burkholderiales
unclassified Comamonadaceae
unclassified Gammaproteobacteria
unclassified Rhodanobacteraceae
BeggiatoaceaeBeggiatoaceae
Acidobacteriae Subgroup 2Acidobacteriae Subgroup 2
Butyricicoccaceae UCG-009Butyricicoccaceae UCG-009
Sutterella
Methylobacterium-MethylorubrumMethylobacterium-Methylorubrum
Ruegeria
Proteus
Bacteria NB1-JBacteria NB1-J

Revision editor(s): Aleru Divine, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2025/01/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine, WikiWorks

Source: Supplementary Data 4 (Sheet 2)

Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4.

Abundance in Group 1: increased abundance in Patients with PTC at clinical stage T4

NCBI Quality ControlLinks
Allofournierella
Alloprevotella
Ardenticatenales
Asticcacaulis
Atopobium
Bergeyella
Candidatus Gastranaerophilales
Capnocytophaga
Crossiella
Eubacterium
Facklamia
Flavonifractor
Gemella
Granulicatella
Haemophilus
Halomonas
Holdemanella
Insolitispirillum
Monoglobus
Pyramidobacter
Sandaracinobacter
Spirochaeta
Streptobacillus
Streptococcus
Sulfurisoma
Truepera
Craucococcus-CaldovatusCraucococcus-Caldovatus
Peptostreptococcales-TissierellalesPeptostreptococcales-Tissierellales
URHD0088URHD0088
Prevotellaceae UCG-004Prevotellaceae UCG-004

Revision editor(s): Aleru Divine, WikiWorks