Body site-typical microbiome signatures for children

Study information

Reviewed Marked as Reviewed by Lwaldron on 2023-2-8

study design

meta-analysis

Citation

PMID PubMed identifier for scientific articles.

Study 608

DOI Digital object identifier for electronic documents.

10.5281/zenodo.7544549

URI

https://doi.org/10.5281/zenodo.7544549

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Using the curatedMetagenomicData Biocondutor package (>=3.2.1): we calculated taxa prevalence of healthy child control samples for each body site and at species/genus levels. Lists of typical healthy signatures were provided for each body site at species/genus level.

For body site-typical microbiome signatures for adults, please go to: https://bugsigdb.org/Study_562

Experiment 1

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Reviewed Marked as Reviewed by Lwaldron on 2023-2-8

Curated date: 2022/01/26

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Subjects

Location of subjects: Italy; 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: Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Health study participationHealth study participation

Group 0 name Corresponds to the control (unexposed) group for case-control studies: none

Group 1 name Corresponds to the case (exposed) group for case-control studies: healthy child oral 50% up

Group 1 sample size Number of subjects in the case (exposed) group: 81

Lab analysis

Sequencing type: 16S

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

Statistical test: prevalence>=50% Statistical test: "prevalence>=50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.

Signature 1

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Reviewed Marked as Reviewed by Lwaldron on 2022/05/25

Curated date: 2022/01/26

Curator: Haoyanzh

Revision editor(s): Haoyanzh

Source: 10.5281/zenodo.5565690

Description: healthy child oral genus in >=50% study samples

Abundance in Group 1:

NCBI	Quality Control	Links
Streptococcus
Rothia
Veillonella
Prevotella
Gemella
Neisseria
Haemophilus

Revision editor(s): Haoyanzh

Signature 2

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Reviewed Marked as Reviewed by Lwaldron on 2022/05/25

Curated date: 2022/01/26

Curator: Haoyanzh

Revision editor(s): Haoyanzh

Source: 10.5281/zenodo.5565690

Description: healthy child oral species in >= 50% samples

Abundance in Group 1:

NCBI	Quality Control	Links
Streptococcus mitis
Rothia mucilaginosa
Streptococcus parasanguinis
Streptococcus oralis
Prevotella melaninogenica
Gemella haemolysans
Streptococcus infantis
Gemella sanguinis
Neisseria flavescens
Streptococcus salivarius
Veillonella dispar

Revision editor(s): Haoyanzh

Experiment 2

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Needs review

Curated date: 2022/01/26

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Differences from previous experiment shown

Subjects

Location of subjects: Bangladesh; China; Estonia; Finland; Germany; India; Ireland; Italy; Luxembourg; Netherlands; Russian Federation; Spain; Sweden; United Kingdom; United Republic of Tanzania; United States of America

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Group 1 name Corresponds to the case (exposed) group for case-control studies: healthy child stool 50% up

Group 1 sample size Number of subjects in the case (exposed) group: 3375

Lab analysis

Statistical Analysis

Statistical test: prevalance>=50% Statistical test: "prevalance>=50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.