Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles

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Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/22

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Subjects

Location of subjects: Finland

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: Amniotic fluid Acqua amnii,Liquor amnii,Amniotic fluid,amniotic fluid

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Vesicle membrane Vesicle membrane,vesicle membrane

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Amniotic fluid (AM)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Amniotic fluid-derived extracellular vesicles (AM EVs)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Amniotic fluid-derived extracellular vesicles from Amniotic samples

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 24

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

Statistical test: ANCOM

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma, MyleeeA

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid (AM) vs. amniotic fluid-derived extracellular vesicles (AM EV)

Abundance in Group 1: increased abundance in Amniotic fluid-derived extracellular vesicles (AM EVs)

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Alistipes
Alloprevotella
Bacteroides
Bradyrhizobium
Deinococcus
Dermacoccus
Dolosigranulum
Gemella
Granulicatella
Lawsonella
Neisseria
Peptoniphilus
Porphyromonas
Prevotella
Staphylococcus
Streptococcus
Veillonella
Vibrionimonas
Williamsia
Escherichia-ShigellaEscherichia-Shigella

Revision editor(s): Iman-Ngwepe, Fiddyhamma, MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/10/22

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid (AM) vs. amniotic fluid-derived extracellular vesicles (AM EV)

Abundance in Group 1: decreased abundance in Amniotic fluid-derived extracellular vesicles (AM EVs)

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Deinococcota

Revision editor(s): Fiddyhamma

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Amniotic fluid , Feces Acqua amnii,Liquor amnii,Amniotic fluid,amniotic fluid,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: Maternal feces (FE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Maternal feces collected before cesarean section

Group 1 sample size Number of subjects in the case (exposed) group: 22

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid (AM) vs. Maternal Feces (FE)

Abundance in Group 1: increased abundance in Maternal feces (FE)

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Bradyrhizobium
Dermacoccus
Faecalibacterium
Staphylococcus

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/10/22

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid (AM) vs. Maternal Feces (FE)

Abundance in Group 1: decreased abundance in Maternal feces (FE)

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Bacteroidota
Bacillota

Revision editor(s): Fiddyhamma

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Feces-derived extracellular vesicles (FE EV)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Feces-derived extracellular vesicles from Feces samples

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: increased

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Amniotic fluid-derived extracellular vesicles (AM EV)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Maternal feces (FE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Maternal feces collected before cesarean section

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: increased

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Feces-derived extracellular vesicles (FE EV)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Feces-derived extracellular vesicles from Feces samples

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid-derived extracellular vesicles (AM EV) vs. fecal-derived extracellular vesicles (FE EV)

Abundance in Group 1: increased abundance in Feces-derived extracellular vesicles (FE EV)

NCBI	Quality Control	Links
Fusobacteriota

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/10/22

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1: Table 8

Description: The differentially abundant genera in the amniotic fluid-derived extracellular vesicles (AM EV) vs. fecal-derived extracellular vesicles (FE EV)

Abundance in Group 1: decreased abundance in Feces-derived extracellular vesicles (FE EV)

NCBI	Quality Control	Links
Fusobacterium
Bacteroides
Finegoldia

Revision editor(s): Fiddyhamma

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-10-22

Curated date: 2024/03/25

Curator: Iman-Ngwepe

Revision editor(s): Iman-Ngwepe, Fiddyhamma

Differences from previous experiment shown

Subjects

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 0 name Corresponds to the control (unexposed) group for case-control studies: Maternal feces (FE)

Group 0 sample size Number of subjects in the control (unexposed) group: 22

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1