Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-24

Curated date: 2024/03/23

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Subjects

Location of subjects: Iran

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: 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Sample treatment protocol Sample treatment protocol,sample treatment protocol

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: RNAlater - Day 4

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: RNAlater fecal samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran

Group 0 sample size Number of subjects in the control (unexposed) group: 69

Group 1 sample size Number of subjects in the case (exposed) group: 64

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: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.01

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

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Needs review

Curated date: 2024/03/25

Curator: EGO

Revision editor(s): EGO, Scholastica, WikiWorks

Source: Additional files 2 Table S2

Description: Differential abundance analysis of phylum and genus level changes comparing RNAlater fecal samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran

Abundance in Group 1: increased abundance in

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Actinomycetota
Collinsella

Revision editor(s): EGO, Scholastica, WikiWorks

Signature 2

Needs review

Curated date: 2024/03/25

Curator: EGO

Revision editor(s): EGO, Scholastica, WikiWorks

Source: Additional files 2 Table S2

Description: Differential abundance analysis of phylum and genus level changes comparing RNAlater fecal samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran

Abundance in Group 1: decreased abundance in

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Coprococcus 3Coprococcus 3

Revision editor(s): EGO, Scholastica, WikiWorks

Experiment 2

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Curated date: 2024/03/26

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Fecal occult blood test [FOBT] cards - Day 0

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Fecal occult blood test [FOBT] cards fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran

Group 1 sample size Number of subjects in the case (exposed) group: 70

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Needs review

Curated date: 2024/03/26

Curator: EGO

Revision editor(s): EGO, Scholastica, WikiWorks

Source: Additional files 2 Table S4

Description: Differential abundance analysis of phylum and genus level changes comparing RNAlater to FOBT card fecal samples frozen immediately (day-0) from Gonbad and Yazd, Iran

Abundance in Group 1: increased abundance in

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Actinomycetota
Bacillota
Bifidobacterium
Collinsella
Eggerthella
Enterorhabdus
Senegalimassilia
Eggerthellaceae bacterium
Lactobacillus
Lactococcus
Streptococcus
Clostridium
Mogibacterium
Clostridiales Family XIII bacterium
Anaerostipes
Blautia
CAG-56CAG-56
Coprococcus 1Coprococcus 1
Coprococcus 2Coprococcus 2
Coprococcus 3Coprococcus 3
Dorea
Fusicatenibacter
Lachnospiraceae FCS020 groupLachnospiraceae FCS020 group
Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group
Marvinbryantia
Anaerobutyricum hallii
Eubacterium ventriosum
Eubacterium xylanophilum
Ruminococcus gauvreauii
Mediterraneibacter gnavus
[Ruminococcus] torques
Lachnospiraceae
Intestinibacter
Romboutsia
Terrisporobacter
Butyricicoccus
Faecalibacterium
Negativibacillus
uncultured Oscillospiraceae bacterium
Ruminococcus
Subdoligranulum
Eubacterium coprostanoligenes
Holdemanella
Solobacterium
Megasphaera
Mitsuokella

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Signature 2

Needs review

Curated date: 2024/03/26

Curator: EGO

Revision editor(s): EGO, Scholastica, WikiWorks

Source: Additional files 2 Table S8

Description: Differential abundance analysis of phylum level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran

Abundance in Group 1: decreased abundance in

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Bacteroidota
Cyanobacteriota
Lentisphaerota
Pseudomonadota
Mycoplasmatota
Bacteroides
Barnesiella
Butyricimonas
Odoribacter
metagenome
gut metagenome
Alloprevotella
Prevotella 2Prevotella 2
Prevotella 7Prevotella 7
Prevotella 9Prevotella 9
Prevotellaceae NK3B31 groupPrevotellaceae NK3B31 group
uncultured Prevotellaceae bacterium
Alistipes
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Parabacteroides
Candidatus Gastranaerophilales
Christensenellaceae R-7 groupChristensenellaceae R-7 group
Clostridiales vadinBB60 groupClostridiales vadinBB60 group
Butyrivibrio
GCA-900066575GCA-900066575
Lachnospira
uncultured Lachnospiraceae bacterium
Lachnospira eligens
Eubacterium ruminantium
Candidatus Soleaferrea
Oscillibacter
Ruminiclostridium 6Ruminiclostridium 6
uncultured Oscillospiraceae bacterium
Eubacteriales
Asteroleplasma
Erysipelotrichaceae UCG-004Erysipelotrichaceae UCG-004
Victivallis
Rhodospirillales
Bilophila
Desulfovibrio
Succinivibrio
Parasutterella
Sutterella
Burkholderiaceae
Candidatus Izemoplasmatales
Mollicutes
Puniceicoccaceae

Revision editor(s): EGO, Scholastica, WikiWorks

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-24

Curated date: 2024/07/23

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Scope mouthwash - Day 0

Group 1 name Corresponds to the case (exposed) group for case-control studies: Scope mouthwash - Day 4

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Scope mouthwash samples after incubation at room temperature for four days (day-4) from Gonbad and Yazd, Iran

Group 0 sample size Number of subjects in the control (unexposed) group: 70

Group 1 sample size Number of subjects in the case (exposed) group: 55

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-24

Curated date: 2024/07/23

Curator: Scholastica

Revision editor(s): Scholastica, WikiWorks

Source: Additional files 2 Table S6

Description: Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran

Abundance in Group 1: increased abundance in

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Bacillota
Actinomycetaceae
Bifidobacterium
Streptococcus
Peptococcus
uncultured Oscillospiraceae bacterium
Solobacterium
Selenomonas 3Selenomonas 3
Veillonellaceae
Lautropia
Pseudomonas

Revision editor(s): Scholastica, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-24

Curated date: 2024/07/23

Curator: Scholastica

Revision editor(s): Scholastica, WikiWorks

Source: Additional files 2 Table S6

Description: Differential abundance analysis of phylum and genus level changes comparing Scope mouthwash samples after incubation at room temperature for four days (day-4) to frozen immediately (day-0) from Gonbad and Yazd, Iran

Abundance in Group 1: decreased abundance in

NCBI	Quality Control	Links
Pseudomonadota
Rothia
Porphyromonas
Alloprevotella
Prevotella 7Prevotella 7
Gemella
Neisseria
Aggregatibacter
Haemophilus

Revision editor(s): Scholastica, WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-7-24

Curated date: 2024/07/23

Curator:

Revision editor(s):

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: OMNIgene ORAL kit

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Scope mouthwash oral samples from Gonbad and Yazd, Iran

Group 0 sample size Number of subjects in the control (unexposed) group: 77

Group 1 sample size Number of subjects in the case (exposed) group: 125

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Needs review

Curated date: 2024/07/23

Curator: Scholastica

Revision editor(s): Scholastica, WikiWorks

Source: Additional files 2 Table S8

Description: Differential abundance analysis of phylum and genus level changes comparing OMNIgene ORAL kit samples to Scope mouthwash oral samples from Gonbad and Yazd, Iran

Abundance in Group 1: increased abundance in

NCBI	Quality Control	Links
Abiotrophia
Alloscardovia
Bacteroidota
Campylobacter
Campylobacterota
Capnocytophaga
Gemella
Geobacillus
Lactobacillus
Lautropia
Patescibacteria group
Phocaeicola
Pseudomonas
Scardovia
Selenomonas
Spirochaetota
Veillonellaceae
uncultured Oscillospiraceae bacterium
Prevotella 6Prevotella 6
Selenomonas 3Selenomonas 3
candidate division SR1 bacterium MGEHA
Treponema 2Treponema 2

Revision editor(s): Scholastica, WikiWorks

Signature 2