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

Curator: EGO

Revision editor(s): EGO, Scholastica

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: Microbiome measurement Microbiome measurement,microbiome measurement

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

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

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

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

Curated date: 2024/03/25

Curator: EGO

Revision editor(s): EGO, Scholastica

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 RNAlater - Day 4

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Actinomycetota
Collinsella

Revision editor(s): EGO, Scholastica

Signature 2

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

Curated date: 2024/03/25

Curator: EGO

Revision editor(s): EGO, Scholastica

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 RNAlater - Day 4

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Coprococcus 3Coprococcus 3

Revision editor(s): EGO, Scholastica

Experiment 2

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

Curated date: 2024/03/26

Curator: EGO

Revision editor(s): EGO, Scholastica

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

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

Curated date: 2024/03/26

Curator: EGO

Revision editor(s): EGO, Scholastica

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 Fecal occult blood test [FOBT] cards - Day 0

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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

Revision editor(s): EGO, Scholastica

Signature 2

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

Curated date: 2024/03/26

Curator: EGO

Revision editor(s): EGO, Scholastica

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 Fecal occult blood test [FOBT] cards - Day 0

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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

Experiment 3

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: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,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

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 Scope mouthwash - Day 4

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

Revision editor(s): Scholastica

Signature 2

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

Curated date: 2024/07/23

Curator: Scholastica

Revision editor(s): Scholastica

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 Scope mouthwash - Day 4

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Pseudomonadota
Rothia
Porphyromonas
Alloprevotella
Prevotella 7Prevotella 7
Gemella
Neisseria
Aggregatibacter
Haemophilus

Revision editor(s): Scholastica

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: Scholastica

Revision editor(s): Scholastica

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

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

Curated date: 2024/07/23

Curator: Scholastica

Revision editor(s): Scholastica

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 Scope mouthwash

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

Signature 2