Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Claregrieve1, WikiWorks

Subjects

Location of subjects: Spain

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: Obsessive-compulsive disorder Anancastic neurosis,obsessive compulsive disorder,obsessive-compulsive disorder,OCD,Obsessive-compulsive disorder

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: OCD T0 (Baseline)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Obsessive-compulsive disorder (OCD), which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 0 was the baseline timepoint prior to three months of pharmacological treatment and cognitive behavioral therapy (referred to as T0).

Group 0 sample size Number of subjects in the control (unexposed) group: 33

Group 1 sample size Number of subjects in the case (exposed) group: 32

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: LEfSe

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.0

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: decreased

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Source: Figure 3A

Description: Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint

Abundance in Group 1: increased abundance in OCD T0 (Baseline)

NCBI	Quality Control	Links
Alistipes
Anaerostipes
Barnesiellaceae
Coprobacter
Flavonifractor
Hungatella
Oscillibacter
Rikenellaceae
Mollicutes
Oscillospiraceae bacterium

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit

Source: Figure 3A

Description: Differential microbial abundance in stool samples between controls and OCD patients at the T0 timepoint

Abundance in Group 1: decreased abundance in OCD T0 (Baseline)

NCBI	Quality Control	Links
Agathobacter
Butyricicoccus
Catenibacterium
Clostridiaceae
Clostridium
Coprococcus
Dialister
Howardella
Lachnospira
Negativicutes
Paraprevotella
Prevotellaceae
Romboutsia
Selenomonadales
Veillonellaceae

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

Group 1 name Corresponds to the case (exposed) group for case-control studies: OCD T0

Group 0 sample size Number of subjects in the control (unexposed) group: 32

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: 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 Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Source: Figure 4A

Description: Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients

Abundance in Group 1: increased abundance in OCD T0

NCBI	Quality Control	Links
Oribacterium
Actinomyces
Actinomycetales
Atopobiaceae
Atopobium
Coriobacteriales
Coriobacteriia
Lachnoanaerobaculum
Lachnospiraceae
Mogibacterium
Oribacterium sp.

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/24

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Source: Figure 4A

Description: Differential microbial abundance in oropharyngeal samples between controls and T0 OCD patients

Abundance in Group 1: decreased abundance in OCD T0

NCBI	Quality Control	Links
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Peptostreptococcaceae bacterium

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Aiyshaaaa

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/28

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Claregrieve1, WikiWorks

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 1 name Corresponds to the case (exposed) group for case-control studies: OCD T3

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with obsessive-compulsive disorder (OCD) which is a neuropsychiatric condition characterized by intrusive and unwanted thoughts (termed obsessions) and repetitive behaviors or mental acts (termed compulsions), which are carried out to at least partially alleviate the anxiety or distress brought on by the obsessions. Timepoint 3 is following three months of pharmacological treatment and cognitive behavioral therapy (referred to as T3).

Group 0 sample size Number of subjects in the control (unexposed) group: 33

Group 1 sample size Number of subjects in the case (exposed) group: 31

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: 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 Claregrieve1 on 2023-5-22

Curated date: 2023/03/29

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Atrayees

Source: Figure S4

Description: Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint

Abundance in Group 1: increased abundance in OCD T3

NCBI	Quality Control	Links
Alistipes
Anaerostipes
Anaerotruncus
Barnesiellaceae
Bilophila
Coprobacter
Eisenbergiella
Flavonifractor
Holdemania
Hungatella
Oscillibacter
Pygmaiobacter
Rikenellaceae
Ruminiclostridium

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit, Atrayees

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/29

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit

Source: Figure S4

Description: Differential microbial abundance in stool samples between controls and OCD patients at the T3 timepoint

Abundance in Group 1: decreased abundance in OCD T3

NCBI	Quality Control	Links
Catenibacterium
Coprococcus
Intestinibacter
Lachnospira sp.
Paraprevotella
Peptostreptococcaceae
Prevotellaceae
Romboutsia
Veillonellaceae

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Merit

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2023/03/29

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

Group 0 sample size Number of subjects in the control (unexposed) group: 32

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: 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 Claregrieve1 on 2023-5-22

Curated date: 2023/03/29

Curator: Kahvecirem

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Aiyshaaaa

Source: Figure S6

Description: Differential microbial abundance in oropharyngeal samples between controls and T3 OCD patients

Abundance in Group 1: increased abundance in OCD T3

NCBI	Quality Control	Links
Actinomyces
Actinomycetaceae
Actinomycetales
Atopobiaceae
Atopobium
Catonella
Coriobacteriales
Coriobacteriia
Lachnospiraceae
Mogibacterium

Revision editor(s): WikiWorks, Claregrieve1, Kahvecirem, Aiyshaaaa

Signature 2