Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/03/05

Curator: Uhabiba14

Revision editor(s): Uhabiba14, MyleeeA, Fiddyhamma

Subjects

Location of subjects: China; Germany

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: Male homosexuality Male homosexuality,male homosexuality

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Men with 0-3 sexual partners

Group 1 name Corresponds to the case (exposed) group for case-control studies: Men with >3 sexual partners

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category with more than 3 sexual partners (in the last 12 months).

Group 0 sample size Number of subjects in the control (unexposed) group: 38

Group 1 sample size Number of subjects in the case (exposed) group: 29

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

Lab analysis

Sequencing type: WMS

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

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)?: No

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

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/03/05

Curator: Uhabiba14

Revision editor(s): Uhabiba14, Fiddyhamma, MyleeeA

Source: figure 4 (c) and Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with behaviors having >3 (and 0–3) sexual partners.

Abundance in Group 1: decreased abundance in Men with >3 sexual partners

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Blautia massiliensis (ex Durand et al. 2017)
Candidatus Neoanaerotignum tabaqchaliae
Clostridia bacterium
Lachnospira pectinoschiza
Methanomassiliicoccales archaeon
Oscillibacter
Bacteroidales incertae sedis
Clostridia incertae sedis

Revision editor(s): Uhabiba14, Fiddyhamma, MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/03/05

Curator: Uhabiba14

Revision editor(s): Uhabiba14, MyleeeA, Fiddyhamma

Source: figure 4C and SupplementaryTable S4

Description: Species-level taxonomic biomarkers identified using LEfSe58 to associate with behaviors having ( 0–3) sexual partners. Only taxonomically known species are displayed

Abundance in Group 1: increased abundance in Men with >3 sexual partners

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Anaerotignum faecicola
Bacteroidaceae bacterium
Brachyspira pilosicoli
Campylobacteraceae bacterium
Candidatus Gastranaerophilales bacterium
Lacrimispora amygdalina
Oscillospiraceae bacterium
Prevotella pectinovora
Prevotellamassilia timonensis
Segatella copri clade CSegatella copri clade C
Segatella copri clade BSegatella copri clade B

Revision editor(s): Uhabiba14, MyleeeA, Fiddyhamma

Experiment 2

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Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Condom use (Always during RAI)

Group 1 name Corresponds to the case (exposed) group for case-control studies: No Condom use (during RAI)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who never use Condom during Receptive Anal intercourse.

Group 0 sample size Number of subjects in the control (unexposed) group: 12

Group 1 sample size Number of subjects in the case (exposed) group: 37

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 Months

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with Condom use (Always during RAI) and No Condom use (during RAI).

Abundance in Group 1: increased abundance in No Condom use (during RAI)

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Clostridia incertae sedis
Clostridiales bacterium
Lachnospiraceae bacterium
Lachnospiraceae incertae sedis
Rikenellaceae bacterium
Roseburia hominis
Roseburia sp.
unclassified Oscillospiraceae

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with Condom use (Always during RAI) and No Condom use (during RAI).

Abundance in Group 1: decreased abundance in No Condom use (during RAI)

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Candidatus Cibiobacter qucibialis
Clostridia bacterium
Lachnospira pectinoschiza

Revision editor(s): MyleeeA

Experiment 3

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Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: No Oral Sex

Group 1 name Corresponds to the case (exposed) group for case-control studies: Yes Oral Sex

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who practice Oral sex.

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 42

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.

Abundance in Group 1: increased abundance in Yes Oral Sex

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Bacteroidaceae bacterium
Clostridia bacterium
Desulfovibrio piger
Phascolarctobacterium succinatutens
Prevotella pectinovora
Prevotella sp.
Lachnospiraceae incertae sedis
Oscillospiraceae bacterium
Clostridia incertae sedis
Rikenellaceae incertae sedis
[Ruminococcus] torques

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with No Oral sex and Yes Oral sex.

Abundance in Group 1: decreased abundance in Yes Oral Sex

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Bacteroides thetaiotaomicron
Bifidobacterium bifidum
Bilophila wadsworthia
Campylobacter gracilis
Candidatus Avimicrobium caecorum
Clostridia bacterium
Clostridium disporicum
Erysipelotrichaceae bacterium
Lachnospiraceae bacterium
Phascolarctobacterium faecium
Phocaeicola massiliensis
Anaeromassilibacillus sp.
Merdimonas faecis
Mesosutterella multiformis
[Ruminococcus] lactaris
Oscillospiraceae bacterium
Bacilli incertae sedis

Revision editor(s): MyleeeA

Experiment 4

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Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Condom use (Sometimes during RAI)

Group 1 name Corresponds to the case (exposed) group for case-control studies: No Condom use (during RAI)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who never use Condom during Receptive Anal intercourse.

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 37

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Experiment 5

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Curated date: 2024/04/13

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Condom use (Always during RAI)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Condom use (Sometimes during RAI)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who sometimes use Condom during Receptive Anal intercourse.

Group 0 sample size Number of subjects in the control (unexposed) group: 12

Group 1 sample size Number of subjects in the case (exposed) group: 15

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

Experiment 6

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Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who were positive to sexually transmitted infection.

Group 0 sample size Number of subjects in the control (unexposed) group: 44

Group 1 sample size Number of subjects in the case (exposed) group: 23

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe associated with Positive STI and Negative STI .

Abundance in Group 1: decreased abundance in STI Positive

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Roseburia faecis
Sutterella wadsworthensis
unclassified Oscillospiraceae
Sutterella seckii

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe associated with Positive STI and Negative STI

Abundance in Group 1: increased abundance in STI Positive

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Clostridia bacterium
Brachyspira pilosicoli
unclassified Oscillospiraceae
unclassified Bacilli
unclassified Rikenellaceae
Lentisphaeria bacterium
Oscillospiraceae bacterium
Eubacteriaceae bacterium

Revision editor(s): MyleeeA

Experiment 7

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Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA, Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: No RAI

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men in the risk increasing category who practice Receptive Anal intercourse.

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 46

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.

Abundance in Group 1: increased abundance in Yes RAI

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Clostridium sp.
Phascolarctobacterium succinatutens
unclassified Rikenellaceae

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/15

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S4

Description: Species-level taxonomic biomarkers identified using LEfSe to associate with No Receptive Anal Intercourse and Yes Receptive Anal Intercourse.

Abundance in Group 1: decreased abundance in Yes RAI

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Alistipes finegoldii
Bifidobacterium longum
Candidatus Avimicrobium caecorum
Clostridia bacterium
Mesosutterella multiformis
unclassified Bacilli
Mycoplasmatales bacterium
Oscillospiraceae bacterium
[Clostridium] nexile
unclassified Clostridia

Revision editor(s): MyleeeA

Experiment 8

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Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.

Group 0 sample size Number of subjects in the control (unexposed) group: 93

Group 1 sample size Number of subjects in the case (exposed) group: 93

Lab analysis

Statistical Analysis

Statistical test: Fisher's Exact Test

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: Not specified

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Westernized.

Abundance in Group 1: increased abundance in Westernized

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Alphaproteobacteria bacterium
Bacilli bacterium
Bacteroidaceae bacterium
Bacteroidales bacterium
Blastocystis sp. subtypes
Brachyspira pilosicoli
Campylobacteraceae bacterium
Candidatus Gastranaerophilales bacterium
Clostridia bacterium
Clostridiaceae bacterium
Clostridiales bacterium
Clostridium sp.
Desulfovibrionaceae bacterium
Dorea longicatena
Duodenibacillus massiliensis
Opitutales bacterium
Oscillospiraceae bacterium
Propionibacterium freudenreichii
Selenomonadales bacterium
Victivallis vadensis
unclassified Bacteroidales
unclassified Clostridia
unclassified Coriobacteriia
Helicobacteraceae bacterium

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Westernized.

Abundance in Group 1: decreased abundance in Westernized

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Akkermansia muciniphila
Alistipes inops
Anaerostipes caccae
Bacteroides fragilis
Bacteroides intestinalis
Bacteroides stercoris
Bacteroides xylanisolvens
Bifidobacterium bifidum
Bilophila wadsworthia
Blautia
Blautia faecis
Blautia obeum
Blautia sp.
Clostridia bacterium
Dialister invisus
Dorea longicatena
Eisenbergiella massiliensis
Eubacteriaceae bacterium
Eubacterium sp.
Mediterraneibacter glycyrrhizinilyticus
Mogibacterium diversum
Monoglobus pectinilyticus
Phocaeicola plebeius
Prevotella marseillensis
Romboutsia timonensis
Sellimonas intestinalis
Solobacterium
Streptococcus infantis
Streptococcus mitis
Streptococcus sp.
Turicibacter sanguinis
Veillonella rogosae
unclassified Bacilli
Coriobacteriia bacterium
Candidatus Avimonas narfae
unclassified Clostridia
[Clostridium] scindens
Lachnospira hominis
[Clostridium] symbiosum
Lawsonibacter hominis
[Ruminococcus] lactaris
Neglectibacter timonensis
Negativibacillus massiliensis
Thomasclavelia ramosa
[Clostridium] innocuum

Revision editor(s): MyleeeA

Experiment 9

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Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men who have sex with Men (Prevotella Family comparison)

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

Group 1 sample size Number of subjects in the case (exposed) group: 84

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S2

Description: Species differentially enriched in MSM relative to non-MSM. Log2-transformed abundances of Prevotellaceae members with a minimum abundance of 0.1 at 90th percentile in all subjects.

Abundance in Group 1: increased abundance in MSM

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Segatella copri clade HSegatella copri clade H
Paraprevotella clara
Prevotella
Segatella copri clade ASegatella copri clade A
Segatella copri clade BSegatella copri clade B
Segatella copri clade CSegatella copri clade C
Segatella copri clade DSegatella copri clade D
Segatella copri clade ESegatella copri clade E
Prevotella pectinovora
Prevotella sp.

Revision editor(s): MyleeeA

Experiment 10

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Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men who have sex with Men

Group 0 sample size Number of subjects in the control (unexposed) group: 31

Group 1 sample size Number of subjects in the case (exposed) group: 93

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Non MSM.

Abundance in Group 1: increased abundance in MSM

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Bacillota bacterium
Bacteroidaceae bacterium
Clostridia bacterium
Desulfovibrio piger
Eubacterium sp.
Faecalibacterium prausnitzii
Fusobacterium mortiferum
Lachnospiraceae bacterium
Holdemanella biformis
Lentisphaeria bacterium
Methanomassiliicoccales archaeon
Mitsuokella jalaludinii
Phascolarctobacterium succinatutens
Prevotella
Prevotella pectinovora
Rikenellaceae bacterium
Roseburia sp.
Slackia isoflavoniconvertens
Streptococcus parasanguinis
unclassified Clostridia
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Rikenellaceae
Prevotella sp. Marseille
Catenibacterium sp.
Segatella copri clade ASegatella copri clade A
Segatella copri clade CSegatella copri clade C
Segatella copri clade DSegatella copri clade D
Segatella copri clade GSegatella copri clade G
Segatella copri clade HSegatella copri clade H
Prevotella sp.
Brachyspira aalborgi
Megasphaera sp.
Bacilli bacterium
Segatella hominis

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/18

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Non MSM.

Abundance in Group 1: decreased abundance in MSM

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Acidaminococcaceae bacterium
Agathobaculum butyriciproducens
Alistipes communis
Alistipes inops
Alistipes onderdonkii
Alistipes putredinis
Anaerotignum faecicola
Bacteroides caccae
Bacteroides cellulosilyticus
Bacteroides finegoldii
Bacteroides fragilis
Bacteroides ovatus
Bacteroides thetaiotaomicron
Bacteroides uniformis
Barnesiella intestinihominis
Bifidobacterium bifidum
Bifidobacterium longum
Bifidobacterium pseudocatenulatum
Blautia faecis
Blautia wexlerae
Candidatus Gastranaerophilales bacterium
Clostridia bacterium
Clostridiaceae bacterium
Clostridium sp.
Dialister invisus
Evtepia gabavorous
Faecalibacterium prausnitzii
Flavonifractor plautii
Fusicatenibacter saccharivorans
Gemmiger
Mediterraneibacter gnavus
Mesosutterella multiformis
Odoribacter splanchnicus
Parabacteroides distasonis
Paraprevotella clara
Parasutterella
Parasutterella excrementihominis
Phascolarctobacterium faecium
Phocaeicola coprocola
Phocaeicola dorei
Phocaeicola plebeius
Phocaeicola vulgatus
Ruminococcus bicirculans (ex Liu et al. 2021)
Ruminococcus callidus
[Ruminococcus] lactaris
[Ruminococcus] torques
unclassified Clostridia
Segatella copri clade BSegatella copri clade B
Clostridium fessum

Revision editor(s): MyleeeA

Experiment 11

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Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).

Group 0 sample size Number of subjects in the control (unexposed) group: 93

Group 1 sample size Number of subjects in the case (exposed) group: 481

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/18

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Non Westernized.

Abundance in Group 1: increased abundance in Non Westernized

NCBI	Quality Control	Links
Anaerotruncus massiliensis (ex Liu et al. 2021)
Angelakisella massiliensis
Bacteroides salyersiae
Bifidobacterium catenulatum
Brachyspira pilosicoli
Butyricimonas
Candidatus Alangreenwoodia gallinarii
Candidatus Allobutyricicoccus pentlandensis
Candidatus Allochristensenella caecavium
Candidatus Avimonas narfae
Candidatus Geddesella stercoravicola
Candidatus Metalachnospira gallinarum
Candidatus Neochristensenella gallicola
Candidatus Neoruminococcus faecicola
Candidatus Pseudolachnospira avium
Clostridia bacterium
Clostridiaceae bacterium
Clostridiales bacterium
Clostridium sp.
Coprobacter fastidiosus
Eisenbergiella tayi
Erysipelotrichaceae bacterium
Eubacterium sp.
Flavonifractor sp.
Holdemania filiformis
Hydrogeniiclostridium mannosilyticum
Intestinimonas massiliensis (ex Afouda et al. 2020)
Intestinimonas timonensis
Lachnoclostridium sp.
Lachnospiraceae bacterium
Massiliimalia timonensis
Megasphaera elsdenii
Merdimmobilis hominis
Merdimonas faecis
Oscillibacter sp.
Phocaeicola vulgatus
Prevotella bivia
Propionibacterium freudenreichii
Rothia mucilaginosa
Sanguibacteroides justesenii
unclassified Oscillospiraceae
Oscillospiraceae bacterium
Massilimicrobiota sp.

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/19

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table S3

Description: Species enriched in MSM and Non Westernized.

Abundance in Group 1: decreased abundance in Non Westernized

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Actinomyces sp.
Bacteroidaceae bacterium
Prevotellamassilia timonensis
Segatella copri clade CSegatella copri clade C
Prevotella sp.
Candidatus Gastranaerophilales bacterium
TM7 phylum sp. oral taxon 348
Candidatus Nanosynsacchari sp. TM7_ANC_38.39_G1_1
Elusimicrobiales bacterium
Bacilli bacterium
unclassified Bacilli
Leuconostoc
Lactococcus petauri
Lactococcus plantarum
Streptococcus sp.
Clostridia bacterium
unclassified Clostridia
Clostridium disporicum
Clostridium sp.
Mogibacterium diversum
Eubacteriaceae bacterium
Blautia
Blautia faecis
Coprococcus catus
Lachnospiraceae bacterium
unclassified Lachnospiraceae
Lachnospira eligens
[Ruminococcus] lactaris
Roseburia sp.
Oscillospiraceae bacterium
unclassified Oscillospiraceae
Ruminococcus bicirculans (ex Liu et al. 2021)
Erysipelotrichaceae bacterium
Selenomonas
Veillonella parvula
Veillonella rogosae
Lentisphaeria bacterium
Escherichia marmotae
Spirochaetia bacterium

Revision editor(s): MyleeeA

Experiment 12

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Westernization describes a population with incremental urbanization, profound lifestyle changes, including but not limited to, transition from autarchic means of producing food to controlled food production chain, increased hygiene and accessibility to modern medicals, introduction of food sterilization, increased exposure to pollutants, and switch from high-fiber simple diets to high-fat high-protein processes that has been undergoing for centuries.

Lab analysis

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3A

Description: Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).

Abundance in Group 1: increased abundance in Westernized

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Prevotellaceae
Segatella/PrevotellaSegatella/Prevotella

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3A

Description: Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).

Abundance in Group 1: decreased abundance in Westernized

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Bacteroidaceae
Bacteroides

Revision editor(s): MyleeeA

Experiment 13

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Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Non-Westernized describes a population practicing a traditional lifestyle relating to factors such as diet, hygiene, and with limited access to modern medical healthcare and pharmaceuticals (e.g., antibiotics).

Group 1 sample size Number of subjects in the case (exposed) group: 389

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3A

Description: Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).

Abundance in Group 1: increased abundance in Non Westernized

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Bacteroidaceae
Bacteroides

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3A

Description: Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).

Abundance in Group 1: decreased abundance in Non Westernized

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Prevotellaceae
Segatella/PrevotellaSegatella/Prevotella

Revision editor(s): MyleeeA

Experiment 14

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Two Chinese cities - GuangDong and TangShan - which are located in Southern China and have been experiencing rapid urbanization in the last decade. They were used to represent populations from non-Western but relatively urbanized communities.

Group 1 sample size Number of subjects in the case (exposed) group: 66

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-5-2

Curated date: 2024/04/17

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 3A

Description: Differential abundance of Bacteroidaceae and Prevotellaceae families and Bacteroides and Segatella/Prevotella genera between MSM (n = 93), Westernized (n = 481), non-Westernized (n = 389), and urban Chinese (n= 66) samples (Wilcoxon rank-sum test with FDR correction).

Abundance in Group 1: increased abundance in China (Urban)

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Prevotellaceae
Segatella/PrevotellaSegatella/Prevotella

Revision editor(s): MyleeeA

Signature 2