Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices
From BugSigDB
Jump to:navigation, search
Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J
Journal
Cell reports. Medicine
Year
2024
Keywords:
MSM, Prevotella, RAI, Segatella, gut microbiome, non-Westernized microbiota, oral sex, sex partner, sexual orientation
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Curated date: 2024/03/05
Curator: Uhabiba14
Revision editor(s): WikiWorks, MyleeeA, Uhabiba14, Fiddyhamma
Subjects
- 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): WikiWorks, MyleeeA, Uhabiba14, Fiddyhamma
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
Revision editor(s): WikiWorks, MyleeeA, Uhabiba14, Fiddyhamma
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Curated date: 2024/03/05
Curator: Uhabiba14
Revision editor(s): WikiWorks, MyleeeA, Uhabiba14, 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
Revision editor(s): WikiWorks, MyleeeA, Uhabiba14, Fiddyhamma
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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 8
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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
Source: Supplementary Table S3
Description: Species enriched in MSM and Westernized.
Abundance in Group 1: increased abundance in Westernized
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Source: Supplementary Table S3
Description: Species enriched in MSM and Westernized.
Abundance in Group 1: decreased abundance in Westernized
Experiment 10
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
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
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
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
Source: Supplementary Table S3
Description: Species enriched in MSM and Non MSM.
Abundance in Group 1: increased abundance in MSM
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-2
Source: Supplementary Table S3
Description: Species enriched in MSM and Non MSM.
Abundance in Group 1: decreased abundance in MSM
Retrieved from "https://bugsigdb.org/w/index.php?title=38366600&oldid=154530"
