Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18
study design
cross-sectional observational, not case-control
Citation
PMID PubMed identifier for scientific articles.
36329122
DOI Digital object identifier for electronic documents.
https://doi.org/10.1038/s41598-022-21779-z
URI
Authors
Clarke T, Brinkac L, Greco C, Alleyne AT, Carrasco P, Inostroza C, Tau T, Wisitrasameewong W, Torralba MG, Nelson K, Singh H
Journal
Scientific reports
Year
2022
Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.

Experiment 3


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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Location of subjects
Barbados
Chile
South Africa
Thailand
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
Lifestyle measurement Lifestyle measurement,lifestyle measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, Chile, South Africa
Group 1 name Corresponds to the case (exposed) group for case-control studies
Thailand
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Thailand refers to the samples from healthy females aged between 18 and 26 years, based in Thailand.
Group 0 sample size Number of subjects in the control (unexposed) group
138
Group 1 sample size Number of subjects in the case (exposed) group
68
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants currently taking antibiotics were excluded from the study.

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).
raw counts
Statistical test
DESeq2
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


Signature 1

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S8

Description: Differentially abundant taxa in stool samples for Thailand location.

Abundance in Group 1: increased abundance in Thailand

NCBI Quality ControlLinks
Escherichia coli   
Fusobacterium mortiferum   
Phocaeicola coprocola DSM 17136   
Phocaeicola massiliensis   
Phocaeicola plebeius   
Ruminococcus sp. 5_1_39BFAA   
unclassified Alistipes   
unclassified Sutterella   
uncultured meganomonasuncultured meganomonas
Parabacteroides merdae   

Revision editor(s): KateRasheed

Signature 2

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S8

Description: Differentially abundant taxa in stool samples for Thailand location.

Abundance in Group 1: decreased abundance in Thailand

NCBI Quality ControlLinks
uncultured Pseudobutyrivibrio sp.   
uncultured Prevotellaceae bacterium   
Ruminococcaceae_UCG-002Ruminococcaceae_UCG-002
unclassified Akkermansia   
Bacteroides ovatus   
Uncultured prevotellaUncultured prevotella
unclassified Ruminococcus   
unclassified Subdoligranulum   
Ruminococcaceae_UCG-014Ruminococcaceae_UCG-014
unclassified Blautia   
Ruminococcus bicirculans (ex Liu et al. 2021)   
uncultured Bacteroides sp.   
unclassified Faecalibacterium   
uncultured Christensenellaceae bacterium   
uncultured Dorea sp.   
Ruminococcaceae_UCG-005Ruminococcaceae_UCG-005

Revision editor(s): KateRasheed

Experiment 4


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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Chile, South Africa, Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
Barbados
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados.
Group 0 sample size Number of subjects in the control (unexposed) group
174
Group 1 sample size Number of subjects in the case (exposed) group
32

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S9

Description: Differentially abundant taxa in stool samples for Barbados location.

Abundance in Group 1: increased abundance in Barbados

NCBI Quality ControlLinks
uncultured Pseudobutyrivibrio sp.   
Bacteroides ovatus   
Lachnospiraceae_UCG-004Lachnospiraceae_UCG-004
Lachnospiraceae_UCG-005Lachnospiraceae_UCG-005
uncultured Bacteroides sp.   

Revision editor(s): KateRasheed

Signature 2

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S9

Description: Differentially abundant taxa in stool samples for Barbados location.

Abundance in Group 1: decreased abundance in Barbados

NCBI Quality ControlLinks
Uncultured prevotellaUncultured prevotella
Phocaeicola plebeius   
unclassified Alistipes   
Phocaeicola coprocola DSM 17136   
Escherichia coli   
unclassified Akkermansia   
Eubacterium coprostanoligenes   
Fusobacterium mortiferum   
Ruminococcaceae_UCG-005Ruminococcaceae_UCG-005

Revision editor(s): KateRasheed

Experiment 5


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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, South Africa, and Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
Chile
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.
Group 0 sample size Number of subjects in the control (unexposed) group
137
Group 1 sample size Number of subjects in the case (exposed) group
69

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S10

Description: Differentially abundant taxa in stool samples for Chile location.

Abundance in Group 1: increased abundance in Chile

NCBI Quality ControlLinks
Ruminococcaceae_UCG-005Ruminococcaceae_UCG-005

Revision editor(s): KateRasheed

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Source: Table S10

Description: Differentially abundant taxa in stool samples for Chile location.

Abundance in Group 1: decreased abundance in Chile

NCBI Quality ControlLinks
Phocaeicola plebeius   
Bacteroides stercoris ATCC 43183   
Phocaeicola massiliensis   
uncultured Faecalibacterium sp.   
Phocaeicola coprocola DSM 17136   
uncultured Prevotellaceae bacterium   
unclassified Bifidobacterium   
Fusobacterium mortiferum   
Escherichia coli   
Lachnospiraceae_UCG-004Lachnospiraceae_UCG-004
unclassified Roseburia   
Lachnospiraceae_UCG-005Lachnospiraceae_UCG-005

Revision editor(s): KateRasheed

Experiment 6


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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, Chile, and Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
South Africa
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.
Group 0 sample size Number of subjects in the control (unexposed) group
169
Group 1 sample size Number of subjects in the case (exposed) group
37

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S11

Description: Differentially abundant taxa in stool samples between South Africa and other location.

Abundance in Group 1: increased abundance in South Africa

NCBI Quality ControlLinks
uncultured Faecalibacterium sp.   
unclassified Bifidobacterium   
Ruminococcaceae_UCG-002Ruminococcaceae_UCG-002
unclassified Faecalibacterium   

Revision editor(s): KateRasheed

Signature 2

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S11

Description: Differentially abundant taxa in stool samples between South Africa and other location.

Abundance in Group 1: decreased abundance in South Africa

NCBI Quality ControlLinks
Bacteroides ovatus   
Fusobacterium mortiferum   
Phocaeicola coprocola DSM 17136   
Phocaeicola plebeius   
unclassified Alistipes   
unclassified Bacteroides   
unclassified Blautia   
unclassified Fusicatenibacter   
unclassified Parabacteroides   
Lachnospiraceae_UCG-004Lachnospiraceae_UCG-004

Revision editor(s): KateRasheed

Experiment 7


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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Cheek Buccae,Jowl,Cheek,cheek
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, Chile, and South Africa
Group 1 name Corresponds to the case (exposed) group for case-control studies
Thailand
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Thailand refers to the oral samples from healthy females aged between 18 and 26 years, based in Thailand.
Group 0 sample size Number of subjects in the control (unexposed) group
138
Group 1 sample size Number of subjects in the case (exposed) group
68

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S12

Description: Differentially abundant taxa in oral samples between Thailand and other location.

Abundance in Group 1: increased abundance in Thailand

NCBI Quality ControlLinks
Streptococcus sanguinis   
unclassified Haemophilus   
uncultured Aggregatibacter sp.   
uncultured Bergeyella sp.   
uncultured gemellauncultured gemella
uncultured Neisseria sp.   

Revision editor(s): KateRasheed

Signature 2

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S12

Description: Differentially abundant taxa in oral samples between Thailand and other location.

Abundance in Group 1: decreased abundance in Thailand

NCBI Quality ControlLinks
unclassified Veillonella   
Prevotella melaninogenica   
uncultured Granulicatella sp.   
unclassified Prevotella   
Prevotella_7_unclassifiedPrevotella_7_unclassified
Streptococcus thermophilus   
Veillonella sp. oral taxon 780   
uncultured Bacteroidota bacterium   
uncultured Rothia sp.   
Prevotella pallens   
Segatella oris   
unclassified Alloprevotella   
Prevotella_6_unclassifiedPrevotella_6_unclassified

Revision editor(s): KateRasheed

Experiment 8


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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Chile, South Africa, Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
Barbados
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Barbados refers to the samples from healthy females aged between 18 and 26 years, based in Barbados
Group 0 sample size Number of subjects in the control (unexposed) group
174
Group 1 sample size Number of subjects in the case (exposed) group
32

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S13

Description: Differentially abundant taxa in oral samples between Barbados and other locations.

Abundance in Group 1: increased abundance in Barbados

NCBI Quality ControlLinks
Actinomyces sp. oral clone DR002   
Alistipes_sp._627Alistipes_sp._627

Revision editor(s): KateRasheed

Signature 2

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Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S13

Description: Differentially abundant taxa in oral samples between Barbados and other locations.

Abundance in Group 1: decreased abundance in Barbados

NCBI Quality ControlLinks
uncultured Dialister sp.   
uncultured Prevotella sp.   
Cronobacter muytjensii   
Phocaeicola plebeius   
unclassified Succinivibrio   
unclassified Actinomyces   
unclassified Atopobium   
Schaalia odontolytica   
Phocaeicola coprocola DSM 17136   

Revision editor(s): KateRasheed

Experiment 9


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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, South Africa, Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
Chile
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Chile refers to the samples from healthy females aged between 18 and 26 years, based in Chile.
Group 0 sample size Number of subjects in the control (unexposed) group
137
Group 1 sample size Number of subjects in the case (exposed) group
69

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S14

Description: Differentially abundant taxa in oral samples between Chile and other locations.

Abundance in Group 1: increased abundance in Chile

NCBI Quality ControlLinks
unclassified Streptococcus   

Revision editor(s): KateRasheed

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S14

Description: Differentially abundant taxa in oral samples between Chile and other locations.

Abundance in Group 1: decreased abundance in Chile

NCBI Quality ControlLinks
Neisseria oralis   
Prevotella melaninogenica   
Prevotella pallens   
unclassified Actinomyces   
unclassified Prevotella   
unclassified Veillonella   
uncultured Bacteroidota bacterium   
Prevotella_7_unclassifiedPrevotella_7_unclassified
Streptococcus thermophilus   

Revision editor(s): KateRasheed

Experiment 10


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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Barbados, Chile, Thailand
Group 1 name Corresponds to the case (exposed) group for case-control studies
South Africa
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
South Africa refers to the samples from healthy females aged between 18 and 26 years, based in South Africa.
Group 0 sample size Number of subjects in the control (unexposed) group
169
Group 1 sample size Number of subjects in the case (exposed) group
37

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S15

Description: Differentially abundant taxa in oral samples between South Africa and other locations.

Abundance in Group 1: increased abundance in South Africa

NCBI Quality ControlLinks
unclassified Veillonella   
Prevotella melaninogenica   
uncultured Granulicatella sp.   
unclassified Prevotella   
uncultured Porphyromonas sp.   
Veillonella sp. oral taxon 780   
Streptococcus thermophilus   
uncultured Bacteroidota bacterium   
unclassified Alloprevotella   

Revision editor(s): KateRasheed

Signature 2

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-11-18

Curated date: 2024/11/12

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Table S15

Description: Differentially abundant taxa in oral samples between South Africa and other locations.

Abundance in Group 1: decreased abundance in South Africa

NCBI Quality ControlLinks
uncultured gemellauncultured gemella
uncultured Neisseriales bacterium   
unclassified Rothia (in: high G+C Gram-positive bacteria)   
uncultured Aggregatibacter sp.   
uncultured Lautropia sp.   
uncultured Bergeyella sp.   
unclassified Haemophilus   

Revision editor(s): KateRasheed

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