Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/07

Curator: Joan Chuks

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Subjects

Location of subjects: United States of America

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: Insulin sensitivity measurement insulin sensitivity test,Insulin sensitivity measurement,insulin sensitivity measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Insulin Sensitive (IS) Individuals

Group 1 name Corresponds to the case (exposed) group for case-control studies: Insulin Resistant (IR) Individuals

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals who are at risk for type 2 diabetes or voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.

Group 0 sample size Number of subjects in the control (unexposed) group: 28

Group 1 sample size Number of subjects in the case (exposed) group: 30

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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

Matched on Factors on which subjects have been matched on in a case-control study: date

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Signature 1

Needs review

Curated date: 2024/04/08

Curator: Joan Chuks

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Source: Table S1D + Figure S1M

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Agathobacter
Anaerotignum
Bacteroidaceae
Bacteroidales
Bacteroides thetaiotaomicron
Bacteroidia
Bacteroidota
Blautia
Enterocloster
Enterococcaceae
Enterococcus
Lachnospiraceae
Phocaeicola
unclassified Bacteroidaceae
unclassified Blautia
unclassified Phocaeicola
unclassified Agathobacter
unclassified Anaerotignum
unclassified Enterocloster

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Signature 2

Needs review

Curated date: 2024/04/08

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Source: Table S1D + Figure S1M

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Actinomycetes
Acutalibacter
Barnesiellaceae
Beduinibacterium
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Bifidobacterium adolescentis
Bifidobacterium longum
Butyricicoccus
Christensenella
Colidextribacter
Coprobacillus
Coprococcus
Corynebacteriaceae
Corynebacterium
Desulfovibrio
Desulfovibrio desulfuricans
Eubacteriales Family XIII. Incertae Sedis
Faecalicatena
Haemophilus
Ihubacter
Kiloniellaceae
Kineothrix
Lachnotalea
Mailhella
Mogibacterium
Monoglobus
Mycobacteriales
Odoribacter
Odoribacteraceae
Oscillibacter
Oscillospiraceae
Oxalobacter
Oxalobacteraceae
Pasteurellaceae
Pasteurellales
Porphyromonas
Porphyromonas gingivalis
Rhodospirillales
Synergistaceae
Synergistales
Synergistia
Synergistota
Turicibacter
Turicibacter sanguinis
unclassified Acutalibacter
unclassified Bacillota
unclassified Bacteroidales
unclassified Butyricicoccus
unclassified Christensenella
unclassified Clostridiaceae
unclassified Colidextribacter
unclassified Coprobacillus
unclassified Coprococcus
unclassified Desulfovibrio
unclassified Eggerthellaceae
unclassified Erysipelotrichaceae
unclassified Eubacteriales
unclassified Faecalicatena
unclassified Haemophilus
unclassified Ihubacter
unclassified Kineothrix
unclassified Lachnotalea
unclassified Mailhella
unclassified Monoglobus
unclassified Odoribacter
unclassified Oscillibacter
unclassified Oscillospiraceae
unclassified Oxalobacter
unclassified Turicibacter
unclassifed Beduinibacteriumunclassifed Beduinibacterium
Christensenellaceae

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/08

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Skin of body

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

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

Signature 1

Needs review

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Source: Table S1D + Figure S1M

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Aggregatibacter segnis
Alishewanella
Alloprevotella
Alloprevotella tannerae
Anaerococcus octavius
Anaerococcus provencensis
Anaerococcus vaginalis
Aquihabitans daechungensis
Atopobium
Bacteroidales
Bacteroidia
Bacteroidota
Campylobacter
Campylobacter showae
Campylobacter ureolyticus
Campylobacteraceae
Campylobacterales
Campylobacterota
Candidatus Saccharibacteria
Capnocytophaga sputigena
Clostridia
Coriobacteriia
Desulfovibrionaceae
Dialister micraerophilus
Dietzia
Dietziaceae
Empedobacter
Epsilonproteobacteria
Ethanoligenens
Eubacteriaceae
Eubacteriales
Eubacteriales Family XIII. Incertae Sedis
Eubacterium
Facklamia languida
Flavobacteriales
Flavobacteriia
Flavobacterium lindanitolerans
Fulvivirgaceae
Gardnerella
Gemmataceae
Intrasporangiaceae
Intrasporangium
Kingella
Kingella oralis
Lawsonella
Lawsonellaceae
Lysobacter
Megasphaera
Methylophilus
Micropruina
Mogibacterium
Negativicoccus
Negativicutes
Ohtaekwangia
Paracoccus siganidrum
Peptoniphilaceae
Peptoniphilus
Porphyromonas bennonis
Prevotella
Prevotella bivia
Prevotella histicola
Prevotella melaninogenica
Prevotella nigrescens
Prevotellaceae
Rickettsiella
Rothia koreensis
Segatella salivae
Tepidimonas
Thermoactinomycetaceae
Veillonellaceae
Veillonellales
Weeksellaceae
Armatimonadetes_gp5Armatimonadetes_gp5
unclassified Peptoniphilus
unclassified Oribacterium
unclassified Rhodospirillales
unclassified Armatimonadetes_gp5unclassified Armatimonadetes_gp5
unclassified Eubacterium
unclassified Empedobacter
unclassified Tepidimonas
unclassified Aggregatibacter
unclassified Ethanoligenensunclassified Ethanoligenens
unclassified Intrasporangium
unclassified Methylophilus
unclassified Lawsonella
unclassified Negativicoccus
unclassified Ohtaekwangia
unclassified Lysobacter
unclassified Rickettsiella
unclassified Alishewanella
unclassified Blastocatellaceae
unclassified Candidatus Saccharibacteria
unclassified Prevotella
unclassified Lachnoanaerobaculum
unclassified Mogibacterium

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Signature 2

Needs review

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Source: Table S1D + Figure S1M

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Actinomycetota
Actinotignum
Aurantimonadaceae
Barnesiella
Barnesiellaceae
Beijerinckiaceae
Cutibacterium
Dialister
Flavisolibacter
Lachnobacterium
Micrococcales
Paracoccaceae
Paracoccus
Paracoccus yeei
Patulibacter minatonensis
Propionibacteriales
Ralstonia
Rhodobacterales
Roseburia
Roseisolibacter
Sphingomonadaceae
Sphingomonadales
Sphingomonas
Sphingomonas ginsengisoli (ex Hoang et al. 2012)
Staphylococcus haemolyticus
Xanthomonas
unclassified Actinotignum
unclassified Barnesiella
unclassified Beijerinckiaceae
unclassified Dialister
unclassified Lachnobacterium
unclassified Ralstonia
unclassified Roseburia
unclassified Roseisolibacter
unclassified Sphingomonas
unclassified Xanthomonas
unclassified Flavisolibacter
unclassified Cutibacterium
Propionibacteriaceae

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Anterior naris Anterior nostril,Anterior naris,anterior naris

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Source: Table S1D

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Anaerococcus senegalensis
Brevibacterium
Caulobacteraceae
Cytophagaceae
Micrococcus luteus
Porphyromonas endodontalis
Salinimicrobium
Staphylococcus capitis
unclassified Mycobacterium
unclassified Salinimicrobium
unclassified Brevibacterium
unclassified Caulobacteraceae

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Adeitan

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Source: Table S1D

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Aerococcus
Allorhizobium
Anaerobutyricum
Anaerostipes
Azonexaceae
Bacteroides fragilis
Bacteroides thetaiotaomicron
Bacteroides xylanisolvens
Blastococcus
Butyricimonas
Capnocytophaga canimorsus
Chloroflexia
Clostridium
Coprococcus
Dorea longicatena
Enterocloster
Gammaproteobacteria
Gemelliphila palaticanis
Geodermatophilaceae
Geodermatophilales
Halomonadaceae
Halomonas
Helicobacteraceae
Ihubacter
Methylobacillus
Microbacterium oleivorans
Microbacterium testaceum
Mollicutes
Monoglobus
Moraxella
Moraxellaceae
Mycoplasmatota
Neisseria flavescens
Nitriliruptoria
Oceanospirillales
Odoribacteraceae
Paludibacter
Paludibacteraceae
Rhodocyclales
Rhodospirillaceae
Sanguibacter
Segatella salivae
Sphingosinicellaceae
Subdoligranulum
Xanthomonas
unclassified Aerococcus
unclassified Allorhizobium
unclassified Anaerobutyricum
unclassified Anaerostipes
unclassified Blastococcus
unclassified Butyricimonas
unclassified Clostridium
unclassified Coprococcus
unclassified Enterocloster
unclassified Halomonas
unclassified Ihubacter
unclassified Leuconostoc
unclassified Micrococcales
unclassified Microvirga
unclassified Monoglobus
unclassified Moraxella
unclassified Odoribacter
unclassified Paludibacter
unclassified Subdoligranulum
Armatimonadetes_gp5Armatimonadetes_gp5
unclassified Armatimonadetes_gp5unclassified Armatimonadetes_gp5
unclassified Clostridium_XlVaunclassified Clostridium_XlVa
Clostridium_XlVaClostridium_XlVa
Cyanobacteriota
Streptophyta
unclassified Streptophyta

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Posterior wall of oropharynx Posterior wall of oropharynx,posterior wall of oropharynx

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-23

Curated date: 2024/04/12

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Source: Table S1D

Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)

Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals

NCBI	Quality Control	Links
Abiotrophia
Abiotrophia defectiva
Aerococcaceae
Cytophagales
Cytophagia
Erythrobacteraceae
Lachnoanaerobaculum umeaense
Olsenella
Prevotella micans
Staphylococcaceae
Staphylococcus
unclassified Staphylococcus
unclassified Olsenella
unclassified Aggregatibacter

Revision editor(s): Joan Chuks, Aleru Divine, WikiWorks

Signature 2