Using the curatedMetagenomicData Biocondutor package (>=3.2.1): we calculated taxa prevalence of healthy adult control samples for each body site (including vagina, skin, feces, nasal cavity, milk, oral cavity) and at species/genus levels. Lists of typical healthy signatures are provided in this study by different thresholds of prevalence level.
For body site-typical microbiome signatures for children, please go to:
https://bugsigdb.org/Study_608
Experiment 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Subjects
- Location of subjects
- Italy
- Luxembourg
- 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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult vagina 50% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
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
- Statistical test
- prevalence>50% Statistical test: "prevalence>50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Source: 10.5281/zenodo.5565690
Description: healthy adult vagina genus >=50%
Abundance in Group 1: Quality Control | Links |
---|
Lactobacillus | | |
Revision editor(s): Haoyanzh
Signature 3
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Source: 10.5281/zenodo.5565690
Description: healthy adult vagina species >=50%
Abundance in Group 1: Quality Control | Links |
---|
Lactobacillus crispatus | | |
Revision editor(s): Lwaldron,
Haoyanzh
Experiment 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- India
- Italy
- Malaysia
- Singapore
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult skin 50% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 362
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>50% Statistical test: "prevalence>50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult skin genus >=50%
Abundance in Group 1: Quality Control | Links |
---|
Staphylococcus | | |
Cutibacterium | | |
Enchelyodon sp. | | |
Corynebacterium | | |
Streptococcus | | |
Micrococcus | | |
Finegoldia | | |
Moraxella | | |
Rothia | | |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult skin species in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Corynebacterium pseudogenitalium | | |
Cutibacterium acnes | | |
Cutibacterium granulosum | | |
Cutibacterium namnetense | | |
Finegoldia magna | | |
Malassezia globosa | | |
Malassezia restricta | | |
Micrococcus luteus | | |
Moraxella osloensis | | |
Staphylococcus capitis | | |
Staphylococcus epidermidis | | |
Staphylococcus hominis | | |
Streptococcus mitis | | |
Streptococcus oralis | | |
Revision editor(s): Haoyanzh
Experiment 3
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Location of subjects
- Australia
- Canada
- China
- Denmark
- Finland
- France
- Germany
- India
- Ireland
- Israel
- Italy
- Japan
- Luxembourg
- Netherlands
- South Korea
- Spain
- Switzerland
- United Kingdom
- United Republic of Tanzania
- United States of America
- 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 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 50% prevalence threshold
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- feces from healthy adult
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- non-disease adult participants from curatedMetagenomicData
- Group 0 sample size Number of subjects in the control (unexposed) group
- 0
- Group 1 sample size Number of subjects in the case (exposed) group
- 9623
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no (n=5572), yes (n=276)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool genus in >= 50% samples
Abundance in Group 1: Quality Control | Links |
---|
Adlercreutzia | | |
Agathobaculum | | |
Akkermansia | | |
Alistipes | | |
Anaerobutyricum | | |
Anaerostipes | | |
Bacteroides | | |
Barnesiella | | |
Bifidobacterium | | |
Bilophila | | |
Blautia | | |
Butyricimonas | | |
Clostridium | | |
Collinsella | | |
Coprococcus | | |
Dorea | | |
Escherichia | | |
Eubacterium | | |
Faecalibacterium | | |
Flavonifractor | | |
Fusicatenibacter | | |
Gemmiger | | |
Gordonibacter | | |
Intestinibacter | | |
Lachnospira | | |
Lawsonibacter | | |
Mediterraneibacter | | |
Odoribacter | | |
Oscillibacter | | |
Parabacteroides | | |
Parasutterella | | |
Phascolarctobacterium | | |
Phocaeicola | | |
Prevotella | | |
Roseburia | | |
Ruminococcus | | |
Ruthenibacterium | | |
Streptococcus | | |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool species in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Faecalibacterium prausnitzii | | |
Fusicatenibacter saccharivorans | | |
Bacteroides uniformis | | |
Agathobacter rectalis | | |
Blautia wexlerae | | |
Anaerostipes hadrus | | |
Agathobaculum butyriciproducens | | |
Dorea longicatena | | |
Anaerobutyricum hallii | | |
Dorea formicigenerans | | |
Collinsella aerofaciens | | |
Phocaeicola vulgatus | | |
Blautia obeum | | |
Roseburia inulinivorans | | |
Parabacteroides distasonis | | |
Gemmiger formicilis | | |
Coprococcus comes | | |
Ruthenibacterium lactatiformans | | |
Roseburia hominis | | |
Lachnospira eligens | | |
[Ruminococcus] torques | | |
Roseburia faecis | | |
Bacteroides ovatus | | |
Odoribacter splanchnicus | | |
Alistipes putredinis | | |
Coprococcus catus | | |
Firmicutes bacterium CAG:83 | | |
Streptococcus salivarius | | |
Bifidobacterium longum | | |
Bacteroides thetaiotaomicron | | |
Alistipes finegoldii | | |
Eubacterium ramulus | | |
Oscillibacter sp. 57_20 | | |
Alistipes shahii | | |
Roseburia intestinalis | | |
Flavonifractor plautii | | |
Ruminococcus bromii | | |
Parabacteroides merdae | | |
Adlercreutzia equolifaciens | | |
Oscillibacter sp. CAG:241 | | |
Bacteroides caccae | | |
Ruminococcus bicirculans (ex Wegman et al. 2014) | | |
Barnesiella intestinihominis | | |
Gordonibacter pamelaeae | | |
Bifidobacterium adolescentis | | |
Bacteroides xylanisolvens | | |
environmental samples | | |
Phocaeicola dorei | | |
Eubacterium sp. CAG:38 | | |
Escherichia coli | | |
[Eubacterium] siraeum | | |
Streptococcus parasanguinis | | |
Bilophila wadsworthia | | |
Lachnospira pectinoschiza | | |
Eubacterium ventriosum | | |
[Clostridium] leptum | | |
Akkermansia muciniphila | | |
Roseburia sp. CAG:471 | | |
Parasutterella excrementihominis | | |
Butyricimonas virosa | | |
Collinsella intestinalis | | |
Segatella copri | | |
Firmicutes bacterium CAG:110 | | |
Intestinibacter bartlettii | | |
Canna indica | | |
Revision editor(s): Haoyanzh
Experiment 4
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Location of subjects
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- nasal cavity from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 92
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult nasal cavity genus in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Cutibacterium | | |
Staphylococcus | | |
Corynebacterium | | |
Malassezia | | |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult nasal cavity species in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Cutibacterium acnes | | |
Staphylococcus epidermidis | | |
Corynebacterium accolens | | |
Malassezia restricta | | |
Cutibacterium granulosum | | |
Revision editor(s): Haoyanzh
Experiment 5
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Philippines
- United States of America
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oral cavity from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 659
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No (n=16)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult oral cavity genus in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Streptococcus | | |
Rothia | | |
Actinomyces | | |
Veillonella | | |
Prevotella | | |
Fusobacterium | | |
Gemella | | |
Neisseria | | |
Haemophilus | | |
Porphyromonas | | |
Campylobacter | | |
Schaalia | | |
Capnocytophaga | | |
Leptotrichia | | |
Corynebacterium | | |
Lautropia | | |
Aggregatibacter | | |
Tannerella | | |
Alloprevotella | | |
Granulicatella | | |
Serinicoccus | | |
Lachnoanaerobaculum | | |
Parvimonas | | |
Selenomonas | | |
Treponema | | |
Abiotrophia | | |
Kingella | | |
Mogibacterium | | |
Stomatobaculum | | |
Solobacterium | | |
Cardiobacterium | | |
Megasphaera | | |
Eikenella | | |
Peptostreptococcus | | |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult oral cavity species in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Streptococcus oralis | | |
Veillonella parvula | | |
Streptococcus mitis | | |
Haemophilus parainfluenzae | | |
Rothia dentocariosa | | |
Gemella haemolysans | | |
Streptococcus sanguinis | | |
Rothia mucilaginosa | | |
Gemella sanguinis | | |
Gemella morbillorum | | |
Fusobacterium nucleatum | | |
Actinomyces oris | | |
Streptococcus infantis | | |
Prevotella melaninogenica | | |
Schaalia odontolytica | | |
Neisseria flavescens | | |
Neisseria sicca | | |
Campylobacter concisus | | |
Porphyromonas somerae | | |
Fusobacterium periodonticum | | |
Lautropia mirabilis | | |
Streptococcus parasanguinis | | |
Capnocytophaga leadbetteri | | |
Leptotrichia wadei | | |
Rothia aeria | | |
Veillonella dispar | | |
Capnocytophaga sputigena | | |
Capnocytophaga gingivalis | | |
Haemophilus haemolyticus | | |
Corynebacterium matruchotii | | |
Granulicatella adiacens | | |
Veillonella infantium | | |
Lockhartia amoena | | |
Streptococcus gordonii | | |
Campylobacter showae | | |
Tannerella serpentiformis | | |
Leptotrichia sp. oral taxon 215 | | |
Veillonella atypica | | |
Prevotella nigrescens | | |
Streptococcus salivarius | | |
Streptococcus cristatus | | |
Aggregatibacter sp. oral taxon 458 | | |
Actinomyces sp. HMSC035G02 | | |
Lachnoanaerobaculum saburreum | | |
Aggregatibacter segnis | | |
Segatella oris | | |
Neisseria elongata | | |
Parvimonas micra | | |
Lancefieldella parvula | | |
Actinomyces sp. ICM47 | | |
Neisseria subflava | | |
Prevotella pallens | | |
Leptotrichia sp. oral taxon 212 | | |
Streptococcus australis | | |
Oribacterium sinus | | |
Lancefieldella rimae | | |
Corynebacterium durum | | |
Streptococcus pseudopneumoniae | | |
Capnocytophaga ochracea | | |
Veillonella sp. T11011-6 | | |
Actinomyces naeslundii | | |
Actinomyces graevenitzii | | |
Segatella salivae | | |
Porphyromonas endodontalis | | |
Alloprevotella tannerae | | |
Stomatobaculum longum | | |
Streptococcus sp. HMSC034E03 | | |
Solobacterium moorei | | |
Alloprevotella sp. oral taxon 473 | | |
Abiotrophia sp. HMSC24B09 | | |
Prevotella histicola | | |
Neisseria mucosa | | |
Capnocytophaga granulosa | | |
Segatella oulorum | | |
[Eubacterium] brachy | | |
Mogibacterium diversum | | |
Haemophilus sputorum | | |
Streptococcus sp. A12 | | |
Leptotrichia sp. oral taxon 225 | | |
Cardiobacterium hominis | | |
Abiotrophia defectiva | | |
Megasphaera micronuciformis | | |
Streptococcus sp. HMSC067H01 | | |
Prevotella jejuni | | |
Eikenella corrodens | | |
Prevotella sp. oral taxon 306 | | |
Haemophilus quentini | | |
Leptotrichia sp. oral taxon 879 | | |
[Eubacterium] sulci | | |
Peptostreptococcus stomatis | | |
Leptotrichia buccalis | | |
Prevotella denticola | | |
Revision editor(s): Haoyanzh
Experiment 6
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Milk Mammary gland milk,Milk,milk
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- milk from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult milk genus in >=50% samples
Abundance in Group 1: Quality Control | Links |
---|
Streptococcus | | |
Revision editor(s): Haoyanzh
Experiment 7
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Luxembourg
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not specified
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult vagina 70% up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>70% Statistical test: "prevalence>70%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult vagina genus in >=70% samples
Abundance in Group 1: Quality Control | Links |
---|
Lactobacillus | | |
Revision editor(s): Haoyanzh
Experiment 8
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- India
- Italy
- Malaysia
- Singapore
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult skin 70% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 362
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>70% Statistical test: "prevalence>70%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult skin genus in >=70% samples
Abundance in Group 1: Quality Control | Links |
---|
Corynebacterium | | |
Cutibacterium | | |
Malassezia | | |
Staphylococcus | | |
Streptococcus | | |
Revision editor(s): Haoyanzh,
Lwaldron
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult skin species in >=70% samples
Abundance in Group 1: Quality Control | Links |
---|
Cutibacterium acnes | | |
Staphylococcus epidermidis | | |
Malassezia restricta | | |
Staphylococcus capitis | | |
Cutibacterium granulosum | | |
Revision editor(s): Haoyanzh
Experiment 9
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Australia
- Canada
- China
- Denmark
- Finland
- France
- Germany
- India
- Ireland
- Israel
- Italy
- Japan
- Luxembourg
- Netherlands
- South Korea
- Spain
- Switzerland
- United Kingdom
- United Republic of Tanzania
- United States of America
- 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 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 70% prevalence threshold
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- feces from healthy adult
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- non-disease adult participants from curatedMetagenomicData
- Group 0 sample size Number of subjects in the control (unexposed) group
- 0
- Group 1 sample size Number of subjects in the case (exposed) group
- 9623
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no (n=5572), yes (n=276)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 70% Statistical test: "prevalence > 70%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool genus in >= 70% samples
Abundance in Group 1: Quality Control | Links |
---|
Adlercreutzia | | |
Agathobaculum | | |
Alistipes | | |
Anaerobutyricum | | |
Anaerostipes | | |
Bacteroides | | |
Bifidobacterium | | |
Blautia | | |
Clostridium | | |
Collinsella | | |
Coprococcus | | |
Dorea | | |
Eubacterium | | |
Faecalibacterium | | |
Flavonifractor | | |
Fusicatenibacter | | |
Gemmiger | | |
Lachnospira | | |
Mediterraneibacter | | |
Odoribacter | | |
Oscillibacter | | |
Parabacteroides | | |
Phocaeicola | | |
Roseburia | | |
Ruminococcus | | |
Streptococcus | | |
Ruthenibacterium | | |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool species in >= 70% samples
Abundance in Group 1: Quality Control | Links |
---|
Faecalibacterium prausnitzii | | |
Fusicatenibacter saccharivorans | | |
Bacteroides uniformis | | |
Agathobacter rectalis | | |
Blautia wexlerae | | |
Anaerostipes hadrus | | |
Agathobaculum butyriciproducens | | |
Dorea longicatena | | |
Anaerobutyricum hallii | | |
Dorea formicigenerans | | |
Collinsella aerofaciens | | |
Phocaeicola vulgatus | | |
Blautia obeum | | |
Roseburia inulinivorans | | |
Parabacteroides distasonis | | |
Gemmiger formicilis | | |
Coprococcus comes | | |
Ruthenibacterium lactatiformans | | |
Roseburia hominis | | |
Lachnospira eligens | | |
[Ruminococcus] torques | | |
Roseburia faecis | | |
Bacteroides ovatus | | |
Odoribacter splanchnicus | | |
Alistipes putredinis | | |
Coprococcus catus | | |
Firmicutes bacterium CAG:83 | | |
Streptococcus salivarius | | |
Bifidobacterium longum | | |
Bacteroides thetaiotaomicron | | |
Alistipes finegoldii | | |
Eubacterium ramulus | | |
Oscillibacter sp. 57_20 | | |
Alistipes shahii | | |
Roseburia intestinalis | | |
Flavonifractor plautii | | |
Revision editor(s): Haoyanzh
Experiment 10
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 0% prevalence threshold
Lab analysis
Statistical Analysis
- Statistical test
- prevalence &;amp;gt; 0% Statistical test: "prevalence &;amp;gt; 0%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy stool genus in any adult sample
Abundance in Group 1: Quality Control | Links |
---|
Abiotrophia | | |
Acholeplasma | | |
Achromobacter | | |
Acidaminococcus | | |
Acidipropionibacterium | | |
Acidovorax | | |
Acinetobacter | | |
Actinobaculum | | |
Actinomyces | | |
Actinotignum | | |
Adlercreutzia | | |
Aeriscardovia | | |
Aerococcus | | |
Aeromonas | | |
Agathobaculum | | |
Aggregatibacter | | |
Agitococcus | | |
Akkermansia | | |
Alcaligenes | | |
Aliarcobacter | | |
Alistipes | | |
Alkalihalobacillus | | |
Alkalilimnicola | | |
Alkaliphilus | | |
Alkanindiges | | |
Allisonella | | |
Alloprevotella | | |
Alloscardovia | | |
Allosphingosinicella | | |
Amedibacillus | | |
Amnimonas | | |
Anaerobiospirillum | | |
Anaerobutyricum | | |
Anaerococcus | | |
Anaerofilum | | |
Anaerofustis | | |
Anaeroglobus | | |
Anaeromassilibacillus | | |
Anaerosporobacter | | |
Anaerostipes | | |
Anaerotignum | | |
Anaerotruncus | | |
Aneurinibacillus | | |
Aquamicrobium | | |
Arachnia | | |
Arcanobacterium | | |
Arthrospira | | |
Aspergillus | | |
Atlantibacter | | |
Atopobium | | |
Bacillus | | |
Bacteroides | | |
Barnesiella | | |
Bavariicoccus | | |
Bifidobacterium | | |
Bilophila | | |
Blautia | | |
Bordetella | | |
Bosea | | |
Brachybacterium | | |
Brachyspira | | |
Brevibacillus | | |
Brevibacterium | | |
Brevundimonas | | |
Brochothrix | | |
Brucella | | |
Burkholderia | | |
Butyricicoccus | | |
Butyricimonas | | |
Butyrivibrio | | |
Caldibacillus | | |
Calidifontibacter | | |
Candida | | |
Methanomethylophilus | | |
Candidatus Stoquefichus | | |
Capnocytophaga | | |
Cardiobacterium | | |
Carnobacterium | | |
Catenibacterium | | |
Caulobacter | | |
Cedecea | | |
Cellulosilyticum | | |
Cellulosimicrobium | | |
Cetobacterium | | |
Chelatococcus | | |
Chlamydia | | |
Christensenella | | |
Chryseobacterium | | |
Clavibacter | | |
Cloacibacillus | | |
Cloacibacterium | | |
Clostridioides | | |
Clostridium | | |
Collinsella | | |
Comamonas | | |
Companilactobacillus | | |
Coprobacillus | | |
Coprobacter | | |
Coprococcus | | |
Coptotermes heimi | | |
Corticimicrobacter | | |
Corynebacterium | | |
Criibacterium | | |
Cronobacter | | |
Cryobacterium | | |
Cytobacillus | | |
Delftia | | |
Dellaglioa | | |
Denitrobacterium | | |
Dermabacter | | |
Desemzia | | |
Desulfobulbus | | |
Desulfomicrobium | | |
Desulfovibrio | | |
Devosia | | |
Dialister | | |
Dielma | | |
Dorea | | |
Duganella | | |
Dysgonomonas | | |
Edwardsiella | | |
Eggerthella | | |
Eggerthia | | |
Eikenella | | |
Eisenbergiella | | |
Elizabethkingia | | |
Elusimicrobium | | |
Empedobacter | | |
Enhydrobacter | | |
Enorma | | |
Ensifer | | |
Entamoeba | | |
Enterobacter | | |
Enterocloster | | |
Enterococcus | | |
Epilithonimonas | | |
Eremococcus | | |
Erwinia | | |
Erysipelothrix | | |
Escherichia | | |
Eubacterium | | |
Ewingella | | |
Exiguobacterium | | |
Ezakiella | | |
Facklamia | | |
Faecalibacterium | | |
Faecalicatena | | |
Faecalicoccus | | |
Faecalitalea | | |
Fannyhessea | | |
Filifactor | | |
Fimbriiglobus | | |
Finegoldia | | |
Flavobacterium | | |
Flavonifractor | | |
Franconibacter | | |
Fretibacterium | | |
Frischella | | |
Fructilactobacillus | | |
Fusicatenibacter | | |
Fusobacterium | | |
Gardnerella | | |
Gemella | | |
Gemmata | | |
Gemmiger | | |
Geobacillus | | |
Geodermatophilus | | |
Georgenia | | |
Gilliamella | | |
Globicatella | | |
Gluconacetobacter | | |
Gluconobacter | | |
Glutamicibacter | | |
Gordonia | | |
Gordonibacter | | |
Granulicatella | | |
Haematobacter | | |
Haemophilus | | |
Hafnia | | |
Harryflintia | | |
Helcococcus | | |
Helicobacter | | |
Hephaestia | | |
Herbaspirillum | | |
Holdemanella | | |
Holdemania | | |
Hornefia | | |
Hungatella | | |
Hydrocarboniphaga | | |
Hydrogenibacillus | | |
Hydrogenophilus | | |
Hypogastrura sp. BOLD:AAI2333 | | |
Ignavigranum | | |
Ileibacterium | | |
Immundisolibacter | | |
Influenza A virus (A/Thailand/VIROAF2CS/2012(H3N2)) | | |
Intestinibacter | | |
Intestinimonas | | |
Jeotgalibacillus | | |
Jonquetella | | |
Kaistella | | |
Kerstersia | | |
Kingella | | |
Klebsiella | | |
Kluyvera | | |
Knoellia | | |
Kosakonia | | |
Kouleothrix | | |
Kurthia | | |
Kytococcus | | |
Lachnoclostridium | | |
Lachnospira | | |
Lacrimispora | | |
Lacticaseibacillus | | |
Lactiplantibacillus | | |
Lactobacillus | | |
Lactococcus | | |
Lactonifactor | | |
Lancefieldella | | |
Lapidilactobacillus | | |
Latilactobacillus | | |
Lautropia | | |
Lawsonella | | |
Lawsonia | | |
Lawsonibacter | | |
Leclercia | | |
Leifsonia | | |
Leishmania | | |
Lentilactobacillus | | |
Leptospira | | |
Leptotrichia | | |
Leptotrichia sp. oral taxon 223 | | |
Leucobacter | | |
Leuconostoc | | |
Levilactobacillus | | |
Ligilactobacillus | | |
Limnochorda | | |
Limosilactobacillus | | |
Liquorilactobacillus | | |
Listeria | | |
Loigolactobacillus | | |
Luteipulveratus | | |
Lysinibacillus | | |
Lysobacter | | |
Macrococcus | | |
Mageeibacillus | | |
Malassezia | | |
Mammaliicoccus | | |
Heyndrickxia | | |
Marmoricola | | |
Marvinbryantia | | |
Massilia | | |
Mediterranea | | |
Mediterraneibacter | | |
Megamonas | | |
Megasphaera | | |
Meiothermus | | |
Melaminivora | | |
Melissococcus | | |
Mesorhizobium | | |
Phytobacter | | |
Methanobrevibacter | | |
Methanomassiliicoccus | | |
Methanosphaera | | |
Methylibium | | |
Methyloceanibacter | | |
Methylorubrum | | |
Microbacterium | | |
Microcoleus | | |
Microlunatus | | |
Micropruina | | |
Microvirgula | | |
Mitsuokella | | |
Mixta | | |
Mobiluncus | | |
Modestobacter | | |
Moellerella | | |
Mogibacterium | | |
Monoglobus | | |
Moraxella | | |
Morganella | | |
Morococcus | | |
Mucispirillum | | |
Muribaculum | | |
Murimonas | | |
Mycobacterium | | |
Mycobacteroides | | |
Mycolicibacter | | |
Mycolicibacterium | | |
Mycoplasma | | |
Mycoplasmopsis | | |
Nakamurella | | |
Nannocystis | | |
Negativicoccus | | |
Neisseria | | |
Nesterenkonia | | |
Nocardia | | |
Nocardioides | | |
Nocardiopsis | | |
Novosphingobium | | |
Odoribacter | | |
Oenococcus | | |
Oligella | | |
Olsenella | | |
Oribacterium | | |
Ornithinimicrobium | | |
Oscillatoria | | |
Oscillibacter | | |
Ottowia | | |
Paenibacillus | | |
Paeniclostridium | | |
Paludisphaera | | |
Parabacteroides | | |
Paraclostridium | | |
Paracoccus | | |
Paraprevotella | | |
Parascardovia | | |
Parasutterella | | |
Pasteurella | | |
Patulibacter | | |
Roseateles | | |
Paucilactobacillus | | |
Pauljensenia | | |
Pectobacterium | | |
Pediococcus | | |
Pedobacter | | |
Pelistega | | |
Peptacetobacter | | |
Peptoanaerobacter | | |
Peptococcus | | |
Peptoniphilus | | |
Peptostreptococcus | | |
Peribacillus | | |
Phascolarctobacterium | | |
Phocaeicola | | |
Photobacterium | | |
Phyllobacterium | | |
Phytobacter | | |
Planifilum | | |
Planomicrobium | | |
Plantibacter | | |
Plesiomonas | | |
Pluralibacter | | |
Prauserella | | |
Prevotella | | |
Priestia | | |
Prolinoborus | | |
Propionibacterium | | |
Propionimicrobium | | |
Proteus | | |
Providencia | | |
Pseudarthrobacter | | |
Pseudescherichia | | |
Pseudoalteromonas | | |
Pseudocitrobacter | | |
Pseudoflavonifractor | | |
Pseudoglutamicibacter | | |
Pseudoleptotrichia | | |
Pseudomonas | | |
Pseudonocardia | | |
Pseudoramibacter | | |
Pseudoxanthomonas | | |
Psychrobacillus | | |
Psychrobacter | | |
Pulveribacter | | |
Pyramidobacter | | |
Pyrococcus | | |
Rahnella | | |
Ralstonia | | |
Raoultella | | |
Rheinheimera | | |
Rhizobium | | |
Rhodanobacter | | |
Rhodococcus | | |
Rickettsia | | |
Rikenella | | |
Robinsoniella | | |
Rodentibacter | | |
Roseburia | | |
Roseicella | | |
Roseiflexus | | |
Roseomonas | | |
Rossellomorea | | |
Rothia | | |
Rotylenchus urmiaensis | | |
Rouxiella | | |
Rubellimicrobium | | |
Rubrobacter | | |
Ruminococcus | | |
Ruthenibacterium | | |
Saccharomyces | | |
Saccharopolyspora | | |
Salinicoccus | | |
Salinicola | | |
Salipiger | | |
Salmonella | | |
Sanguibacter | | |
Sarcina | | |
Scardovia | | |
Schaalia | | |
Schizophyllum sp. | | |
Schleiferilactobacillus | | |
Selenomonas | | |
Sellimonas | | |
Serinicoccus | | |
Serratia | | |
Sharpea | | |
Shewanella | | |
Shuttleworthella | | |
Siccibacter | | |
Simonsiella | | |
Skermanella | | |
Slackia | | |
Sneathia | | |
Sodalis | | |
Solibacillus | | |
Solimonas | | |
Solobacterium | | |
Sphingobacterium | | |
Sphingobium | | |
Sphingomonas | | |
Sphingopyxis | | |
Spiroplasma | | |
Sporosarcina | | |
Staphylococcus | | |
Starkeya | | |
Stenotrophomonas | | |
Stomatobaculum | | |
Streptococcus | | |
Streptomyces | | |
Subdoligranulum | | |
Succinatimonas | | |
Superficieibacter | | |
Synechococcus | | |
Synergistes | | |
Tannerella | | |
Tatumella | | |
Tepidimonas | | |
Tepidiphilus | | |
Terrisporobacter | | |
Tersicoccus | | |
Tetragenococcus | | |
Nostocoides | | |
Thermoleophilum | | |
Thermomonas | | |
Thermus | | |
Thiohalorhabdus | | |
Thomasclavelia | | |
Tolypothrix | | |
Tractidigestivibacter | | |
Treponema | | |
Tropheryma | | |
Trueperella | | |
Tsukamurella | | |
Turicibacter | | |
Turicimonas | | |
Tyzzerella | | |
Ureaplasma | | |
Vagococcus | | |
Varibaculum | | |
Variovorax | | |
Veillonella | | |
Vibrio | | |
Victivallis | | |
Weeksella | | |
Heyndrickxia | | |
Williamsia | | |
Winkia | | |
Xanthomonas | | |
Yersinia | | |
Yokenella | | |
Zymomonas | | |
Revision editor(s): Haoyanzh
Experiment 11
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 30% prevalence threshold
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- prevelance > 30% Statistical test: "prevelance > 30%" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Source: 10.5281/zenodo.5565690
Description: healthy stool genus prevalence >=30%
Abundance in Group 1: Quality Control | Links |
---|
Faecalibacterium | | |
Bacteroides | | |
Roseburia | | |
Blautia | | |
Mediterraneibacter | | |
Dorea | | |
Eubacterium | | |
Phocaeicola | | |
Fusicatenibacter | | |
Parabacteroides | | |
Alistipes | | |
Anaerostipes | | |
Coprococcus | | |
Collinsella | | |
Agathobaculum | | |
Anaerobutyricum | | |
Ruminococcus | | |
Bifidobacterium | | |
Lachnospira | | |
Streptococcus | | |
Gemmiger | | |
Ruthenibacterium | | |
Oscillibacter | | |
Clostridium | | |
Odoribacter | | |
Flavonifractor | | |
Adlercreutzia | | |
Prevotella | | |
Barnesiella | | |
Gordonibacter | | |
Phascolarctobacterium | | |
Lawsonibacter | | |
Escherichia | | |
Bilophila | | |
Akkermansia | | |
Butyricimonas | | |
Parasutterella | | |
Intestinibacter | | |
Lactobacillus | | |
Thomasclavelia | | |
Slackia | | |
Enterocloster | | |
Coprobacter | | |
Eggerthella | | |
Dialister | | |
Veillonella | | |
Enorma | | |
Intestinimonas | | |
Haemophilus | | |
Anaeromassilibacillus | | |
Holdemanella | | |
Methanobrevibacter | | |
Holdemania | | |
Paraprevotella | | |
Tractidigestivibacter | | |
Turicibacter | | |
Turicimonas | | |
Actinomyces | | |
Revision editor(s): Haoyanzh