Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Honduras
- 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
- Health-related quality of life measurement HRQOL,Health-related quality of life measurement,health-related quality of life measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Health associated(Healthy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Disease associated(Chronically diseased individuals)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Disease associated has to do with chronically diseased individuals who had at least one chronic condition. Examples of the chronic conditions include: diabetes, asthma, heart disease, arthritis, etc
- Group 1 sample size Number of subjects in the case (exposed) group
- 468
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).
- centered log-ratio
- Statistical test
- MaAsLin2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration, Confounders controlled for: "sequencing batch" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sequencing batch, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. S4B
Description: Differential abundance in healthy vs chronically diseased individuals using MaAsLin2.
Abundance in Group 1: decreased abundance in Disease associated(Chronically diseased individuals)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4B
Description: Differential abundance in healthy vs chronically diseased individuals using MaAsLin2
Abundance in Group 1: increased abundance in Disease associated(Chronically diseased individuals)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Clostridia | ||
| Coprococcus | ||
| Spirochaetia bacterium | ||
| uSGB1663uSGB1663 | ||
| uSGB27424uSGB27424 |
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on Physiological Variables
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals refers to those with unhealthy phenotypes like BMI <18 and BMI >25 to account for underweight and overweight individuals; diastolic pressure >89 to account for hypertensive individuals; Haemoglobin A1c, Haemoglobin total, heart disease, oxygen saturation.
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Mixed-Effects Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "batch effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.batch effect, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration, body mass index
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on physiological variables
Abundance in Group 1: increased abundance in Unhealthy individuals based on Physiological Variables
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on physiological variables
Abundance in Group 1: decreased abundance in Unhealthy individuals based on Physiological Variables
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on acute conditions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals refers to those with unhealthy phenotypes like Bristol, diarrhea, cough.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on acute conditions
Abundance in Group 1: increased abundance in Unhealthy individuals based on acute conditions
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus parasanguinis | ||
| Streptococcus salivarius | ||
| Lachnospiraceae bacterium |
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on acute conditions
Abundance in Group 1: decreased abundance in Unhealthy individuals based on acute conditions
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae_unclassified_SGB15236Ruminococcaceae_unclassified_SGB15236 | ||
| GGB9602_SGB15031GGB9602_SGB15031 | ||
| SGB3940SGB3940 | ||
| SGB15408SGB15408 | ||
| SGB13987SGB13987 |
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on Chronic conditions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals based on Chronic conditions refers to those with unhealthy phenotypes like diabetes, allergies, heart disease, asthma, stomach illness, intestinal illness, arthritis
- Group 1 sample size Number of subjects in the case (exposed) group
- 688
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, sex, Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "batch effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.batch effect, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on chronic conditions
Abundance in Group 1: increased abundance in Unhealthy individuals based on Chronic conditions
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on chronic conditions
Abundance in Group 1: decreased abundance in Unhealthy individuals based on Chronic conditions
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals based on medication use refers to those with unhealthy phenotypes like antibiotics, painkillers, anti-diarreal, anti-fungal, anti-parasitic, anti-hypertensive and vitamins
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on medication use.
Abundance in Group 1: increased abundance in Unhealthy individuals based on medication use
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on medication use.
Abundance in Group 1: decreased abundance in Unhealthy individuals based on medication use
Revision editor(s): KateRasheed
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on mental health
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals based on mental health refers to those with unhealthy phenotypes like dementia, reserved, anxiety, depression, openness, nervous, cognitive impairment.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on mental health
Abundance in Group 1: increased abundance in Unhealthy individuals based on mental health
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on mental health
Abundance in Group 1: decreased abundance in Unhealthy individuals based on mental health
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unhealthy individuals based on alcohol and cigarette
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unhealthy individuals based on unfavourable habits(alcohol and cigarette) refers to those with unhealthy phenotypes like alcohol daily frequency, cigarette use, cigarette frequency.
- Group 1 sample size Number of subjects in the case (exposed) group
- 972
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, sex, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "batch effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.batch effect, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration, body mass index
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on alcohol and cigarette.
Abundance in Group 1: increased abundance in Unhealthy individuals based on alcohol and cigarette
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterella wadsworthensis | ||
| Flavonifractor plautii |
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between healthy and unhealthy individuals based on alcohol and cigarette.
Abundance in Group 1: decreased abundance in Unhealthy individuals based on alcohol and cigarette
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus bovis |
Revision editor(s): KateRasheed
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overall health phenotype sub-category
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Overall health phenotype sub-category refers to those with phenotypes like fair, poor, very good, excellent
- Group 1 sample size Number of subjects in the case (exposed) group
- 1394
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, sex, Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "batch effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.batch effect, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration
Signature 1
Source: Table S1
Description: Differential abundant taxa between healthy and overall healthy phenotype sub-category(fair).
Abundance in Group 1: increased abundance in Overall health phenotype sub-category
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes finegoldii |
Revision editor(s): KateRasheed
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental exposure measurement Environmental exposure measurement,environmental exposure measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individual unexposed to animals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individual exposed to animals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individual exposed to animals refers to the villagers who reported having exposure to different types of animals, including wild animals, farm animals, and pets, affording possible zoonotic transmission.
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S1
Description: Differential abundant taxa between individuals exposed or unexposed to animals
Abundance in Group 1: decreased abundance in Individual exposed to animals
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between individuals exposed or unexposed to animals
Abundance in Group 1: increased abundance in Individual exposed to animals
Revision editor(s): KateRasheed
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Food frequency consumption(Never/Rarely)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Food frequency consumption(Everyday)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Food frequency consumption(Everyday) refers to individuals who consumed various categories of food everyday especially Beans and Tortillas
Lab analysis
Statistical Analysis
Signature 1
Source: Table S1
Description: Differential abundant taxa between food frequency consumption(never/rarely) and food frequency consumption(always).
Abundance in Group 1: increased abundance in Food frequency consumption(Everyday)
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between food frequency consumption(never/rarely) and food frequency consumption(always).
Abundance in Group 1: decreased abundance in Food frequency consumption(Everyday)
Revision editor(s): KateRasheed
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects from the least well-off households based on economic factors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects from the wealthier households based on economic factors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects from the wealthier households based on economic factors such as income(travel, monthly expenditure) and household essentials(Household size, Household wealth index, TV, No electronics, Earth/sand floor, Ceramic floor, Glass windows, Unfinished windows, Clay/mud walls, Cement walls, Concrete roof, Sleeping rooms). The household wealth index is constructed based on these household essentials.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S1
Description: Differential abundant taxa between subjects from the least well-off households and subjects from the wealthier households.
Abundance in Group 1: increased abundance in Subjects from the wealthier households based on economic factors
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between subjects from the least well-off households and subjects from the wealthier households based on economic factors.
Abundance in Group 1: decreased abundance in Subjects from the wealthier households based on economic factors
Revision editor(s): KateRasheed
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Self reported educational attainment Self reported educational attainment,self reported educational attainment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects from the least well-off households based on educational attainment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects from wealthier households based on educational attainment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects from wealthier households based on educational attainment refers to those that attained Primary(1-3), Middle (4–6), and Secondary (>6)
- Group 1 sample size Number of subjects in the case (exposed) group
- 1620
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S1
Description: Differential abundant taxa between Primary (1–3) and Middle (4–6)/Secondary (>6) educational levels.
Abundance in Group 1: increased abundance in Subjects from wealthier households based on educational attainment
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between Primary (1–3) and Middle (4–6)/Secondary (>6) educational levels.
Abundance in Group 1: decreased abundance in Subjects from wealthier households based on educational attainment
Revision editor(s): KateRasheed
Experiment 13
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Social interaction measurement Social interaction measurement,social interaction measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects from the least well-off households based on social factors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects from the wealthier households based on social factors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects from the wealthier households refers to those with these social phenotypes: Friend ties (same building), Friend ties (different building), Betweeness (friendship), Transitivity (friendship), Familial ties (same building), Familial ties (different building), Transitivity (familial), Betweeness (familial), Degree (all ties), Kin percentage (to the third degree), Altruism, washing hands, living with partners, number of partners.
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on social factors.
Abundance in Group 1: increased abundance in Subjects from the wealthier households based on social factors
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on social factors.
Abundance in Group 1: decreased abundance in Subjects from the wealthier households based on social factors
Revision editor(s): KateRasheed
Experiment 14
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Environmental factor environment factor,Environmental factor,environmental factor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects from the least well-off households based on village factors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects from wealthier households based on village factors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects from wealthier households based on village factors such as Distance to village center, Distance to main road, Number of churches, Altitude.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village factors.
Abundance in Group 1: increased abundance in Subjects from wealthier households based on village factors
| NCBI | Quality Control | Links |
|---|---|---|
| SGB4750SGB4750 | ||
| Enterobacter hormaechei | ||
| SGB4395SGB4395 | ||
| Lachnospira pectinoschiza | ||
| Clostridiales_unclassified_SGB15145Clostridiales_unclassified_SGB15145 | ||
| Collinsella aerofaciens |
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village factors.
Abundance in Group 1: decreased abundance in Subjects from wealthier households based on village factors
| NCBI | Quality Control | Links |
|---|---|---|
| SGB9313SGB9313 | ||
| SGB8644SGB8644 | ||
| Clostridia_unclassified_SGB13966Clostridia_unclassified_SGB13966 |
Revision editor(s): KateRasheed
Experiment 15
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Water [H]O[H],[OH2],acqua,agua,aqua,BOUND WATER,dihydridooxygen,dihydrogen oxide,eau,H2O,HOH,hydrogen hydroxide,InChI=1/H2O/h1H2,InChIKey=XLYOFNOQVPJJNP-UHFFFAOYAF,oxidane,Wasser,Water,water
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Subjects from the least well-off households based on water sources
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Subjects from wealthier households based on water sources
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects from wealthier households based on water sources refers to those with water sources such as: dug well, spring, tube well
- Group 1 sample size Number of subjects in the case (exposed) group
- 1610
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on water sources.
Abundance in Group 1: increased abundance in Subjects from wealthier households based on water sources
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia_unclassified_SGB14065Clostridia_unclassified_SGB14065 | ||
| Catenibacterium sp. AM22-15 |
Revision editor(s): KateRasheed
Signature 2
Source: Table S1
Description: Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village sources.
Abundance in Group 1: decreased abundance in Subjects from wealthier households based on water sources
| NCBI | Quality Control | Links |
|---|---|---|
| SGB4750SGB4750 |
Revision editor(s): KateRasheed
Experiment 16
Subjects
- 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
- Phenotypes without strain-phylogenetic information
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenotypes with strain-phylogenetic information
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Sex" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Sex, Confounders controlled for: "Bristol stool scale" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Bristol stool scale, Confounders controlled for: "sampling date" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling date, Confounders controlled for: "batch effect" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.batch effect, Confounders controlled for: "DNA concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.DNA concentration
Signature 1
Source: Table S9
Description: Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.
Abundance in Group 1: increased abundance in Phenotypes with strain-phylogenetic information
Revision editor(s): KateRasheed
Signature 2
Source: Table S9
Description: Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.
Abundance in Group 1: decreased abundance in Phenotypes with strain-phylogenetic information
Revision editor(s): KateRasheed
