Mica | Microbiome in health and disease and in ageing

INTIMIC-KP Use Cases 3 and 4 (Microbiome in health and disease and in ageing, WP6)

Networks -

Variables -

Approach: Prospective
Type: Qualitative
Procedures: Studies responsible for data processing
Participant Inclusion: Age range: 18+ years
Infrastructure: Data hosted in Opal servers on study site

Associated initiative Federated analysis in INTIMIC-KP Contingency Table

Information Content

**Study question** “Differences in the microbiome composition between obese and non-obese adult individuals across different epidemiological studies” **Outcome variables** * Microbial alpha diversity assessed using the Shannon-Weiner diversity index (H’), which accounts for both the number of phylotypes (richness by means of ACE and Chao indices) and the proportion of the total accounted for by each phylotype (evenness) * Microbial beta diversity using the Bray-Curtis dissimilarity and Unweighted UniFrac. * Firmicutes to Bacteroidetes ratio (at phylum level) * Candidate list of bacteria identified in individual stool samples (at Phylum and Genus level) (see Table A3 in appendix). * Enterotype determination (high-level classification of microbiome compositional states) **Exposure variables** 1. Anthropometric measurements: Height, Weight, Waist Circumference: * Obesity defined by body mass index (BMI) ≥30 kg/m2 (as compared to non-obesity, BMI <30 kg/m2). Or: * Abdominal obesity based on waist circumference ≥102 cm in men and ≥88 cm in women, or waist-to-hip ratio ≥0.95 in men and ≥0.80 in women (as compared to non-obesity based on waist circumference <102 cm in men and <88 cm in women, or waist-to-hip ratio <0.95 in men and <0.80 in women). * Overweight defined by BMI ≥ 25 kg/m2 (as compared to non-overweight (BMI<25 kg/m2) 2. Dietary intake (see **Table 1**): Healthy Eating Index (HEI-2015): the HEI-2015 consists of 13 food items. The first 6 items include (1) **total vegetables**; (2) **total fruits**; (3) **whole fruits**; (4) **greens and beans**; (5) **seafood and plant proteins**; and (6) **total proteins**, which can be scored from 0 to 5 points each. The remaining 7 items include (7) **whole grains**; (8) **low-fat dairy**; (9) **fatty acids ratio** (polyunsaturated fatty acids plus monounsaturated fatty acids to saturated fatty acids); (10) **refined grains**; (11) **sodium**; (12) **added sugars**; and (13) **saturated fats**, which can be scored from 0 to 10 points each. Most food components (except for fatty acids ratio, added sugars, and saturated fats) are scored on a density basis per 1000 kcal or as a percentage of energy. Four components (sodium, refined grains, added sugars, and saturated fats) are reverse scored (i.e., higher intakes receive lower scores). Total HEI-2015 scores are computed by aggregating scores across individual dietary components such that total scores ranged from zero (poor diet quality) to 100 (optimal diet quality). Because HEI-2015 does not include a specific component for alcohol, we should run additional sub-analyses adjusting for alcohol intake **Table 1. List of dietary intake variables** | Nutrients Intake | Units | | -------- | -------- | | Total energy intake | Kcal/day| |Total Protein | % of TE | |Plant proteins |% of TE | |Total fat | % of TE | |Saturated fat | % of TE| |Polyunsaturated fat | % of TE| |Monounsaturated fats | % of TE| |Carbohydrates | % of TE| |Total Sugar | % of TE| |Alcohol | % of TE or g/day| |Dietary fibre | g/day| |Salt | g/day| |Sodium | g/day| |**Food group intake** | | |Total fruits | g/day | |Whole fruits | g/day | |Total vegetables | g/day | |Whole grains | g/day | |Refined grains| g/day | |White meat | g/day | |Red meat | g/day | |Fish and Seafood | g/day | |Dairy | g/day | |Fruit juice | g/day | |Processed meat | g/day | |Sugar sweetened carbonated drinks | g/day | |Sweets and pastries | g/day | |Nuts | g/day | TE: total Energy. Taken from (Celis-Morales 2019) with amendments. **Covariates** * Sociodemographic: Age, sex, education, smoking * Related with BMI and microbiome: cardiometabolic diseases, physical activity, energy intake, alcohol intake * Confounding microbiome composition: current medication, current use of antibiotics (or use of antibiotics in the past year), regular use of probiotics * Study source (to account for technical and data processing issues) * Related to collection and measurement of microbiome data: DNA extraction kit, gene region, sequencing platform used

Additional Information

**Study inclusion criteria** 1. Study design: Cross-sectional data from either cross-sectional or cohort (baseline or single follow-up data) or case-control (controls only) or intervention study (control arm) 2. Mandatory data: Data on microbiome and anthropometric measurements (to address the primary aim) 3. Additional data: dietary intake (to address the secondary aim) 4. Age range: 18+ years

Studies Included

Study	Population	Data Collection Event
EPIC-Potsdam	EPIC-Potsdam Selection Criteria Minimum age 35 Maximum age 65 Newborns Twins Countries Germany International/National/Regional (region name) Brandenburg Ethnic Origin Health Status Recruitment Sources of recruitment General population Number of participants Number of participants 27,548 Number of participants with biosamples Supplementary Information Files No files could be found. EPIC-Potsdam	EPIC-DZD Start Date 2014 End Date 2020 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Special dietary aspects collected (e.g. supplements, probiotics, prebiotics and synbiotics) Methods 24-hour dietary recall FFQ 24-hour dietary recall Administration method Face-to-face interview FFQ Type of questionnaire Semi-quantitative Administration method Self-reported Administration type Web/computer-based Reference period Year Anthropometric measurements Weight/height Measured Waist/hip circumference Measured Sociodemographic information Information collected Sex, age, residence, education, etc. Questionnaire name/set of questions Questionnaire name/set of questions Administration method Self-reported Medication Information collected Drug dosage and drug name Antibiotics Last treatment and frequency collected Health status Information collected Various Measurements Various Biological samples and laboratory measurements Samples collected Blood, urine, feces, hair Biomarkers Lipids Measurement(s) Various Medium Plasma, serum Glucose Measurement(s) Various Medium Plasma, serum, RBC Inflammation markers Measurement(s) Various Medium Plasma Adiposity biomarkers Measurement(s) Various Medium Plasma Other biomarkers Measurement(s) Various Medium Plasma, serum Microbiome Microbial material 16S rDNA (V3-V4 region) Number of samples/number of individuals 3,299 Library source and library selection Metabarcoding Medium/tissue Feces Sampling collection method Invitek tubes with DNA stabilizer (collected at home by participants) Sequencing platform Illumina MiSeq v3 Read length/depth 2x300bp/~20,000 reads Further details 16S amplicon sequenced Information on type of meal last eaten prior to sample extraction available no Files No files could be found. EPIC-DZD
DONALD Study	DONALD Selection Criteria Minimum age 0 Newborns Twins Countries Germany International/National/Regional (region name) Dortmund and surrounding regions Ethnic Origin Health Status Healthy Other criteria Supplementary Information Eligible are healthy infants (i.e., no prevalent diseases affecting growth and/or diet) from the city of Dortmund and surrounding communities, whose parents are willing to participate in a long-term study and of whom at least one has sufficient knowledge of the German language. Recruitment Sources of recruitment General population Number of participants Number of participants No Limit Number of participants with biosamples No Limit Files No files could be found. DONALD	DONALD Start Date 1985 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Special dietary aspects collected (e.g. supplements, probiotics, prebiotics and synbiotics) Methods Food records 24-hour dietary recall Food records Administration method Self-reported Administration type Paper-based Number of recorded days 2-7 Portion size estimation Standard portion sizes with aids such as pictures, models, standard household measure, utensils, etc. Instrument validity Bokhof B, Günther AL, Berg-Beckhoff G, Kroke A, Buyken AE. Validation of protein intake assessed from weighed dietary records against protein estimated from 24 h urine samples in children, adolescents and young adults participating in the Dortmund Nutritional and Longitudinally Designed (DONALD) Study. Public Health Nutr. 2010 Jun;13(6):826-34. doi: 10.1017/S136898000999317X. Epub 2010 Jan 15. PMID: 20074394 Alcohol consumption Questionnaire name/set of questions Set of questions Administration method Self-reported Administration type Paper-based Tobacco consumption Questionnaire name/set of questions Set of questions Administration method Self-reported Administration type Paper-based Physical activity Questionnaire name/set of questions Adolescent Physical Activity Recall Questionnaire (APARQ) by Booth et al., 2002 (https://doi.org/10.1097/00005768-200212000-00019) Administration method Face-to-face interview Administration type Paper-based Sedentary behaviours Questionnaire name/set of questions Modified questions according to the German Health Interview and Examination Survey for Children and Adolescents (KiGGS); Opper et al. 2007 (https://doi.org/10.1007/s00103-007-0251-5) Administration method Face-to-face interview Administration type Paper-based Anthropometric measurements Weight/height Measured Waist/hip circumference Measured Other measurements Upper arm circumference (every visit), abdominal circumference (0-2 years), head circumference (0-5 years), skinfolds (biceps, triceps, subscapular and suprailiac skin fold; every visit), Upper + lower leg circumference (approx. 4 x during childhood and adolescence), pelvis + shoulder width (approx. 4 x during childhood and adolescence), waist + hip circumference (from 3 years onwards), sitting height (from 3 years onwards) Sociodemographic information Information collected Among others: Sex, age, socioeconomic factors (e.g. parental employment, parental education) and early life factors (e.g. birth weight, pregnancy duration, breastfeeding duration) Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Administration type Paper-based Medication Health status Information collected blood pressure, grip strength, family history of diseases, chronic diseases Questionnaire name/set of questions measured or set of questions Administration method Face-to-face interview Administration type Paper-based Biological samples and laboratory measurements Samples collected 24h-urine samples (from 3 years onwards), spot urine samples (0,25 - 3 years), blood samples (from 18 years onwards), stool samples (subsample from 18 years onwards), saliva (once during adolescence) Number of samples Biomarkers Lipids Measurement(s) HDL, LDL and other Medium Serum Glucose Measurement(s) Glucose Medium Plasma Inflammation markers Measurement(s) IL-6, IL-18 and other Medium plasma or serum Adiposity biomarkers Measurement(s) Leptin Medium serum Other biomarkers Measurement(s) liver enzymes (ALT, AST, GGT) and others Medium plasma Metabolomics Measurement(s) HP-LC and others Medium Urine, plasma Untargeted approach yes Targeted groups Amino acids Genomics DNA available yes Extraction protocol/ method Chemagic Magnetic Separation Module (Lymphocytes); or salting out by prepIT purifier von Oragene (Saliva) Genotyping whole genome: Illumina Infinium Global Screening Array v2.0. Microbiome Microbial material V3–V4 variable region of the 16S rRNA gene Number of samples/number of individuals 128 Medium/tissue Faeces Sampling collection method Solution: RNAlater Time spent in room temperature Approximately 3 days Sequencing platform MiSeq Information on type of meal last eaten prior to sample extraction available no Files No files could be found. DONALD
NU-AGE	Italian_cohort Selection Criteria Minimum age 65 Maximum age 79 Newborns Twins Countries Italy Ethnic Origin Health Status Other criteria Free of major overt chronic diseases for at least 2 years (e.g., cancer, severe organ disease), living independently, and free of dementia Recruitment Sources of recruitment General population Number of participants Number of participants 201 Number of participants with biosamples Files No files could be found. Italian_cohort	elderly-microbiome-study-_italian-cohort-from-nu-age Start Date 2012 End Date 2015 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Special dietary aspects collected (e.g. supplements, probiotics, prebiotics and synbiotics) Methods Food records Other methods Food records Administration method Face-to-face interview Administration type Paper-based Number of recorded days 2-7 Portion size estimation Standard portion sizes with aids such as pictures, models, standard household measure, utensils, etc. Instrument validity No Instrument development Already existing Instrument reference Ostan et al., Front Physiol 2018 Other methods Instrument(s) access 7-day food record template available Alcohol consumption Information collected Intake Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Administration type Paper-based Physical activity Information collected Scores (ADLs, IADLs, PASE) Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Domains covered Total physical activity Sedentary behaviours Information collected Scores (ADLs, IADLs, PASE) Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Anthropometric measurements Weight/height Measured Waist/hip circumference Measured Other measurements Body composition (DXA) Sociodemographic information Information collected Sex, age Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Medication Information collected Drug name Questionnaire name/set of questions Set of questions Antibiotics Yes (recent use of antibiotics was an exclusion criterion) Administration method Face-to-face interview Health status Questionnaire name/set of questions Blood pressure, hand grip strength, clinical data, family history of diseases, etc. Administration method Face-to-face interview Measurements Various Biological samples and laboratory measurements Samples collected Blood, feces Number of samples 402 Biomarkers Lipids Measurement(s) Various Medium Serum Glucose Measurement(s) Various Medium Inflammation markers Measurement(s) Various Adiposity biomarkers Measurement(s) Various Other biomarkers Measurement(s) Various Metabolomics Measurement(s) UPLC/Q-TOF-MS Medium Serum Untargeted approach yes Microbiome Microbial material 16S rDNA (V3-V4) Number of samples/number of individuals 201 Library source and library selection Metagenome (following the 16S Metagenomic Sequencing Library Preparation protocol by Illumina) Medium/tissue Faeces Sampling collection method Sterile collection tube Time spent in room temperature Few minutes Sequencing platform Illumina MiSeq Read length/depth 2x250 bp Further details True sequencing Preservation method No, immediately -20°C until delivery to the lab (where stored at -80°C) Information on type of meal last eaten prior to sample extraction available no Files No files could be found. elderly-microbiome-study-_italian-cohort-from-nu-age
ErNst	ernst Selection Criteria Minimum age 18 Maximum age 79 Newborns Twins Countries Germany International/National/Regional (region name) Europe Ethnic Origin not assessed Health Status healthy (without any known or apparent acute or chronic illness/disease) Recruitment Sources of recruitment General population Other : Recruitment through Study Center via database for study participants (through mail and E-Mail), leaflets, homepage etc. Number of participants Number of participants 117 Number of participants with biosamples 106 Supplementary Information Total number of participants was 117. Of these, full sets of biosamples (stool) and FFQs were obtained from 106 of these (53 M 53 F). Files No files could be found. ernst	ernst Start Date 2018-10 End Date 2018-12 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Methods 24-hour dietary recall FFQ 24-hour dietary recall Administration method Face-to-face interview Administration type Web/computer-based Number of recalls 1 Portion size estimation Standard portion sizes with aids such as pictures, models, standard household measure, utensils, etc. Instrument validity Testing validity of the updated instrument was one of the study aims. Instrument development Updated version of GloboDiet Instrument reference Slimani et al. (1999), doi:10.1016/s0169-2607(98)00088-1; Slimani et al. (2011), doi: 10.1038/ejcn.2011.83 FFQ Questionnaire name/set of questions DEGS FFQ/RKI (modified version) Type of questionnaire Semi-quantitative Administration method Self-reported Administration type Paper-based Number of food items 48 Reference period 1 month (30 days) Frequency categories 11 Portion size estimation Standard portion sizes without aids Reproducibility no Instrument validity no Instrument development Adapted from DEGS FFQ/RKI Instrument reference Haftenberger et al., Nutrition Journal volume 9, Article number: 36 (2010); doi: 10.1186/1475-2891-9-36. Alcohol consumption Information collected Categorical (no, occassionally, regularly) Questionnaire name/set of questions Single question Administration method Self-reported Administration type Paper-based Tobacco consumption Information collected Frequency of smoking cigarettes and other tobacco products; history (total years of smoking) Questionnaire name/set of questions Set of questions Administration method Self-reported Administration type Paper-based Physical activity Device type Accelerometer (ActiHeart/ CamNtech) Device model ActiHeart (Software version: 4.0.131) Measurement period 24h Measurement position Chest lead: one electrode is adhered at V1 or V2 (4th intercostals) and the second electrode is placed approximately 10cm away on the left side at V4 or V5 Anthropometric measurements Weight/height Measured Other measurements Body composition (BIA) Sociodemographic information Information collected Sex, age Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Administration type Web/computer-based Medication Information collected Drug dosage and name Questionnaire name/set of questions Set of questions Antibiotics Yes (treatment within last 6 months) Administration method Self-reported Administration type Paper-based Health status Information collected Medical history Questionnaire name/set of questions Various Administration method Face-to-face interview Biological samples and laboratory measurements Samples collected Urine (24h), stool Number of samples 109 (urine), 106 (stool) Biomarkers Other biomarkers Measurement(s) Sodium, potassium, nitrogen, osmolality, creatinine Medium Urine Microbiome Microbial material DNA Number of samples/number of individuals 212 Library source and library selection 16S Amplicons (V4 region) Medium/tissue Faeces Sampling collection method Frozen (-20°) Time spent in room temperature Short (immediatey freezing after collection) Sequencing platform MiSeq Read length/depth 2x301/20000 - ca. 100000 on average per sample Further details Amplicon sequencing Preservation method Immediate -20, transport on cooling packages, mid-/long-term storage at -80 until aliquotation and DNA isolation Preservation buffer None Information on type of meal last eaten prior to sample extraction available no Files No files could be found. ernst
FoCus	focus Selection Criteria Minimum age 18 Maximum age 83 Newborns Twins Countries Germany Territory International/National/Regional (region name) Europe Ethnic Origin Health Status Recruitment Sources of recruitment General population Specific population Specific Population Clinic patients Other specific population : Number of participants Number of participants 1,811 Number of participants with biosamples Files No files could be found. focus	FoCus_baseline Start Date 2014 End Date 2015 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Methods FFQ FFQ Questionnaire name/set of questions Postadam FFQ Type of questionnaire Semi-quantitative Administration method Self-reported Administration type Paper-based Reference period Year Portion size estimation Not quantified Alcohol consumption Information collected Administration method Self-reported Administration type Paper-based Tobacco consumption Information collected ever/never/current/packs per day Administration method Self-reported Administration type Paper-based Anthropometric measurements Weight/height Self-reported, measured for subset Waist/hip circumference Self-reported, measured for subset Other measurements Various Sociodemographic information Information collected Sex, age, residence, education, etc. Administration method Self-reported Medication Information collected Drug dosage and drug name Antibiotics Last treatment and frequency collected Administration method Self-reported Health status Information collected Various Questionnaire name/set of questions Various Administration method Self-reported Measurements Various Biological samples and laboratory measurements Samples collected Blood, urine, stool Number of samples 1811 Biomarkers Lipids Measurement(s) Various Medium Serum Glucose Measurement(s) Various Medium Serum Inflammation markers Measurement(s) Various Medium Serum Adiposity biomarkers Measurement(s) Various Medium Serum Other biomarkers Measurement(s) Various Medium Serum Metabolomics Measurement(s) Direct infusion high resolution mass spectrometry Medium Serum, urine Untargeted approach yes Targeted groups Several Genomics DNA available yes Number of samples/number of individuals 1,811 Extraction protocol/ method Mircoarray Microbiome Microbial material DNA, 16s rRNA V3 and V4 region Number of samples/number of individuals 1,545 Library source and library selection Serum and urine metabolome Medium/tissue Faeces Sampling collection method Samples on dry ice Time spent in room temperature none Sequencing platform Illumina MiSeq Further details 16s Preservation method Cooled immediatley -80 within 24 hours Information on type of meal last eaten prior to sample extraction available no Files No files could be found. FoCus_baseline
MeaTIc	meatic Selection Criteria Minimum age 18 Maximum age 50 Newborns Twins Countries Italy Ethnic Origin Health Status healthy volounteers undergoing an intervention trial Recruitment Sources of recruitment General population General Population Volunteer enrolment Number of participants Number of participants 113 Number of participants with biosamples Files No files could be found. meatic	meatic Start Date 2020 End Date 2021 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Special dietary aspects collected (e.g. supplements, probiotics, prebiotics and synbiotics) Methods FFQ Food records Other methods FFQ Questionnaire name/set of questions Italian medium-FFQ Type of questionnaire Semi-quantitative Administration method Self-reported Administration type Paper-based Number of food items 27 Reference period year Frequency categories varying Portion size estimation Standard portion sizes without aids Reproducibility no Instrument validity no Instrument development already existing instrument (medium-FFQ) Instrument reference https://pubmed.ncbi.nlm.nih.gov/25830946/ Food records Administration method Self-reported Administration type Paper-based Number of recorded days 2-7 Instrument validity no Instrument development already existing instrument Instrument reference 3-day weighted dietary record (WDR) Other methods Other methods Medi-Lite adherence score Instrument(s) access https://pubmed.ncbi.nlm.nih.gov/28276908/ Alcohol consumption Information collected quantity and frequency of consumption of alcoholic drinks Questionnaire name/set of questions medium-FFQ, Medi-Lite adherence score Administration method Self-reported Administration type Paper-based Tobacco consumption Information collected consumption (yes/no) Questionnaire name/set of questions Set of questions Administration method Face-to-face iinterview Administration type Paper-based Physical activity Information collected frequency, duration and types of PA Questionnaire name/set of questions set of questions Administration method Face-to-face interview Domains covered leisure, occupation Anthropometric measurements Weight/height Measured Waist/hip circumference no Other measurements body composition (BIA) Sociodemographic information Information collected sex, age, residence, country of birth, country of citizenship at time of data collection Questionnaire name/set of questions set of questions Administration method Face-to-face interview Medication Information collected drug name Questionnaire name/set of questions set of questions Antibiotics yes Administration method Face-to-face interview Health status Information collected disease diagnosis Questionnaire name/set of questions set of questions Administration method Face-to-face interview Measurements various Biological samples and laboratory measurements Samples collected blood, urine, stool Number of samples 113 Biomarkers Lipids Measurement(s) HDL, LDL, cholesterol Medium Serum Glucose Measurement(s) glucose Medium serum Other biomarkers Measurement(s) Folate, vitamin B12, iron, ferritin, triglycerides, AST, ALT, uric acid, urea, creatinine, pro- and anti-inflammatory profile, cytokines, urinary biomarkers of lipid peroxidation, Markers of global peroxidation of fecal water (TBARs) and specific peroxidation of omega-3 and omega-6 PUFA in fecal water Medium other Metabolomics Measurement(s) SCFAs, Aminoacids, Bile acids, Fecal water untargeted metabolomics Medium other Untargeted approach no Targeted groups lipids, aminoacids, secondary bile acids Microbiome Microbial material DNA, 16S rRNA (V3 and V4 hypervariable regions), Fecal microbiota profiles Number of samples/number of individuals 113 Library source and library selection Metagenome, serum and urine metabolome Medium/tissue faeces Sampling collection method samples on dry ice Time spent in room temperature none Sequencing platform Illumina MiSeq Preservation method Immediate -20, dry ice/-80 within 4-24h Information on type of meal last eaten prior to sample extraction available no Files No files could be found. meatic
MetaCardis	MetaCardis population Selection Criteria Minimum age 18 Maximum age 75 Newborns Twins Countries Germany France Denmark International/National/Regional (region name) Europe Ethnic Origin Health Status Multiple graduated groups ranging from healthy, metabolic syndrome, obese, morbidly obese, T2D, acute CAD, chronic CAD w/o HF, chronic CAD w HF, HF w/o CAD Recruitment Sources of recruitment General population Other : Recruitment through clinics and through advertisement (for controls) Number of participants Number of participants 2,189 Number of participants with biosamples 2,189 Supplementary Information 1101 M 1088 F Files No files could be found. MetaCardis population	metacardis Start Date 2013 End Date 2015 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Methods 24-hour dietary recall FFQ 24-hour dietary recall Instrument development 24h was done in subset of subjects to validate FFQ Instrument reference https://www.ncbi.nlm.nih.gov/pubmed/28024800 FFQ Questionnaire name/set of questions MetaCardis FFQ Type of questionnaire Semi-quantitative Administration method Self-reported Administration type Web/computer-based Number of food items Country-dependent Reference period Varying Frequency categories Varying Portion size estimation Standard portion sizes without aids Reproducibility Tested Instrument validity Tested Instrument development Newly developed Instrument reference https://www.ncbi.nlm.nih.gov/pubmed/28024800 Alcohol consumption Questionnaire name/set of questions Set of questions Tobacco consumption Questionnaire name/set of questions Set of questions Physical activity Information collected Various Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Domains covered Leisure, occupation Sedentary behaviours Questionnaire name/set of questions Set of questions Anthropometric measurements Weight/height Measured Waist/hip circumference Waist circumference (measured) Other measurements Various Sociodemographic information Information collected Sex, age, residence, country of birth, country of citizenship at time of data collection, economic income status, education, etc. Questionnaire name/set of questions Set of questions Administration method Face-to-face interview Medication Information collected Drug dosage and drug name Questionnaire name/set of questions Medical records Antibiotics Last treatment and frequency collected Health status Information collected Various, focused on CMD and comorbidities Questionnaire name/set of questions Various Administration method Face-to-face interview Measurements Various Biological samples and laboratory measurements Samples collected Blood, urine, stool Number of samples 2189 Biomarkers Lipids Measurement(s) Various Medium Serum Glucose Measurement(s) Various Medium Serum Inflammation markers Measurement(s) Various Medium Serum Adiposity biomarkers Measurement(s) Various Medium Serum Other biomarkers Measurement(s) Various Medium Serum Metabolomics Measurement(s) NMR, HP-LC, others Medium Serum, urine Untargeted approach yes Targeted groups Several: lipids, aminoacyls, others Microbiome Microbial material DNA, shotgun Number of samples/number of individuals 2,189 Library source and library selection Metagenome, serum and urine metabolome Medium/tissue Faeces Sampling collection method Samples on dry ice Time spent in room temperature None Sequencing platform Ion-Proton Read length/depth ~150/23M+-4M Further details Shotgun metagenome Preservation method Immediate -20, dry ice/-80 within 4-24h Information on type of meal last eaten prior to sample extraction available no Files No files could be found. metacardis
Diet4MicroGut	diet4microgut Selection Criteria Minimum age 18 Maximum age 60 Newborns Twins Countries Italy International/National/Regional (region name) 4 cities in Southern and Northern Italy Ethnic Origin Health Status healthy Recruitment Sources of recruitment General population Other : recruitment through advertisement, exclusion criteria applied Number of participants Number of participants 153 Number of participants with biosamples Files No files could be found. diet4microgut	diet4microgut Start Date 2012 End Date 2013 Measurements & methods Dietary intake yes/no Information collected on habitual food intake collected Information collected on type of diet (vegetarian/vegan/omnivore) Special dietary aspects collected (e.g. supplements, probiotics, prebiotics and synbiotics) Methods Food records Food records Administration type Paper-based Number of recorded days 2-7 Portion size estimation Not quantified Instrument validity No Instrument development Already existing instrument - self-completed 7-days food diary Alcohol consumption Questionnaire name/set of questions Set of questions Tobacco consumption Questionnaire name/set of questions Set of questions Sedentary behaviours Questionnaire name/set of questions Set of questions Administration method Self-reported Anthropometric measurements Weight/height Self-reported Other measurements Weight, height, BMI Sociodemographic information Information collected Sex, age Questionnaire name/set of questions Set of questions Administration method Self-reported Medication Information collected Drug dosage and drug name Questionnaire name/set of questions Set of questions Antibiotics Yes (antibiotics in the previous 3 months were considered an exclusion factor) Administration method Self-reported Health status Information collected Gastrointestinal diseases, metabolic diseases, cancer, allergies, cardiovascular diseases, neurodegenerative diseases, constipation, arthritis, pregnancy, breastfeeding were exclusion factors Questionnaire name/set of questions Set of questions Administration method Self-reported Measurements No Biological samples and laboratory measurements Samples collected Urine, saliva, stool Number of samples 459 Biomarkers Metabolomics Measurement(s) NMR, GC-MS Medium Feces, urine Untargeted approach yes Proteomics Measurement(s) YES on a subset Medium Feces Untargeted approach no Targeted protein groups No Genomics DNA available yes Number of samples/number of individuals 80 Extraction protocol/ method Powe Soil kit (qiagen) Genotyping No Microbiome Microbial material 16S rRNA V1-V3 regions (454 reads) on 153 subjects, Illumina shotgun on a subset of 50 subjects Number of samples/number of individuals 153 Library source and library selection Metagenome (16S and shotgun), fecal and urinary metabolome, fecal proteome only on a subset Medium/tissue Feces, urine Sampling collection method Samples self-collected and transported refrigerated to the laboratory within 24 h, then stored at -80°C Time spent in room temperature None Sequencing platform 454 Junior (16S seq), Illumina NextSeq (shotgun) Read length/depth ~500bp, about 4000 reads/sample (16S seq); about 50M/sample, 2x150bp (shotgun) Further details Shotgun metagenome; 16S rRNA sequencing Preservation method Samples self-collected and transported refrigerated to the laboratory within 24 h, then stored at -80°C Information on type of meal last eaten prior to sample extraction available no Files No files could be found. diet4microgut

Initiatives Included

Harmonization

: Complete - study-specific variable is the same as DataSchema variable (status = identical) or needs transformation to generate DataSchema variable (status = compatible)
: Partial - categorical study-specific variable (status = proximate) or other types (status = tentative) could generate DataSchema variable but with loss of information
: Impossible - study does not collect DataSchema variable (status = unavailable) or cannot be used to generate DataSchema variable (status = incompatible)
: Undetermined - harmonization status not determined
: Not Applicable - harmonization status is not relevant

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Variable	EPIC-Potsdam	DONALD Study	NU-AGE	ErNst	FoCus	MeaTIc	MetaCardis	Diet4MicroGut

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Harmonization Protocol / Microbiome in health and disease and in ageing

INTIMIC-KP Use Cases 3 and 4 (Microbiome in health and disease and in ageing, WP6)

Information Content

Additional Information

Studies Included

Initiatives Included

Harmonization

Files

Variables Classifications

Harmonization Protocol / Microbiome in health and disease and in ageing

INTIMIC-KP Use Cases 3 and 4 (Microbiome in health and disease and in ageing, WP6)

Information Content

Additional Information

Studies Included

EPIC-Potsdam

Selection Criteria

Recruitment

Number of participants

Files

EPIC-DZD

Measurements & methods

Dietary intake

24-hour dietary recall

FFQ

Anthropometric measurements

Sociodemographic information

Medication

Health status

Biological samples and laboratory measurements

Biomarkers

Lipids

Glucose

Inflammation markers

Adiposity biomarkers

Other biomarkers

Microbiome

DONALD

Selection Criteria

Recruitment

Number of participants

Files

DONALD

Measurements & methods

Dietary intake

24-hour dietary recall

Food records

Alcohol consumption

Tobacco consumption

Physical activity

Sedentary behaviours

Anthropometric measurements

Sociodemographic information

Medication

Health status

Biological samples and laboratory measurements

Biomarkers

Lipids

Glucose

Inflammation markers

Adiposity biomarkers

Other biomarkers

Metabolomics

Genomics

Microbiome

Italian_cohort

Selection Criteria

Recruitment

Number of participants

Files

elderly-microbiome-study-_italian-cohort-from-nu-age

Measurements & methods

Dietary intake

Food records

Other methods

Alcohol consumption

Physical activity

Sedentary behaviours

Anthropometric measurements

Sociodemographic information

Medication

Health status

Biological samples and laboratory measurements

Biomarkers

Lipids

Glucose

Inflammation markers

Adiposity biomarkers

Other biomarkers

Metabolomics