Shotgun Metagenomic Data

Human (CHAMP)

Stool

1. Human stool by antibiotic treatment - Wilmann et al 2019
2. Preterm Infant Probiotic Supplementation - Nguyen et al 2021 - PRJNA630999
3. Infant stool by time points - Backhed et al 2015
4. Infant stool by time points - Matharu et al 2022
5. Clostridioides difficile-colonized patients - Fishbein et al 2022 - PRJNA748262
6. HIV InfectionStatus Fecal WGS - Noguera-Julian et al 2016 - PRJNA307231
7. Hazda Hunter Gatherer v Italy Gut Biome WGS - Rampelli et al 2015 - PRJNA278393
8. Infant Probiotic Supplementation - Henrick et al 2021 - PRJNA390646

Skin

1. Skin Microbiome by Antibiotics - Jo et al 2021
2. Skin Microbiome in Cutaneous Lymphoma - Salava et al 2020 - PRJEB36953
3. Skin Biopsy Metatranscriptomics - Leishmaniasis Cohort - Christensen et al 2016 - PRJNA307599

Oral

1. Oral Disease Cohort - healthy vs mucositis vs peri-implantitis - Bazzani et al 2024 - PRJNA547717
2. Healthy Saliva WGS - PMC8727345
3. Human Oral Microbiome - Caselli et al 2020 - PRJEB36291

Vaginal

1. Healthy Vaginal MetaAnalysis

Urine

1. Urinary Tract Infection Microbiome - Neugent et al 2022 - PRJNA801448

Cerebral Spinal Fluid

1. CLIMB CSF Shunt Infection Microbiome - Hodor et al 2021 - PRJNA707514

Eye

1. Ocular Surface Microbiome in Dry Eyes - Tong et al 2022 - PRJNA886972

Milk

1. Human and Bovine Milk - Yap et al 2020 - PRJEB38099

Tumor

1. GI Tumor Microenvironment - WGS - Roelands et al 2023 - PRJNA941834

Non-Human (Kepler)

Environmental

1. Aral Sea Desiccation Study - Wicaksono et al 2022 - PRJEB51329
2. Honey Microbiome - Bovo et al 2020 - PRJEB36075
3. Citrus Rhizosphere and Soil - Xu et al 2018 - PRJNA362455
4. Global Wastewater Microbiome Consortium - Wu et al 2019 - PRJNA509305

Food

1. Ground Beef by Antibiotic Treatment - Doster et al 2020 - PRJNA608954
2. Food Microbiota WGS - Bloomfield et al 2023 - PRJNA849983

Wastewater

1. Global Wastewater Microbiome Consortium - Wu et al 2019 - PRJNA509305

Monkey

1. Rhesus Monkey Gut Microbiome in Parkinsons Disease - Yan et al 2021 - PRJNA574851

Mouse

1. Mouse Gut (High vs. Low Fiber Diet) - PRJEB37383

Fish

1. Fish Microbiome by Longitudinal Antibiotic Treatment - Kayani et al 2022 - PRJNA781418

Horse

1. Horse by breed-conservation status (Equus przewalskii vs. Equus hemionus hemionus - Tang et al 2022 - PRJNA814825

Dog

1. Dog Gut Microbiome by breed (Labrador vs. Beagle) - Coelho et al 2018 - PRJEB20308

Pig

1. Pig Gut Longitudinal Fecal by Post-Weaning Diarrhea Treatment - Guitart-Matas 2024 - PRJNA1010706
   1. Groups: amoxicillin, colistin, gentamicin, trimethoprim/sulfamethoxazole, oral vaccine, control, no_treatment_control_with_acidified_water
2. Pig Stool by Drug Treatment - Sanjuan et al 2024a - PRJNA984595
3. Pig Lung Metagenomics (healthy vs. severe lesions) - Li et al 2023 - PRJNA732170
4. Weaning Piglet Gut Microbiome - Holman et al 2021 - PRJNA629856

Cat

1. Feline Gut (Obese vs. Healthy) - Ma et al 2022 - PRJNA758898

Poultry

1. Gnotobiotic chick cecum dynamics post-inoculation - Thomas et al 2019 - PRJNA415593
2. Chicken Gut Sampling - Kang et al 2021 - PRJNA658643
3. Chicken Cecal Microbiome during Salmonella Infection - Bogomolnaya et al 2022 - PRJNA906507

Bovine

1. Cow Rumen Microbiome by Breed - Sandri et al 2018 - PRJNA381851

Other

1. Microbiota of Domestic Kitchen Sponges - Brandau et al 2022 - PRJEB49259

Amplicon Data

1. Gut Decontamination for Stem Cell Transfer Patients - 16S V4 - Bekker et al 2019 - PRJEB28845
2. Antarctic Snow Algae Mycobiome - ITS - Davey et al 2019 - PRJEB23732
3. Antarctic Snow Algae Microbiome - 16S V4 - Davey et al 2019 - PRJEB23732
4. Anaerobic Food Waste Digesters - 16S V4 - Svensson et al 2019 - PRJNA430711
5. Mice on SPF or GF Diet - 16S V3_4 - Wu et al 2022 - PRJNA768608
6. Umbilical Cord Serum Microbiome - 16S V1_3 - Turturice et al 2019 - PRJNA473573