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Technical Appendix
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Technical Appendix
Available Example Datasets
These datasets can be deposited into your account upon request for demo purposes
Shotgun Metagenomic Data
Human (CHAMP)
Stool
Human stool by antibiotic treatment - Wilmann et al 2019
Preterm Infant Probiotic Supplementation - Nguyen et al 2021 - PRJNA630999
Infant stool by time points - Backhed et al 2015
Infant stool by time points - Matharu et al 2022
Clostridioides difficile-colonized patients - Fishbein et al 2022 - PRJNA748262
HIV InfectionStatus Fecal WGS - Noguera-Julian et al 2016 - PRJNA307231
Hazda Hunter Gatherer v Italy Gut Biome WGS - Rampelli et al 2015 - PRJNA278393
Infant Probiotic Supplementation - Henrick et al 2021 - PRJNA390646
Skin
Skin Microbiome by Antibiotics - Jo et al 2021
Skin Microbiome in Cutaneous Lymphoma - Salava et al 2020 - PRJEB36953
Skin Biopsy Metatranscriptomics - Leishmaniasis Cohort - Christensen et al 2016 - PRJNA307599
Oral
Oral Disease Cohort - healthy vs mucositis vs peri-implantitis - Bazzani et al 2024 - PRJNA547717
Healthy Saliva WGS - PMC8727345
Human Oral Microbiome - Caselli et al 2020 - PRJEB36291
Vaginal
Healthy Vaginal MetaAnalysis
Urine
Urinary Tract Infection Microbiome - Neugent et al 2022 - PRJNA801448
Cerebral Spinal Fluid
CLIMB CSF Shunt Infection Microbiome - Hodor et al 2021 - PRJNA707514
Eye
Ocular Surface Microbiome in Dry Eyes - Tong et al 2022 - PRJNA886972
Milk
Human and Bovine Milk - Yap et al 2020 - PRJEB38099
Tumor
GI Tumor Microenvironment - WGS - Roelands et al 2023 - PRJNA941834
Non-Human (Kepler)
Environmental
Aral Sea Desiccation Study - Wicaksono et al 2022 - PRJEB51329
Honey Microbiome - Bovo et al 2020 - PRJEB36075
Citrus Rhizosphere and Soil - Xu et al 2018 - PRJNA362455
Global Wastewater Microbiome Consortium - Wu et al 2019 - PRJNA509305
Food
Ground Beef by Antibiotic Treatment - Doster et al 2020 - PRJNA608954
Food Microbiota WGS - Bloomfield et al 2023 - PRJNA849983
Wastewater
Global Wastewater Microbiome Consortium - Wu et al 2019 - PRJNA509305
Monkey
Rhesus Monkey Gut Microbiome in Parkinsons Disease - Yan et al 2021 - PRJNA574851
Mouse
Mouse Gut (High vs. Low Fiber Diet) - PRJEB37383
Fish
Fish Microbiome by Longitudinal Antibiotic Treatment - Kayani et al 2022 - PRJNA781418
Horse
Horse by breed-conservation status (
Equus przewalskii
vs.
Equus hemionus hemionus
- Tang et al 2022 - PRJNA814825
Dog
Dog Gut Microbiome by breed (Labrador vs. Beagle) - Coelho et al 2018 - PRJEB20308
Pig
Pig Gut Longitudinal Fecal by Post-Weaning Diarrhea Treatment -
Guitart-Matas 2024
- PRJNA1010706
Groups: amoxicillin, colistin, gentamicin, trimethoprim/sulfamethoxazole, oral vaccine, control, no_treatment_control_with_acidified_water
Pig Stool by Drug Treatment - Sanjuan et al 2024a - PRJNA984595
Pig Lung Metagenomics (healthy vs. severe lesions) - Li et al 2023 - PRJNA732170
Weaning Piglet Gut Microbiome - Holman et al 2021 - PRJNA629856
Cat
Feline Gut (Obese vs. Healthy) - Ma et al 2022 - PRJNA758898
Poultry
Gnotobiotic chick cecum dynamics post-inoculation - Thomas et al 2019 - PRJNA415593
Chicken Gut Sampling - Kang et al 2021 - PRJNA658643
Chicken Cecal Microbiome during Salmonella Infection - Bogomolnaya et al 2022 - PRJNA906507
Bovine
Cow Rumen Microbiome by Breed - Sandri et al 2018 - PRJNA381851
Other
Microbiota of Domestic Kitchen Sponges - Brandau et al 2022 - PRJEB49259
Amplicon Data
Gut Decontamination for Stem Cell Transfer Patients - 16S V4 - Bekker et al 2019 - PRJEB28845
Antarctic Snow Algae Mycobiome - ITS - Davey et al 2019 - PRJEB23732
Antarctic Snow Algae Microbiome - 16S V4 - Davey et al 2019 - PRJEB23732
Anaerobic Food Waste Digesters - 16S V4 - Svensson et al 2019 - PRJNA430711
Mice on SPF or GF Diet - 16S V3_4 - Wu et al 2022 - PRJNA768608
Umbilical Cord Serum Microbiome - 16S V1_3 - Turturice et al 2019 - PRJNA473573
Assistant
Responses are generated using AI and may contain mistakes.
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GTDB vs. NCBI Taxonomic Nomenclature
The Cosmos-Hub utilizes GTDB-based nomenclature for taxonomic assessment.
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Shotgun Metagenomic Data
Human (CHAMP)
Stool
Skin
Oral
Vaginal
Urine
Cerebral Spinal Fluid
Eye
Milk
Tumor
Non-Human (Kepler)
Environmental
Food
Wastewater
Monkey
Mouse
Fish
Horse
Dog
Pig
Cat
Poultry
Bovine
Other
Amplicon Data