datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
gut-microbiome-allergy-data
Dataset Card for Gut Microbiome–Food Allergy Prediction Datasets
Dataset Summary
This repository contains multiple human gut microbiome datasets curated for predicting food allergy development.
Each dataset corresponds to a distinct cohort with longitudinal microbiome sampling, providing both metadata and derived embeddings suitable for machine learning.
The datasets are designed to support binary classification of subjects into healthy vs allergic categories, enabling… See the full description on the dataset page: https://huggingface.co/datasets/hugging-science/gut-microbiome-allergy-data.qiime2_antibiotic_microbiome_analysis
Soil Microbiome Responses to Antibiotic Contamination: A Dual-Marker Amplicon Analysis
Overview
This repository contains a fully reproducible computational pipeline for the analysis of soil microbial community responses to escalating antibiotic concentrations. The study employs a dual-marker amplicon sequencing approach, simultaneously profiling bacterial communities via the 16S rRNA gene (V3-V4 region) and fungal communities via the internal transcribed spacer… See the full description on the dataset page: https://huggingface.co/datasets/QasimHussain/qiime2_antibiotic_microbiome_analysis.Human_Gut_Microbiome_Atlas
Deep Metagenomics of the Human Gut Microbiome in IBD: A Multi-Omics Data Atlas
A curated longitudinal dataset and computational framework for dissecting the temporal ecology of Inflammatory Bowel Disease (IBD).
Abstract
This project presents a comprehensive, high-resolution computational analysis of the human gut microbiome in Inflammatory Bowel Disease (IBD), leveraging deep metagenomic sequencing data from the HMP2 (Integrative Human Microbiome Project)… See the full description on the dataset page: https://huggingface.co/datasets/QasimHussain/Human_Gut_Microbiome_Atlas.colorectal-carcinoma-microbiome-fengqThe dataset contains 16S rRNA gene sequencing data from healthy controls and colorectal cancer patients. The dataset was used in the paper "Gut microbiome development along the colorectal adenoma-carcinoma sequence" by Feng et al. (2015).bio-faiss-microbiome-v1
bio-faiss-microbiome-v1
A FAISS index + metadata for scientific retrieval
Contents
index.faiss: FAISS index (cosine w/ inner product).
meta.jsonl: one JSON per chunk; fields include chunk_id, paper_id, title, section, subsection, paragraph_index, keywords, boost.
Build provenance
Chunking: hierarchical (section→paragraph→~380-token chunks, ~15% overlap)
Embedder: bio-protocol/scientific-retriever (mean-pooled, L2-normalized)
Similarity: cosine via inner… See the full description on the dataset page: https://huggingface.co/datasets/bio-protocol/bio-faiss-microbiome-v1.Human_Gut_Microbiome_Data
Human Gut Microbiome Dataset (40-class)
Pre-processed, train/val/test-split human gut microbiome dataset used to train and evaluate
MicrobiomeFM, a Transformer-based foundation model for multi-class disease classification
from shotgun metagenomic data.
This release contains the 40-class filtered version of the dataset that the published
results were obtained on (test accuracy ≈ 96.05%, weighted F1 ≈ 0.950, macro F1 ≈ 0.691).
It is derived from the curatedMetagenomicData (cMD)… See the full description on the dataset page: https://huggingface.co/datasets/mohitraiyani27/Human_Gut_Microbiome_Data.huberman_lab_How_to_Enhance_Your_Gut_Microbiome_for_Brain__Overall_Healthmicrobiome-health-ibdBioFactory-Asian-Oral-Microbiome-Preview
🦷 World's First Chinese-Anchored Oral Multi-Omics Synthetic Dataset (v2026)
3,872 production records · PERMANOVA p=0.994 · MMD=0.060 · 100% synthetic = zero GDPR risk
📄 Full Whitepaper ·
📋 1-Page Executive Summary ·
🔬 38-Sample Preview ·
📧 Enterprise: jerry820402@hotmail.com
English Executive Summary
This is the world's first Asian/Chinese-specific oral microbiome multi-omics synthetic dataset, generated via Evo foundation model inference on 8× NVIDIA A800… See the full description on the dataset page: https://huggingface.co/datasets/jerry982/BioFactory-Asian-Oral-Microbiome-Preview.microbiome-training-pmc_extracted_methods_batch_0microbiome-uc-ibdmicrobiome-16s-v1_0_4microbiome-training-pmc-expertqa_abstracts_2-sep_answers-v1_0_4microbiome-american_gut_project-v1_0_4microbiome-leuconostoc-brachyspira
Leucnostoc and Brachyspira Microbiome Findings
This dataset contains scientific findings about bacteria in the human gut microbiome in health and ulcerative colitis.
Dataset Structure
The dataset follows the same structure as TinyStories, with a single 'text' field containing scientific findings from research papers.
Example:
Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species.. The… See the full description on the dataset page: https://huggingface.co/datasets/polejowska/microbiome-leuconostoc-brachyspira.microbiome-cmd-v1_0_4microbiome-american_gut_project_disease-v1_0_4microbiome-16s_to_functions-v1_0_4microbiome-summariesssa-breast-gut-microbiome
SSA Breast Gut Microbiome Dataset (Women, Multi-ancestry) | Africa (Electric Sheep Africa metadata inventory)
Size category: 10K<n<100K - Formats: parquet - Sector: health - Engineered by Electric Sheep Africa
TL;DR
This dataset is part of the Electric Sheep Africa catalog on Hugging Face. It is indexed for African data discovery with standardized metadata, loading guidance, provenance notes, and analyst-oriented context.
What This Dataset Covers… See the full description on the dataset page: https://huggingface.co/datasets/electricsheepafrica/ssa-breast-gut-microbiome.microbiome-summaries-2cases_microbiomeThis dataset contains 105 patient descriptions that are looking for clinical trials investigating interventions targeting their microbiome.
The dataset was intentionally distributed across 18 disease categories of various disease settings, locations spread accross 17 countries, and broad spectrum of age ranges.
Disease Categories covered by the dataset:
Cardiovascular Diseases
Musculoskeletal Issues
Type 2 Diabetes
Skin Diseases
Gastrointestinal Disorders
Digestive Disorders
Mental Health… See the full description on the dataset page: https://huggingface.co/datasets/Elysr/cases_microbiome.microbiome-summaries-3microbiome-disease-dataset
Dataset Card for Dataset Name
This dataset card aims to be a base template for new datasets. It has been generated using this raw template.
Dataset Details
Dataset Description
Curated by: [More Information Needed]
Funded by [optional]: [More Information Needed]
Shared by [optional]: [More Information Needed]
Language(s) (NLP): [More Information Needed]
License: [More Information Needed]
Dataset Sources [optional]
Repository: [More… See the full description on the dataset page: https://huggingface.co/datasets/elizah521/microbiome-disease-dataset.ABX-HT-006_microbiome_diversity_collapse-v0.1ABX-HT-006 Microbiome Diversity Collapse
Purpose
Detect early microbiome collapse that predicts C. difficile risk.
Core pattern
host_stress_index high
abx_exposure_index high
microbiome_coherence_index drops
shannon_drop_vs_expected stays high
domination_rise_vs_expected stays high
later_cdiff_flag appears
Files
data/train.csv
data/test.csv
scorer.py
Schema
Each row is one timepoint in a within series microbiome time course.
Required columns
row_id
series_id
timepoint_d
host_model
drug… See the full description on the dataset page: https://huggingface.co/datasets/ClarusC64/ABX-HT-006_microbiome_diversity_collapse-v0.1.RAG-Immunotherapy-Microbiome-CDSmpegg_microbiome_fastq_train_unified
MPEG-G Microbiome FASTQ — Train (Unified)
This dataset consolidates the converted FASTQ files for the MPEG-G Microbiome challenge (train split).
Structure
train/fastq/ — per-sample FASTQ files (<sample_id>.fastq.gz)
unified_train.csv — manifest with sample_id, label, filename
Labels are from the original Train.csv, and FASTQs are normalized to gzipped form.
zindi-mpeg-microbiome-fastq-demo-packmicrobome-expert-qa