# The Human Gut Mycobiome Atlas

Author: Xinyu Wang, Kailang Huang, and Ju-Sheng Zheng  

Affiliation: Westlake University  

Contact: [wangxinyu30@westlake.edu.cn](mailto:wangxinyu30@westlake.edu.cn)

## Files

### Metadata and Supplementary Tables

- `metadata.csv`: Sample metadata.
- `supplemental_tables.xlsx`: Supplementary tables associated with this project.

### Diversity Data

- `alpha_diversity.csv`: Alpha diversity metrics for microfungal species hypotheses (SHs) across all samples.
- `beta_diversity.rds`: Robust Aitchison distance matrix for samples with ≥10,000 microfungal reads, calculated from raw counts of 688 genera after aggregating taxa with prevalence <0.1% into “Other” and unclassified taxa into “Unknown”.

### Feature Tables, Taxonomy, and Reference Sequences

- `otu_gen.csv`: Genus-level feature table.
- `tax_gen.csv`: Genus-level taxonomic assignment table.
- `otu_sh.csv`: SH-level feature table.
- `tax_sh.csv`: SH-level taxonomic assignment table.
- `refseq_sh.fasta`: Representative SH sequences.

### Phyloseq Objects

- `ps_fdp_gen.rds`: Genus-level phyloseq object for samples with ≥10,000 microfungal reads after depth filtering.
- `ps_fdp_sh.rds`: SH-level phyloseq object for samples with ≥10,000 microfungal reads after depth filtering.
- `ps_nfdp_gen.rds`: Genus-level phyloseq object for all samples without depth filtering.
- `ps_nfdp_sh.rds`: SH-level phyloseq object for all samples without depth filtering.

## Notes

- Non-depth-filtered files retain samples with more than one microfungal read after MycoGAP processing. Apply additional depth filtering as needed before analysis.
- `beta_diversity.rds`, `ps_fdp_gen.rds`, and `ps_fdp_sh.rds` are based on samples with ≥10,000 microfungal reads.
- Load `.rds` files in R with `readRDS()`.
- The phyloseq R package is required to use the phyloseq objects.
- Sample metadata and SH reference sequences are already included in the SH-level phyloseq objects.

## References

- [MycoGAP: ITS data processing](https://github.com/WeStrainGroup/MycoGAP)
- [Fungi_Atlas: atlas construction code](https://github.com/WeStrainGroup/Fungi_Atlas)
- [HuGMycoA: R package for atlas usage](https://github.com/WeStrainGroup/HuGMycoA)
- [Atlas website](https://zheng.lab.westlake.edu.cn/Resource/Resource_GlobalFungi.htm)

## License

This dataset is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0). Commercial use is not permitted without prior written permission from the authors.