This database provides query and download capabilities for individual genomes. To selectively retrieve or download specific genomic data, please utilize the Data Viewer for Genomes interface. Additionally, we offer bulk download options including all genome files and pre-compiled Kraken2 database files. These Kraken2 database files can be directly downloaded for analyzing giant panda gut microbiome data, supporting various analytical approaches such as metagenomics, meta-transcriptomics, and microbial single-cell RNA sequencing. More about the update log for Pbac database could be found here.

1. Pbac v2 database source download

Pbac v2 constitutes a substantial improvement over v1, achieved through combined culturomics and PacBio HiFi sequencing. This methodological integration significantly increased the recovery of high-quality (≥90% complete, <5% contamination) and near-complete genomes, establishing an enhanced genomic collection.

Key advancements include:

(1) ​Expanded species representation: 466 species-level genomes (84% increase from v1).

(2) Novel taxa identification: 213 previously undocumented species and five new genus.

​(3) Validation metrics: Core genomes show 92.7% metagenomic and 91.9% metatranscriptomic mapping efficiency.

This resource advances research on bacterial adaptations in bamboo-digesting ecosystems and supports conservation genomics for endangered bears.

* High-quality reference genomes (Completeness ≥80%, Contamination ≤5%) were selected, and rRNA/tRNA sequences were masked. This reference genome sequence set was used for microbial scRNA-Seq data analysis in our study. A total number of 339 genomes were selected from the 466 genomes in the Pbac v2 database.

2. Pbac V1 database

Pbac v1 (Panda Gut Microbiome Database): A Curated Resource for Giant Panda Gut Microbial Genomes​
As the inaugural version of our database, Pbac v1 provides a comprehensive collection of curated giant panda gut metagenome-assembled genomes (MAGs). We generated these MAGs through an integrated approach combining Illumina and Nanopore sequencing technologies, resulting in 2,684 medium- to high-quality MAGs that satisfied the following criteria: ≥50% completeness, <10% contamination, and ≥500 kb length. Notably, 960 MAGs exceeded stringent high-quality benchmarks (≥90% completeness with <5% contamination). Cluster analysis at 99% average nucleotide identity (ANI) identified 1,193 non-redundant MAGs, including 354 high-quality representatives. Taxonomic annotation revealed: (1) 672 MAGs mapped to 219 established bacterial species; (2) 521 MAGs forming 228 novel phylogenetic clusters, warranting new genus or species designations. 
 

Please cite the following publications if you use Pbac database:

(1) Deng, F., Wang, C., Li, D. et al. (2023)The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo. Microbiome 11, 180. https://doi.org/10.1186/s40168-023-01603-0

(2) Deng, F., Han, Y., Huang, Y., et al. (2024). A comprehensive analysis of antibiotic resistance genes in the giant panda gut. iMeta 3, e171. https://doi.org/10.1002/imt2.171

(3) Deng, F., Han, Y., Li, M., et al. (2025). HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly. iMetaOmics 2 (3), e70041.  https://doi.org/10.1002/imo2.70041