Bat Shotgun Metagenomic Flow-work

The data analysis of shotgun metagenomic data from bats fecal samples was so complex that there are 4 different parts of it!
See lab journals and some supplementary files in directories:

• 📁 01_QC_n_tax_id - quality control & taxonomic identification step
• 📁 02_Diff_analysis - microbial community analysis (relative abundance, differential abundance analysis, α & β diversities assessment)
• 📁 03_Metagenomes - assembling metagenomes and analyzing them from quality control to the detailed functional profiling
• 📁 04_Densoviruses - analyzing densoviruses (genome annotation, ANI, phylogenomics)

Pipeline:

Figure 1. Pipeline overview.

Citation

The paper has been published on June 20, 2025 in International Journal of Molecular Sciences

Popov, I.V.; Manakhov, A.D.; Gorobets, V.E.; Diakova, K.B.; Lukbanova, E.A.; Malinovkin, A.V.; Venema, K.; Ermakov, A.M.; Popov, I.V. Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities. Int. J. Mol. Sci. 2025, 26, 5941. https://doi.org/10.3390/ijms26135941