Abstract: SA-PO0726
Deep Shotgun Metagenomic Analysis of the Oral Microbiome Identifies Extrachromosomal Mobile Genetic Elements Associated with IgAN
Session Information
- Glomerular Diseases: Profiling Through Multiomics
November 08, 2025 | Location: Exhibit Hall, Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Glomerular Diseases
- 1401 Glomerular Diseases: Mechanisms, including Podocyte Biology
Authors
- Hamaguchi, Sho, Laboratory for Symbiotic Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Masuoka, Hiroaki, Laboratory for Symbiotic Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Kurokawa, Rina, Laboratory for Symbiotic Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Nihei, Yoshihito, Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Mori, Kazuaki, Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Aoki, Ryousuke, Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Suzuki, Hitoshi, Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Suzuki, Yusuke, Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Suda, Wataru, Laboratory for Symbiotic Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
Background
Exogenous antigens are implicated in the pathogenesis of IgA nephropathy (IgAN), and our recent studies showed that antigenic stimulation of the upper respiratory mucosa induces nephritogenic IgA antibodies. However, the specific antigens involved remain unclear. This study aimed to analyze the oral microbiome of IgAN patients using deep shotgun metagenomic sequencing and identify microorganisms associated with the disease pathogenesis.
Methods
Saliva samples were collected from 44 patients with IgAN, 25 with chronic tonsillitis, and 11 healthy individuals. Shotgun sequencing was performed on extracted DNA. Universal single-copy marker genes were used to analyze bacterial species and their relative abundances. Additionally, de novo assembly of short reads was conducted to generate contigs, which were classified into three categories—chromosome, plasmid, and phage—based on genomic features. Subsequently, the diversity and abundance of the contigs were compared among categories.
Results
Shotgun sequencing yielded an average of 56 million paired-end reads per sample. Bacterial species analysis showed few species consistently enriched in IgAN patients. However, contig-based analysis revealed that only plasmid contigs showed significant beta diversity differences. Among these, certain bacterial plasmids were significantly increased in IgAN patients (Fig.1). To validate this, the host strain was isolated from saliva of IgAN patients. Subsequent long-read sequencing confirmed it harbored a plasmid and comparative genome analysis showed this plasmid was significantly abundant in IgAN patients.
Conclusion
While previous studies on disease-associated microbiomes have primarily focused on the relationship between bacterial species and disease, our findings suggest that plasmids, as mobile genetic elements within the commensal microbiome, may play a critical role in the pathogenesis of IgAN.
Fig.1 Volcano plots show plasmid contigs; those significantly enriched in IgAN patients appear in the upper-right. Most enriched plasmids originate from a single bacterial genus (red dots).