Network-Based Exploration of Candidate Biodegradable Plastic-Degrading Bacteria Using Metagenomic and Functional Gene Data from Enrichment Cultures

Biodegradable plastics have been proposed as an alternative to mitigate the environmental persistence of conventional petroleum-based plastics, however, securing bacterial resources capable of degradation is essential to achieve stable biodegradation under treatment conditions such as composting. Although bacteria that can degrade biodegradable plastics have been reported, there remains a need to obtain degrader resources applicable across different plastic types and diverse environmental conditions. Conventional approaches based on strain isolation followed by degradation activity tests are labor-intensive and time-consuming, which limits efficient screening and isolation of target degraders. To address these limitations, we introduced a network-based analytical framework that leverages metagenomic information from enrichment cultures and functional gene information to identify candidate bacteria contributing to biodegradable plastic degradation. Two composts were used as inocula, and enrichment cultures were conducted for 100 days at mesophilic (35 °C) and thermophilic (58 °C) conditions using Polylactic acid (PLA) or Polybutylene adipate terephthalate (PBAT) as the sole carbon source. Bacterial community structure was characterized across 20 enrichment cultures using 16S rRNA gene amplicon sequencing. To evaluate functional potential related to biodegradable plastic degradation, predicted functional gene profiles were inferred at the KEGG Orthology (KO) level using PICRUSt2. Co-occurrence network analysis was then performed to link changes in genus-level dominance with shifts in predicted functional gene abundances and to explore candidate bacterial resources with high degradation potential for PLA and PBAT. As a result, genera whose dominance increased over time and showed positive associations with predicted secondary-metabolism–related functional genes (K10804, K01432, K15739, and K00467)—processes involved in polymer breakdown to lower-molecular-weight compounds and/or transformation and accumulation of intermediates such as lactate—were highlighted as candidate degraders, including Pseudoxanthomonas, Thermoflavifilum, and Thermopolyspora. This study provides microbiological insights for inoculum design and process optimization for composting-based biodegradation, and demonstrates that a network analysis approach integrating community and predicted functional gene information can be applied to explore diverse microbial resources in future studies.

 

Keywords

Biodegradable plastics, Bacterial resource, Metagenome, Functional genes, Network analysis

 

Acknowledgement

This research was supported by Particulate Matter Management Specialized Graduate Program through the Korea Environmental Industry & Technology Institute (KEITI) funded by the Ministry of Environment (MOE), and by the Ministry of Trade, Industry and Energy (MOTIE) (RS-2025-07902968).