Enabling mangrove restoration by AI-tailored microbiome fortification

Overview

This short collaboration (2023, funded under the KAUST Center for Living Innovation programme) developed AI-tailored microbiome work in support of coastal mangrove restoration in Saudi Arabia. The project ran as a sister activity to the BORG group's larger desert-microbiome programme with the NTGC, applying analogous metagenomic and functional-annotation pipelines to mangrove sediment and root-associated communities rather than to arid-soil systems. Heribert Hirt (DARWIN21, KAUST) was the Principal Investigator, with Hoehndorf as Co-Investigator providing the computational microbiome analysis.

Because the engagement was brief and exploratory, no peer-reviewed publications resulted directly from this award; the bioinformatic methods developed and refined during the collaboration (in particular DeepGOMeta-based functional annotation of environmental metagenomes) have since been redeployed on related mangrove and coastal sediment datasets in subsequent projects.

Period: 2023–2023

Funding

• KAUST Climate and Livability Initiative (CoI) — USD 25,000

Team

• Heribert Hirt — PI (KAUST (Center for Desert Agriculture))
• Robert Hoehndorf — CoI (KAUST (Professor of Computer Science))

Software

• DeepGOMeta — DeepGO trained specifically for metagenomic communities; predicts functional roles of proteins recovered from environmental samples and links them to biogeochemical processes. https://github.com/bio-ontology-research-group/deepgometa

Topics: Genomics, Microbial communities, Neuro-symbolic AI