High-throughput Detection of AD/KS Domains with OpenTrons Flex

Mon, 01 Jan 0001 00:00:00 +0000

Project Description

PKS and NRPS gene clusters are responsible for producing many clinically and industrially important natural products. However, full genome sequencing of large strain collections remains costly and time-consuming.

Targeted detection of AD and KS domains provides a powerful intermediate strategy to:

Rapidly assess biosynthetic potential
Prioritize strains for whole-genome sequencing
Enable scalable, cost-effective bioprospecting pipelines

Automation is essential to make this approach feasible at scale.

Project Goals

This project aims to:

Develop a fully automated OpenTrons Flex protocol for AD/KS domain amplification
Implement combinatorial PCR strategies for broad domain coverage
Integrate automated wet-lab workflows with long-read sequencing (ONT PromethION)
Enable high-throughput screening of microbial strain libraries
Establish a reproducible, modular pipeline for biosynthetic domain discovery

Acknowledgements

This project conducted in collaboration with Universitas Teknologi Sumbawa (UTS), Synbio.id and Integrated Genome Factory internship program.

Whole Genome Sequencing, Assembly, and Annotation of Rare Actinomycetota Strains

Mon, 01 Jan 0001 00:00:00 +0000

Project Description

This project focuses on the whole genome sequencing, assembly, and functional annotation of rare Actinomycetota strains collected from diverse Indonesian environments. Actinomycetota are renowned for their exceptional capacity to produce bioactive secondary metabolites, including antibiotics, anticancer compounds, and industrially relevant enzymes—yet many rare lineages remain genomically unexplored.

Through the generation of high-quality, near-complete genome assemblies, this project aims to unlock the biosynthetic potential of underrepresented Actinomycetota and establish a foundational genomic resource for natural product discovery, comparative genomics, and synthetic biology applications.

Project Goals

The main objectives of this project are to:

Generate high-contiguity whole-genome assemblies of rare Actinomycetota strains
Perform comprehensive genome annotation, including biosynthetic gene cluster (BGC) detection
Enable genome-guided bioprospecting of secondary metabolites
Build a curated genomic dataset to support downstream comparative and functional analyses
Strengthen national capacity in long-read microbial genomics

Acknowledgements

This project is funded by the Riset Inovasi Indonesia Maju (RIIM) – Ekspedisi Grant, in collaboration with Universitas Teknologi Sumbawa (UTS), Synbio.id, and Integrated Genome Factory.

High-throughput Detection of AD/KS Domains with OpenTrons Flex | BEAMS Lab

High-throughput Detection of AD/KS Domains with OpenTrons Flex

Project Description

Project Goals

Acknowledgements

Whole Genome Sequencing, Assembly, and Annotation of Rare Actinomycetota Strains

Project Description

Project Goals

Acknowledgements