Live Microbiome Engineering for Circular Bioprocessing: A Virtual Live Lab in Metagenomics & Predictive Optimization

This 5-day hands-on workshop explores how metagenomics, microbial ecology, functional guilds, microbial interactions and predictive analytics can be integrated for microbiome engineering and circular bioprocessing.

Participants will progress from microbial-community profiling and interaction analysis to microbiome–process prediction and bioreactor modelling. The workshop concludes with a MicrobeAI Virtual Live Lab, where participants apply the complete workflow through microbial-community analysis, perturbation, virtual bioreactor simulation and predictive optimization.

To develop practical skills for connecting microbiome composition, microbial functions and community interactions with bioprocess performance, and to apply these concepts through computational analysis and virtual experimentation.

Participants will learn to:

• Analyse taxonomic and functional microbiome profiles

• Interpret microbial interactions and metabolic relationships

• Understand syntrophy and functional microbial guilds

• Explore synthetic microbial-community design

• Connect microbiome characteristics with bioprocess performance

• Apply predictive analytics to microbiome–process datasets

• Understand microbial perturbation and bioreactor modelling

• Apply virtual experimentation for microbiome optimization

📅 Day 1 – Metagenomics to Functional Microbiome Intelligence

• Introduction to microbiome engineering and microbial-community analysis

• Understanding shotgun metagenomics and microbiome sequencing data

• Microbial abundance and taxonomic profiling

• Functional profiling of genes and metabolic pathways

• Connecting microbial identity with biological function

• Core and variable microbiome concepts

• Functional redundancy and microbial ecosystem resilience

• Identification of important microbial groups and functional signatures

Hands-On Activity:

• Explore a microbiome dataset and generate microbial-abundance profiles

• Compare taxonomic and functional characteristics across samples

• Visualize major microbial-community patterns

Hands-On Tools: Python, Pandas, Matplotlib, Google Colab, MetaPhlAn/HUMAnN concepts

📅 Day 2 – Microbial Interaction Networks, Syntrophy & Synthetic Consortia

• Microbial cooperation, competition, mutualism and commensalism

• Cross-feeding and metabolite exchange between microorganisms

• Syntrophic interactions in microbial ecosystems

• Metabolic dependencies and division of labour

• Identification of potential keystone microorganisms

• Microbial interaction-network concepts

• Principles of synthetic microbial-consortium design

• Community stability, resilience and bioaugmentation strategies

Hands-On Activity:

• Construct and analyse a simplified microbial interaction network

• Identify important microbial groups and functional relationships

• Design a conceptual synthetic microbial consortium

Hands-On Tools: Python, NetworkX, Pandas, Google Colab, Microbial Interaction Dataset

📅 Day 3 – Microbiome–Bioprocess Integration & Predictive Analytics

• Introduction to microbiome-driven circular bioprocessing

• Hydrolysis, acidogenesis, acetogenesis and methanogenesis

• Functional microbial guilds in anaerobic bioprocesses

• Integration of microbiome and reactor-performance data

• VFAs, methane production and process-stability indicators

• Identification of microbiome features associated with process outcomes

• Machine-learning approaches for bioprocess prediction

• Feature importance and biological interpretation of predictive models

Hands-On Activity:

• Integrate microbiome and reactor-performance datasets

• Build a basic machine-learning model for process prediction

• Identify microbial features associated with predicted bioprocess performance

Hands-On Tools: Python, Pandas, Scikit-learn, Matplotlib, Google Colab

📅 Day 4 – Functional Microbial Guilds & Predictive Bioreactor Modelling

• Functional guilds and their roles in microbial bioprocesses

• Hydrolytic and fermentative microbial communities

• Acidogenic and acetogenic microbial functions

• Syntrophic microbial cooperation and metabolite transfer

• Methanogenic pathways and methane formation

• Microbial-community perturbation concepts

• Introduction to ADM1-based anaerobic digestion modelling

• Scenario analysis, process stability and bioaugmentation strategies

Hands-On Activity:

• Map major microbial guilds to anaerobic digestion stages and process outputs

• Compare microbial-community scenarios and predicted reactor responses

• Evaluate potential microbial or process interventions for improved performance

Hands-On Tools: Python, Pandas, Google Colab, ADM1 Modelling Concepts

📅 Day 5 – MicrobeAI Virtual Live Lab: Microbiome Engineering & Predictive Optimization

• Introduction to the MicrobeAI integrated virtual workflow

• Microbiome input assessment and community analysis

• Functional microbial-guild interpretation

• Analysis of hydrolytic, fermentative, acetogenic and methanogenic groups

• Microbial-community perturbation and scenario design

• Connecting community changes with virtual bioreactor behaviour

• Analysis of VFAs, H₂, CO₂, CH₄ and process-stability responses

• Comparison of baseline, perturbed and alternative scenarios

• Identification of microbial and process bottlenecks

• Predictive interpretation and microbiome-engineering recommendations

Hands-On Activity: MicrobeAI Integrated Virtual Live Lab

• Perform the complete microbiome analysis → guild interpretation → community perturbation → bioreactor simulation workflow

• Compare baseline and intervention scenarios and interpret predicted biological and process responses

• Develop a microbiome-engineering recommendation for improved virtual bioprocess performance

Hands-On Tools: MicrobeAI Virtual Live Lab, Functional Guild Analysis, Bioreactor Simulation Environment, Predictive Analysis

After completing the workshop, participants will be able to:

• Analyse taxonomic and functional microbiome profiles

• Interpret microbial interactions and metabolic relationships

• Identify major functional microbial guilds

• Understand syntrophy and synthetic-community design

• Connect microbial-community features with bioprocess performance

• Integrate microbiome and reactor-performance datasets

• Build basic predictive models for microbiome–process analysis

• Interpret microbial perturbation strategies

• Understand microbiome-to-bioreactor relationships

• Compare baseline and alternative microbial scenarios

• Identify potential microbial and process bottlenecks

• Apply virtual experimentation for predictive microbiome engineering

• Microbiology and Biotechnology students

• Bioinformatics and Computational Biology researchers

• Microbial Ecology researchers

• Environmental Biotechnology researchers

• Synthetic Biology researchers

• Bioprocess and Biochemical engineers

• Wastewater and Anaerobic Digestion researchers

• Bioenergy and Circular Bioeconomy researchers

• Industrial microbiologists

• Ph.D. scholars and research fellows

• Faculty members and academicians

• Industry professionals working in microbial and bioprocess technologies