Next-Generation Synthetic Microbiomics: From AI-Driven Design to Clinical Application

Dear Colleagues,

The human microbiome and environmental microbial communities play pivotal roles in health, disease, and ecosystem stability. While traditional microbiome research has focused on descriptive analysis, the field of synthetic biology offers the tools to move from correlation to causation through the construction of defined synthetic communities. However, engineering stable, functional, and predictable microbial consortia remains a significant challenge. The integration of high-throughput automation, microfluidic technologies, and advanced artificial intelligence is now revolutionizing our ability to design and optimize these complex systems. We are pleased to invite you to contribute to this Special Issue, which seeks to bridge the gap between computational design, automated testing, and clinical application.

This Special Issue aims to provide a comprehensive overview of the current state of "Synthetic Microbiomics." It fits squarely within the scope of the journal by focusing on the engineering principles governing microbial interactions and community dynamics. We aim to publish a collection of articles that demonstrate novel strategies for manipulating microbiome structure and function. By combining engineering approaches with biological discovery, this issue will explore how synthetic consortia can be designed to perform complex tasks that are difficult or impossible for monocultures.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

• Design and Assessment: Strategies for the bottom-up assembly of synthetic microbial communities, including the evaluation of community structure, stability, and metabolic cross-feeding.
• High-Throughput Automation: Utilization of droplet microfluidics and automated platforms for the rapid assembly, phenotypic screening, and functional testing of synthetic consortia.
• AI and Computational Biology: Application of artificial intelligence, particularly protein language models (PLMs) and deep learning, for mining novel functional elements and predicting community dynamics.
• Clinical Applications: Development of engineered probiotics and live biotherapeutic products (LBPs), with a specific emphasis on next-generation Fecal Microbiota Transplantation (FMT) and modulation of the gut microbiome.

We look forward to hearing from you.

Dr. Haokui Zhou
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the Special Issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. SynBio is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.