A blog about fermentation, engineering, and cell-ag. We run wild experiments on microbes and try to eat them, all with the help of computers and math.
Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications
Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth or provide nutrients, or pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and can assemble stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. This review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.
SLIME MOLD TIME MOLD on Twitter / X
we'd love to make this happen! happy to discuss and brainstorm any time :) we even wrote a little bit about it in the past, check out this old post:https://t.co/krgMioxZtb— SLIME MOLD TIME MOLD (@mold_time) September 15, 2025
Reinventing the wheel: milk, microbes, and the fight for real cheese
"Reinventing the Wheel is equal parts popular science, history, and muckraking. Over the past hundred and fifty years, dairy farming and cheesemaking have been transformed, and this book explores what has been lost along the way. Today, using cutting-edge technologies like high-throughput DNA sequencing, scientists are beginning to understand the techniques of our great-grandparents. The authors describe how geneticists are helping conservationists rescue rare dairy cow breeds on the brink of extinction, microbiologists are teaching cheesemakers to nurture the naturally occurring microbes in their raw milk rather than destroying them, and communities of cheesemakers are producing "real" cheeses that reunite farming and flavor, rewarding diversity and sustainability at every level."--Provided by publisher.
Cognition without brains? Learning and memory in microorganisms
Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learning-like behaviours. However, a factor limiting progress in this field is the lack of shared, microbe-specific frameworks that allow microbiologists to easily compare discoveries with concepts developed in cognitive sciences. In this review, we aim to bridge this gap by providing a conceptual overview of the definitional requirements for memory and learning to classify microbial behaviours and capabilities. Additionally, we identify and address problems that cause conceptual ambiguity in the microbial cognition literature, thereby facilitating more productive debates on the topic. Finally, we provide a novel perspective on how microbes might ‘learn’ from each other.
Let’s Become Fungal!
Inspired by conversations with: Francisca Álvarez Sánchez, Carolina Caycedo, Annalee Davis, Maya Errázuriz, Juan Ferrer, Lilian Fraiji, Giuliana Furci, Sofía Gallisá Muriente, Yina Jiménez Suriel, Patricia Kaishian, Mirla Klijn and Olaf Boswijk, Lola Malavasi and Daniela Morales Lisac, Martina Manterola and Carmen Serra, Camila Marambio, Mariana Martínez Balvanera, Claudia Martínez Garay, Lina Meija and Luciana Fleischman, Tomaz Morgado Françozo and Marília Carneiro Brandão, Marion Neumann, Maria Alice Neves, Tara Rodríguez Besosa, Raquel Rosenberg, Juli Simon, Ela Spalding, Gianine Tabja, Gabriela Flores del Pozo and Lucia Monge, Fer Walüng, Tatyana Zambrano
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.
b.next: rebuilding biology for engineering
TILOS HOT-AI Workshop: The Architecture of Intelligence with John Doyle
A diverse and distinct microbiome inside living trees
Nature - Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood...
Use of generative artificial intelligence | ÉPICBiodiversity
An alternative version of this document was initially drafted by Timothée Poisot with input from members of the Viral Emergence Research Initiative, and further revised based on a conversation with group members. For this reason, it is excluded from the CC BY-NC-SA license under which the rest of the website is published, and may not be reproduced without permission.
AI creates first synthetic viruses
Genomic language model has huge potential to redesign organisms such as bacteria
As promised, here's a takehome from my workshop with @tessa.germnetwork.com and @anna.germnetwork.com at @atmosphereconf.org
Dive into research resources
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