Framework for microbiome-inspired functional synthetic communities
One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...
ISBB 2026 registration is now open! 🧫🧬
📍Parma, Italy (University of Parma)
📅 17-19 Sept 2026
Updated programme + confirmed speakers now online. Early reg: 5 May 2026 | Abstracts: 30 June 2026.
Website/registration: www.bifidosympo26.it
#ISBB2026 #Bifidobacterium #microbiome #microbiology
BioBloom, a method for barcoded saturation mutagenesis of an entire bacterial genome https://www.biorxiv.org/content/10.64898/2026.02.04.703572v1
Excited to share our latest publication, led by Dr. Ellie McCallum and Juan Burckhardt!
bit.ly/4kfzQaf
You can access the article for free here: authors.elsevier.com/a/1mWb4L7PXu... And more information is available on the updated preprint: www.biorxiv.org/content/10.1...
Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
High-throughput transposon mutagenesis defines the essential genome of diverse phages https://www.biorxiv.org/content/10.64898/2025.12.19.695335v1
📍Our paper is out!📍
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!
link.springer.com/article/10.1...
Characterizing phage gene essentiality with PhageMaP:
• High-throughput approach to generate genome-wide loss-of-function phage libraries.
• Interrogates gene essentiality w/insights into phage genome organization, host antiviral defense & gene function
www.cell.com/cell-host-mi...
A special thanks to Gigi Storz for making this article happen!
I particularly like the table of online resources, like a database of bacterial genome sequences and a literature search tool for protein sequences.
It has contributions from early-career scientists like @bridgesbio.bsky.social, Leah Guthrie, McKenzie Lehman, Elizabeth Kellogg, @drsamwellie.bsky.social, Andrew Pountain, and Andrew Varble.
A future perspective article on the next 10 years in microbial molecular biology and physiology is online now.
journals.asm.org/doi/10.1128/... 🧵👇
Original article: www.biorxiv.org/content/10.1...
Original code: github.com/czbiohub-sf/...
My fork (up-to-date versions of dependencies, some debugging): github.com/AnthonyShive...
Adapting the “Well-Lit” device to our workload, we operated 3 devices assembled at $150 each to do the work—2,760 total transfers—in two days. I refuse to go back to printing out an excel sheet, and I think more people should know about this.
A "Well-Lit" device
I reused “Well-Lit” tech from the pandemic, with thanks to Rafael Gómez-Sjöberg, Joana Cabrera, and @andercot.bsky.social.
We had a huge task—picking bacterial stocks from >200 96-well plates and re-arranging them—and the lab's anaerobic liquid handler was broken without the funds to repair. 🧵
Berkeley Lab released a news article describing our recent work on the genetics of the infant-specialized bifidobacteria biosciences.lbl.gov/2025/05/01/h...
All of our measurements of gene-environment interactions, both in vitro and in vivo, are available through the Fitness Browser: fit.genomics.lbl.gov, which has a lot of nice tools for parsing these large datasets.
A heart-felt thanks to the many co-authors who came together to make this happen!
Small molecules produced by bacteria influence the host and support bacterial growth.
We also screened a subset of the ordered mutant collection for small molecule production.
We identified new genes involved in aromatic lactic acid production, an important set of signals to the developing infant, and connected production of these small molecules to growth of bifidobacteria.
Host, diet, and co-colonization status in colonization experiments.
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
Biosynthetic pathways clarified in study
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
An insertion pool as multicolored bacterial cells next to an insertion density map for the genome.
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
Silhouettes of infant, mouse, chick, and bacteria.
Interested in the influence of the infant microbiome on health? Quickly interrogating non-model organisms using omic approaches?
A new publication, describing genome-scale resources in bifidobacteria, is now available online: doi.org/10.1016/j.ce...
#microbiome #microsky
Combinations of host (left: animal silhouettes), diet (middle: food pellets), and co-colonization status (right: bacterial cells) defined the colonization experiments.
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
Two biosynthetic pathways where gene assignments were clarified. Left: amino acid biosynthesis. Right: nucleotide biosynthesis.
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
Multicolored bacteria on the left represent a pool of random transposon insertion mutants. On the right, a plot of insertion density across the genome along with parameters of pool size (230,000 insertions) and average gap size between insertions.
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
