Anthony Shiver
@anthonyshiver.bsky.social
Researcher in the life sciences. Expertise in systems biology, biophysics, applied math.
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. 🧵
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. 🧵
June 18, 2025 at 8:19 PM
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. 🧵
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. 🧵
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.
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.
March 13, 2025 at 10:35 PM
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.
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.
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.
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.
March 13, 2025 at 10:35 PM
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.
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.
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.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
March 13, 2025 at 10:35 PM
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.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
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.
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.
March 13, 2025 at 10:35 PM
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.
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.
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
A new publication, describing genome-scale resources in bifidobacteria, is now available online: doi.org/10.1016/j.ce...
#microbiome #microsky
March 13, 2025 at 10:35 PM
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
A new publication, describing genome-scale resources in bifidobacteria, is now available online: doi.org/10.1016/j.ce...
#microbiome #microsky
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.
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.
March 13, 2025 at 10:04 PM
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.
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.
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.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
March 13, 2025 at 10:04 PM
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.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
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.
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.
March 13, 2025 at 10:04 PM
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.
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?
How did we do this?
March 13, 2025 at 10:04 PM
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?
How did we do this?