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Anthony Shiver

@anthonyshiver.bsky.social
95 followers 276 following 20 posts

Researcher in the life sciences. Expertise in systems biology, biophysics, applied math.

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Anthony Shiver @anthonyshiver.bsky.social · 17/07/2026
The labs of KC Huang and Justin Sonnenburg at Stanford are working on an exciting and impactful project related to infant probiotics and are hiring a Life Science Research Professional to be part of that team. Take a look at the posting if you're interested. Please share/apply
careersearch.stanford.edu
Life Science Research Professional 2
Applying a comprehensive understanding for the theories and methods of a life science discipline, perform work directly involved in research projects, interpreting results and participation in experim...
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Reposted by Anthony Shiver
Typas Lab @typaslab.bsky.social · 12/03/2026
Featuring leading voices in microbiome research, with sessions on multi-omics, genetic tools, ecological context functions, and new model species. Focusing on research that moves from descriptive to molecular understanding and functional discoveries.
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Indra Roux @indraroux.bsky.social · 10/03/2026
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...
Framework for microbiome-inspired functional synthetic communities
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Hall Lab @halllab.bsky.social · 16/02/2026
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
bifidosympo26.it
ISBB 2026 – The 2nd International Symposium on Bifidobacterial Biology
The 2nd International Symposium on Bifidobacterial Biology (ISBB) – Parma, Italy – September 18–19, 2026.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 06/02/2026
BioBloom, a method for barcoded saturation mutagenesis of an entire bacterial genome www.biorxiv.org/content/10.64898/20…
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Carolina Tropini (TropiniLab@UBC) @ctropini.bsky.social · 28/01/2026
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...
bit.ly
Glowing bacterial sensors detect gut illness in mice before symptoms emerge
UBC researchers have engineered gut bacteria that dim their fluorescent glow in the presence of illness.
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Reposted by Anthony Shiver
Ran Blekhman @blekhman.bsky.social · 18/01/2026
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...
doi.org
Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications
Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 20/12/2025
High-throughput transposon mutagenesis defines the essential genome of diverse phages www.biorxiv.org/content/10.64898/20…
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Yoav Gilad @ygilad.bsky.social · 15/12/2025
academicjobs.uchicago.edu/positions/16...
academicjobs.uchicago.edu
Academic Jobs | The University of Chicago
The University of Chicago is a private, nondenominational, culturally rich and ethnically diverse coeducational research university located in Hyde Park, Chicago.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/12/2025
📍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...
link.springer.com
Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites - Analytical and Bioanalytical Chemistry
The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 23/07/2025
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...
cell.com
Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts
Chen et al. report PhageMaP, a high-throughput approach to generate and characterize genome-wide loss-of-function phage libraries. PhageMaP systematically interrogates conditional gene essentiality, p...
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Anthony Shiver @anthonyshiver.bsky.social · 02/07/2025
A special thanks to Gigi Storz for making this article happen!
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Anthony Shiver @anthonyshiver.bsky.social · 02/07/2025
I particularly like the table of online resources, like a database of bacterial genome sequences and a literature search tool for protein sequences.
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Anthony Shiver @anthonyshiver.bsky.social · 02/07/2025
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.
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Anthony Shiver @anthonyshiver.bsky.social · 02/07/2025
A future perspective article on the next 10 years in microbial molecular biology and physiology is online now. journals.asm.org/doi/10.1128/... 🧵👇
journals.asm.org
An exciting future for microbial molecular biology and physiology | mBio
The first two bacterial genomes were sequenced nearly 30 years ago (1, 2). The cost of one of those sequences, that of Haemophilus influenzae, was over 1,000,000 U.S. dollars and took multiple years (...
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Anthony Shiver @anthonyshiver.bsky.social · 18/06/2025
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...
biorxiv.org
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Anthony Shiver @anthonyshiver.bsky.social · 18/06/2025
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.
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Anthony Shiver @anthonyshiver.bsky.social · 18/06/2025
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. 🧵
A "Well-Lit" device
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Anthony Shiver @anthonyshiver.bsky.social · 11/06/2025
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...
biosciences.lbl.gov
Barcoded Transposons Help Mine the Secrets of the Human Gut - Biosciences Area
Researchers have demonstrated a high-impact approach for dissecting complex host-microbe interactions in the infant microbiome, revealing new possibilities for studying the broader microbial world.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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!
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
Small molecules produced by bacteria influence the host and support bacterial growth.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
Host, diet, and co-colonization status in colonization experiments.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
Biosynthetic pathways clarified in study
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
An insertion pool as multicolored bacterial cells next to an insertion density map for the genome.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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?
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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
Silhouettes of infant, mouse, chick, and bacteria.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
Combinations of host (left: animal silhouettes), diet (middle: food pellets), and co-colonization status (right: bacterial cells) defined the colonization experiments.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
Two biosynthetic pathways where gene assignments were clarified. Left: amino acid biosynthesis. Right: nucleotide biosynthesis.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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.
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.
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Anthony Shiver @anthonyshiver.bsky.social · 13/03/2025
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?
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