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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

We further applied our framework to published datasets and found candidate transfer events in longitudinal human metagenomes. Huge thanks to my co-authors and to the Sonnenburg and Huang Labs.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Diet and community ecology gated both steps. Pectin fibers were correlated with costly prophage activation and donor lysis, and a diversity-generating retroelement diversified the phage's receptor-binding protein in correlation with transfer, consistent with host-range expansion.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Counterintuitively, more donors ≠ more transfers. A prophage from the invader P. vulgatus repeatedly transferred into resident Bacteroides intestinalis in all mice on a high-fiber diet, even when the donor was rare, but failed to transfer on a low-fiber diet, where the donor was abundant.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

We tested it in a defined gut community in mice invaded by Phocaeicola vulgatus. We found that activation is common, but successful transfer between species is rare.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

The beauty of the approach is that we don't have to select for transfer to see it. No antibiotic selection, no engineered markers. No expectations of what will transfer. We read the junctions directly, so we observe gene flow as ecology permits, not as we decide.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Our trick: read the junctions. Look for evidence of circular DNA fragments, define their boundaries, and then look for evidence of integration in other bacterial genomes. This enables tracking over time, from activation to integration. Tracking gene movement in real time!

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Horizontal gene transfer is the primary mechanism of adaptive bacterial evolution. But most methods give a snapshot. They can't distinguish an element moving now from ancestral transfer or show the order of events, unlike Hi-C, long-read, or single-cell methods, which can, but at steep cost.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026

Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵

doi.org

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Reposted by Saria McKeithen-Mead, PhD

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 Saria McKeithen-Mead, PhD

Sarafan ChEM-H @stanford-chemh.bsky.social · 10/09/2025

Next Generation Faculty Symposium SESSION 3: Immunology and Cell-Cell Interactions More on the speakers: www.berkeleystanfordnextgensymposium.com/speakersalumni

Saria McKeithen-Mead, PhD, is a Postdoctoral Research Fellow at Stanford University (sariam@stanford.edu); Juan Inclan Rico, PhD,
is a Postdoctoral Research Fellow at the University of Pennsylvania (jmirico.k16@gmail.com); Christian Dzuvor, PhD, is a Postdoctoral Research Fellow at Harvard University (christian_dzuvor@hsph.harvard.edu)

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 03/09/2025

Honored to be selected to speak at this symposium. Please tune in on Sept. 10th if you’re interested in hearing what I’ve learned while mapping HGT in the gut microbiome! www.berkeleystanfordnextgensymposium.com

berkeleystanfordnextgensymposium.com

Stanford.Berkeley.UCSF Next Generation Faculty Symposium

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Reposted by Saria McKeithen-Mead, PhD

George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 28/02/2025

JB Editor's Choice: McKeithen-Mead, Grossman et al. explore the mechanism whereby ICEBs1, an integrative and conjugative element (ICE) of B. subtilis, inhibits the host SOS response and RecA function. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology

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Reposted by Saria McKeithen-Mead, PhD

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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Saria McKeithen-Mead, PhD @sciria.bsky.social · 26/01/2025

If you're excited about MGEs and the transference of this type of perspective to the gut microbiome, I hope to update everyone soon on some work I've been doing regarding HGT in the mammalian gut. Here's a snapshot of things to come.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 26/01/2025

And 2) show that the timing of integration in transconjugants is critically important and links two essential functions of the ICE lifecycle: replication and integration.

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 26/01/2025

In the paper, we delve a bit into why MGEs may have evolved these functions. If interested in more work like this, please check out some of my other publications where 1) we characterize how an integrative and conjugative element finds its integration site: doi.org/10.1093/nar/...

doi.org

Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer

Abstract. Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 26/01/2025

Though not fully elucidated here, this seems to differ from the mechanism utilized by PsiB encoded by F-plasmid as it is active in donors and is not believed to interact directly with RecA. Alam Heredia has done excellent follow-up characterizing the mechanism of action here: doi.org/10.1101/2024...

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 26/01/2025

We show that ICEBs1 in Bacillus subtilis encodes genes that inhibit RecA filament formation. This prevents activation of co-resident prophages following a DNA damage event and inhibits ICEBs1-mediated activation of the SOS response during rolling-circle replication.

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