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We also need funding for interdiscliplinary teams that can combine deep knowledge of site history, hydrology, biogeochemistry, informatics, modeling and more to not only do the work but also understand it in context and work out how to scale up to the wider world. 23/23

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If we want to keep pushing on these questions, we need sustained investment in long-term observation of model ecosystems. These analyses are data- and timepoint-hungry. When you're patching together stopgap funding to keep your team employed, you can't dream up a sampling plan like this. 22/23

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We have no idea where biological reality sits between these extremes. Seems like the kind of thing we ought to figure out, right? Because microbial adaptibility affects everything in a changing world: soil health and crop yields, climate, human health, you name it. 21/23

(2) Activity is stochastic, say Poisson-distributed. In a population with 38 MGEs/cell, 1% activity means almost a third of cells have at least one MGE firing. At 66 MGEs/cell, 1% activity means about half of cells have at least one MGE firing, and >14% have 2 or more. 20/23

Extreme scenarios: (1) All that activity is concentrated in a minority of cells that are freaking out and have every MGE active. Huge combinatorial potential in those cells; elsewhere, pretty chill. 19/23

We looked at activity in 3 different ways, capturing 3 different timescales. The most straightforward is expression of MGE recombinase genes. By that measure, ~1% were active at any given time. Seems like very few, until you remember: 38-66 MGEs per genome. 18/23

Figure 5B from Guo et al. 2026. Three bar plots showing MGE activity as measured by recombinase transcription; by the occurrence of identical MGEs in distinct genomic contexts; and by the prevalence of loci where metagenomic coverage of the MGE recombinase is significantly lower than that of flanking sequence, suggesting that the population includes both +MGE and -MGE variants. Measured activity levels are lowest for the transcriptomic measure, which captures the shortest timespan, and vary across MGE types, wtih phage and insertion sequences/transposons dominating activity across measures.

That is, these wildly abundant elements are poised to affect the adaptibility and activity of pathways that feed into global biogeochemical cycles. How often do they actually move around? 17/23

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We could make confident functional predictions for a subset of those, and the answer is: MGEs affect genes doing all the things. Antibiotic resistance, stress response, sure, fine, yes. But >50% of genes annotated affect "domestic" processes involved in being a cell. Notably, nutrient cycling. 16/23

Figure 4 from Guo et al. 2026. Figure highlighting MGE-affected functions of interest and their distribution across habitats, host phyla, and MGE types. Highlighted functions depicted in a cartoon cell span cellular activities including transport, signaling, antiviral defense, genome maintenance and expression, and cycling of carbon, nitrogen, and sulfur.

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But for a tiny subset of our MGEs, we could identify genes we were highly confident were MGE-affected, either because they were being moved or because they were host genes being interrupted by transposons. 15/23

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With our 2.1M hits plus a new bound on how much we're missing, we estimate that microbial genomes in the wild have an average of 38-66 MGEs each. How do they affect their hosts? Most of the time, we can't say: defining MGE boundaries is really hard, and it's even harder in metagenomes. 14/23

Just as you'd expect, short-read-only MAGs recover just 35-60% of the MGE recombinases detectable in hybrid assemblies. Just as you'd expect, it's worst for recombinases that move more and have higher nucleotide diversity. Coverage makes a real difference. 13/23

So @aroneys.bsky.social and @benjwoodcroft.bsky.social benchmarked with 6 samples sequenced with both short and long reads. Among the very high quality MAGs (>95% complete, <5% contam) recovered, they found 17 species-level clusters with members from both hybrid and short-only assemblies. 12/23

Unsurprisingly, most (>5 out of 6) of our hits were in contigs that failed to make it into MAGs. (Again: this was all a crazy idea; MGEs live to thwart us.) We figured we were probably missing even more that never made it into contigs. 11/23

And did we ever find them! 2.1M MGE recombinases, out of 131.5M predicted genes altogether. Which is to say: about 1 in 63 genes in these soil metagenomes was an MGE recombinase. That's a lot! More than 7X as common as the most common family of actual host genes detected (rpoE). 10/23

Figure 2B&C from Guo et al. 2026. Panel B shows the proportion of MGE recombinases among all predicted genes; C shows MGE recombinase counts and counts of the four most abundant KEGG gene families.

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

First question: how many MGEs in our metagenomes? With Matt's postdoc Jiarong Guo taking point, we used an excellent set of HMMs developed with high-quality genomic sequence data in the lab of the late great Peer Bork (doi.org/10.1093/nar/...) to go looking for MGE recombinases in our data. 9/23

doi.org

Abstract. Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and

emerge-db.asc.ohio-state.edu

Since 2010, the IsoGenie Consortium and its successor EMERGE have been sampling soils from Stordalen Mire, a thawing permafrost peatland in northern Sweden. The complete dataset is pretty mind-blowing. emerge-db.asc.ohio-state.edu 8/23

EMERGE-DB

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In fact there just aren't that many datasets out there where this plan would have been merely crazy rather than obviously doomed. But we had one, from a fascinating site, and between @emerge-bii.bsky.social and the VirSoil Consortium we had the team to analyze it. (Photo: Scott Saleska) 7/23

Aerial photo of the field site, showing a peatland crossed by boardwalks, pocked with small pools, and flanked by lakes. The boardwalk passes a small hut housing research instrumentation. Photo by Scott Saleska.

So yield was always a worry, and we knew we had to start with a whole lot of raw sequence. Plus, going after a mechanism of change means you have to have a lot of timepoints. You can't see change in a single snapshot. So having deep sequencing across a time series was key. 6/23

What's so crazy about that? The thing is, all the signals that people exploit to get from short-read sequence to high-quality metagenome-assembled genomes are thwarted by MGEs. Active MGEs break contigs, screw up binning, and get squashed out of consensus sequences. 5/23

Matt's idea: we should join forces with @simrouxvirus.bsky.social to survey all the mobile genetic elements in the soil microbiome of a complex natural ecosystem: how many MGEs are there? how are they distributed? how active are they? what functions do they affect? 4/23

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These mobile genetic elements constitute the "mobilome". To a first approximation, what we know about MGEs comes from isolates and relatively simple systems. Or, if people look at a complex system, they only look at one slice of the mobilome, like its impact on antimicrobial resistance. 3/23

Matt and I have been working together on and off since I was in grad school, with a common interest in how gene flow shapes microbial systems. Genes get moved around within and between host cells by viruses, integrons, transposons, and more, and when they move they can alter host genes too. 2/23

Figure 1A from Guo et al. 2026. Diagram of the ways a mobile genetic element's cargo genes and the genomic context into which it inserts can impact the host: knocking in cargo functions, knocking out host functions, and/or bringing host genes under MGE regulatory control.

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Sarah Bagby @scbagby.bsky.social · 08/05/2026

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

Screenshot of an email header with subject line "Crazy ideas"

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I feel that the local science center could have done with one more round of review before going with "Voices of the Titanic Immersive Experience" for the new exhibit.

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Sarah Bagby @scbagby.bsky.social · 03/11/2025

Microbial eukaryote folks, you've got two more weeks to apply for this TT job: apply.interfolio.com/174456. We're a supportive department with a great breadth of interests, with really sharp students, in a very livable city with the nation's best park system. Come join us!

apply.interfolio.com

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

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Ben Monreal @benmonreal.bsky.social · 09/08/2025

Fellow Clevelanders will have seen @neorsd.org's update on the end of their Shaker Dam engineering work. I have some technical-detail thoughts about this, as an engineering-adjacent STEM person and a fan of the lake and brook. Keep reading for a summary (incl. links to slides and video): 1/8

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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

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The Tennessee Holler @thetnholler.bsky.social · 18/03/2025

NEBRASKA CROWD: “TAX THE RICH! TAX THE RICH!” @USRepMikeFlood: “So your proposal to solve (the debt) is tax the rich?” NEBRASKA CROWD: *CHEERS WILDLY* (not sure this went quite as he planned 😬)

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Joshua Weitz @joshuasweitz.bsky.social · 22/02/2025

No PhD students or severely reduced # of admits -> *undergraduates* looking now to start the next phase of their career in support of research & discovery will be stuck without an option. This is far from the only place in a similar situation, whether announced publicly yet or not.

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Alexandria Ocasio-Cortez @aoc.bsky.social · 21/02/2025

Medicaid is not for sale. NASA is not for sale. The Post Office is not for sale. America is not for sale. We have an obligation to resist kings. We outnumber them. And they can be overwhelmed.

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Scott Delaney @scott-delaney.bsky.social · 21/02/2025

NIH indirects case update: Hearing ongoing now, and I'll try to live tweet some notable exchanges. Prior to more detailed arguments, Judge Kelley starts off with a few point questions to both sides: (I'm paraphrasing here)

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Mike Dickison @adzebill.bsky.social · 01/02/2025

The Internet Archive has to date downloaded 500 terabytes of US government websites, which it crawls at the end of every presidential term. The whole archive is fully searchable. This effort's housed by a donation-funded nonprofit, not a branch of the US government. blog.archive.org/2024/05/08/e...

blog.archive.org

End of Term Web Archive – Preserving the Transition of a Nation | Internet Archive Blogs

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Nicole Bedera @nbedera.bsky.social · 01/02/2025

I know that all these institutions know how to push back because when Obama directed them to enforce pre-existing Title IX law, universities said no. They flat out refused until there was a working group and specific guidelines. And even then, they *still* refused.

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Kelly Zamudio @kzutaustin.bsky.social · 16/01/2025

Everyone, plz share with your stellar undergrads! The UDE program (Undergraduate Diversity at Evolution) pairs students from diverse backgrounds with mentors to attend the Evolution meeting each year. Encourage your undergrads to apply!

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Patrick R. Secor @prsecor.bsky.social · 06/01/2025

Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 13 deadline 🧫🧪🦠#microsky

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Sarah Bagby @scbagby.bsky.social · 22/11/2024

For myself, Emacs org-mode, always. For my group, the goal is GitHub task lists in private repos; right now it's a mix of that and Slack. For wider collaborations, Basecamp and a whole lot more Google docs than I would like. The best tool is the one people are willing to use to get the job done.

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Ben Vezina @bananabenana.bsky.social · 21/11/2024

(1/6) Our new short paper on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought. #MicroSky

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Vivek Mutalik @vivekmutalik.bsky.social · 21/11/2024

#phagesky Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF Tapping the treasure trove of atypical phages www.sciencedirect.com/science/arti...

sciencedirect.com

Tapping the treasure trove of atypical phages

With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncover…

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Brooke Conti @brookeconti.bsky.social · 15/11/2024

Ohio friends: consider contacting Gov Dewine to urge him not to sign the "bathroom bill" (SB 104). Educators are in a particularly good position to made the case against this on practical grounds, though I also brought up the specter of conference/business boycotts, as in NC.

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Sarah Bagby @scbagby.bsky.social · 14/11/2024

FWIW, we've switched over to CheckM2 (reduces bias against small genomes), and our are-these-bugs-the-same step is usually dereplication with dRep or galah. But I'd agree with the above---"good enough" depends on what you need it for; there's lots to learn even from fragmented assemblies.