Mike Lee

Contrasting Responses of Oceanic and Coastal Synechococcus to Iron Limitation and Warming Interactions Oceanic Synechococcus respond to the interactive effects of iron (Fe) limitation and ocean warming by regulating photosynthesis, nutrient metabolism, and heat shock gene expression, while a coastal s...

Happy to share that the 1st chapter of my PhD on how coastal & oceanic Synechococcus deal with iron × warming interactions is now published in Environmental Microbiology Reports!
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Home Resources for the STAMPS 2025 course at the MBL in Woods Hole, MA, USA - mblstamps/stamps2025

Here at STAMPS 2025 we will be using bluesky and specifically #stamps2025 to social-media-ify our teaching on microbiome data analysis techniques! cc @amydwillis.bsky.social

We do not choose our families but we can choose people who push us A thought in structures that helps us become who we want to become

New blog post I wrote on 'how we do not choose our families but we can choose people who push us', and ONLY for my scientist colleagues who are looking for things to procrastinate with style (by requiring them to be longer than a post on BlueSky) :p

merenlab.org/2025/07/16/s...

2015: US brokers deal with Iran to lessen sanctions on them if they start reducing their efforts on developing nuclear weapons 2015-2018: the international nuclear watchdog agency regularly investigates and reports that Iran is adhering to the deal (reducing uranium quantities, reducing enrichment of uranium, reducing centrifuges, allowing surprise inspections by the watchdog group) 2018: Trump reneges on the US-brokered arrangement and reimposes sanctions on Iran 2021-: Iran is enriching uranium beyond the previously agreed upon limit and is now restricting access of the international nuclear watchdog agency to do inspections 2025: Trump has the US bomb Iranian nuclear facilities, announcing the attack on his social media website while adding “NOW IS THE TIME FOR PEACE!”

Tomorrow at 12:45-1:30 in the EEB Track Hub in the poster hall #ASMmicrobe I am talking about microbial diversity including Asgard archaea, and an expanded tree of life from marine sediments.

Awesome! 🦠

I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

This is an amazing group to work with! 🦠

Base-modified nucleotides mediate immune signaling in bacteria Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of othe...

Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...

For people with hmmalign experience. When running post-alignment trim (i.e. clipkit/trimal), how do you handle insertion gap added by hmmalign?

AFAIK many trimmers don't count '.' as AA gap character - and manually adjusting '.' to recognized gap character can significantly alter results 💻🧬🦠🧫

Pseudomonas aeruginosa clinical isolates can encode plastic-degrading enzymes that allow survival on plastic and augment biofilm formation Howard et al. demonstrate that clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa can encode functional plastic-degrading enzymes and that these enzymes can influence bacterial bio...

Pseudomonas aeruginosa clinical isolates can encode plastic-degrading enzymes that allow survival on plastic and augment biofilm formation

This strain encodes a polyesterase that degrades polycaprolactone, and it can use it as a sole carbon source:

www.cell.com/cell-reports...

#MicroSky

Strain-level metagenomic profiling using pangenome graphs with PanTax Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting...

Strain-level metagenomic profiling using pangenome graphs with PanTax

#MicroSky

#MicroSky

This is important work for the exciting next stage of metagenomics #MicroSky

Super cool! #MicroSky

Me being cuddled by our two cats, one in my lap, the other sprawled out next to me

Happy #Caturday 😺

🧪This mesmerizing green and purple cloud happens inside our gastrointestinal tract everyday! Swimming bacteria use chemotaxis to rapidly find nutrients. Takes only a few seconds.

WAY faster than phagocytes (~20 min). Bacteria will literally swim circles around them 🦠💨

#MicroSky #IDSky #GastroSky

A chemical radar allows bacteria to detect and kill predators Pseudomonas syringae can detect and kill microbial predators via a chemical radar (Cra), which also allows the bacterium to infect plants despite predation pressure.

Biology is so cool

- P. syringae produces syringafactin, which is deacylated by amoebae

- Deacylated syringafactin binds to CraR, triggering amoebicidal pyrofactin synthesis

- Cra allows P. syringae to infect Arabidopsis thaliana in the presence of amoebae

#MicroSky

The first #anvio workshop at our brand new @hifmb.de building in Oldenburg has just started with around 50 individuals who represent a wide range of locations, scientific interests and career levels :')

Very excited for this week and thankful for Iva Veseli and Florian Trigodet!

One cannot simply *stop developing* SPAdes :)

It’s a cliché to say it—and no two historical scenarios offer a perfectly compelling analogy—but what each American is doing now is what they’d be doing were they a German living in Germany and were it 1936-38

There’s no more doubt about who the appeasers or the bad guys are—they’re in the open now

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data www.biorxiv.org/content/10.1... #jcampubs

70% of an E. coli cell is water. The other 30% of mass is *mostly* proteins.

But what's the most abundant protein in the cell?

To my surprise, it's Lpp, a protein that anchors the outer membrane to the peptidoglycan layer. There are ~700,000 of them in each cell.

New blog🔻

Are you affected by the Trump administration’s pause on health communications, science meetings, and reviews? Have you been affected by the Trump administration’s pause on communications, science meetings, and reviews? @statnews would like to hear from you.

Is the communications pause that's been imposed on the US government's health agencies affecting you? @statnews.com would love to hear about it. Please let us know. www.statnews.com/2025/01/25/t...

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Happy to announce EvoQuant LLC is launching consulting services (boinformatics and more) starting Jan 1, 2025

See our new, preliminary, website at: evoquantbio.com

#Bioinformatics #SoftwareDevelopment #DataScience #Python #R #Nextflow #AWS #GCP

Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins Abstract. Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and publ

Out now in @genomebiolevol.bsky.social! With colleagues at NBACC and PNNL, we helped answer a long-standing question about how widely-divergent cyanobacteria produce saxitoxin, a major cause of paralytic shellfish poisoning. We assembled a new genome for a producer of saxitoxin and ...

Can’t be less, ha. Welcome!