Mike Lee

High-resolution sampling of microbial biomolecules provides a window into how microbes rapidly respond to environmental variability. This dataset offers metagenomes, metatranscriptomes, and high-throughput transfer RNA transcripts, as well as rich biogeochemical data and high-quality MAGs.

A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts - Scientific Data Scientific Data - A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts

I am happy to share that our data descriptor on the Hawaiʻi Diel Sampling is now published! 🌊🦠https://www.nature.com/articles/s41597-025-06166-3

Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.

Schedule | Ocean Sciences Meeting 2026 The #OSM26 schedule at a glance, available session formats, keynote and plenary speakers, special events, and more will be highlighted here. Please check back regularly for more details and updates.

Check out this line-up of plenary speakers for the Ocean Sciences Meeting (OSM) taking place in Scotland in February of 2026!

Britney Schmidt in particular is one of our favorites 🚀

www.agu.org/ocean-scienc...

#MicroSky

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

QUESTION: anyone knows of a published example of a gene/operon which is toxic in Pseudomonas aeruginosa if in high copy plasmids, but ok in low copy? Got plenty of examples of my own for E. coli (esp of membrane protein genes), but struggling to find for Pae… Cheers!

#microsky #synbio

Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome” - NCBI Insights NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowl...

To maybe spare someone else the headache I just went through trying to figure out why I couldn’t find any NCBI assembly tables letting me parse by “representative” genomes, they purged the term last year and solely use “reference” now. #MicroSky

A Population-Based Study of Measles, Mumps, and Rubella Vaccination and Autism | NEJM It has been suggested that vaccination against measles, mumps, and rubella (MMR) is a cause of autism. We conducted a retrospective cohort study of all children born in Denmark from January 1991 th...

Many studies have shown that there is no relationship between MMR vaccine and the development of autism. Here are two of the best.

This one followed every single child born in Denmark from 1991 through 1998 (n=537,303). There was no association.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution An integrated analysis framework shows a strong association between within-population genetic variation and protein structure.

It's like you can see the interaction between ecology and evolution happening right in front of you. 💚🦠🧬
#mevosky #bluesci

www.science.org/doi/10.1126/...

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