Mike Lee
@astrobiomike.org
Former musician-wannabe. Current micro. ecologist/bioinformatician PhD. Deep biosphere/oceans (USC) -> Astrobiology/Space Bio (NASA) 👽 -> National Biodefense (DHS) Bioinf-beginners go to http://microbialomics.org | For phylogenomics, GToTree :) | he/him
🎉 We are honoured and excited to share that our team has been named a finalist in the the Australian Research Data Commons Eureka Prize for Excellence in #DataPlatforms! 🎉 Check out our video at: www.youtube.com/watch?v=1nzt... @ardc.edu.au @eurekaprizes.bsky.social #EurekaPrizes
Genome Taxonomy Database – Finalist, 2026 Eureka Prize for Excellence in Data Platforms
YouTube video by Australian Museum
youtube.com
Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/
Excited to share our review relating to the giant extrachromosomal elements (ECEs) We cover: why long-read metagenomics enables their discovery, genomic comparisons across recently characterized examples, and limitations of current classification tools. www.cell.com/trends/genet...
Giants within: a new class of microbial mobile elements
Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field ha...
cell.com
Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...
Treemble: a graphical tool to generate Newick strings from phylogenetic tree images
AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
doi.org
Notice for users submitting MAGs to INSDC Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen... What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
Genome
Download a genome data package including genome, transcript and protein sequence, annotation and a data report
ncbi.nlm.nih.gov
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵
We've got a new paper about the consequences of microfaunal predation for bacterial community structure and function. 🧪🦠 #microbiome #MicroSky www.nature.com/articles/s41...
Predator-driven microbial feedback loops promote plant health - Nature Communications
Top-down trophic interactions are critical drivers of microbiome dynamics but are difficult to predict. Here, the authors demonstrate that nematode-driven shifts in microbiomes enhance pathogen suppre...
nature.com
In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...
AI is starting to look like pseudoscience
Not all of it, but some scientists are too eager to believe their own hype
stevensalzberg.substack.com
Interesting work on epigenetics and aging www.cell.com/cell/fulltex...
Loss of epigenetic information as a cause of mammalian aging
Aging is characterized by changes in cellular identity and function over time. This process is driven by changes in chromatin factor localization during DNA break repair, which alters the epigenome an...
cell.com
Myloasm - long-read metagenomics assembler 🦠 Open preprint: www.biorxiv.org/content/10.1... Publication: www.nature.com/articles/s41... GitHub: github.com/bluenote-157...
GitHub - bluenote-1577/myloasm: A new high-resolution long-read metagenome assembler for even noisy reads
A new high-resolution long-read metagenome assembler for even noisy reads - bluenote-1577/myloasm
github.com
How much protein diversity can Life on Earth actually generate? With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks. 📚Paper: www.nature.com/articles/s41... 💻Code: github.com/bbuchfink/di...
Absolutely astounding paper. Massive 36,000 AA proteins facilitate cell-cell interactions in this bacterial symbiosis. Really beautiful scientific work.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5mo agoInterspecies transfer of giant virulence-factor-like proteins in a bacterial symbiosis https://www.biorxiv.org/content/10.64898/2026.03.19.712371v1
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.
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.
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
nature.com
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...
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.
agu.org
ace-gtdb.bsky.social@ace-gtdb.bsky.social · 10mo agoOur @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-...
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-...
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
academic.oup.com
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
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...
ncbiinsights.ncbi.nlm.nih.gov
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.
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...
nejm.org
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
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo agoHigh-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
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/...
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.
science.org
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/...
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...
enviromicro-journals.onlinelibrary.wiley.com
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
Home
Resources for the STAMPS 2025 course at the MBL in Woods Hole, MA, USA - mblstamps/stamps2025
github.com
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...
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
merenlab.org
