iiinova — where your digital self keeps evolving

Reposted by Mike Lee

Karen Lloyd @karenlloyd.bsky.social · 16/09/2026

I wrote a blog post about aeornophiles for Small Things Considered. smallthingsconsidered.blog/schaechter/2...

smallthingsconsidered.blog

Aeonophiles

by Karen G. Lloyd — The story behind some extremely long-lived microbial cells.

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Reposted by Mike Lee

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 11/09/2026

Marine biology friends, my upcoming online take-at-your-own-pace “foundations of marine biology” course will include two regular features and I welcome your suggestions for both! 🧪🌎🦑🐟 #SciComm

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Stephen Turner @stephenturner.us · 21/08/2026

vscode in the terminal 😵‍💫 terminal-code.com github.com/zenbu-labs/t...

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Reposted by Mike Lee

ace-gtdb.bsky.social @ace-gtdb.bsky.social · 30/07/2026

🎉 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

youtube.com

Genome Taxonomy Database – Finalist, 2026 Eureka Prize for Excellence in Data Platforms

YouTube video by Australian Museum

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Reposted by Mike Lee

Amy D Willis @amydwillis.bsky.social · 20/07/2026

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/

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Yuya Kiguchi @ykiguchi.bsky.social · 01/06/2026

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...

cell.com

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...

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Reposted by Mike Lee

ace-gtdb.bsky.social @ace-gtdb.bsky.social · 10/04/2026

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.

ncbi.nlm.nih.gov

Genome

Download a genome data package including genome, transcript and protein sequence, annotation and a data report

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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 15/04/2026

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.ecogenomic.org

GTDB - Genome Taxonomy Database

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

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Reposted by Mike Lee

Daan Speth @daanspeth.bsky.social · 25/03/2026

We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵

Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories

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Reposted by Mike Lee

Steven Salzberg @stevensalzberg.bsky.social · 30/03/2026

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...

stevensalzberg.substack.com

AI is starting to look like pseudoscience

Not all of it, but some scientists are too eager to believe their own hype

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Mike Lee @astrobiomike.org · 28/03/2026

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.com

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

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Reposted by Mike Lee

Hajk-Georg Drost @hajkdrost.bsky.social · 24/03/2026

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...

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Alex Crits-Christoph @acritschristoph.bsky.social · 21/03/2026

Absolutely astounding paper. Massive 36,000 AA proteins facilitate cell-cell interactions in this bacterial symbiosis. Really beautiful scientific work.

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Reposted by Mike Lee

Sarah J Tucker @sjtucker.bsky.social · 05/12/2025

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.

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Reposted by Mike Lee

Sarah J Tucker @sjtucker.bsky.social · 05/12/2025

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.

nature.com

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

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Reposted by Mike Lee

Blue Marble Space @bluemarblespace.bsky.social · 13/11/2025

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...

agu.org

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.

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Reposted by Mike Lee

ace-gtdb.bsky.social @ace-gtdb.bsky.social · 22/10/2025

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-...

academic.oup.com

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

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Emmanuele Severi @emmseveri.bsky.social · 13/10/2025

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

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Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 22/09/2025

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.

nejm.org

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...

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Reposted by Mike Lee

Jim Shaw @jimshaw.bsky.social · 08/09/2025

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

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Reposted by Mike Lee

Ran Duan @drduanran.bsky.social · 19/07/2025

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/...

enviromicro-journals.onlinelibrary.wiley.com

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...

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Reposted by Mike Lee

Titus Brown @titus.idyll.org · 15/07/2025

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

github.com

Home

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

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Reposted by Mike Lee

A. Murat Eren (Meren) @merenbey.bsky.social · 16/07/2025

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...

merenlab.org

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

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Reposted by Mike Lee

Brett Baker @archaeal.bsky.social · 20/06/2025

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.

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Daan Speth @daanspeth.bsky.social · 10/06/2025

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.

globdb.org

home | GlobDB

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Mike Lee @astrobiomike.org · 05/06/2025

This is an amazing group to work with! 🦠

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naturepoker @binomicalabs.org · 10/05/2025

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 💻🧬🦠🧫

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Alex Crits-Christoph @acritschristoph.bsky.social · 08/05/2025

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...

cell.com

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...

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Mike Lee @astrobiomike.org · 28/04/2025

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

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Baylink Lab @baylinklab.bsky.social · 07/04/2025

🧪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

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