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
Deep biosphere/oceans (USC) -> Astrobiology/Space Bio (NASA) 👽 -> National Biodefense (DHS)
Bioinf-beginners go to http://microbialomics.org | For phylogenomics, GToTree :) | he/him
Pinned
Mike Lee
@astrobiomike.org
· Nov 16
This has been my license plate for about 10 years over 3 cars and 2 states, I’m so thrilled we’re on our way #2EUROPA! Go, #EuropaClipper!!
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/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
October 27, 2025 at 4:37 AM
Reposted by Mike Lee
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/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
October 22, 2025 at 2:20 PM
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/nar/advance-...
Reposted by Mike Lee
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
#microsky #synbio
October 13, 2025 at 12:48 PM
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
October 1, 2025 at 3:52 PM
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
Reposted by Mike Lee
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.
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...
www.nejm.org
September 22, 2025 at 2:37 PM
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.
This one followed every single child born in Denmark from 1991 through 1998 (n=537,303). There was no association.
Reposted by Mike Lee
American Academy of Pediatrics vaccine schedule for newborns - 18 yrs is the one to use. Just published August 19, 2025 ❤️ downloads.aap.org/AAP/PDF/AAP-...
September 18, 2025 at 10:35 PM
Reposted by Mike Lee
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Mike Lee
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/...
#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.
www.science.org
August 26, 2025 at 4:09 PM
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/...
#mevosky #bluesci
www.science.org/doi/10.1126/...
Reposted by Mike Lee
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/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
July 19, 2025 at 1:04 PM
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/doi/10.1111/...
Reposted by Mike Lee
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
July 15, 2025 at 1:26 PM
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
Reposted by Mike Lee
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/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
July 16, 2025 at 11:00 AM
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/2025/07/16/s...
Reposted by Mike Lee
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.
June 20, 2025 at 3:23 PM
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.
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.
home | GlobDB
globdb.org
June 11, 2025 at 12:27 AM
Awesome! 🦠
Reposted by Mike Lee
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.
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.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
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.
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! 🦠
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
jobs.awi.de
June 5, 2025 at 11:34 AM
This is an amazing group to work with! 🦠
Reposted by Mike Lee
Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...
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...
www.science.org
April 25, 2025 at 6:55 AM
Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...
Reposted by Mike Lee
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 💻🧬🦠🧫
AFAIK many trimmers don't count '.' as AA gap character - and manually adjusting '.' to recognized gap character can significantly alter results 💻🧬🦠🧫
May 10, 2025 at 12:23 AM
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 💻🧬🦠🧫
AFAIK many trimmers don't count '.' as AA gap character - and manually adjusting '.' to recognized gap character can significantly alter results 💻🧬🦠🧫
Reposted by Mike Lee
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...
This strain encodes a polyesterase that degrades polycaprolactone, and it can use it as a sole carbon source:
www.cell.com/cell-reports...
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...
www.cell.com
May 8, 2025 at 9:06 PM
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...
This strain encodes a polyesterase that degrades polycaprolactone, and it can use it as a sole carbon source:
www.cell.com/cell-reports...
TaxonKit v0.20.0 is adapted to recent rank changes in NCBI Taxonomy.
github.com/shenwei356/t...
Also updated
- taxid-changelog to May, 2025 github.com/shenwei356/t...
- gtdb-taxdump to GTDB r226 github.com/shenwei356/g...
- ictv-taxdump to VMR_MSL40 github.com/shenwei356/i...
github.com/shenwei356/t...
Also updated
- taxid-changelog to May, 2025 github.com/shenwei356/t...
- gtdb-taxdump to GTDB r226 github.com/shenwei356/g...
- ictv-taxdump to VMR_MSL40 github.com/shenwei356/i...
Release TaxonKit v0.20.0 · shenwei356/taxonkit
Changes
TaxonKit v0.20.0
This version is mainly for maintaining compatibility with NCBI's recent changes(1, 2).
Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing t...
github.com
May 7, 2025 at 3:30 AM
New paper out!
We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp!
Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive.
It also represents a novel, deep-branching lineage in the archaeal tree.
We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp!
Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive.
It also represents a novel, deep-branching lineage in the archaeal tree.
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome https://www.biorxiv.org/content/10.1101/2025.05.02.651781v1
May 3, 2025 at 3:03 PM
This is important work for the exciting next stage of metagenomics #MicroSky
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
www.biorxiv.org
April 28, 2025 at 11:04 AM
This is important work for the exciting next stage of metagenomics #MicroSky
Super cool! #MicroSky
Fresh in @NatureBiotech! We developed a synthetic biology tool for tracking gene transfer in microbial communities and applied it to study plasmid hosts in a wastewater microbiome. Awesome collab with James Chappell & @joffsilberg.bsky.social and incredible students. www.nature.com/articles/s41...
Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology
Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.
www.nature.com
April 27, 2025 at 2:58 PM
Super cool! #MicroSky
