Lightnews — Scholar-powered news

Mike Lee @astrobiomike.org · 7d

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

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Reposted by Mike Lee

Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 16d

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...

www.nejm.org

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Reposted by Mike Lee

Alyson Smith @pedsaly.bsky.social · 19d

Alyson Smith @pedsaly.bsky.social · Aug 28

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-...

American Academy of Pediatrics Recommended Child and Adolescent Immunization Schedule
Table 1 for Ages 18 Years or Younger, United States, 2025
Published August 19, 2025. View full document and notes here: https://downloads.aap.org/AAP/PDF/AAP-Immunization-Schedule.pdf

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Reposted by Mike Lee

Jim Shaw @jimshaw.bsky.social · Sep 7

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 · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Reposted by Mike Lee

Rhys Allen @rhysallensysbio.bsky.social · Aug 26

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.

www.science.org

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Reposted by Mike Lee

Ran Duan @drduanran.bsky.social · Jul 19

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

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Reposted by Mike Lee

Titus Brown @titus.idyll.org · Jul 15

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

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Reposted by Mike Lee

A. Murat Eren (Meren) @merenbey.bsky.social · Jul 16

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

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Mike Lee @astrobiomike.org · Jun 22

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!”

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Reposted by Mike Lee

Brett Baker @archaeal.bsky.social · Jun 20

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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Mike Lee @astrobiomike.org · Jun 11

Awesome! 🦠

Daan Speth @daanspeth.bsky.social · Jun 10

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.

home | GlobDB

globdb.org

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Reposted by Mike Lee

Daan Speth @daanspeth.bsky.social · Jun 10

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.

home | GlobDB

globdb.org

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Mike Lee @astrobiomike.org · Jun 5

This is an amazing group to work with! 🦠

A. Murat Eren (Meren) @merenbey.bsky.social · Jun 5

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...

PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)

Layout AWI HIPP extern, englisch

jobs.awi.de

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Reposted by Mike Lee

Christian Frezza @frezzalab.bsky.social · Apr 25

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

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Reposted by Mike Lee

naturepoker @binomicalabs.org · May 10

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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Reposted by Mike Lee

Alex Crits-Christoph @acritschristoph.bsky.social · May 8

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...

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

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Mike Lee @astrobiomike.org · May 7

#MicroSky

Wei Shen 沈伟 @shenwei356.bsky.social · May 6

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...

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

Mike Lee @astrobiomike.org · May 4

Strain-level metagenomic profiling using pangenome graphs with PanTax

#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...

www.biorxiv.org

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Mike Lee @astrobiomike.org · May 3

#MicroSky

Ryo Harada @ryoharada.bsky.social · May 3

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.

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · May 2

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

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Mike Lee @astrobiomike.org · Apr 28

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

Florian Trigodet @floriantrigodet.bsky.social · Apr 28

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 🧵

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

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Mike Lee @astrobiomike.org · Apr 27

Super cool! #MicroSky

lauren-stadler.bsky.social @lauren-stadler.bsky.social · Mar 18

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

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Mike Lee @astrobiomike.org · Apr 27

a man sitting on a couch with the words " that 's a shame " written below him

ALT: a man sitting on a couch with the words " that 's a shame " written below him

media.tenor.com

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Mike Lee @astrobiomike.org · Apr 12

Happy #Caturday 😺

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

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Reposted by Mike Lee

Baylink Lab @baylinklab.bsky.social · Apr 7

🧪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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Mike Lee @astrobiomike.org · Apr 5

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

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.

www.cell.com

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