Lightnews — Scholar-powered news

Ilnam Kang @ilnamkang.bsky.social · 3h

Targeted protein evolution in the gut microbiome by diversity-generating retroelements
www.science.org/doi/10.1126/...

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...

www.science.org

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Reposted by Ilnam Kang

Stephen Turner @stephenturner.us · 13h

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪
MetaGraph: metagraph.ethz.ch
Code: github.com/ratschlab/me...

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Reposted by Ilnam Kang

Cameron Thrash @jcamthrash.bsky.social · 14h

Carbon source diversity shapes bacterial interspecies interactions academic.oup.com/ismej/advanc... #jcampubs

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Reposted by Ilnam Kang

Cameron Thrash @jcamthrash.bsky.social · 14h

SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen academic.oup.com/ismej/advanc... #jcampubs 🌊

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Reposted by Ilnam Kang

Cameron Thrash @jcamthrash.bsky.social · 15h

Active microorganisms and potential metabolic pathways mediating anaerobic degradation of DMSP in anoxic saltmarsh sediment academic.oup.com/ismecommun/a... #jcampubs

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Reposted by Ilnam Kang

Cameron Thrash @jcamthrash.bsky.social · 15h

Cellular-level control on global ocean deoxygenation driven by phytoplankton ecophysiology www.biorxiv.org/content/10.1... #jcampubs

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Reposted by Ilnam Kang

Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 17h

🚀 Released gbdraw v0.6.0!

- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.

- Added links to relevant sections of the documentation throughout the web app help menu.

Try out:👉 gbdraw.streamlit.app

A grid of 12 circular E. coli genome maps showing dinucleotide skew plots for GC, CG, AG, GA, CT, TC, TG, GT, CA, AC, AT, and TA. Each circle displays color-coded genome annotations (CDS, rRNA, tRNA, etc.) around the outer ring, with inner line plots showing positive and negative dinucleotide skew values.
Below the grid, a linear representation of two E. coli genomes shows annotated tracks, GC content, and GC skew plots, with two genomes linked with ribbons representing BLASTN hits. Note that the lower track (pathogenic strain O157:H7 Sakai) has multiple prophage insertions (shaded with orange) that are absent from the upper track (the laboratory strain K-12). Further below are five linear genome comparison diagrams of Hepatoplasmataceae mollicutes, each with colored gene annotations, GC content and GC skew plots, and gray ribbons indicating TBLASTX hits across genomes.

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Reposted by Ilnam Kang

Tominaga K. (tomiken) @pacyc184.bsky.social · 1d

Global Deep Terrestrial Biosphere Core Microbiome | ISME Communications | Oxford Academic https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycaf176/8276778?rss=1&login=false

A Global Deep Terrestrial Biosphere Core Microbiome

Abstract. The deep biosphere encompasses life beneath the Earth’s surface and constitutes a substantial portion of the planet’s microbial biomass. This stu

dx.doi.org

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Reposted by Ilnam Kang

Cathy Hernandez @cathyhernandez.bsky.social · 1d

Very happy to share that I will be starting as an Assistant Professor in the department of Biological Sciences at the University of South Carolina in January! My group will be working on environmental phage ecology and evolution, and I am recruiting for the upcoming year (more info below).

A graphic advertising phage ecology and evolution research at the University of South Carolina, showing a central image of a tide pool flanked by a photo of an agar plate containing diverse microbes and a TEM image of a virus particle.

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Reposted by Ilnam Kang

RuthLeyMicro @microbiome.bsky.social · 5d

Thinking about a postdoc in microbiome science?
Our lab at the MPI for Biology (Tübingen) builds on the culture I established at Cornell: collaborative, creative, and internationally diverse. Postdocs lead their own projects with secure funding. Join us!
#PostdocJobs #HostMicrobe #AcademicJobs

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Reposted by Ilnam Kang

Nils Rädecker @radecker.bsky.social · 3d

🪸🧪 We’re hiring! Join our ERC-funded group at the @hifmb.de in Oldenburg, Germany to explore the cellular origins of photosymbiosis:⁣
⁣
𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.⁣
Deadlines: Oct 29 & Nov 5. Links below. ⁣

Questions: [email protected]⁣
#Photosymbiosis #HIFMB #ERC #AcademicJobs

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Reposted by Ilnam Kang

Alejandro Rodríguez-Gijón @alejandrorgijon.bsky.social · 3d

I am extremely happy to share our latest manuscript "Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance". This project started back in 2021-2022 and after a long time, it sees the light today!

www.nature.com/articles/s41...

Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance - Scientific Reports

Scientific Reports - Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance

www.nature.com

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Reposted by Ilnam Kang

Paul Rainey @paulbrainey.bsky.social · 3d

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...

Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology

The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

www.evolbio.mpg.de

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Reposted by Ilnam Kang

Oliver Schwengers @oschwengers.bsky.social · 3d

Dear community, Bakta needs your help!

To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)

(1/2)

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Reposted by Ilnam Kang

Michael Brockhurst @brockhurstlab.bsky.social · 4d

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

www.biorxiv.org

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Reposted by Ilnam Kang

Michael Wagner @michiwagner4.bsky.social · 4d

Interested in an exciting 2.5 year PostDoc position with a focus on the characterization of novel #nitrifiers? This is a collaborative project between our nitrification group @cemess.bsky.social and C. Singleton and P. Nielsen at @aau.dk

🧪 #MicroSky

www.stillinger.aau.dk/videnskabeli...

Postdoc in Identification and characterization of novel nitrifiers

At the Faculty of Engineering and Science, Department of Chemistry and Bioscience, a 2.5 year position as Postdoc in “Identification and characterization of ...

www.stillinger.aau.dk

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Reposted by Ilnam Kang

Jelena Godrijan 🫧❾🌊🦋 @godi.bsky.social · 7d

🌊🔬 Looking for a postdoc to join our team!
Cocco-Channel project ➡️ studying coccolithophore phycospheres and their role in ocean carbon cycling.
✔️ Plus if you bring experience in microbial ecology, molecular/microscopy tools & fieldwork
👉 More info: euraxess.ec.europa.eu/jobs/375178
#protistsonsky

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Reposted by Ilnam Kang

Mya Breitbart @viromegirl.bsky.social · 7d

We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...

Apply - Genomics

www.marine.usf.edu

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Reposted by Ilnam Kang

Emmanuele Severi @emmseveri.bsky.social · 7d

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

#microsky #phagesky

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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Reposted by Ilnam Kang

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 10d

Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions https://www.biorxiv.org/content/10.1101/2025.09.29.679331v1

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Reposted by Ilnam Kang

Paul Carini @uncultured.carinilab.com · 9d

Neat paper!

Way back when, we speculated SAR11 could assimilate glycolate by oxidizing to glyoxylate and slapping an ammonia on it to produce glycine. Perhaps other taxa assimilate it similarly.
www.nature.com/articles/ism...

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Reposted by Ilnam Kang

raw9371 @raw937.bsky.social · 9d

Multiomic analysis of the only megaphage in culture. In press today.

Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv...

#phage #bacteriophage

Unlocking the genomic repertoire of a cultivated megaphage - npj Viruses

npj Viruses - Unlocking the genomic repertoire of a cultivated megaphage

share.google

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Reposted by Ilnam Kang

Tominaga K. (tomiken) @pacyc184.bsky.social · 10d

Giant virus genomes are unlikely to be reservoirs of antibiotic resistance genes | Nature Communications https://www.nature.com/articles/s41467-025-63367-5

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Reposted by Ilnam Kang

Lucas Farnung @lucas.farnunglab.com · 10d

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

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Reposted by Ilnam Kang

Ryan Wick @rrwick.bsky.social · 11d

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
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Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

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