Arkadiy Garber
@ironark.bsky.social
150 followers 440 following 79 posts
Phd Candidate, Microbiology at ASU https://mccutcheonlab.org/ Founder of MAB: midauthorbio.com GitHub: https://github.com/Arkadiy-Garber https://github.com/Middle-Author-Bioinformatics Google Scholar: https://scholar.google.com/citations?user=SGPloYgAAA
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ironark.bsky.social
Cool system. I was surprised to learn about circadian rhythms in bacteria. To aid in the identification of this system in genomes and metagenomes, @zombiephylotype.bsky.social and I included this pathway as part of our MagicLamp functional annotation suite: www.magiclamp.midauthorbio.com
Reposted by Arkadiy Garber
sse-evolution.bsky.social
Now accepting proposals for new Research Synthesis Working Groups! Each funded group will present a symposium at the Evolution meeting, collaborate on a publication, and establish a lasting research network. Submit your proposal by January 6: www.evolutionsociety.org/content/soci...
Text: Society for the Study of Evolution Call for Proposals: Research Synthesis Working Groups. Deadline: January 6.
Reposted by Arkadiy Garber
lancetmicrobe.bsky.social
New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
Reposted by Arkadiy Garber
filiphusnik.bsky.social
Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...
Reposted by Arkadiy Garber
oschwengers.bsky.social
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)
Reposted by Arkadiy Garber
Reposted by Arkadiy Garber
nanamikubota.bsky.social
Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...
ironark.bsky.social
Thank you for the kind words! Glad it's been useful :)
ironark.bsky.social
Look at all that iron 🤩
Reposted by Arkadiy Garber
jingnandu.bsky.social
Our new paper is out now in Neuron! 🎉 With @vaibhavtripathi.bsky.social @maxwellelliott.bsky.social Joanna Ladopoulou, Wendy Sun, Mark Eldaief, and Randy Buckner

Paper link: www.sciencedirect.com/science/arti...
Reposted by Arkadiy Garber
thedailypub.bsky.social
Holobionts, the combo of a host and its tiny partners, are like living networks. Turns out, microbes can jump between hosts and parasites, tweaking health and immunity in ways that go beyond quick chemical signals. These sneaky micro-travelers could redefine what it means to be a pathogen or a fr...
Holobiont-holobiont interactions across host-ectoparasite systems.
Published in Parasites & vectors
doi.org
Reposted by Arkadiy Garber
asaflevylab.bsky.social
A recent cool preprint by John Whitney's lab on a new family of antibacterial proteins secreted by Gram-positive bacteria that enter and kill a broad spectrum of bacteria. Cell entry is receptor-independent and relies on cleavage by a co-secreted protease and the PMF.
www.biorxiv.org/content/10.1...
Proteolytically activated antibacterial toxins inhibit the growth of diverse Gram-positive bacteria
Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacterial proteins that share this broad-spectrum activity ...
www.biorxiv.org
Reposted by Arkadiy Garber
vscooper.micropopbio.org
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...
www.linkedin.com
Reposted by Arkadiy Garber
uncultured.carinilab.com
What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.
Reposted by Arkadiy Garber
vscooper.micropopbio.org
Delighted and deeply relieved that our R25-SEPA supporting EvolvingSTEM will continue another year.

I've never been happier to see a NOA, and this is just a noncompeting renewal.

I appreciate the troopers inside NIH for keeping the candles lit.

1000's of students & ~50 teachers will benefit!
Reposted by Arkadiy Garber
femsmicro.org
To maintain genome integrity, extreme organisms like archaea rely heavily on repair pathways.

This #FEMSmicroBlog explains how the halophile model organism Haloferax volcanii repairs DNA double strand breaks quickly and efficiently. #FascinatingMicrobes
#FEMSmicroBlog: Halophile archaea healing themselves
This #FEMSmicroBlog explains how the halophile model organism Haloferax volcanii repairs DNA double strand breaks quickly and efficiently. #FascinatingMicrobes
buff.ly
Reposted by Arkadiy Garber
biorxiv-microbiol.bsky.social
Nitrate-responsive Mycobacterial Intracytoplasmic Membranes dampen Inflammation during Mycobacterium tuberculosis Infection https://www.biorxiv.org/content/10.1101/2025.09.17.676823v1
Reposted by Arkadiy Garber
microbiologysociety.org
Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK. Published in MGen: doi.org/10.1099/mgen... #MGen
Fig. 1.
Loss of AMR-carrying transposable element in the S. Typhimurium genome of Patient 4. Clinker [81] schematic comparing two isolates collected from the same faecal sample from an acute case (Patient 4), with no difference in time of collection. Isolate 3 represents the consensus sequence found in 19 of 20 colonies, while isolate 10 shows a loss of a region flanked by ISs (orange) that includes four AMR genes (red, dark blue, yellow and light blue). Genes are shown as directional arrows, with identical sequences coloured consistently. Homology between the isolates is indicated by black bars; regions lacking these links are absent in isolate 10.
Reposted by Arkadiy Garber
jcamthrash.bsky.social
Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia www.biorxiv.org/content/10.1... #jcampubs