Arkadiy Garber
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ironark.bsky.social
Arkadiy Garber
@ironark.bsky.social
PhD, Microbiology
MS, Geological Sciences
BS, Neuroscience

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
Pinned
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
cool! tools to making it easier to work with 𝘐𝘥𝘦𝘰𝘯𝘦𝘭𝘭𝘢 𝘴𝘢𝘬𝘢𝘪𝘦𝘯𝘴𝘪𝘴 (now 𝘗𝘪𝘴𝘤𝘪𝘯𝘪𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘢𝘬𝘢𝘪𝘦𝘯𝘴𝘪𝘴) for PET degradation

#MicroSky
November 12, 2025 at 8:11 PM
Reposted by Arkadiy Garber
“Non-photosynthetic Plastid Replacement by a
Primary Plastid in the Making”. This is cool as hell 😎
www.biorxiv.org/content/bior...
www.biorxiv.org
November 12, 2025 at 1:30 AM
Reposted by Arkadiy Garber
Plastic degradation by enzymes from uncultured deep sea microorganisms academic.oup.com/ismej/articl... #jcampubs
Plastic degradation by enzymes from uncultured deep sea microorganisms
Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are
academic.oup.com
November 11, 2025 at 3:06 PM
Great opening: "Once considered a bag of enzymes, bacterial cells do not simply hold their proteins in the bag but have evolved multiple protein secretion systems to release proteins outside for crucial functions"

Review on the T6SS structure and effectors.

journals.asm.org/doi/10.1128/...
Not just passengers: effectors contribute to the assembly of the type VI secretion system as structural building blocks | Journal of Bacteriology
Once considered a bag of enzymes, bacterial cells do not simply hold their proteins in the bag but have evolved multiple protein secretion systems to release proteins outside for crucial functions. These secretion systems are often required for mediating intra- and inter-cellular interactions in diverse polymicrobial environments, virulence, and survival during pathogen-host interactions (1–3). Therefore, bacterial secretion systems have received tremendous attention and broad interest despite their non-essential role in survival in pure cultures. Among the known systems, most secrete proteins across the double membrane of Gram-negative bacteria through one- or two-step mechanisms (4). One-step systems (T1SS, T3SS, T4SS, T6SS, and T7SS) form trans-membrane tunnels that translocate substrates directly from the cytoplasm to the extracellular environment (5–9). Two-step systems (T2SS and T5SS) use Sec or Tat translocation systems to move effectors across the inner membrane to the periplasm before secretion across the outer membrane (10, 11). These systems secrete diverse effectors involved in stress mitigation, nutrient acquisition, host-microbe interactions, and modulation of polymicrobial communities (12–16).
journals.asm.org
November 10, 2025 at 7:23 PM
Reposted by Arkadiy Garber
Microorganisms like bacteria can cleverly adapt to rapidly changing environments, such as exposure to drugs, because their evolution isn't random. They have a knack for directed evolution, which means they can adjust purposefully to external changes. This insight reshapes how we understand human...
Humans and Microbes: A Systems Theory Perspective on Coevolution.
Published in Bio Systems
doi.org
November 2, 2025 at 2:00 PM
Reposted by Arkadiy Garber
By studying the process through which a soil bacterium naturally produces a well-known drug, scientists have discovered a powerful antibiotic that could help to fight drug-resistant infections.

🦠🧪

www.nature.com/articles/d41...
Powerful new antibiotic that can kill superbugs discovered in soil bacteria
Surprise discovery could pave the way for new treatments against drug-resistant infections.
www.nature.com
November 2, 2025 at 2:09 PM
Reposted by Arkadiy Garber
In a new study an international team led by the University of Vienna reports the discovery and extraction of ancient DNA from a tiny 5 cm long Neanderthal bone found in the Crimean peninsula.
Neanderthal DNA reveals ancient long-distance migrations
Tiny 5 cm long bone allows insights into crucial period when Neanderthals disappeared and Homo sapiens replaced them
www.univie.ac.at
November 2, 2025 at 4:38 PM
Reposted by Arkadiy Garber
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com

rdcu.be/eLtCH
November 2, 2025 at 5:52 PM
Reposted by Arkadiy Garber
Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.
October 23, 2025 at 10:09 AM
Reposted by Arkadiy Garber
Good opportunity to be on Mark's podcast. Highly recommend! #microsky
Just looking for two guests for my #MattersMicrobial podcast. Slots open between 7AM and noon on Friday, November 28th and Friday, December 26th. DM me, email, and please spread the #GoodMicrobialWord. Always looking for #MicrobialEnthusiasts.
a man in a cowboy hat is standing in the desert looking at something .
ALT: a man in a cowboy hat is standing in the desert looking at something .
media.tenor.com
November 2, 2025 at 11:29 PM
Reposted by Arkadiy Garber
Direct carbon monoxide fixation via the bacterial and archaeal Wood–Ljungdahl pathways www.biorxiv.org/content/10.1... #jcampubs
November 1, 2025 at 6:28 AM
Reposted by Arkadiy Garber
Forgot to post the recently published version of this paper on the role of a minor pilin-like protein in surface sensing journals.asm.org/doi/10.1128/...
October 31, 2025 at 6:54 PM
Reposted by Arkadiy Garber
We are really proud of this report from our 3 colloquia convened by the AAM and supported by the Moore Foundation. A few experts even said they would use it as their introductory textbook for this area. Please check it out!
asm.org ASM @asm.org · 13d
How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...
Early Microbial Evolution | ASM.org
How did life begin, and why does it matter? Scientists are tracing early microbial life—from LUCA to multicellularity—to unlock insights for biotech, climate science and even space exploration.
asm.org
October 30, 2025 at 3:14 PM
Reposted by Arkadiy Garber
ICYMI: Our latest shows what happens to transcriptional and metabolic profiles in a desiccated soil bacterium.

To simplify things, I've attached a visual abstract.

Comments on the preprint are welcome!
#microsky #microbesky

www.biorxiv.org/content/10.1...
October 30, 2025 at 7:35 PM
Reposted by Arkadiy Garber
How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...
Early Microbial Evolution | ASM.org
How did life begin, and why does it matter? Scientists are tracing early microbial life—from LUCA to multicellularity—to unlock insights for biotech, climate science and even space exploration.
asm.org
October 30, 2025 at 2:09 PM
Reposted by Arkadiy Garber
First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience

Our latest in @natrevneuro.nature.com
Link: rdcu.be/eMX3E

@jeffcolgren.bsky.social @msarscentre.bsky.social
The evolutionary origins of synaptic proteins and their changing roles in different organisms across evolution
Nature Reviews Neuroscience - Recent studies have shed further light on the evolutionary origins of chemical synapses, In this Review, Colgren and Burkhardt explore how ancient proteins were...
rdcu.be
October 27, 2025 at 6:48 PM
Reposted by Arkadiy Garber
How to become a "hot RNA" 🌡️? The answers were kindly provided by hyperthermophilic archaea: rRNA modifications are key! Check out this new publication presenting pan-modification profiling of the epitranscriptome. www.cell.com/cell/fulltex.... (1/3)
Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome
Pan-Mod-seq enables systematic, multi-modification mapping of rRNA across life. Applying it to diverse organisms reveals that hyperthermophiles dynamically install stabilizing modifications to support...
www.cell.com
October 27, 2025 at 1:19 PM
Reposted by Arkadiy Garber
Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC url: academic.oup.com/nar/article/...
Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC
Abstract. Natural chromosomal transformation (NCT) in Bacillus subtilis requires RecA and its accessory proteins including RecX and RecD2. Inactivation of
academic.oup.com
October 25, 2025 at 12:10 PM
Reposted by Arkadiy Garber
The fall armyworm is tough to beat because its gut bacteria help it resist pesticides. One key bacterium, Enterococcus casseliflavus EMBL-3, supplies tryptophan, which gets turned into a compound that boosts a detox enzyme. This process helps the worm resist chlorantraniliprole. Targeting these b...
Cooperative Microbial Metabolism Enhances Tryptophan-Mediated Insecticide Detoxification in the Fall Armyworm.
Published in The ISME journal
doi.org
October 24, 2025 at 7:00 PM
Reposted by Arkadiy Garber
This looks to be a great meeting convened by @microbiologysociety.org
microbiologysociety.org/event/societ...
Microbes in Microbiomes
microbiologysociety.org
October 23, 2025 at 3:23 PM
Reposted by Arkadiy Garber
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs
October 23, 2025 at 5:20 AM
Reposted by Arkadiy Garber
#microsky #mevosky @spp2389.bsky.social

A PhD position is available in my lab to work on:

Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.

Please RT

Deadline: 12.11.25

More infos 👇
shorturl.at/rAKAT
October 15, 2025 at 1:07 PM
Reposted by Arkadiy Garber
What type of #microscopy would allow for watching real time cell division of an anaerobic bacterium (~1 x 0.5 um rod) at resolution high enough to view internal structure? Doubling time of ~2 days.

#MicroSky
October 17, 2025 at 11:11 PM
Reposted by Arkadiy Garber
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
October 17, 2025 at 10:28 AM
Reposted by Arkadiy Garber
We have recently shown the large potential of organellar genome-resolved metagenomics by assembling 100s of new marine plastid MAGs (ptMAGs), including revealing the new deep-branching algal group leptophytes: www.biorxiv.org/content/10.1...
New deep-branching environmental plastid genomes on the algal tree of life
Marine algae support the entire ocean ecosystem and greatly impact planetary biology. The availability of algae in culture poorly represents their large environmental diversity, and we still have a li...
www.biorxiv.org
October 17, 2025 at 7:33 AM