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
#NewResearch

A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.

#MicroSky 🦠

www.nature.com/articles/s41...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology
A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.
www.nature.com
November 26, 2025 at 3:59 PM
Reposted by Arkadiy Garber
In fermented foods microbes convert some of the food substrate into microbial protein. We found that in some fermented foods up to 10% of the total protein is microbial and that some of these microbial proteins have functions that might explain some of the beneficial effects of fermented foods.
Assessing the diversity and functional profile of the “microbial proteome” in fermented foods
Fermented foods are staples in diets worldwide and are known for their health benefits. Microorganisms are the key to fermented food production as they convert raw substrates into digestible, nutritio...
www.biorxiv.org
November 23, 2025 at 8:09 PM
Reposted by Arkadiy Garber
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Reposted by Arkadiy Garber
Magnetotactic bacteria are tiny navigators using Earth's magnetic field to move! Spanning ecosystems from volcanic lakes to deep-sea vents, they create magnetosomes, little mineral magnets. Recent innovations have unveiled their vast diversity, and their biomagnets show promise in cancer therapy,...
Global advances in magnetotactic bacteria: ecology, evolution and biotechnological applications of BioMagnets with a focus on magnetic hyperthermia.
Published in Critical reviews in biotechnology
doi.org
November 20, 2025 at 8:00 AM
Reposted by Arkadiy Garber
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?
November 18, 2025 at 5:29 PM
Reposted by Arkadiy Garber
Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert www.nature.com/articles/s41... #jcampubs
Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert - Scientific Data
Scientific Data - Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert
www.nature.com
November 18, 2025 at 2:05 PM
Reposted by Arkadiy Garber
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
Microbial science moves forward when we do. Submit your early abstract for #ASMicrobe 2026 and join thousands of scientists advancing discovery, collaboration and innovation.

Deadline: Dec. 2, 2 p.m. ET.

Share your science → asm.social/2Gv
November 13, 2025 at 12:32 PM
Reposted by Arkadiy Garber
#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...
Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi - Nature Communications
In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...
www.nature.com
November 12, 2025 at 8:36 PM
Reposted by Arkadiy Garber
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.

We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Reposted by Arkadiy Garber
Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions https://www.biorxiv.org/content/10.1101/2025.11.12.688118v1
November 13, 2025 at 3:17 AM
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 · 27d
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