Arkadiy Garber

h/t @zombiephylotype.bsky.social and Steindler lab @ Haifa University

Diel transcriptional dynamics of a marine sponge and its microbiome in a natural environment - Animal Microbiome Animal Microbiome - Marine sponges are ecologically critical animals that host diverse microbial communities, forming complex symbiotic systems crucial to nutrient cycling and ecosystem functioning...

Thankful to be part of this study looking at how the marine sponge and its microbes change gene activity across day and night in the natural ocean environment:

Diel transcriptional dynamics of a marine sponge and its microbiome in a natural environment
link.springer.com/article/10.1...

Figure from: Likelihood-based fine-tuning of protein language models for few-shot fitness prediction and design

Protein language models capture evolutionary constraints from natural sequences. A team from UCL and InstaDeep compared two strategies for adapting these models to predict protein fitness from limited lab data: using frozen embeddin...

https://www.biorxiv.org/content/10.1101/2024.05.28.596156

Endosymbiotic apicomplexans of marine holobionts: microbial parasites in a warming ocean.

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles | PNAS Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information r...

Thanks Alejandro! Looking forward to checking out these papers.

though - I am getting a "DOI Not Found" error when trying to access the pnas paper. Is this the paper: www.pnas.org/doi/10.1073/...

Of Terms in Bi­ol­ogy: Trans-Trans­la­tion by John McCutcheon, Janie and Christoph — This could become a very short explainer of the term "trans-trans­lation", as gi­ven by Vioque and de la Cruz in their mini­review: "Trans-trans­lation is…

... worked on it in the mid-90s.)

john and I chatted about TmRNA/10Sa RNA in STC... but none of us could have anticipated how useful it might be for endosymbionts. great work 👍

have you ever wondered how endosymbionts cope with the many pseudogenes in their genomes (before they generously reduce them by a factor of ~10)?
arkadiy describes a way, read his paper and learn the surprising role of TmRNA (10Sa RNA still when john @mcsymbiont.bsky.social ...

#SymbioSky #MicroSky

Pseudococcus longispinus mealybug on a potato. Image by Maria Kupper.

To do this research, we relied on two young endosymbiont genomes recently acquired by the long-tailed mealybug (Pseudococcus longispinus) and combined transcriptomics, ribosome profiling, and mass spectrometry proteomics to follow pseudogenes from RNA to ribosome to protein.

Bar chart comparing tmRNA abundance in total RNA versus ribosome-bound RNA for two bacterial endosymbionts, Sodalis and Symbiopectobacterium. tmRNA is low in total RNA for both, but becomes highly enriched in ribosome-bound RNA in Symbiopectobacterium (~40%), while remaining low in Sodalis, indicating stronger ribosome rescue activity in Symbiopectobacterium.

We find a possible role for tmRNA-mediated ribosome rescue as a short-term mechanism to clear aberrant peptides & recycle ribosomes stalled on newly formed pseudogenes. Over longer evolutionary time, pseudogenes lose promoter & ribosome-binding signals, reducing their transcription and translation

Comparative funnel diagram showing pseudogene fate in two bacterial endosymbionts, Sodalis and Symbiopectobacterium. Red bars represent pseudogenes and black bars intact genes across stages from encoding to transcription, ribosome binding, and protein production. In Symbiopectobacterium, many pseudogene transcripts continue binding ribosomes but rarely yield proteins, while Sodalis shows a sharper drop before ribosome association.

We find that pseudogenes remain broadly transcribed and can still associate with ribosomes even after losing function. Yet, they rarely produce stable proteins, suggesting that bacterial cells rely on some sort of mechanism to prevent pseudogene-derived products from mucking up the proteome

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

Efficient and scalable Python implementation of ANCOM-BC for omics differential abundance testing https://www.biorxiv.org/content/10.64898/2026.01.26.701398v1

We introduce a Python implementation of ANCOM-BC that is 100x faster than the original R code, while preserving statistical validity. Scales to much larger omics datasets and enables ML workflows with repeated inference (feature selection, sensitivity, stability, etc.) #Bioinformatics #Microbiome

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

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

A quorum-sensing molecule from Pseudomonas aeruginosa induces defensive multicellularity in a coinfecting pathogen | PNAS Microorganisms commonly exist in polymicrobial communities, where they can respond to interspecies secreted molecules by altering behaviors and phy...

Cool stuff!

“A quorum-sensing molecule from Pseudomonas aeruginosa induces defensive multicellularity in a coinfecting pathogen”

#microsky

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

(1/10)

Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis.

New paper out in @pnas.org, and it made the cover! 👁️

We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.

‼️Check Paula’s 🧵 and the paper👇

𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...

Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria This special issue marking the University of Bath's 60th anniversary offers an opportunity to reflect on nearly a decade of research into the evolution of gene regulatory networks (GRNs) from members....

Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria
(=Pseudomonas fluorescens)
Advanced Science, perspective by @taylorlabgroup.bsky.social & @alanrice.ie
Uni Bath's 60th anniversary special issue
advanced.onlinelibrary.wiley.com/doi/10.1002/...

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

Our new paper on Insertion Sequences (IS) in #Klebsiella

- Lineages have vastly different IS loads and profiles
- An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution.

www.microbiologyresearch.org/content/jour...

Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them Researchers are close to making “reversed” cells that may wipe us off the planet

What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them.

Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...

From infestation to infection: a systematic review of arthropod-mediated microbial transmission in hospitals - PubMed Arthropods in healthcare environments commonly harbor clinically relevant and antimicrobial-resistant microbes, and limited but compelling evidence supports their potential role in patient transmission. Strengthened pest management and environmental hygiene are essential components of infection prev …

Insects in hospitals are potential disease vectors! 🪳🪰

A new systematic review shows that cockroaches, flies, and ants often carry drug-resistant bacteria and can transmit pathogens to patients. 🏥

pubmed.ncbi.nlm.nih.gov/41562025/

#InfectionPrevention #PublicHealth #Microbiology

FEBS Press Circadian clocks have been identified in very few bacterial species, and only the cyanobacterial clock is understood in detail. Bacterial rhythms have primarily been studied in species in isolation o...

so very happy to share this Perspective piece that I wrote with @hollykay1.bsky.social for @febsletters.bsky.social

in this paper we do an extensive (and long overdue) review of rhythms (of all kinds, not just circadian!) in bacteria, and we ask the +

febs.onlinelibrary.wiley.com/doi/10.1002/...

Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...

Enterococcus faecalis redox metabolism activates the unfolded protein response to impair wound healing E. faecalis EET generates ROS, which induces the UPR in keratinocytes, inhibiting in vitro migration.

We’ve discovered how the superbug E. faecalis prevents chronic wounds from healing.

It’s not a toxin. It’s metabolism.

The bacteria use extracellular electron transport (EET) to electrochemically generate ROS, effectively "freezing" skin cells in place.

doi.org/10.1126/sciadv.aeb5297

Middle Author Bioinformatics This website describes a start-up company that specializes in bioinformatics analysis, software development, and teaching/outreach.

Reach out to @midauthorbio.bsky.social. We can help :)

midauthorbio.com#contact

Top: Cicada. Bottom: Bacterial cell being punctured by nanopillars.

Inspired by cicada wings, mechano-bactericidal surfaces are patterned with nanostructures that poke, cut and tear bacteria to death. Can they transform how we combat biofilms to protect human health? asm.org/articles/202...

Transcriptional and metabolic stasis define desiccation-induced dormancy in the soil bacterium Arthrobacter sp. AZCC_0090 until water vapor initiates resuscitation Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration o...

Our revised manuscript is up on BioRxiv and is coming soon to an ASM journal in your neighborhood.

We show that metabolome & transcriptome profiles are frozen in desiccated Arthrobacter and that water vapor induces resuscitation.

Happy to answer any Qs.

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

Microbial Evolution: Impacts on Human Health Call for Papers A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases. This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution. Submission – open until January 31, 2027 Guest editors Robert Woods, MD PhD, University of Michigan Camilo Barbosa, PhD, University of Michigan Silvie Huijben, PhD, Arizona State University

🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health

Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me

This will be great, please submit and share!
academic.oup.com/emph/pages/m...