AA (Adjie) Pratama

Diversity and ecological roles of hidden viral players in groundwater microbiomes - Nature Communications Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect domina...

New paper from @adjiep.bsky.social on viral impacts in groundwater at Nature Comms. Congratulations Adjie and team!

Read: www.nature.com/articles/s41...

#viruses #viromics #groundwater

Another exciting publication from our group this week!
First comprehensive insights into viruses in groundwater microbiomes and their role in biogeochemical cycles.
Congrats to @adjiep.bsky.social and the team!

Very interesting strategy to sense infection!

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Building inclusive microbial communities 🌍
@adjiep.bsky.social (@kuesellab.bsky.social, @uni-jena.de & Sullivan Lab) shares how mentorship & representation can shape a more inclusive future in microbial sciences.
🎤 Meet him at the #ISME Early Career Researchers event on 21 Oct: lnkd.in/dXeyvnZK

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

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

#microsky #microbiome

Systematic genome-wide mapping of host determinants of bacteriophage infectivity Chitboonthavisuk et al. present PHAGEPACK, a CRISPRi-based screen that links host gene perturbations to phage fitness via a phage packaging-based readout. Applied in permissive and non-permissive E. c...

www.cell.com/cell-systems...

#phagesky #phage

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

📸 ISME is calling all microbial ecologists!
Send us your best photos & videos—lab, field, or under the microscope.
Winners will be featured on journal covers or on ISME promotional materials!
Deadline: 11 November 2025
Details 👉 isme-microbes.org/call-for-mic...
#MicrobialEcology

Fascinating preprint. I've always been curious about genome stability of phages.

🧫🦠

Phages communicate across species to shape microbial ecosystems Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

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

#microsky #phagesky #phage

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

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.

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes www.science.org/doi/full/10.... #jcampubs

Had a great time yesterday with Konstantinos Kormas (@kkormas.bsky.social), Irene Ramirez Hernandez & Akbar Adjie Pratama (@adjiep.bsky.social) at the professional pathway lunch, part of @mikrobiokosmos.bsky.social.
Thanks to @isme-microbes.bsky.social for making it possible!
#mbkceesme2025

In this new series, ISME would like to introduce the members of the Early Career Scientist Committee to you, starting with Chair Burak Avcı.

Find out more at isme-microbes.org/meet-ecsc-bu...

Ann Gregory, Co-Chair of the ISME Early Career Scientist Committee, introduces herself and her work on viruses to the ISME community.

Find out more at isme-microbes.org/meet-ecsc-an...

Learn more about new ISME Early Career Scientist Member Pam Engelberts's research, career, and the work she's been doing for BrisJAMS.

isme-microbes.org/meet-ecsc-pa...

New ISME Early Career Scientist Committee Member Akbar Adjie Pratama @adjiep.bsky.social has a joint position in Germany and the U.S.
Learn more about his career and interests at isme-microbes.org/meet-ecsc-ak...

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species https://www.biorxiv.org/content/10.1101/2025.07.30.667625v1

Synteny-aware functional annotation of bacteriophage genomes with Phynteny Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

🚨 New preprint 🚨

My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky

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

Hidden viral players: Diversity and ecological roles of viruses in groundwater microbiomes Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we anal...

“Hidden viral players: Diversity and ecological roles of viruses in groundwater Microbiomes”
We uncover how viruses shape groundwater microbial communities and ecosystem function.

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

Phages and phage-borne enzymes as new antibacterial agents Persistent and resistant infections caused by bacteria are increasing in numbers and pose a treatment challenge to the medical community and public health. However, solutions with new agents that will...

Phages as treatment for infections are coming. Lots of steps to get right first though.
@cmijournal.bsky.social #IDSky #ClinMicro
www.clinicalmicrobiologyandinfection.com/article/S119...

Environmental factors influence airborne microplastic deposition in the soil of urban allotment gardens The widespread contamination of urban soils by airborne microplastics (MPs) is an emerging environmental concern, particularly in urban allotment gard…

New paper out by former postdoc and Humboldt fellow, Luís Fernando Amato-Lourenço et al. with work done in Berlin community gardens

Environmental factors influence airborne microplastic deposition in the soil of urban allotment gardens

www.sciencedirect.com/science/arti...

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research - Nature Biotechnology Overcoming key hurdles for the development of next-generation anaerobic cultivation methods could have major impacts on microbial community research and applications.

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research www.nature.com/articles/s41... #jcampubs

New paper out!
We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp!
Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive.
It also represents a novel, deep-branching lineage in the archaeal tree.

NIOZ - Postdoc position (45 months):“Marine phytoplankton – virus interactions and loss rates from small to ocean scale” The Department of Marine Microbiology and Biogeochemistry (MMB; principal investigator and PHYVIR project coordinator Prof. Dr. Corina Brussaard) of NIOZ is looking for a talented and dedicated Postdo

Another position within the PHYVIR project 😁.
Are you looking for an interesting Postdoc (45 month!) on marine viral ecology? Check out the ad below.
workingat.nioz.nl/o/postdoc-po...

Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats Nature Communications - Biller et al. use long-read sequencing of fractionated ocean nanoparticles, showing that extracellular vesicles and virus-like particles contain distinct pools of genetic...

Exploring the horizontal gene transfer potential of virus-like particles and extracellular vesicles in the pelagic marine environment - www.nature.com/artic...

ISME is looking for the next destination for its symposium! Interested scientists can now submit an Expression of Interest for their city to be the host for ISME22 in 2030.
The deadline for Expressions of Interest is 1 April.
isme-microbes.org/call-for-bid...
#MicrobialEcology #microbes #isme22

Stable states in an unstable landscape: microbial resistance at the front line of climate change Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. We quantified microbial warming response over seven ye...

🚨🚨🚨 New pre-print alert: "Stable states in an unstable landscape: microbial resistance at the front line of climate change" doi.org/10.1101/2025...

Probably the most complex paper I have ever worked on. It took 4 (!) co-first authors to accomplish and literal years to decipher the story.