A genomic catalog of Earth’s bacterial and archaeal symbionts #symbiosis www.nature.com/articles/s41...

A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

nature.com

Research Briefing: Machine learning interprets genome sequences to map possible microbial symbionts www.nature.com/articles/s41... rdcu.be/VJ76sLyg4Q6a

Machine learning interprets genome sequences to map possible microbial symbionts - Nature Biotechnology

A machine-learning framework called symclatron uses genome sequencing content to predict whether uncultivated bacteria and archaea live independently or in close association with hosts. Applied to a g...

nature.com

🍄 @jgi.doe.gov's Fun-Guys and Fun-Gals have been busy this summer! ☀️ New fungal genomes in MycoCosm: ✔️ Hanseniaspora uvarum NRRL Y-1614 ✔️ Semicentenialea rex gs25 v1.0 ✔️ Amoeboaphelidium occidentale KS120 v1.0 ✔️ Neocallimastix sp FC1 v1.0 ✔️ Boletus sp. 2018DF043 v1.0 mycocosm.jgi.doe.gov 🍄🧬🔬

Giant virus evolution unfolding in real time 🦠🔬👀 Analyzing 20 years of metagenomic data from Lake Mendota Cool work by @jgi.doe.gov postdoc Yumary Vasquez. Also involved: @miferg.bsky.social @robinrohwer.bsky.social @quendi.bsky.social @fmschu.bsky.social & others jgi.doe.gov/user-science...

A Broader Sense of Evolution Over Time | Joint Genome Institute

Analyzing how giant viruses—and interns—respond to environmental change.

jgi.doe.gov

A genomic catalog of Earth’s bacterial and archaeal symbionts - @fmschu.bsky.social @jgi.doe.gov www.nature.com/articles/s41...

A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

nature.com

New AI Tool Maps the Global Catalog of Microbial Symbionts 🖥️ 🧬 🦠 Today in @natbiotech.nature.com: The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms. Learn more ⬇️

New AI Tool Maps the Global Catalog of Microbial Symbionts | Joint Genome Institute

The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms.

jgi.doe.gov

A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨 New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more 🔓 www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov

A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

nature.com

Joint Genome Institute@jgi.doe.gov · 2mo ago

New AI Tool Maps the Global Catalog of Microbial Symbionts 🖥️ 🧬 🦠 Today in @natbiotech.nature.com: The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms. Learn more ⬇️

Identification of CprV during bacterial sporulation reveals insight into how developing cells monitor compartmental integrity during cellular remodelling and differentiation. @crodrigueslab.bsky.social @warwicklifesci.bsky.social PDF available: www.nature.com/articles/s42...

A safeguarding factor monitors septal pore stability to secure compartmentalization during sporulation in Bacillus subtilis - Communications Biology

Identification of CprV during bacterial sporulation reveals insight into how developing cells monitor compartmental integrity during cellular remodelling and differentiation.

nature.com

Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb

Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

nature.com

The Princess Bride (1987) Director: Rob Reiner

I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)

Evolution induced state shifts in a long-term microbial community experiment (now out, but previously posted here as a preprint) with Ville Mustonen, Lutz Becks @jcairns.bsky.social & others. Experiment continues @utu.fi and now 5+ years www.pnas.org/doi/10.1073/...

Evolution induced state shifts in a long-term microbial community experiment | PNAS

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...

pnas.org

Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com : academic.oup.com/bioinformati... Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social ! See the thread below for more details.

microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and

academic.oup.com

Sebastian Schmidt@tsbschm.bsky.social · 10mo ago

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...

Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images

AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma

doi.org

Very nice experimental study from Jessica Purswani's lab. Full factorial design of microbial consortia where multiple plant growth-promoting functions were measured. doi.org/10.1111/1751...

BSocial Tool Deciphers Highly Functional Plant Growth‐Promoting Bacterial Consortia

The use of the online tool BSocial can be used to decipher microbial social behaviour and select highly functional plant growth-promoting consortia. Positive correlations are observed between species...

doi.org

Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses

Beyond thrilled that our paper ‘Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers’ has been accepted in Nature Communications! 🎉🦠 (1/n) www.nature.com/articles/s41...

Prokaryotic Pangenomes Are Bet-Hedging Devices www.biorxiv.org/content/10.6... #jcampubs

Tired of the uncertainty in dating? This one weird trick will bring back the confidence to your dating!

Cognition without brains? Learning and memory in microorganisms @cp-trendsmicrobiol.bsky.social Review by Andreas Messer, Leonardo Oña, and @kostchristian.bsky.social www.cell.com/trends/micro...

Cognition without brains? Learning and memory in microorganisms

Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learni...

cell.com

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

🪐🌌☄️ 🔭 Largest ever map of universe from #DESIsurvey captures 47 million galaxies and quasars, via @newscientist.com.

Berkeley Lab Press@berkeleylabpress.bsky.social · 7mo ago

"The @desisurvey.bsky.social is still the leading instrument like it in the world," says @berkeleylab.lbl.gov's David Schlegel. It completed its initial 5-year survey and mapped 47 million galaxies and quasars. The experiment will continue observations into 2028.

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

DefensePredictor: A machine learning model to discover prokaryotic immune systems

Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...

science.org

Peter DeWeirdt@pdeweirdt.bsky.social · 2y ago

Excited to share our work using machine learning to predict anti-phage defense systems! 1/n

Excited to share my latest work on synthetic biology and host–microbe interactions, now published in Nature Communications! www.nature.com/articles/s41...

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization - Nature Communications

This study reveals how plant-associated bacteria dynamically reprogram gene expression during root colonization, using a new high-throughput approach that overcomes low bacterial biomass and interfere...

nature.com

Our vision is to lead AI-driven genomic innovation to advance biotechnology. We provide advanced genomic capabilities, large-scale AI-ready data & professional expertise to support the global research community. More at jgi.doe.gov/mission

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

Critical Minerals and Materials Genomics🧬 meets Nanoscience🔬 to enable recovery, reuse, and transformation of CMMs New joint user opportunity from @jgi.doe.gov and @molecularfoundry.lbl.gov at @berkeleylab.lbl.gov Join our informational webinar on Feb 27, 9am PT: jgi.doe.gov/work-with-us...

This study looks at microbiomes in aerial surfaces of plants and their roles in environmental processes, in order to advance microbiome utility across the bioeconomy. @ucmerced.bsky.social 🖥️🧬 🦠 🌱 https://jgi.doe.gov/user-science/science-stories/secrets-needles-what-microbes-do-conifer-leaves

Secrets of the Needles: What Microbes do on Conifer Leaves | Joint Genome Institute

Novel study looks at microbiomes in aerial surfaces of plants, and their roles in plant health and environmental processes

jgi.doe.gov

Deployable high-fidelity metagenome binning at scale with QuickBin https://www.biorxiv.org/content/10.64898/2026.01.08.698506v1