We surveyed 130+ people in climate biotech and interviewed 63 of them. We are excited to share the results: an interactive dashboard where you can explore the data, discover what we found, and develop your own conclusions. View the Climate Biotech Community Survey Dashboard: survey.homeworld.bio

Inspiration for the scientists working on soil: flags stained with soil from all 50 United States. (From Andy Goldsworthy's Red Flags).

Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

Zachary Sun is a great person and it’s been fun to watch his super affordable cell-free protein synthesis reactions absolutely LIGHT up with GFP. If you’re new to cell-free protein synthesis, Sepia Bio’s product is cheap- and good-enough you should think about what you can do with it.

Our new commentary rdcu.be/ftx6h in @natecoevo.nature.com written with folks from @inaturalist.bsky.social and @cornellbirds.bsky.social shows that use of AI to manipulate existing or create new wildlife images undermines the huge value of vast citizen science databases. 🌍🪰🪶 #Ornithology 🧵 1/10

Citizen science platforms must mitigate against the threat of generative AI

Nature Ecology & Evolution - Citizen science platforms must mitigate against the threat of generative AI

rdcu.be

Another barrier to genetic transformation of non-model microbes

Xavier Charpentier@labxc.bsky.social · 4w ago

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Following the formal description of Caldifarcimen microaerophilum, the candidate phylum WOR-3 has been officially renamed Caldifarciminota within the kingdom Pseudomonadati #microbiology #NewSpecies #taxonomy #bacteria #MicroSky @microbiologysociety.org doi.org/10.1099/ijse...

To guess which uncultured bacteria are multicellular, and therefore trickier to culture, might be able to use BGC size as a proxy

Rauf Salamzade@raufs.bsky.social · last mo.

Microbes that have the greatest genomic potential for secondary metabolism tend to be multicellular. Here, we show that signatures of ancestral BGC expansions within 3 bacterial phyla and 2 fungal lineages coincide with origins of complex multicellularity [1/12] 🧵 www.nature.com/articles/s41...

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

While some might argue that the golden age of Streptomyces in antibiotic discovery has passed, these organisms can still surprise us 🦠🧫🔬🤓 #microbiology #antibiotics #NaturalProducts #MicroSky @nature.com doi.org/10.1038/s415...

A Streptomyces megacluster encodes synergistic biotin-targeting antibiotics - Nature

In Streptomyces spp., a conserved biosynthetic gene megacluster produces an arsenal of distinct antimicrobials that converge on bacterial biotin biosynthesis as a naturally evolved combination therapy...

doi.org

NBD, only >4 years of microbial enrichment "After approximately 1.5 years of incubation... the enrichment cultures underwent two successive transfers at 4-month intervals... This subculturing process was repeated six times, each at 4-month intervals." Filters used to get the ultrasmall episymbiont.

Masaru Nobu@masarunobu.bsky.social · last mo.

Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...

A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing www.pnas.org/doi/10.1073/... #jcampubs

A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing | PNAS

While methods exist to indirectly quantify the metabolism of biological systems, directly measuring metabolic rates in living samples remains chall...

pnas.org

Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals #microbiology #archaea #ammonia #MicroSky @isme-microbes.bsky.social doi.org/10.1093/isme...

Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals

Abstract. Ammonia-oxidizing archaea (AOA) have repeatedly been detected with molecular methods on human skin, yet their persistence, physiological traits,

doi.org

MicrobioME: a CURE model for diverse microbiology laboratory classrooms journals.asm.org/doi/10.1128/... #jcampubs

Nostalgia Content xkcd.com/3256/

Introducing openRxiv Labs! 🔬 Growing from the strong foundation of bioRxiv & medRxiv, Labs is an experimental space for working with collaborators to push the boundaries of open scientific communication. 👉 Check it out and learn more: openrxiv.org/openrxiv-lab... #OpenScience #Preprints #Scicomm

Launching openRxiv Labs - openRxiv

Over the last thirteen years, bioRxiv and medRxiv have grown into widely used infrastructure for rapid research sharing in biology and medicine. The reliability and researcher-first values that have d...

openrxiv.org

🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5

Enter PHLEGM! 💻🧬 We developed the Phage Homomer Level Estimate and Generation Method to infer oligomeric state using AlphaFold-Multimer and interface quality assessment. We applied it to >22,000 sequences, revealing massive structural diversity. (2/n)

Check out this exciting new paper in @currentbiology.bsky.social from my friend and collaborator @stephaniesimone.bsky.social’s lab on the genomics of novel rhizobium endosymbiosis www.cell.com/current-biol...

The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria

Resolving early steps in how hosts and microbes unite in novel endosymbiosis is critical for understanding key evolutionary innovations and ecosystem functions. Montoya et al. reveal how mobile geneti...

cell.com

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

Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

Lots of folks don't know that certain phage can infect bacteria across taxonomic orders

Cameron Thrash@jcamthrash.bsky.social · 3mo ago

A polyvalent phage shapes bacterial dynamics journals.asm.org/doi/10.1128/... #jcampubs

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

agtools: A Software Framework to Manipulate Assembly Graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

Doing the periodic cleaning of used plasmid miniprep columns and realized in honor of Earth Day it may be worth reminding you molecular biologists: Plasmid miniprep columns can be cleaned and reused essentially indefinitely! Just add 1 M HCl, soak overnight and wash 3x w/ water. Save $ and plastic

A droplet microfluidic-based platform for enhanced DNA delivery in non-model organisms www.biorxiv.org/content/10.6... #jcampubs

Every microbiologist needs a photo this cool. Media is cheap - grow your microbe in giant bags and stand in front of it

The New York Times@nytimes.com · 3mo ago

J. Craig Venter, a scientist and entrepreneur who decoded the human genome, has died at 79.

An Asgard archaeon from a modern analog of ancient microbial mats (Current Biology) Beautiful microscopy of an Asgard archaeon, in the same family as Lokiarchaea, in syntrophy with a sulfate-reducing bacteria Very very nice paper we saw in preprint form: www.cell.com/current-biol...

Biology labs looking to reduce costs or increase throughput should consider switching from kits for DNA and RNA purification and size selection (e.g. plasmid or PCR products) to… magnetic beads. The BOMB platform (Oberacker 2019, 338 citations) claims 10-20x cost reduction.

You can now run a multiple sequence alignment directly on your SeqHub search results. Once the alignment runs, conserved regions are mapped onto the 3D structure of your query protein. Explore results in SeqHub or download as an a3m file.

Read this!

Marta Skreta@martaowesyou.bsky.social · 4mo ago

What if AI could invent enzymes that nature hasn’t seen? 👩‍🔬🧑‍🔬 Introducing 🪩 DISCO: Diffusion for Sequence-structure CO-design 📝 Blog: disco-design.github.io 📄 Paper: arxiv.org/abs/2604.05181 💻 Code: github.com/DISCO-design...