Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

Pelagibacter, resolved www.biorxiv.org/content/10.64898/2026.04...

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

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

A new study exploring the diversity of microbial life encapsulated in global metagenomic contigs reveals there could be at least 250,000 bacterial species and potentially up to 750,000, with only a fraction that have genomic representatives

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

Nice highlight of both Laub's lab and our work !
www.science.org/doi/10.1126/...

Still so much to discover in the amazing world of bacteria immunity 🧬🦠🛡️

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Cultivation and genomic characterization of the first representative of the globally distributed marine UBA868 group | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil

Want to convert old relative abundance ocean amplicon data into absolute abundances? Williams et al. show a flow cytometry "anchor" can provide reasonable absolute abundances, validated by internal-standard corrected metagenomics with single copy genes, and amplicons academic.oup.com/ismecommun/a...

Arbitrium phages can manipulate each other’s lysis/lysogeny decisions Arbitrium phages belonging to different species and genera can influence each other’s infection dynamics by secreting chemically similar, non-cognate signal peptides. These findings indicate that arbitrium-based communication is not as specific as previously thought.

Now online! Arbitrium phages can manipulate each other’s lysis/lysogeny decisions

Predator-prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions Abstract. Vibrio cholerae is a ubiquitous marine bacterium that solubilizes and consumes chitin in the marine water column. In both the marine environment

Predator-prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions

#ISMEJournal from Carey Nadell

academic.oup.com/ismej/advanc...

Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans www.nature.com/articles/s41... #jcampubs 🌊

River Microbiomes as Sentinels of National‐Scale Freshwater Ecosystems River biofilms are complex microbial assemblages that underpin aquatic food webs and play a central role in biogeochemical cycling. By responding to environmental signals over space and time, biofilm...

Using river biofilm microbiomes as sentinels of national-scale freshwater ecosystems

Very impressive coverage of England's river system with 700 sites included!

onlinelibrary.wiley.com/doi/10.1111/...

A methylotroph, a CPR parasite, and their phages (including a filamentous one), what's not to love 😍

Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics Abstract. Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coe

Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics

#ISMEJournal from @joshuasweitz.bsky.social

academic.oup.com/ismej/advanc...

Characterization of phytoplankton-excreted metabolites mediating carbon flux through the surface ocean www.pnas.org/doi/abs/10.1... #jcampubs 🌊

Our new paper on the presence of xenobiotics in marine dissolved organic matter just come out. Thanks to Jarmo Kalinski and our awesome collaborators, we were able to reanalyze more than 20 public LC-MS/MS datasets from seawater and ask how many anthropogenic compounds we can detect. rdcu.be/e8q6C

The archaeal roots of eukaryotic life www.pnas.org/doi/abs/10.1... #jcampubs

In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut?

TLDR: Not much overall, in specific bacterial species.
🧵

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

Water mass specific genes dominate the Southern Ocean microbiome - Nature Communications Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale uniqueness and water-mass–spe...

Water mass specific genes dominate the Southern Ocean microbiome www.nature.com/articles/s41... #jcampubs 🌊

Gracias a Alejandro López y a @elpaismexico.bsky.social por cubrir nuestro último estudio en #melanoma #acral, realizado estudiando pacientes mexicanos 🇲🇽

Con @pbasurto.bsky.social y @christianmolinaag.bsky.social en portada, investigadores clave en este estudio 🤓💻🧬🧫

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

Great to see this amazing resource finally published !

MicrobeAtlas - 2.4 million SSU rRNA gene sequence datasets systematically analysed against an extensive full length reference database enabling tracking of OTUs at global scales!

www.cell.com/cell/fulltex...

Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts Abstract. Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts

Excited to share that @michelle-hauer.bsky.social's paper with @katiekliermicrobe.bsky.social @maggielangwig.bsky.social @karthik-a.bsky.social on phage interactions with chemosynthetic symbionts was published today. #NSF and @schmidtocean.bsky.social supported. academic.oup.com/ismecommun/a...

I'm happy to share our new review with @lau-co89.bsky.social @liigh-unam.bsky.social just published in @genomebiolevol.bsky.social

Recent microbial evolutionary insights from metagenomics
academic.oup.com/gbe/advance-...

Inspired by the session "Molecular evolution through metagenomics" at #SMBE24

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/...

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Matters Microbial #122: Jumbo Marine Viruses and Nanoscopic Warfare YouTube video by MicrobeTV

Also a new Matters Microbial is live on our YouTube channel! @markowenmartin.bsky.social welcomes Dr. Alaina Weinheimer, to the quality quorum to discuss new and intriguing marine viruses, including Jumbo Phages!

LAUNCH DAY🎙️

We're thrilled to share the very first episode of #MVIFconversations w/ Jack Gilbert 💫

Stefanie Malan-Müller & @cpavloud.bsky.social talked with @gilbertjacka.bsky.social about how microbes shape our health and the invisible living world around us.

Give it a listen & spread the word!

Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?

Then come and join our group !

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

Really cool pre-print by Ellie Tong and my supervisor @btemperton.bsky.social that I'm proud to have a even a little role in! Bacterial resistance to one Pseudomonas phage coneys susceptibility to another!! Super cool stuff, exited to see where this leads!

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

New preprint led by Ellie Tong! Using phages targeting the inner core of LPS in PAO1, we found that when bacteria evolved resistance to one phage via genomic deletions, they became vulnerable to another revealing a resistance trade-off. #Microbiology #PhageTherapy
www.biorxiv.org/content/10.6...