morning, Liverpool :: My brain is buzzing this morning from a great day of science talks, posters, and chats yesterday. I can’t wait for day two today! #microevo25

No Evidence the Gut Microbiome Causes Autism neurosciencenews.com/asd-microbio...

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....

Homeward Bound! Yes, the #LTEE is homeward bound. After a few thousand generations in Texas, the lines are coming back to #MSU, along with Jeff Barrick, and his team. telliamedrevisited.wordpress.com/2025/07/28/h...

Avocet wading into your timeline #birds 🌿

Apparently, I’m photographing only grebes right now…. oh well! These two horned grebe chicks hatched a few days apart and the little one definitely wants to hang out with its older sibling while they explore their marsh home! #Birds #photography #wildlife 🪶

OMG you guys! I was totally surprised and thrilled today to learn today that my pine grosbeak photo is an honourable mention in the 2025 @birdscanada.bsky.social calendar photo contest! You can check out the story with other cool photos here: shorturl.at/iXPy9 #birds

I wish all our institutions, leaders, and politicians would do the same. Come on @mcmasteru.bsky.social - do the right thing!

mark, dare to ask dianne about 👇

So humbly honoured to have this recognition. But as we all of know, it really does take a village. This is a tribute to many. It’s important we look wholistically at what enables research innovation. I also invite you to think of all those who support you and be so grateful for them all - as I am.

IMPORTANT IMPORTANT IMPORTANT IMPORTANT Please watch the workshop video and COMMENT by 5:00 Monday 7/14 This is the source of the "no more model organism only grants in NIH-funded research" decree.

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...

Fresh from the press (from my brother Joao Xavier) www.nature.com/articles/s41...

The MERMan contingent at #microbio25 headed home today after a great week in Liverpool for the @microbiologysociety.org annual conference - Thanks to the society and organisers for putting on a great event, and supporting us in presenting 6 talks and 5 posters packed full of microbial evolution!

Paper! @phoebesilva.bsky.social's labour of love* optimising synthetic #CysticFibrosis mucus for growth of NTHi is out #MicroSky #Biofilm www.microbiologyresearch.org/content/jour... *more like seething resentment as the bugs steadfastly refused to grow in most things we threw at them ^_^

Another fabulous way to celebrate the #Solstice

Venn diagram

Angel? Spent some time with Forster’s terns last weekend. Incredible aerial acrobats #birds

Looking for examples of beautiful, controversial or impactful microbial modelling papers - ideally a mixture of the above! It’s for teaching in the context of microbial eco/evo/epi. The modelling should be relatively easy to understand for a master’s student with a biology background.

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation academic.oup.com/nar/advance-... #jcampubs

Attention long read metagenomists! This feels like an important read. Misassemblies stitching together bacteria, archaea, and euks all into the same contigs, yikes! Reports of circularisation isn’t robust. There’s a lot in here to ponder.

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

I was reading Botstein's "A theory of modular evolution for bacteriophages" (1980) and thinking about how concise the arguments are, and about all the ways reviewers nowadays would demand changes that mess up such an elegant paper. #phagesky nyaspubs.onlinelibrary.wiley.com/doi/10.1111/...

The sequel: youtu.be/EFCQoObWtvQ