Polling the council of smart people again. What's the current state of the art tool(s) for calling/identifying AMR genes en masse--e.g. in metagenomic plasmids? Please share for reach. :-)

Does anyone have examples of their own or others of how to best structure a GitHub repository for a scientific peer-reviewed manuscript? #Science 🧪

Hey team! What are your favorite metagenomic plasmid identification tools these days? I have a list circa 1-2 years ago, but like to poll the audience every so often. I'd say GeNomad, PlasForest, PlasX, maybe PPR-Meta would be my go-tos. Any others you think should be included? Please share :-)

Host-asssociated, especially human, metagenomics colleagues! Is there a current best-practice pipeline for removing human (long) reads from a metagenome at this point? We usually just map against the host reference, but are their classifiers that really work well for this?

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments? My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database. Please share around for visibility.

Possums in your yard? News got you down? Fear not, I have made playlists for the A and B sections of my ongoing Statistical Rethinking course. Click the section of your choice, sit back, and forget the possums and decay of the international order while your brain updates. github.com/rmcelreath/s...

If you're doing innovative research about #microbiota and received an MD &/or PhD in last 10 yrs don’t forget to apply for the NOSTER & @science.org Microbiome Prize! Grand Prize: $25K & your essay published in Science Magazine Deadline: Feb 14th Enter: buff.ly/5GKZgUN

Happy “Bowel”-idays!

I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students. I will record lectures & all will be found at this link: github.com/rmcelreath/s...

Hey Team! What do you think are the best free digital notebooks these days. I've used: Evernote--great, but now it's paid TiddlyWiki wasn't bad, but got rid of scrollable code blocks Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki. Suggestions?

We're at 735 registrants and counting! 🎉🦠 If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health. Please share with your networks. 🔗👇 isbscience.org/events/2025-...

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)! We're looking for someone keen on bioinformatics and microbiome evolution. Important info below on eligibility & URSA competition funding👇 www.findaphd.com/phds/project...

Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!

It comes with both great excitement and regret that I have attained a PhD in Microbiology. I'm excited for what comes next, but sad that I can no longer use the phrase "Dear Dr. Sieler" to filter out 90% of the spam emails I receive. 🪦 RIP my inbox

This candid photo taken of me on my last slide of my PhD defense really sums it all up, doesn't it? 😆 Thank you to all who attended in person, virtually, or wished me well wishes. I'm officially a PhD! Still processing that, but happy to moving on to the next chapter of my life 🚀 #Phd

I designed a limited run of zebrafish gut microbiome-themed stickers for anyone attending my defense next Monday. Love the holographic effect on them! #Zebrafish #Gutmicrobiome #stickers

A host has never been just a host. A host has always lived as a multiscale holobiont made from context-sensitive cells of host and microorganisms. It is ultimately this dynamic composition that determines forms, functions, and their endless variations. www.science.org/doi/10.1126/...

My entire PhD dissertation. 5 years. 45k words. Countless laughs and tears :) What a journey

Does anyone have any tips or advice for how to include supplementary tables and figures into your dissertation when you have 100's of them? For example, my first two research chapters I have all of mysupplementary tab/fig in supplementary docs, but how do people incorporate these? #PhD #Gradschool

~25 days until I defend my PhD! “Defining the context dependence of how the zebrafish gut microbiome responds to environmental stressors” Aug 25, 10am PST Please message me if you’d like to attend virtually! #zebrafish #microbiome #microsky

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome. See thread for more information and reach out!

This week's #substack is a recent podcast conversation, where we chat about the human microbiome, health, and some new work from the lab that involves predicting diet from poop DNA. gibbological.substack.com/p/a-conversa...

It’s finally published! Yay 🎉 Check the thread to get the gist or check the article in the link 👇👇

This 4:30am post brought to you by our sponsors at Anxiety and Looming Deadlines. Now back to our regular programming of tossing and turning.

I’m really enjoying the critical discussions happening already at the @microsocequity.bsky.social Microbiome Stewardship Summit! It’s not too late to join the Summit and workshops this week! microbesandsocialequity.com/events/mse-s... #MicrobiomeSky #MicroSky #Microbiomes #Microbiology 🧪🧫

July will have some very cool opportunities for folks interested in #STEM! Check out some of them on my #Substack newsletter. For more updates and regular opportunities in your inbox, subscribe for free ☺️❤️ microbephd.substack.com/p/july-oppor... #scicomm #academicsky #academia #research

Woke up today with a dozen new grey hairs in my beard. Also, definitely unrelated, I have 58 more days until I defend 😳

The virtual Summit on Microbiome Stewardship is just two weeks away!!! Program details and free registration can be found here.  Please note, the webinars and the workshop each require registration to help us manage attendance. Who should attend? Students, and professionals from any discipline,…

Left a couple stickers at the Piedmont Station food cart pod in Portland, Or this weekend.

Did I finish the last book I posted about on here? No. Am I starting a new book and posting about here? Yes.

SciCom folks! Where do y’all buy stickers now? I remember there were suggestions when all the bad stuff about sticker 🫏 came out but I can’t remember any of them! 🧪

T-minus 90 days to PhD defense and all I gotta do is: - Revise peer review edits to manuscript - Complete dissertation 4th chp analysis and write - Write intro and conclusion for diss - Prepare defense presentation - Assist a microbiome analysis workshop - Try not to lose my mind I think that's all

Using museum specimens for microbiome analyses? We tested it out - and it seems these samples could be an untapped resource for understanding host-microbe interactions! ⬇️

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

I’m trademarking “Shit Eating Grin Toothpaste”, a probiotic toothpaste that improves your dental hygiene and mental health. Stay tuned for our next product “FMT: Fecal Microbiota Toothpaste”

Microbiome folks: one of my former students is a Gilliam fellow & is looking for an HHMI lab for a postdoc in the next year-ish. She has a lot of bioinformatics (16S for sure, I am not sure what else) experience. Have any leads?

Just heard two people sneeze at the same time and then say “cheers”

Wow! Very cool. But, I guess this means I need to rerun my transcriptomics data I analyzed a couple weeks ago 🫠

Some exciting news! NCBI has finished the annotation pipeline for our new #zebrafish reference sequence GRCz12tu: www.ncbi.nlm.nih.gov/refseq/annot... This is a big step up in data depth and quality and should be super helpful going forward.

When I was in middle school I used to use thesauruses to find sumptuously decorated words. I need the opposite now, a word squeezer? How can I fit the most words into the fewest characters possible for this dang proposal?

Some samples were clustering very tightly in my transcriptomics data, and I couldn’t figure out why. Nothing about the sample’s metadata, treatment assignment, or microbiome characteristics seemed to line up. Then I looked at what the gene functions were identified as: 🤭

900 People Are Collectively Driving an 'Internet Roadtrip' on Google Street View 🔗 www.404media.co/900-people-a...

A PhD position is available in my lab at the University of Geneva to explore the interaction between gut microbes and behavior in social bees. Please share with potential candidates. Application deadline: May 25th. More info and how to apply: tinyurl.com/PhDmgbee

Since science is on its way out, I’m putting together a portfolio for my stock photo modeling career 📸 Rion Mooneyham

I really dislike how often the bloodborne pathogen trainer is saying the phrase "Portals of Entry"

Woke up today and realized it’s May, and I have 3.5 months until I defend my PhD 😳 Where did the last 3 months go?

Happening this Thursday! RSVP at: tinyurl.com/BoldPhD #academicsky #microsky #blackinmicro #phd #gradschool #stem #brownu

This month's sticker drop from @gutmichaelbio.me are frickin amazing, as always!!

“Home is where the bidet is” embroidered patches just arrived! I think they turned out great 🤎

Are there examples of anaerobic marine eukaryotes (micro or macro) that raise the pH of their surroundings to modulate microbial activity or communities? pH 9-ish.