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gutmichaelbio.me
GutMichaelBiome
@gutmichaelbio.me
1.2K followers 450 following 630 posts
Gut microbiome scientist & stickerer
🐟💩👨🏻‍🔬🧪🧫👨🏻‍💻📊📈🤯
PhD | Sharpton Lab | OSU 🦫
Future Postdoc in Liberti Lab at UniGe🇨🇭
MichaelSieler.com
Posts Replies Media Videos
Reposted by GutMichaelBiome
stevenjrobbins.bsky.social
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?
November 26, 2025 at 9:49 PM
Reposted by GutMichaelBiome
gibbological.bsky.social
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-...
November 26, 2025 at 5:19 PM
Reposted by GutMichaelBiome
gmeric.bsky.social
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...
The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com
PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com
www.findaphd.com
November 12, 2025 at 1:20 PM
Reposted by GutMichaelBiome
stevenjrobbins.bsky.social
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!
November 11, 2025 at 8:21 PM
gutmichaelbio.me
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
August 29, 2025 at 4:29 PM
gutmichaelbio.me
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
Photo of me in the foreground behind some computer monitors. Behind me is a slide that depicts a fish with cursive text saying "that's all folks", a nod to the looney tunes conclusion scene. There's also a sentence that says "please take a sticker!" I'm making a silly face for some reason. Photo credit: Eddie Fuques Close up of me from other photo
August 28, 2025 at 7:58 AM
gutmichaelbio.me
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
Selfie of me with a colorful fabric background, looking down at a sticker I’m holding with my thumb and finger. The sticker is of a cartoon drawing of zebrafish and its gut microbiome. There’s a slight holographic shimmer effect. The fin says “zebrafish (Danio rerio)” Close up photo of my hand holding a sticker that is a cartoon drawing of zebrafish and its gut microbiome. There’s a slight holographic shimmer effect. The fin says “zebrafish (Danio rerio)”
August 20, 2025 at 9:50 PM
Reposted by GutMichaelBiome
symbionticism.bsky.social
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/...
The disciplinary matrix of holobiont biology
Uniting life’s seen and unseen realms guides a conceptual advance in research
www.science.org
August 17, 2025 at 11:23 PM
gutmichaelbio.me
My entire PhD dissertation.

5 years. 45k words. Countless laughs and tears :)

What a journey
Screenshot of all the pages included in my dissertation in one view.
August 4, 2025 at 11:35 PM
gutmichaelbio.me
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
August 1, 2025 at 9:31 PM
gutmichaelbio.me
~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
PhD defense flyer that reads: “Defining the context dependence of how the zebrafish gut microbiome responds to environmental stressors” Michael Sieler PhD Defense Sharpton Lab ALS 4000 AUG 25th, 2025 10:00 A.M., PST Zoom: DM me for Zoom link Oregon State University #zebrafish #microbiome #microsky
July 31, 2025 at 3:15 PM
Reposted by GutMichaelBiome
contaminatedsci.bsky.social
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!
July 22, 2025 at 7:34 PM
Reposted by GutMichaelBiome
gibbological.bsky.social
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...
A conversation about the human gut microbiome
Still working on my next post, so I thought I’d share a recent conversation with Dr.
gibbological.substack.com
July 22, 2025 at 3:56 PM
gutmichaelbio.me
It’s finally published! Yay 🎉

Check the thread to get the gist or check the article in the link 👇👇
July 22, 2025 at 7:02 AM
gutmichaelbio.me
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.
July 11, 2025 at 12:51 PM
gutmichaelbio.me
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 🧪🧫
https://microbesandsocialequity.com/events/mse-summit-2025.html MICROBES AND SOCIAL EQUITY Virtual Conference MSE Summit 2025: Pathways to Microbiome Stewardship 7 - 10 July 2025 + Add to calendar -..========- Virtual (Zoom Webinars + Zoom Meetings) Overview Registration Organizing Team Virtual Access BOOK NOW MICROBES AND SOCIAL EQUITY The 2025 Microbes and Social Equity (MSE) Summit: Pathways to Microbiome Stewardship will be held online from July 7-10, 2025. This virtual summit convenes experts in microbiology, policy, public and environmental health, and social justice to discuss, refine, and expand the draft working definition and guiding principles of microbiome stewardship. A core concept of the Microbes and Social Equity (MSE) group is recognising the links between microbiomes, social equity, and environmental health. Our ability to develop practices and advocate for policy reform that address societal inequities is limited without a strong microbiome stewardship framework. Led by MSE and the Microbiome Stewardship working group, participants will co-develop this framework and use it to plan a pathway to bring their own work in line with principles of conservation and stewardship. Participants will also design case studies or future research which provide tangible and meaningful outcomes relevant to their area of focus. Originally planned as an in-person gathering at the University of Maine, the summit has transitioned to a fully virtual format and opens new opportunities to engage a wider, more global audience in this essential conversation. MICROBES AND SOCIAL EQUITY Why Attend? • Webinars and Case Studies (Monday and Tuesday): Open to everyone, these sessions will feature insightful presentations from leading researchers, policymakers, and community leaders. Join us to hear the latest in microbiome science, social equity, and public health, and leave with new perspectives and ideas to help shape future efforts. • Interactive Workshops (Wednesday and Thursday): Selected participants will come together in these collaborative sessions to co-develop case studies that integrate research, practice, and policy. With a focus on actionable outcomes, these workshops provide an opportunity to work closely with experts and contribute directly to the development of a global microbiome stewardship framework. Participation is by application, ensuring a diverse group of voices and expertise.
July 7, 2025 at 5:04 PM
Reposted by GutMichaelBiome
moadlc.bsky.social
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
July Opportunities for Aspiring MD/PhDs & PhDs!
Are you an undergrad or grad student interested in STEM careers? Check out these opportunities!
microbephd.substack.com
July 3, 2025 at 5:42 PM
gutmichaelbio.me
Woke up today with a dozen new grey hairs in my beard.

Also, definitely unrelated, I have 58 more days until I defend 😳
June 27, 2025 at 2:49 PM
Reposted by GutMichaelBiome
drsueishaq.bsky.social
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,…
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, are encouraged to attend! The summit is highly interdisciplinary and we welcome diverse perspectives: research presentation and workshop activities represent microbiome, ethics, health, food systems, ecology, and environmental sciences, and more!
sueishaqlab.org
June 23, 2025 at 2:56 PM
gutmichaelbio.me
Left a couple stickers at the Piedmont Station food cart pod in Portland, Or this weekend.
Sign that says “woodstocks library and water station”. A “home is where the bidet is” sticker sits tucked into the frame of the sign. Close up of the “home is where the bidet is” sticker tucked into a sign frame.
June 23, 2025 at 3:43 AM
gutmichaelbio.me
Did I finish the last book I posted about on here? No.

Am I starting a new book and posting about here? Yes.
Photo of: “WONDERFUL LIFE The Burgess Shale and the Nature of History” By STEPHEN JAY GOULD
June 2, 2025 at 6:29 AM
Reposted by GutMichaelBiome
binningsingletons.com
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! 🧪
May 29, 2025 at 7:32 PM
gutmichaelbio.me
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
May 29, 2025 at 7:45 PM
Reposted by GutMichaelBiome
kevindkohl.bsky.social
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! ⬇️
May 27, 2025 at 10:21 AM
Reposted by GutMichaelBiome
stevenjrobbins.bsky.social
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...
The planktonic microbiome of the Great Barrier Reef
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...
www.biorxiv.org
May 21, 2025 at 7:34 AM