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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
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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
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
~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
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
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
gutmichaelbio.me
I get my stickers made by my friends at @stickerninja.bsky.social. Their prices are a little higher than others, but your paying for fair employee wages and high quality materials that last forever. I can’t recommend them more highly.

Below is a sticker they printed for me.

stickerninja.com
Photo of a stack of stickers made by Sticker Ninja (Portland, Or). The sticker is rectangular shaped with a white border. The sticker features text that says “greetings from your microbiome. Remember to eat your fiber!” The ‘your gut microbiome’ text is formatted in the style of a vintage postcard with different gastrointestinal elements filled into the text. The background is a pink and purple view of inside a gastrointestinal tract showing villi.
May 29, 2025 at 7:58 PM
gutmichaelbio.me
Here are the troublemakers. The 6 fish that are **f’ing** up my data 😁
Heatmap of significantly expressed genes. Each column is a sample, and every row is a gene. The columns and rows are clustered based on similarity of up or down regulation/expression. There were 5-6 fish that were clustering out to the left here. Once I figured out that it was reproductive genes, it made sense. Whats neat is within this cluster you see some separation or differences between the 6 samples. Those differences are between male and female fish.
May 13, 2025 at 2:05 PM
gutmichaelbio.me
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:

🤭
Screenshot of a heat map, showing the relative affect sizes of genes and what they encode for in my gene expression transcript on mix data. These genes are a subset of thousands of other genes that were highly expressed in a few of my samples of the samples they were present in almost one fish across each of the eight treatments I have. I couldn’t for the life of me make any sense of the metadata that might explain why these fish were clustering together you know maybe they were heavily infection, burdened, or their Microbiome were similar but none of that was the case. I’m still new to analyzing transcript data so I hadn’t gotten to the gene imitation steps yet and when I did, I was shocked to find that pretty much all these genes that are making this group of fish cluster together are related to reproduction. List of gene annotations from the plot: gamete generation germ cell development spermatogenesis male gamete generation sexual reproduction reproductive process reproduction multicellular organism reproduction developmental process involved in reproduction multicellular organismal reproductive process cellular process involved in reproduction in multicel
May 13, 2025 at 1:58 PM
gutmichaelbio.me
Since science is on its way out, I’m putting together a portfolio for my stock photo modeling career

📸 Rion Mooneyham
Photo of me in a white lab coat in the fish room. I’m looking pensively at something. Probably nothing. Photo of me in a lab coat pretending to pipette science stuff. It’s just water. Photo of me smiling at a white board. I’m pointing at something doodles. It looks like I just made a hilarious joke with a colleague off camera (there’s no one there). Photo of me presenting in front of a projector screen. I’m holding what looks like a light saber pool cue for pointing at things.
May 9, 2025 at 6:23 AM
gutmichaelbio.me
Meant to teply to you yesterday, but let’s just say I’m all too familiar with the instant gratification monkey in his presentation 😆
Selfie of me with a stuffed animal monkey sitting on my shoulder. The monkey is from Tim Urban’s‘s TED talk about procrastination. The monkey is called the instant gratification monkey.
May 8, 2025 at 8:16 PM
gutmichaelbio.me
“Home is where the bidet is” embroidered patches just arrived!

I think they turned out great 🤎
An embroidered patch made by Patchdogs (Portland, OR), designed by me (not AI). The patch is circular. The center of the design features a toilet with water spraying upwards like a fountain with a brown colored heart. The background is a light tan/brown color. Surrounding the toilet is the phrase “Home is where the bidet is”. The text is “written” on toilet paper rolls that border the patch design. The patch is approximately 2.5” in diameter. This patch will be sent to June sticker club members at www.GutMichaelBio.me
May 3, 2025 at 8:41 PM
gutmichaelbio.me
This AI gen poster design for the Harvard Chan Microbiome in Public Health Center (HCMPH) symposium looks tacky as hell 👎👎

I would not want my research associated with this image.

What’s going on with the puff balls? Is it DNA or a ladder made of Cheetos? Are those pickles or giant balloons? 🤦🏻‍♂️
Poster for the Harvard Chan Microbiome in Public Health Center (HCMPH) symposium. The design features an AI generated image that looks half-assed and unfinished. Some of the design elements are nonsensical. The laziness of this design makes me feel less interested in attending, and I certainly wouldn’t want my research associated with the design. Yikes.
May 3, 2025 at 3:55 PM
gutmichaelbio.me
It’s 2025, and this mystery still hasn’t been solved…

…that ends TODAY!

www.instagram.com/p/DJKb8vzBtHw/
Selfie of me, holding a “white mystery” airheads candy with proper PPE gloves.
May 2, 2025 at 9:03 PM
gutmichaelbio.me
I’m getting targeted ads on instagram to emigrate to Australia, a quote “safe and secure societies”, and the place that is home to the deadliest creatures on the planet 😂
Instagram add promoting the “National innovation visa” for scientists to immigrate there. One of the supposed benefits stated in the ad is “live in a safe and secure society.” Here’s the full ad text: We're looking for exceptionally talented Americans. Learn more ausintheus Calling innovators, entrepreneurs, creatives. Accelerate your career. Enjoy an enviable lifestyle. Live in a safe and secure society. Australia is not just a great place to live. It's where experts build the future. We're looking for exceptionally talented individuals from across America to join us. Make the smart move to Australia and explore our National Results of searching “which country has the deadliest creatures”: “which country has the deadliest creatures Australia Australia is home to some of the world's deadliest animals, including snakes, spiders, and dangerous sea creatures like great white sharks and jellyfish”
April 28, 2025 at 6:30 AM
gutmichaelbio.me
I don’t have a dog in the fight, but couldn’t the same have been argued for Enron before it imploded?

(Idk if this table is actually true or not, the actual numbers aren’t my point)
Enron's revenues and income Fiscal year Net income Operating cash flow Revenues Enron's cash flow and revenues 1987 -$29 $184 $5,916 $ 120,000 1988 $109 $82 $5,708 $100,000 —Operating cash flow 1989 $226 $194 $9,836 —Revenues 1990 $202 $1,107 $13,165 $80,000 1991 $242 $791 $5,563 $60,000 1992 $306 $293 $6,325 1993 $333 $468 $7,972 $40,000 1994 $453 $504 $8,984 $20,000 1995 $520 -$15 $9,189 $O 1996 $584 $1,040 $13,289 1997 $105 $501 $20,273 -$20,000 1998 $703 $1,640 $31,260 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1999 $893 $1,228 $40,112 2000 $979 $4,779 $100,789 1997 1998 1999 2000 Source of data: Standard & Poor's Compustat
April 24, 2025 at 8:25 PM
gutmichaelbio.me
Maybe the underpaid humans working behind the scenes appreciate a little politeness when you ask them to do your homework assignment
Screenshot of a linked in post: Joshua Weaver, Ph.D. in • Following Product | Data 20m • © Is Al the new millennial? Al is now killing manners. If you need an incentive to be more human, research shows that being nice to Al does lead to better higher quality answers. Claire Anderson in • 3rd+ Founder | Brand Strategist | Art Director I build... 2d • + Follow Sam Altman said that saying "please" and "thank you" to ChatGPT wastes millions in computing power. @ Guilty. But it raises a question: Are we optimizing for efficiency or etiquette in the Al era? Every extra word costs compute power. But also, every interaction shapes how we think, behave, and create. So maybe the real cost isn't in politeness. It's in forgetting that behind the prompt is a human habit being reinforced. Small habits stack. If I train myself to be kind even when no one's watching, l'm more likely to carry that into the rest of my life. Curious where this balance leads us. Are you still saying "please" to your Al? #Al #ChatGPT #SamAltman #FutureOfWork #HumanCenteredDesign #LinkedInPrompt
April 24, 2025 at 5:13 PM
gutmichaelbio.me
New book arrived! Very excited to start reading it tonight.

Picked this book up because it surveys some texts at the intersection of ecology & philosophy of science
Book titled “The philosophy of ecology: from science to synthesis”. Written by and edited by DAVID R. KELLER AND FRANK B. GOLLEY Back cover of the book. This is the first introductory anthology on the philosophy of ecology edited by an ecologist and a philosopher. It illustrates the range of philosophical approaches available to ecologists and provides a basis for understanding the thinking on which many of today's environmental ideas are founded. Collectively, these seminal readings make a powerful statement on the value of ecological knowledge and thinking in alleviating the many problems of modern industrial civilization. Issues covered include « the challenges of defining scientific ecology, tracing its genealogy, and distinguishing the science from various forms of "ecological-like" thinking; « the ontology of ecological entities and processes; « selected concepts of community, stability, diversity, and niche; « the methodology of ecology (rationalism and empiricism, reductionism and holism); and ‹ the significance of evolutionary law for ecological science. David R. Keller is an assistant professor of philosophy and director of the Center for the Study of Ethics at Utah Valley State College. Frank B. Golley is Research Professor of Ecology, professor of zoology, and professor of environmental design at the University of Georgia. His books include A Primer for Environmental Literacy, A History of the Ecosystem Concept, and Tropical Rainforest Systems. CONTENTS List of Figures and Tables ix Preface xi Acknowledgments xili Introduction: Ecology as a Science of Synthesis PART ONE. Entities and Process in Ecology 21 1. Frederic E. Clements, Preface to Plant Succession: An Analysis of the Development of Vegetation 35 2. Henry A. Gleason, The Individualistic Concept of the Plant Association 42 3. Arthur G. Tansley, The Use and Abuse of Vegetational Concepts and Terms 55 4. Daniel Simberloff, A Succession of Paradigms in Ecology: Essentialism to Materialism and Probabilism 71 5. Robert E. Ulanowiez, Life after Newton: An Ecological Metaphysic 81 PART Two. Community, Niche, Diversity, and Stability 101 6. Karl Möbius, An Oyster Bank Is a Biocönose, or a Social Community 111 7. Robert H. Whittaker, Simon A. Levin, and Richard B. Root, On the Reasons for Distinguishing Niche, Habitat, and Ecotope 115 8. Ruth Patrick, Biological Diversity in Ecology 119 9. Andrew Redfearn and Stuart L. Pimm, Stability in Ecological Communities 124 PART THREE. Rationalism and Empiricism 133 10. Karl R. Popper, The Bucket and the Searchlight: Two Theories of Knowledge 141 11. Robert M. May, The Role of Tbeory in Ecology 147 12. Kristin Shrader-Frechette and Earl D. McCoy, Commanity Ecology, Population Biology, and the Method of Case Studies 153 PART FOUR. Reductionism and Helism 171 13. Thomas W. Schoener, Mechanistic Approaches to Ecology: A New Reductionism? 181 14. Eugene P. Odum, The Emergence of Ecology as a New Integrative Discipline 194 15. Donato Bergandi, "Reductionist Holism": An Oxymoron or a Philosophical Chimera of Eugene Odum's Systems Ecology? 204 16. Richard Levins and Richard C. Lewontin, Dialectics and Reductionism in Ecology 218 17. T. F. H. Allen and Thomas B. Starr, Hierarchy: Perspectives for Ecological Complexity 226 PART FIVE. Ecology and Evolution 233 18. David L. Hull, The Metaphysics of Evolution 247 19. Stephen J. Gould and Richard C. Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Program 263 20. Ernst Mayr, How to Carry Out the Adaptationist Program? 277 21. James P. Collins, Evolutionary Ecology and the Use of Natural Selection in Ecological Theory 288 22. Craig Loehle and Joseph H. K. Pechmann, Evolution: The Missing Ingredient in Systems Ecology 304 Afterword 320 Literature Cited 323 Index 361
April 14, 2025 at 5:09 AM
gutmichaelbio.me
Just got the proofs back for June’s sticker club drop. We’re doing patches!

“Home is where the bidet is”
Photo of a proof of an upcoming patch I’ll be sending to sticker club members. The patch features a toilet with water spraying out of it with a brown colored heart. Around this design are the words “home is where the bidet is” in brown and blue colored text. The text is split into two, on top of two rolls of toilet paper that form a circular crest or border around the toilet, water, and heart.
April 11, 2025 at 2:00 PM
gutmichaelbio.me
I almost got it working yesterday 😩
Stepping on a rake meme. Top panel person stepping on a rake in one step, bottom panel someone doing a kick flip over stairs and then hitting their face with the rake. Top panel caption: “writing my own bioinformatics pipelines”. Bottom panel caption: “using nf-core pipelines”
April 8, 2025 at 2:41 PM
gutmichaelbio.me
Woo! Congrats to Robyn. I did a lot of embryo sorting and behavioral microbiome research in her lab during my undergrad. Her lab and team are incredible.

And thanks for featuring my preprint 🥺
Photo of some hours old zebrafish embryos.
April 8, 2025 at 2:33 PM
gutmichaelbio.me
I have a 200ish lines of code for one ggplot. Why? Because I wanted pretty outlines
A simple looking plot that took a lot of code to make
April 3, 2025 at 2:33 PM
gutmichaelbio.me
Really beautiful how the paper ends talking about how knots are an intersection (weaving, if you will) of combinatorial thinking. Knots are everywhere!
We argue that knotting, alongside other important binding techniques (lashing, adhesives, etc.), has catalysed combinatorial thinking, enabling the imagination and experimentation with various combinations of technological elements. This has contributed to the evolution of new technologies and contributed to a combinatorial growth of innovations.
April 3, 2025 at 1:26 PM
gutmichaelbio.me
The granny vs reef knot discussion is really interesting too. Here’s a couple screen shots. The quote in the second screenshot in particular.
Cognitive and cultural adaptations and ethnomathematics Our data suggest that people across the world have paid meticulous attention to knotting, intentionally preferring more robust knots over unsecure ones. The obvious example is the high prevalence of the sheet bend, which is today a reputable knot for its reliability: it is secure yet easy to untie. Another reliable indicator of this is the low presence of the granny knot (ABoK #3). The granny knot is very similar in structure to the reef knot (Fig. 1B–C), both being composite products of two overhand knots. In contemporary knotting traditions, the reef knot is considered an essential knot, whereas the granny knot is notoriously unsecure and prone to slipping. Today, it is regarded a common novice mistake accidentally to tie a granny knot when attempting a reef knot (Van De Griend Reference Van De Griend1994, 14). In short, there is no functional reason to tie a granny knot when one could tie a reef knot. Previous theoretical discussion has suggested that the granny knot is more intuitive to tie than the reef knot, because unlike the reef knot, the granny knot repeats two overhand knots with the same orientation (Van De Griend Reference Van De Griend1994, 14). This has been shown to be the case with experimental work, which suggests that humans have a cognitive or motoric bias to construct the granny knot instead of the reef knot Against this backdrop, it would be reasonable to predict that in naïve knot-tying populations, the granny knot would appear more often than the reef knot (Scanlon et al. Reference Scanlon, Lobb, Tehrani and Kendal2019). Yet in our sample the exact opposite is the case. We document the reef knot in 23 cultures and the granny knot in only 8 (Fig. 5). Evidently, people around the world have knowingly preferred the secure reef knot over the insecure granny knot. This may also be indicated in some ethnographical descriptions. For instance, Navajo knot-tying traditions even involve a tabooFootnote 1 for using the granny knot for anything other than ceremonial purposes (Kluckhohn et al. Reference Kluckhohn, Hill and Kluckhohn1971, 232): The granny knot … was currently known as the ‘knot of the dead,’ and was avoided except in connection with preparation and dressing of the corpse prior to burial. … ‘This knot should never be found on a living person. … There are really two knots, one for the living [the reef knot] and one for the dead [the granny knot].’ A recent experimental study has indicated that individuals without prior knotting experience tend to have poor intuition when judging the strength or physical behaviour of knots (Croom & Firestone Reference Croom and Firestone2024). Given that our data suggest a preference for secure knots, we might infer that experienced string users have a refined cognitive ability to assess knots and/or that cumulative cultural knowledge can surpass individual cognition
April 3, 2025 at 1:26 PM