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GutMichaelBiome

@gutmichaelbio.me
1.2K followers 504 following 667 posts

Gut microbiome scientist & stickerer 🐝 Postdoc in Liberti Lab at UniGe🇨🇭 • Microbiome-gut-brain axis of eusocial bees • 💩👨🏻‍🔬🧪🧫👨🏻‍💻📊📈🤯 Science: MichaelSieler.com Stickers: GutMichaelBio.me

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GutMichaelBiome @gutmichaelbio.me · 17/08/2026
“To bee or not to bee” Had so much fun at the poster session this evening, but my voice is all gone 😪 Thanks for everyone who stopped by! #IUSSI26
Photo of me with my right hand raised dramatically and my left hand holding a glass of wine. Two people are standing across from me, listening to me re-enact hamlet (joke).
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GutMichaelBiome @gutmichaelbio.me · 14/08/2026
Excited share our honeybee microbiota-gut-brain axis research at @uissi-social.bsky.social next week. Here’s a sneak preview! Who else is going?
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GutMichaelBiome @gutmichaelbio.me · 12/08/2026
Bees Do So Much 🐝 for the environment!
Screenshot of a video showing one of my newest sticker designs “bees do so much for the environment”. The sticker depicts a flower with a bumblebee winking. The flower petals are rainbow colored. The petals spell out “B D S M” and “bees do so much”. The bee is flying and its flight trail spells out “for the environment”.
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GutMichaelBiome @gutmichaelbio.me · 26/07/2026
Clouds obscured the view of any mountains in Zermatt, but saw lots of good dogs
Collage of dogs
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GutMichaelBiome @gutmichaelbio.me · 26/07/2026
My mom is visiting me in Switzerland and brought two suitcases with her. One for her stuff and the other packed with my stickers 😄
Bags of various stickers my mom had to schlepp to Switzerland for me. Stickers laid out on a train table with a map background. Described from left to right, top to bottom. 

- GutMichaelBiome intestinal tract
- BDSM: Bacteria Do So Much for your microbiome
- poop (iykyk)
- Greetings from your microbiome remembering to eat your fiber, vintage postcard design
- invasive species 
- milf: mother of like to ferment
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GutMichaelBiome @gutmichaelbio.me · 05/07/2026
🚨NEW STICKER DROP🚨 Mother I’d Like to Ferment Order yours here: gutmichaelbio.me/products/mil... #Kombucha #Scoby #Sticker
My friend holding a Sticker I designed. The sticker features a cartoon SCOBY with a blonde bob of hair and wearing make up and high heels leaning up against a fermentation jar of kombucha. 

Red text above the cartoon says “MILF”. And the red text below says “Mother I’d Like to Ferment”.

Stickers are designed and drawn by me (not AI) and printed by my friends RxSkulls in Portland, OR. 

The sticker is printed with the highest quality UV-resistant vinyl. So it’s built to last 💪
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GutMichaelBiome @gutmichaelbio.me · 28/06/2026
Swiss🇨🇭 travel hack: with the 35+C (~95F) heat in Geneva, avoid the expensive saunas and get a public transit day pass for $12 instead. You can sweat with friends & strangers while seeing the city at the same time! Then jump into the river to cool off. Rinse and repeat as much as you want.
Photo from inside the 12 tram line in Geneva Switzerland. The window is dripping with water because of the heat and humidity inside the tram.
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GutMichaelBiome @gutmichaelbio.me · 07/06/2026
Other than stickers, I also sell my designs on direct-to-print clothes or accessories. Here’s a little round up of some of my favorite stickers :)
Screenshot of my sticker that says “I poop therefore I am -socraFeces” with Socrates, sitting upon a toiletScreenshot of a bumper sticker I made that says I break for microbes with a drawing of a gloved hand holding a Petri dish covered in bacteria coloniesScreenshot of my sticker I made for my PhD dissertation defense of a zebrafish with a gut Microbiome cartoon. Photo of my one of my more “spicier” but popular stickers that says “BDSM: bacteria do so much (for your microbiome” with a silhouette of a bacteria.
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GutMichaelBiome @gutmichaelbio.me · 07/06/2026
Each sticker is designed by me (not AI) and printed by my friends in Portland, OR (Sticker Ninja & RXskulls). They’re made on high quality UV-resistant vinyl, so they won’t degrade with time. I also appreciate they pay their workers fair wages and support socially progressive causes
Photo of some my stickers in front of a water fountain.
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GutMichaelBiome @gutmichaelbio.me · 07/06/2026
Many of my stickers were a limited drop and are currently “out of stock” because I’m doing my postdoc abroad and took my leftover stickers with me. But, I’m working with a friend to help me ship stuff in the US once I restock things (coming soon)!
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GutMichaelBiome @gutmichaelbio.me · 07/06/2026
Yay I love this thread! So many great sci-artists I can’t wait to follow. I’ll make a shameless plug for my silly niche microbiome-themed stickers :)
Screenshot of one of my first stickers. It says “greetings from your microbiome. Remember to eat your fiber” in the style of a vintage postcard. 

GutMichaelBio.me
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GutMichaelBiome @gutmichaelbio.me · 06/06/2026
They don’t name bacteria like they used to :/ Named after the entomologist Sir Vincent Brian Wigglesworth, of course.
Screenshot of a Wikipedia article. 

Text from the screenshot:

Wigglesworthia glossinidia

Wigglesworthia glossinidia is a species of gram-negative bacteria that is a bacterial endosymbiont of the tsetse fly.!"! Because of this relationship, Wigglesworthia has lost a large part of its genome, leaving it with one of the smallest genomes of any living organism, consisting of a single chromosome of 700,000 bp and a plasmid of 5,200. 2! Together with Buchnera aphidicola, Wigglesworthia has been the subject of genetic research into the minimal genome necessary for any living organism.
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GutMichaelBiome @gutmichaelbio.me · 11/05/2026
Here’s a close up of some of the bees wearing their QR codes.
Screenshot of the black and white video footage. A cluster of honeybees is pictured with tiny QR codes on their backs.
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GutMichaelBiome @gutmichaelbio.me · 11/05/2026
My colleagues in the Liberti Lab are running our latest tracking experiment to understand how the gut microbiota influences animal behavior using honeybees. You can watch the live stream here: geneva.tuleu.science/host/palaven... 🐝🧪 @joanitoliberti.bsky.social
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GutMichaelBiome @gutmichaelbio.me · 25/12/2025
Happy “Bowel”-idays!
Holiday card design I made that featured a gingerbread person with my “GutMichaelBiome” intestinal logo super imposed onto them. The card says “Happy Bowelidays!” in red cursive font above the gingerbread person. The background of the card is tan colored with white snow-like dots scattered around.
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GutMichaelBiome @gutmichaelbio.me · 28/08/2025
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 FuquesClose up of me from other photo
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GutMichaelBiome @gutmichaelbio.me · 20/08/2025
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)”
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GutMichaelBiome @gutmichaelbio.me · 05/08/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 31/07/2025
~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
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GutMichaelBiome @gutmichaelbio.me · 07/07/2025
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 NOWMICROBES 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.
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GutMichaelBiome @gutmichaelbio.me · 23/06/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 02/06/2025
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
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GutMichaelBiome @gutmichaelbio.me · 29/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 13/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 13/05/2025
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
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GutMichaelBiome @gutmichaelbio.me · 09/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 08/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 03/05/2025
“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
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GutMichaelBiome @gutmichaelbio.me · 03/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 02/05/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 28/04/2025
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 NationalResults 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”
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GutMichaelBiome @gutmichaelbio.me · 24/04/2025
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
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GutMichaelBiome @gutmichaelbio.me · 24/04/2025
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
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GutMichaelBiome @gutmichaelbio.me · 14/04/2025
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. GOLLEYBack 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 14111. 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
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GutMichaelBiome @gutmichaelbio.me · 11/04/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 08/04/2025
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”
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GutMichaelBiome @gutmichaelbio.me · 08/04/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 03/04/2025
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
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GutMichaelBiome @gutmichaelbio.me · 03/04/2025
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.
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GutMichaelBiome @gutmichaelbio.me · 03/04/2025
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 knotAgainst 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
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GutMichaelBiome @gutmichaelbio.me · 03/04/2025
Picture of me trying to find your lab's website to learn more about your research group #AcademicSky
Picture of a gentleman holding a magnifying glass up to his eye
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
BONUS: Our next study looked at how multiple successive exogenous stressors temporaly impact zebrafish gut microbiota. Analysis forthcoming... stay tuned and thanks for reading along! 13/12 (PS. preprint typos/corrections will be awarded with stickers)
Experimental design schematic. To test the buffering capacity hypothesis in zebrafish, I conduced a multifactorial and longitudinal study

Across 60 days, fish were sequentially exposed different pairwise combinations of antibiotics, a temperature change, and/or an intestinal parasite, resulting in 8 unique exposure regimes.

We started with 720 fish across 24 tanks, each tank containing 30 fish. 3 tanks were assigned to each of the 8 exposure regimes
- At 6 different time points, we collected fecal samples, intestinal samples, and body size measurements. 
- Additionally, at the final time we assessed infection outcomes and mortality.

- Our first sampling time point occurred prior to any exposures (shown here)
- Next half of the tanks were exposed to antibiotics
- Then we further divided each of these tanks into two, and exposed each group to a temperature increase or not
- Finally, each antibiotic and temperature exposure groups were divided again, and exposed to an intestinal parasite or not

As you can see by the final sampling time point, tanks were exposed to one of eight unique combinations of the three exposures.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
A homeorhetic framework (C.H. Waddington), conceptualizing stability as a change along a stable trajectory rather than a fixed state, could improve our ability to measure microbiome stability and dysbiosis across dynamic temporal and spatial scales. 11/12
Depictions of a homeorhetic framework, originally drawn by James Piper as conceptualized by CH Waddington, redrawn by me.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
These results seemingly align with the Anna Karenina Principle (AKP) which describes dysbiotic (unhealthy) GMBs as being very different from one another, while healthy GMBs are more similar to one another. However, the AKP effect diminishes when you consider environmental condtions. 8/12
Left: infection X alpha diversity scores. Right: Beta diversity dissimilarity plot. Colors: orange = low alpha diversity, purple = high alpha diversity. Purple/high group is composed of 67% 32°C reared infected fish, while orange/low alpha diversity group is composed of 67% 28°C infected fish.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
IMO, the most interesting observations were the infection by microbiome results. We found that gut diversity was highest or lowest among heavily infected fish, which also manifested in beta diversity space where infected fish differed from uninfected fish. 7/12
scatter plot showing worm (infection) counts on y-axis, and normalized alpha diversity scores on x-axis. Each diamond represents a unique sample from an individual fish. Highly infected fish display either very high or very low alpha diversity scores, while uninfected fish alpha diversity scores center around the median.Beta diversity dissimilarity plot showing how similar samples are in composition to one another. Where each diamond represents a unique sample from an individual fish. The closer the points are to each other the more similar in microbial composition they are, and the further apart the more dissimilar they are. Highly infected fish are dispersed from each other and differ from uninfected fish.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
Gut microbiota of fish reared at diff temps diversified and varied along different trajectories. This effect was exacerbated by parasite exposure. 6/12
Simpson's Index for diversity of parasite unexposed and exposed fish. Gut microbial alpha-diversity significantly differs between parasite exposed fish reared at 28°C and 32°C water temperature relative to unexposed control fish, but gut microbial alpha-diversity does not differ between parasite unexposed and exposed fish reared at 35°C water temperature. (D) Capscale ordinations based on the Bray-Curtis dissimilarity of gut microbiome composition constrained on the main and interaction effects of temperature and parasite exposure (treatment) of post-exposure samples after 0 dpe. The analysis shows gut microbiome composition differs between fish reared at different water temperatures prior to parasite exposure, and parasite exposure further drives these temperature associated differences in microbiome community composition. Ribbons and ellipses indicate 95% confidence interval. Ribbons and ellipses indicate 95% confidence interval. Only statistically significant relationships are shown. A "*" indicates statistical significance below the "0.05" level. Black arrows indicate statistically significant covariates and direction of greatest change in the indicated covariates.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
We found that fish reared in diff water temps responded differently to parasitic infection. Surprisingly, fish at higher temps were "protected" against infection, while fish at lower temps experienced higher infection. 5/12
Infection outcome analysis of fish exposed to P. tomentosa (n = 89) by temperature. Fish reared at 28°C and 32°C water temperatures had significantly different infection burden to fish reared at 35°C water temperature. Only one fish in our microbiome analysis reared at 35°C was identified as being positively infected by wet mount. Only statistically significant relationships are shown. A “*” indicates statistical significance below the “0.05” level.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
To test this, we reared 260 zebrafish across 3 increasing tank water temps (28, 32, 25°C) and then exposed a subset of each temp group to an intestinal parasitic worm, and measured their gut microbiota responses and infection outcomes at 5 time points across 42 days. 4/12
Experimental design showing treatments and husbandry events during the course of the study. Symbols indicate when an experimental event occurred at each time point. (1) 260 fish were assigned and acclimated to one of three water temperature groups (e.g., 28°C, 32°C, or 35°C) and reared from 0 to 164 days post fertilization (dpf). (2a) At 164 dpf (or 0 days post exposure; DPE), fecal collections were collected from a random selection of five fish per tank (n = 60). Additionally, histological and wet mount assessments were conducted on selected fish to assess presence of infection and infection burden. (1b) Afterwards, a cohort of fish from each water temperature group were exposed to Pseudocapillaria tomentosa. (3-6) Subsequent fecal samples were collected and histopathological assessments were conducted at 14 dpe (n = 54), (3) 21 dpe (n = 48), (4) 28 dpe (n = 47), and (5) 42 dpe (n = 51).
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
Climate change is anticipated to inc global temps impacting wildlife & humans. E.g., increased parasite pressure on aquatic organisms as water temps inc globally. B/c gut microbiota (GMB) interface w/ gut parasites, we hypothesized that GMB response would vary across vaying env conditions. 2/12
Figure sourced from NASA showing climate changes over the last 50 years on Earth.
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GutMichaelBiome @gutmichaelbio.me · 31/03/2025
I'm very excited to share our preprint on @biorxiv-microbiol.bsky.social demonstrating environmentally contingent gut microbiota reponses to intestinal infection in #Zebrafish. 🧵 1/12 doi.org/10.1101/2025... #MicrobiomeSky #MicroSky #MicrobialEcology #ClimateChange #Preprint
Cartoon remix I drew of the dog in a burning building meme featuring two zebrafish sitting at a table drinking coffee with a parasitic worm in the background. The room is filling with flames and smoke. One fish says "This is fine". The meme represents how we are ignoring the growing stressors of climate change.
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