Through the conversation.
20 sections010:00 – 4:47Introduction to the Podcast and the Microbiome
Hosts Dave Pietraszewski and David Pinsof introduce the podcast, discuss the growing cultural and scientific interest in the microbiome, and introduce guest Katrine Whiteson from UC Irvine, who studies the microbiome from an evolutionary perspective.
it is the coolest, hottest topic in science now
“it is the coolest, hottest topic in science now” 2:22
it's coming from an evolutionary perspective, thinking about the ways in which our diet might be mismatched from the way that we're designed
“coming from an evolutionary perspective, thinking about the ways in which our diet might be mismatched from the way that we're designed” 4:01
024:52 – 12:03Studying Saliva, Fermented Beverages, and Indigenous Diets
Katrine Whiteson discusses her collaboration with John Patton, detailing salivary science research and the significance of chicha, a traditional fermented beverage in Ecuador, contrasting indigenous diets with modern processed foods and their impact on human microbiomes.
chicha is a fermented beverage that people in Ecuador and other parts of South America make
“chicha is a fermented beverage that people in Ecuador and other parts of South America make” 7:32
we live in a world where most of the industrialized world is consuming something like 70% of our calories are processed foods
“we live in a world where most of the industrialized world is consuming something like 70% of our calories are processed foods” 10:50
Host Dave Pietraszewski and guest Katrine Whiteson discuss how modern food processing and the loss of dietary fiber have dramatically shifted human microbiomes, correlating with rises in autoimmune diseases, allergies, and certain cancers. They explore historical human populations, such as in Canombo, who lack these conditions, and mention international efforts like the Global Microbiome Conservancy to preserve historical microbes.
we are now pro more prone to autoimmune diseases, allergies.
“we are now pro more prone to autoimmune diseases, allergies.” 12:45
there's actually a really cool global movement to try to preserve the microbes of human history.
“there's actually a really cool global movement to try to preserve the microbes of human history.” 13:48
0415:20 – 24:07Defining the Microbiome and Modern Antibiotic Overuse
David Pinsof and Katrine Whiteson break down what a microbiome actually is, noting that no bodily environment is truly sterile and that dense microbial communities in the gut assist with metabolism and fiber breakdown. They also discuss armpit microbiomes, body odor, and the historical overprescription of antibiotics in medicine and agriculture.
nothing is sterile, despite what you might read in medical textbooks
“Nothing is sterile, despite what you might read in medical textbooks” 16:23
we weren't thinking about the downside of hurting the microbiome because it wasn't even appreciated really.
“we weren't thinking about the downside of hurting the microbiome because it wasn't even appreciated really.” 23:26
Host David Pinsof and guest Katrine Whiteson discuss what dietary fiber actually is biochemically, distinguishing it from general roughage like lettuce, and examine how fiber-rich foods like beans, lentils, and chia seeds can easily fill the average dietary gap. They also address common misconceptions around internet health fads.
fiber is the parts of carbohydrates that are big long chains that hum the linkages between those chains, human enzymes can't even break down
“fiber is the parts of carbohydrates that are big long chains that hum the linkages between those chains, human enzymes can't even break down” 25:33
if you just ate a cup of beans or lentils every day, you would fill your fiber gap
“if you just ate a cup of beans or lentils every day, you would fill your fiber gap” 28:42
Katrine Whiteson explains why commercial probiotics largely fail to colonize the gut and can sometimes interfere with medical treatments or recovery after antibiotics. Instead, she and the hosts emphasize that eating fiber and fermented foods like yogurt supports microbiome diversity by nurturing the beneficial microbes already present.
probiotics are really not what they say they are
“probiotics are really not what they say they are” 29:59
eating fermented foods together with fiber is the best thing we know to do
“eating fermented foods together with fiber is the best thing we know to do” 34:15
0736:11 – 40:35Household Microbiome Sampling and Ancient Prevatella Strains
Katrine Whiteson discusses a household-level microbiome study in Conombo comparing saliva, chicha, and fecal samples. The researchers found high diversity and an abundance of the fiber-degrading microbe Prevatella, which is largely missing in industrialized populations. Whiteson hypothesizes that these ancient microbes may have been passed down through human generations since leaving Africa.
And what people were finding was that the microbes in the in the gut microbiome were, first of all, just super diverse.
“the microbes in the in the gut microbiome were, first of all, just super diverse.” 38:09
And more than half of the reads mapped to this vanishing microbe called Previtella.
“more than half of the reads mapped to this vanishing microbe called Previtella.” 39:00
0840:38 – 48:12Health Implications, Infant Microbiomes, and Fiber Interventions
Dave Pietraszewski and David Pinsof ask about health implications related to ancestral differences in the microbiome. Katrine Whiteson explains how industrialized populations have lost key microbes like bifidobacteria needed to break down breast milk sugars, which impacts immune development. She also discusses the near-term health benefits of increasing dietary fiber to support a healthier microbiome.
So the US and Europe, for the most part, they are completely lacking this bifidobacteria that contains genes that can break down breast milk sugars
“they are completely lacking this bifidobacteria that contains genes that can break down breast milk sugars” 42:09
And there now have been many intervention studies showing that even short term, you will push your microbiome towards a healthier state by eating more fiber.
“you will push your microbiome towards a healthier state by eating more fiber.” 44:53
Dave Pietraszewski, David Pinsof, and guest Katrine Whiteson discuss the potential causal pathways linking gut microbiome health to conditions like cancer, explaining how short-chain fatty acids from fiber support colon cell metabolism and how the immune system surveys and removes precancerous cells.
when you are eating enough fiber, then the microbes in your colon are taking the fiber and producing these actually quite smelly volatile molecules
“When you are eating enough fiber, then the microbes in your colon are taking the fiber and producing these actually quite smelly volatile molecules.” 49:06
one of the most important functions of our immune system is to survey and prevent cancer cells from taking off
“one of the most important functions of our immune system is to survey and prevent cancer cells from taking off.” 50:59
The hosts and Katrine Whiteson explore how the gut interacts with the nervous and immune systems, dietary exposure tolerances, the abundance of undiscovered microbial molecules, and how food processing and economic profitability impact human health and dietary choices.
90% of the serotonin in our bodies is produced by cells in our gut
“90% of the serotonin in our bodies is produced by cells in our gut.” 54:43
maybe like five or 10% of the molecules can even be identified
“maybe like five or 10% of the molecules can even be identified.” 56:05
Dave Pietraszewski, David Pinsof, and guest Katrine Whiteson discuss the ubiquity of processed food and sugar in modern society, noting that simple dietary changes like increasing fiber intake through inexpensive foods such as beans, frozen berries, and homemade kombucha can be practical and beneficial.
the amount of sugar a person eats in a day today is more than the amount of sugar a person would eat in a year 300 years ago
“the amount of sugar a person eats in a day today is more than the amount of sugar a person would eat in a year 300 years ago” 1:02:03
The speakers examine the physiological effects of processed foods, with Katrine Whiteson explaining that removing fiber from food starves beneficial gut microbes. This causes microbes to consume the protective gut mucus lining, potentially leading to weakened barrier function and health issues.
the major problem is that one pretty universal step in all processed food is removing the fiber
“the major problem is that one pretty universal step in all processed food is removing the fiber” 1:06:38
one signature of the gut microbiomes of people in the industrialized world are microbes that eat gut mucus
“one signature of the gut microbiomes of people in the industrialized world are microbes that eat gut mucus” 1:07:53
Dave Pietraszewski, David Pinsof, and Katrine Whiteson discuss consumer food preferences, the hidden societal costs of highly processed, low-fiber diets, and how temporal discounting influences eating habits. They also compare laxatives like Miralax and Metamucil, highlighting how fiber intake supports a healthy microbiome and influences infection and health outcomes.
Katrine Whiteson explains that Miralax and Metamucil affect the microbiome differently, noting that fiber-based Metamucil leads to better infection outcomes in mice compared to Miralax.
“the mice that get mirrorax will get a terrible infection and very likely die from sepsis.” 1:19:42
The hosts and Katrine Whiteson explore the mystery of the enteric nervous system in the gut, discussing why there are so many neurons there and how gut microbes interact with neuroendocrine cells. They examine research on how microbes assist in transporting serotonin and communicating with the brain to influence well-being.
Katrine Whiteson highlights research showing that gut microbes can transport serotonin and potentially signal neuroendocrine cells in the gut to produce more of it.
“we have microbes that can transport serotonin.” 1:22:31
Dave Pietraszewski, David Pinsof, and guest Katrine Whiteson discuss physiological delivery systems, food cravings, and whether research supports the satisfying feelings associated with exercise and eating well, drawing connections between psychology, physiology, and microbiology.
I mean, we also we s we now have like urban cases of scurvy, for example, where people are just like eating toast
“urban cases of scurvy, for example, where people are just like eating toast” 1:25:20
So I on that side I definitely know. I don't know as much about that on the food side, but I mean there is a lot of food research.
“I on that side I definitely know. I don't know as much about that” 1:26:37
Katrine Whiteson explains what phages are, detailing her lab's work using wastewater samples at UC Irvine to hunt and isolate therapeutic viruses that can target and kill antibiotic-resistant bacterial infections.
Most viruses are not pathogens, but there are viruses everywhere. So every single one of these bacteria that we've been talking about in our microbiomes probably has about 10 viruses infecting it.
“Most viruses are not pathogens, but there are viruses everywhere.” 1:28:16
So we'll get the pathogen from the clinical microlab, we'll hunt a phage out of the wastewater.
“we'll get the pathogen from the clinical microlab, we'll hunt a phage out of the” 1:32:10
Katrine Whiteson and the hosts discuss the challenges of antibiotic discovery and how academic labs are stepping in to develop personalized bacteriophage therapies. Whiteson shares a successful case study of treating a patient with chronic sinusitis using a custom-produced phage named Ludmilla, detailing the regulatory approvals, rigorous safety testing, and meticulous laboratory procedures required.
And the phages are an alternative, but they're still a little bit homemade. Like we don't have them at an industrial scale at all.
“And the phages are an alternative, but they're still a little bit homemade. Like we don't have them at an industrial scale at all.” 1:37:20
So I changed tax about a year ago and I said that we would accept chronic cases.
“So I changed tax about a year ago and I said that we would accept chronic cases.” 1:39:04
The speakers examine the economic hurdles and funding constraints facing translational microbiology and academic research, noting how regulatory pathways like FDA compassionate exemptions are surprisingly workable despite funding scarcity. Finally, they share anecdotes about colleague John Patton and anthropological fieldwork involving traditional beverages.
The reason I'm able to do it mainly in this case is because of this amazing student who cared so much about doing it?
“The reason I'm able to do it mainly in this case is because of this amazing student who cared so much about doing it?” 1:43:40
I honestly the the FDA's compassionate exemption route is functioning pretty well, in my opinion.
“I honestly the the FDA's compassionate exemption route is functioning pretty well, in my opinion.” 1:44:59
Hosts Dave Pietraszewski and David Pinsof thank guest Katrine Whiteson for her inspiring and evolutionarily grounded research on the microbiome and fiber. Following her departure, the hosts review dietary fiber sources, organic berries, and compare various supplements like psyllium husk versus polyethylene glycol.
The hosts express deep appreciation for Katrine Whiteson's impactful and evolutionary-informed scientific work.
“change the way I think about the world, and and you are in that category.” 1:49:27
The hosts discuss recommended fiber supplements and whole foods for maintaining good digestive health.
“psyllium husk or the derivatives are.” 1:51:18
The hosts transition into a casual discussion about films like Oppenheimer, historical recordings, and their immense admiration for Charles Darwin. They discuss what it would be like to share modern scientific discoveries with Darwin and briefly touch upon popular evolutionary psychology books like The Moral Animal.
David Pinsof expresses that Charles Darwin is at the top of his list of historical figures he would love to meet.
“Top of my list.” 1:53:54
The hosts discuss Robert Wright's book The Moral Animal and its role as a popular introduction to evolutionary psychology.
“That's a lot of people's intro gateway drug to Yeah, a lot of their gateway drugs.” 1:55:19