The Top Five Mysteries of the Human Gut Microbiome
A scholar of science, circa 2218, might look back on this era and wonder why, all of a sudden, scientists became so obsessed with human stool. Or more accurately, the microorganisms therein.
Although every human is nearly identical genetically, each person carries around a massively different variety of microbial genes from bacteria, fungi, viruses, and archaea.
This scholar might find, for example, the seven-fold increase in PubMed articles on "gut microbiome" in the half-decade between 2012 and 2017; the plastic detritus of millions of fecal sample collection kits, and evidence that freezers in research labs worldwide had filled up with fecal samples. What's happened?
Human genome science has led to some important medical insights over time. Now it's moving over for the microorganisms. Because, although every human is nearly identical genetically, each person carries around a massively different variety of microbial genes from bacteria, fungi, viruses, and archaea—genes that are collectively called the microbiome.
Thinking that more knowledge about the gut microbiome is going to solve every problem in medicine is pure hubris. And yet these microorganisms seem to be at the nexus of humans and our environment, capable of changing us metabolically and adjusting our immune systems. What might they have the power to do?
Here are five of the most important questions that lie ahead for microbiome science.
1) What makes a gut microbiome 'healthy'?
The words "healthy microbiome" should raise a red flag. Because, currently, if scientists examine the gut microbial community of a single individual they have no way of knowing whether or not it qualifies as healthy—nor even what parameter to look at in order to find out. Is it only the names of the bugs that matter, or is it their diversity? Alternatively, is it function—what they're genetically equipped to do?
The words "healthy microbiome" should raise a red flag.
The focused efforts of the Human Microbiome Project were supposed to accomplish the apparently simple task of defining a healthy microbiome, but no clear answers emerged. If researchers could identify the parameters of a healthy microbiota per se, they might have a way to know whether manipulations—from probiotics to fecal transplant—were making a difference that could lead to a good health outcome.
2) Diet can manipulate gut microbes. How does this affect health?
"Many kinds of bacteria in our gut, they're changeable by changing our diet," says Liping Zhao of Shanghai Jiao Tong University in China, citing two large population studies from 2016. What's murkier is how this effects a change in health status.
Zhao's research focuses on making the three-way link between diet, gut microbiota, and health outcome. Meanwhile, researchers like Genelle Healey at the University of British Columbia (UBC) are working to track how the gut microbiome and health respond to a dietary intervention in a personalized way.
Knowing how the diet-induced changes in gut microbes affected health in the long term would allow every individual to toss out the diet books and figure out a dietary pattern—probably as personal as their gut microbes—that would result in their best health down the line.
If scientists could find how to harness one or more microorganisms to have specific effects on the immune system, they might be able to crack a new class of therapeutics.
3) How can gut microorganisms be used to fine-tune the immune system?
Many chronic diseases—autoimmune conditions but also, according to the latest research, obesity and cardiovascular disease—are immune mediated. Kenya Honda of Keio University School of Medicine in Tokyo, Yasmine Belkaid of the US National Institutes of Health (NIH), June Round at University of Utah, and many other researchers are chasing the ways in which gut microbes 'talk' to the immune system. But it's more than just studying certain bugs.
"It's an incredibly complex situation and we can't just label bugs as pro-inflammatory or anti-inflammatory. It's very context-dependent," says Justin Sonnenburg of Stanford. But if scientists could find how to harness a microorganism or group of them to have specific effects on the immune system, they might be able to crack a new class of therapeutics that could change the course of immune-mediated diseases.
4) How can a person's gut microbiome be reconfigured in a lasting way?
Measures of the adult microbiome over time show it has a high degree of stability—in fact, it can be downright stubborn. But a new, stable gut microbial ecology can be achieved when someone receives a fecal transplant for recurrent C. difficile infection. Work by Eric Alm of Massachusetts Institute of Technology (MIT) and others have shown the recipient's gut microbiota ends up looking more like the donor's, with engraftment of particular strains.
But what are the microorganisms' 'rules of engraftment'? Knowing this, it might be possible to intervene in a number of disease-associated microbiome states, changing them in a way that changed the course of the disease.
Is the infant microbiome, as shaped by birth mode and diet, responsible for health issues later in life?
5) How do early-life shapers of the gut microbiome affect health status later on?
Researchers have found two main factors that appear to shape the gut microbiome in early life, at least temporarily: mode of birth (whether vaginal or Cesarean section), and early life diet (whether formula or breast milk). These same factors are associated with an increased risk of immune and metabolic diseases. So is the infant microbiome, as shaped by birth mode and diet, responsible for health issues later in life?
Brett Finlay of the University of British Columbia has made these 'hygiene hypothesis' compatible links between the absence of certain bacteria in early life and asthma later on. "I think the bugs are shaping and pushing how our immune system develops, and if very early in life you don't have those things, it goes to a more allergic-type immune system. If you do have those bugs it gets pushed towards more normal," he says. The work could lead to targeted manipulation of the microbiome in early life to offset negative health effects.
Stronger psychedelics that rewire the brain, with Doug Drysdale
A promising development in science in recent years has been the use technology to optimize something natural. One-upping nature's wisdom isn't easy. In many cases, we haven't - and maybe we can't - figure it out. But today's episode features a fascinating example: using tech to optimize psychedelic mushrooms.
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These mushrooms have been used for religious, spiritual and medicinal purposes for thousands of years, but only in the past several decades have scientists brought psychedelics into the lab to enhance them and maximize their therapeutic value.
Today’s podcast guest, Doug Drysdale, is doing important work to lead this effort. Drysdale is the CEO of a company called Cybin that has figured out how to make psilocybin more potent, so it can be administered in smaller doses without side effects.
The natural form of psilocybin has been studied increasingly in the realm of mental health. Taking doses of these mushrooms appears to help people with anxiety and depression by spurring the development of connections in the brain, an example of neuroplasticity. The process basically shifts the adult brain from being fairly rigid like dried clay into a malleable substance like warm wax - the state of change that's constantly underway in the developing brains of children.
Neuroplasticity in adults seems to unlock some of our default ways of of thinking, the habitual thought patterns that’ve been associated with various mental health problems. Some promising research suggests that psilocybin causes a reset of sorts. It makes way for new, healthier thought patterns.
So what is Drysdale’s secret weapon to bring even more therapeutic value to psilocybin? It’s a process called deuteration. It focuses on the hydrogen atoms in psilocybin. These atoms are very light and don’t stick very well to carbon, which is another atom in psilocybin. As a result, our bodies can easily breaks down the bonds between the hydrogen and carbon atoms. For many people, that means psilocybin gets cleared from the body too quickly, before it can have a therapeutic benefit.
In deuteration, scientists do something simple but ingenious: they replace the hydrogen atoms with a molecule called deuterium. It’s twice as heavy as hydrogen and forms tighter bonds with the carbon. Because these pairs are so rock-steady, they slow down the rate at which psilocybin is metabolized, so it has more sustained effects on our brains.
Cybin isn’t Drysdale’s first go around at this - far from it. He has over 30 years of experience in the healthcare sector. During this time he’s raised around $4 billion of both public and private capital, and has been named Ernst and Young Entrepreneur of the Year. Before Cybin, he was the founding CEO of a pharmaceutical company called Alvogen, leading it from inception to around $500 million in revenues, across 35 countries. Drysdale has also been the head of mergers and acquisitions at Actavis Group, leading 15 corporate acquisitions across three continents.
In this episode, Drysdale walks us through the promising research of his current company, Cybin, and the different therapies he’s developing for anxiety and depression based not just on psilocybin but another psychedelic compound found in plants called DMT. He explains how they seem to have such powerful effects on the brain, as well as the potential for psychedelics to eventually support other use cases, including helping us strive toward higher levels of well-being. He goes on to discuss his views on mindfulness and lifestyle factors - such as optimal nutrition - that could help bring out hte best in psychedelics.
Show links:
Doug Drysdale full bio
Doug Drysdale twitter
Cybin website
Cybin development pipeline
Cybin's promising phase 2 research on depression
Johns Hopkins psychedelics research and psilocybin research
Mets owner Steve Cohen invests in psychedelic therapies
Doug Drysdale, CEO of Cybin
How the body's immune resilience affects our health and lifespan
Story by Big Think
It is a mystery why humans manifest vast differences in lifespan, health, and susceptibility to infectious diseases. However, a team of international scientists has revealed that the capacity to resist or recover from infections and inflammation (a trait they call “immune resilience”) is one of the major contributors to these differences.
Immune resilience involves controlling inflammation and preserving or rapidly restoring immune activity at any age, explained Weijing He, a study co-author. He and his colleagues discovered that people with the highest level of immune resilience were more likely to live longer, resist infection and recurrence of skin cancer, and survive COVID and sepsis.
Measuring immune resilience
The researchers measured immune resilience in two ways. The first is based on the relative quantities of two types of immune cells, CD4+ T cells and CD8+ T cells. CD4+ T cells coordinate the immune system’s response to pathogens and are often used to measure immune health (with higher levels typically suggesting a stronger immune system). However, in 2021, the researchers found that a low level of CD8+ T cells (which are responsible for killing damaged or infected cells) is also an important indicator of immune health. In fact, patients with high levels of CD4+ T cells and low levels of CD8+ T cells during SARS-CoV-2 and HIV infection were the least likely to develop severe COVID and AIDS.
Individuals with optimal levels of immune resilience were more likely to live longer.
In the same 2021 study, the researchers identified a second measure of immune resilience that involves two gene expression signatures correlated with an infected person’s risk of death. One of the signatures was linked to a higher risk of death; it includes genes related to inflammation — an essential process for jumpstarting the immune system but one that can cause considerable damage if left unbridled. The other signature was linked to a greater chance of survival; it includes genes related to keeping inflammation in check. These genes help the immune system mount a balanced immune response during infection and taper down the response after the threat is gone. The researchers found that participants who expressed the optimal combination of genes lived longer.
Immune resilience and longevity
The researchers assessed levels of immune resilience in nearly 50,000 participants of different ages and with various types of challenges to their immune systems, including acute infections, chronic diseases, and cancers. Their evaluation demonstrated that individuals with optimal levels of immune resilience were more likely to live longer, resist HIV and influenza infections, resist recurrence of skin cancer after kidney transplant, survive COVID infection, and survive sepsis.
However, a person’s immune resilience fluctuates all the time. Study participants who had optimal immune resilience before common symptomatic viral infections like a cold or the flu experienced a shift in their gene expression to poor immune resilience within 48 hours of symptom onset. As these people recovered from their infection, many gradually returned to the more favorable gene expression levels they had before. However, nearly 30% who once had optimal immune resilience did not fully regain that survival-associated profile by the end of the cold and flu season, even though they had recovered from their illness.
Intriguingly, some people who are 90+ years old still have optimal immune resilience, suggesting that these individuals’ immune systems have an exceptional capacity to control inflammation and rapidly restore proper immune balance.
This could suggest that the recovery phase varies among people and diseases. For example, young female sex workers who had many clients and did not use condoms — and thus were repeatedly exposed to sexually transmitted pathogens — had very low immune resilience. However, most of the sex workers who began reducing their exposure to sexually transmitted pathogens by using condoms and decreasing their number of sex partners experienced an improvement in immune resilience over the next 10 years.
Immune resilience and aging
The researchers found that the proportion of people with optimal immune resilience tended to be highest among the young and lowest among the elderly. The researchers suggest that, as people age, they are exposed to increasingly more health conditions (acute infections, chronic diseases, cancers, etc.) which challenge their immune systems to undergo a “respond-and-recover” cycle. During the response phase, CD8+ T cells and inflammatory gene expression increase, and during the recovery phase, they go back down.
However, over a lifetime of repeated challenges, the immune system is slower to recover, altering a person’s immune resilience. Intriguingly, some people who are 90+ years old still have optimal immune resilience, suggesting that these individuals’ immune systems have an exceptional capacity to control inflammation and rapidly restore proper immune balance despite the many respond-and-recover cycles that their immune systems have faced.
Public health ramifications could be significant. Immune cell and gene expression profile assessments are relatively simple to conduct, and being able to determine a person’s immune resilience can help identify whether someone is at greater risk for developing diseases, how they will respond to treatment, and whether, as well as to what extent, they will recover.