Essentials: How to Build, Maintain & Repair Gut Health | Dr. Justin Sonnenburg
In this episode of the Huberman Lab, Dr. Justin Sonnenburg explains how the gut microbiome—a complex ecosystem of bacteria, fungi, and other microorganisms—develops and functions in the human body. He describes how factors like birth method, diet choices, and antibiotic use shape our microbiome from infancy, and discusses the significant differences between gut health in industrialized versus traditional populations.
Sonnenburg outlines how modern lifestyle factors, particularly processed foods and repeated antibiotic exposure, can permanently reduce microbial diversity in the gut. He presents research-backed approaches for maintaining and restoring gut health, including the benefits of consuming varied fiber sources and fermented foods. The discussion also covers the relationship between environmental microbial exposure and immune system development, offering practical insights for achieving a balanced approach to hygiene.
This is a preview of the Shortform summary of the Dec 11, 2025 episode of the Huberman Lab
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1-Page Summary
Understanding the Gut Microbiome
Justin Sonnenburg explains that the gut microbiome is a complex ecosystem containing trillions of microbial cells, including bacteria, archaea, fungi, and bacteriophages. These organisms interact in intricate ways, with bacteriophages playing a particularly interesting role by regulating bacterial populations through predator-prey relationships.
According to Sonnenburg, newborns acquire their gut microbiome primarily after birth, not in the womb. The development of an infant's microbiota is shaped by various factors, including birth method, diet choices, pet exposure, and antibiotic use. These early influences can have lasting effects on both microbial diversity and long-term health outcomes.
Individual Variability and Modern Challenges
Research has revealed significant differences between the gut microbiomes of people in industrialized societies versus traditional populations. Sonnenburg notes that modern Western lifestyles, particularly the use of antibiotics and processed foods, may have led to less diverse and potentially less healthy microbiomes in industrialized populations.
Factors That Influence Gut Microbiome Health
Sonnenburg explains that processed foods can disrupt the gut microbiome by lacking essential fibers and containing harmful additives. Artificial sweeteners, in particular, can contribute to metabolic syndrome, while emulsifiers may disrupt the protective mucus layer in the gut.
While the gut microbiome typically rebounds after antibiotic treatment, Sonnenburg points out that repeated exposure, especially combined with poor diet, can lead to permanent losses in microbial diversity. Research in mice has shown that by the fourth generation on a low-fiber, high-fat diet with antibiotics, about 70% of microbial species went extinct.
Strategies For Maintaining or Restoring a Healthy Microbiome
Studies show that a high-fiber, plant-rich diet is crucial for maintaining a healthy gut microbiome. Sonnenburg recommends consuming diverse fiber sources rather than supplements, as variety helps promote overall microbiota diversity.
Fermented foods have also shown promise in boosting microbial diversity and reducing inflammation. Research participants who consumed six daily servings of naturally fermented foods like yogurt, kefir, and kimchi experienced increased microbiota diversity and decreased inflammatory markers.
Regarding hygiene, Sonnenburg advocates for a balanced approach to microbial exposure, suggesting that some exposure to environmental microbes is essential for developing a robust immune system while maintaining appropriate hygiene in high-risk situations.
1-Page Summary
Additional Materials
Clarifications
- The gut microbiome refers to the community of microorganisms living in the digestive tract, mainly the intestines. These microbes include bacteria, viruses, fungi, and other tiny life forms that help digest food, produce vitamins, and protect against harmful pathogens. The balance and diversity of these microbes are crucial for overall health and immune function. Changes in the gut microbiome can influence digestion, metabolism, and even mood.
- Bacteria and archaea are single-celled microorganisms, but archaea have unique genetic and biochemical traits that distinguish them from bacteria. Fungi in the gut are mostly microscopic yeasts and molds that can influence digestion and immunity. Bacteriophages are viruses that specifically infect and kill bacteria, helping control bacterial populations. Together, these diverse microbes form a dynamic community that impacts health and disease.
- Bacteriophages are viruses that specifically infect bacteria. They attach to bacterial cells, inject their genetic material, and use the bacteria to reproduce, often killing the host cell. This predation controls bacterial population sizes and diversity within the gut ecosystem. By targeting certain bacteria, bacteriophages help maintain balance and prevent overgrowth of harmful species.
- Microbial diversity refers to the variety of different microbial species living in the gut. Higher diversity generally means a more resilient and stable ecosystem that can better support digestion, immune function, and protection against harmful pathogens. Low diversity is linked to increased risk of diseases like obesity, allergies, and inflammatory bowel conditions. Maintaining diverse microbes helps the gut adapt to dietary changes and environmental stresses.
- Newborns acquire their microbiome mainly during and after birth through exposure to their mother's vaginal and skin microbes, as well as the environment. The womb is generally sterile, meaning it lacks microbial colonization under normal conditions. Initial microbial exposure helps train the infant's immune system and establish gut function. Factors like delivery method (vaginal vs. cesarean) influence the types of microbes first encountered.
- The birth method affects initial microbial exposure: vaginal birth transfers beneficial bacteria from the mother, while C-section often results in different microbial colonization. Diet influences which microbes thrive, with breast milk providing prebiotics that promote healthy bacteria growth. Pet exposure introduces diverse environmental microbes, potentially enhancing immune system development. Antibiotics can kill both harmful and beneficial bacteria, disrupting microbiome balance and delaying its maturation.
- Traditional populations often have more diverse gut microbiomes due to diets rich in fiber and fewer processed foods. Their microbiomes include bacteria that help digest complex plant materials and resist pathogens. Industrialized populations typically have less microbial diversity, linked to higher rates of chronic diseases. Environmental exposures and lifestyle differences also shape these distinct microbial communities.
- Processed foods often lack dietary fibers, which are crucial nutrients that feed beneficial gut bacteria and support their growth. Without fiber, these bacteria starve, reducing microbial diversity and weakening gut health. Additives like emulsifiers can damage the gut’s mucus lining, making it easier for harmful bacteria to cause inflammation. Artificial sweeteners may alter bacterial metabolism, potentially leading to negative effects on blood sugar regulation and metabolism.
- Artificial sweeteners are synthetic sugar substitutes used to provide sweetness without calories. Emulsifiers are additives that help mix ingredients like oil and water in processed foods. Both can alter gut bacteria, potentially leading to inflammation and metabolic changes. These changes may increase the risk of conditions like obesity and insulin resistance.
- Antibiotics kill both harmful and beneficial bacteria in the gut, causing a temporary imbalance. The gut microbiome rebounding means these beneficial bacteria regrow and restore balance after treatment ends. This recovery is crucial because a balanced microbiome supports digestion, immunity, and overall health. However, repeated antibiotic use can impair this recovery, leading to lasting damage.
- Microbial species extinction means certain types of gut microbes completely disappear and cannot be recovered. This loss reduces the gut ecosystem's complexity and resilience, impairing digestion and immune function. In mice, extinction after repeated antibiotics and poor diet suggests similar risks for humans, potentially leading to chronic health issues. It highlights the importance of preserving microbial diversity for long-term health.
- A high-fiber, plant-rich diet provides diverse types of dietary fibers that serve as food for beneficial gut bacteria. These fibers are fermented by microbes, producing short-chain fatty acids that nourish gut cells and reduce inflammation. Different fibers support different bacterial species, promoting a balanced and resilient microbiome. Without fiber, many beneficial microbes starve and decline, reducing overall microbial diversity.
- Fiber supplements typically contain isolated types of fiber, often from a single source, providing limited variety for gut microbes. Diverse fiber sources come from different plant foods, offering a wide range of fiber types that feed various beneficial bacteria. This variety supports a richer and more resilient gut microbiome by promoting multiple microbial species. Whole foods also provide additional nutrients and compounds that supplements usually lack.
- Fermented foods are foods transformed by beneficial bacteria or yeasts through a natural process called fermentation. This process produces probiotics, which are live microorganisms that can colonize the gut and support a healthy microbiome. Probiotics from fermented foods help increase microbial diversity by introducing new beneficial strains. They also reduce inflammation by strengthening the gut barrier and modulating immune responses.
- Inflammatory markers are substances in the blood that indicate the presence of inflammation in the body. Common markers include C-reactive protein (CRP) and cytokines, which rise when the immune system responds to injury or infection. Chronic high levels of these markers are linked to diseases like heart disease, diabetes, and autoimmune disorders. Monitoring them helps assess health and the effectiveness of treatments.
- Balanced microbial exposure means encountering a variety of harmless microbes from the environment, which helps train the immune system to distinguish between harmful and non-harmful agents. This exposure supports immune tolerance, reducing the risk of allergies and autoimmune diseases. Over-sanitizing limits this training, potentially leading to immune system overreactions. Therefore, moderate contact with everyday microbes is essential for a well-functioning immune system.
- Maintaining hygiene prevents harmful infections, especially in vulnerable settings like hospitals. However, excessive cleanliness can limit exposure to beneficial environmental microbes that help train and strengthen the immune system. Early-life microbial exposure supports immune tolerance and reduces allergy and autoimmune risks. Thus, balanced hygiene protects health while allowing immune development.
Counterarguments
- While the gut microbiome is indeed complex, the specific roles and interactions of its constituents, such as bacteriophages, are still not fully understood, and more research is needed to clarify these relationships.
- The extent to which newborns acquire their microbiome after birth versus in utero is still debated, with some research suggesting that there may be some microbial transfer before birth.
- The impact of birth method on the microbiome is complex, and while cesarean deliveries have been associated with different initial microbiota, the long-term health implications of these differences are not yet clear.
- The assertion that modern Western lifestyles have led to less diverse microbiomes could be oversimplified, as there are many factors at play, and some studies suggest that urban living can also introduce a variety of beneficial microbes.
- The claim that processed foods universally disrupt the gut microbiome may not account for the complexity of food processing and the potential for some processed foods to have neutral or even beneficial effects on gut health.
- The role of artificial sweeteners in metabolic syndrome is still controversial, with some studies showing no direct causation and suggesting that other lifestyle factors may be more significant contributors.
- The impact of emulsifiers on the gut mucus layer and health is an area of active research, and not all emulsifiers may have the same effect; some may be benign or even beneficial.
- The resilience of the gut microbiome after antibiotic treatment varies greatly among individuals, and some may experience long-term changes even after a single course of antibiotics.
- The findings from mouse models, such as the extinction of microbial species on a low-fiber, high-fat diet with antibiotics, may not directly translate to humans due to differences in physiology and environmental exposures.
- While a high-fiber, plant-rich diet is generally recommended for gut health, individual responses to dietary fiber vary, and some people may experience adverse effects from high-fiber diets, such as those with certain gastrointestinal disorders.
- The benefits of fermented foods are supported by some studies, but the evidence is not yet conclusive, and the optimal types and amounts of fermented foods for gut health are still being determined.
- The recommendation for six daily servings of fermented foods may not be suitable for everyone and could lead to excessive calorie intake or other issues in some individuals.
- The concept of balanced microbial exposure is a general guideline, and the specific types and amounts of microbial exposure that are beneficial versus harmful are not well-defined and likely vary from person to person.
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Understanding the Gut Microbiome
Gut microbiome research, as explained by Justin Sonnenburg, is delving into the incredible complexity and importance of the microbial community living within our gastrointestinal tracts.
The Gut Microbiome: A Dense, Diverse Ecosystem Impacting Health
The gut microbiome, or microbiota, is a dense ecosystem within the gut, comprising trillions of microbial cells. Justin Sonnenburg explains that most of these microbes are bacteria, but they also include archaea, eukaryotes such as fungi, and a vast number of bacteriophages. Bacteriophages, which are viruses that infect bacterial cells, contribute to the complex interplay of the gut ecosystem by acting in predator-prey dynamics.
The Gut Microbiome Includes Bacteria, Archaea, Eukaryotes, and Viruses Interacting Complexly
The gut microbiome is made up of a wide array of organisms that interact in a complex manner. This ecosystem is predominantly bacterial but includes other forms of life such as archaea—organisms similar to bacteria but genetically distinct—and eukaryotes like fungi. The bacteriophages present in the gut outnumber bacteria by 10 to 1 and play a crucial role in shaping bacterial populations through their infectious processes.
Newborns Acquire Their Gut Microbiome From Birth and Early Exposures, Shaping Its Development
Sonnenburg provides insight into the establishment of the gut microbiome, dispelling the idea that significant microbial colonization occurs in the womb. He compares newborns to new ecosystems or islands, initially devoid of species, ready to be colonized by microbes. The specific trajectory of a newborn's microbiota development is influenced by factors such as the method of birth, diet (breastfeeding or formula feeding), pet exposure, and antibiotic use. These early influences can have a long-lasting impact on microbial diversity and subsequently affect the immune system and metabolism later in life.
Individual Variability in Human Gut Microbiome Challenges Defining "Healthy"
Despite the revelations of the microbiome's influence on health, Sonnenburg explains that tremendous variability exists between individuals, making it challenging to pin down a standard "healthy" microbiome.
Microbiomes in Industrialized Vs. Traditional Populations Less Diverse, Healthy
Research indicates that the gut mi ...
Here’s what you’ll find in our full summary
Understanding the Gut Microbiome
Additional Materials
Clarifications
- Archaea are single-celled microorganisms distinct from bacteria at the genetic and biochemical levels. Unlike bacteria, their cell membranes contain unique lipids that help them survive extreme environments. They often play specialized roles in processes like methane production and nutrient cycling. Understanding archaea helps reveal the full diversity and function of the gut microbiome.
- Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike bacteria and archaea. In the gut microbiome, eukaryotes mainly include fungi and protozoa. These organisms can influence digestion, immune responses, and interact with bacteria. Their presence adds to the complexity and balance of the gut ecosystem.
- Bacteriophages, or phages, are viruses that specifically infect bacteria by attaching to their surface and injecting their genetic material. Once inside, phages hijack the bacterial machinery to produce new virus particles, often killing the bacteria in the process. This predator-prey relationship helps regulate bacterial populations and maintain balance in the gut ecosystem. Phages also influence bacterial evolution by transferring genes between bacteria.
- Predator-prey dynamics in microbial populations refer to interactions where one organism (the predator) consumes or infects another (the prey). In the gut, bacteriophages act as predators by infecting and killing specific bacteria, controlling their numbers. This interaction helps maintain balance and diversity within the microbial community. Such dynamics influence which bacterial species thrive or decline, affecting overall gut health.
- Microbial colonization in newborns begins immediately after birth when microbes from the mother and environment start to populate the sterile gut. This early colonization is crucial because it helps train the infant’s immune system to distinguish between harmful and harmless microbes. Proper microbial development supports digestion, nutrient absorption, and protection against pathogens. Disruptions in this process can increase the risk of allergies, infections, and chronic diseases later in life.
- The birth method affects initial microbial exposure: vaginal birth transfers beneficial bacteria from the mother, while C-section limits this. Diet shapes microbiome by providing different nutrients that promote growth of specific microbes; breast milk contains prebiotics and beneficial bacteria. Pet exposure introduces diverse microbes, potentially enhancing immune system training. Antibiotics can kill both harmful and beneficial bacteria, disrupting microbiome balance and reducing diversity.
- Microbial diversity refers to the variety of different microbial species living in the gut. Higher diversity generally means a more resilient and stable ecosystem that can better support digestion, immune function, and protection against harmful pathogens. Low diversity is often linked to health problems like inflammation, allergies, and metabolic disorders. Maintaining diverse microbes helps the gut adapt to changes and maintain overall health.
- Traditional populations typically have more diverse gut microbiomes due to varied diets rich in fiber and less exposure to antibiotics. Industrialized populations often consume processed foods high in fat and sugar, which reduce microbial diversity. Hygiene practices and medical interventions in i ...
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Factors That Influence Gut Microbiome Health
Understanding the factors that affect gut microbiome health is critical. Justin Sonnenburg details how processed foods and antibiotics impact gut microbiome composition and function, noting the resilience of the microbiome in adapting to these changes.
Processed Foods Disrupt Gut Microbiome, Promote Inflammation
Processed Foods Lack Fibers Nourishing Microbiome
Sonnenburg explains that processed foods often contain components harmful to our gut microbiome. Specifically, these foods lack the necessary fibers that nourish our microbiome, leading to potential imbalances and health issues.
Artificial Sweeteners Negatively Impact the Gut Microbiome
Artificial sweeteners, Sonnenburg notes, have a massive negative impact on the gut microbiome, contributing towards metabolic syndrome. Additionally, emulsifiers in processed foods disrupt the mucus layer, which can lead to inflammation and metabolic syndrome, as seen in animal models. In contrast, Sonnenburg suggests that non-caloric plant-based sweeteners might be less negative due to their higher potency and therefore require smaller amounts for the same level of sweetness. Traditional populations have used plant-based sweeteners without issues, which implies that natural compounds might be handled better by our bodies than synthetic ones, but Sonnenburg indicates that more research is required.
Antibiotics Disrupt Gut Microbiome, but It Often Rebounds After Treatment
Sonnenburg points out that individuals who take oral antibiotics experience a significant change in their gut microbiome due to the death of many microbes and a shift in composition. Importantly, after the antibiotic treatment ends, the microbiota usually returns to a similar state as it was in before the antibiotics, provided that no pathogens take over the now-vacant niches.
Repeated Antibiotic Exposure May Permanently Reduce ...
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Factors That Influence Gut Microbiome Health
Additional Materials
Clarifications
- The gut microbiome is the community of trillions of microorganisms living in the digestive tract. These microbes help digest food, produce vitamins, and support the immune system. A balanced microbiome protects against harmful bacteria and inflammation. Disruptions can lead to digestive issues, metabolic problems, and weakened immunity.
- Fibers are types of carbohydrates found in plant foods that humans cannot digest. Instead, gut bacteria ferment these fibers, producing beneficial compounds like short-chain fatty acids. These compounds help maintain gut lining health and regulate inflammation. Thus, fibers act as food for beneficial microbes, supporting a balanced microbiome.
- Metabolic syndrome is a group of conditions including high blood pressure, high blood sugar, excess body fat around the waist, and abnormal cholesterol levels. It increases the risk of heart disease, stroke, and type 2 diabetes. Gut health influences metabolic syndrome by affecting inflammation, nutrient absorption, and energy balance. Disruptions in the gut microbiome can worsen these metabolic processes, contributing to the syndrome.
- Emulsifiers are additives used in processed foods to help mix ingredients like oil and water that normally separate. In the gut, they can thin or disrupt the protective mucus layer lining the intestines. This disruption allows bacteria to come into closer contact with gut cells, triggering inflammation. Chronic inflammation can contribute to metabolic and digestive disorders.
- Artificial sweeteners are synthetic compounds created to mimic sugar's sweetness without calories. Non-caloric plant-based sweeteners come from natural sources like stevia or monk fruit and are also low or zero calorie. The body may metabolize natural sweeteners differently, potentially causing fewer negative effects on gut bacteria. However, scientific consensus on their comparative impact is still developing.
- Traditional populations’ long-term use of plant-based sweeteners suggests these compounds are less likely to disrupt the gut microbiome because the body and microbes have co-evolved with them. This historical exposure implies better microbial adaptation and tolerance compared to synthetic sweeteners, which are relatively new. It provides a natural context for assessing safety and potential impacts on gut health. Understanding this helps guide research on sweetener effects and dietary recommendations.
- Antibiotics kill many bacteria in the gut, including beneficial ones, disrupting the microbial community. "Vacant niches" refer to empty spaces or roles in the gut ecosystem left by bacteria that were killed. These empty niches can be quickly filled by other microbes, sometimes harmful pathogens. This competition influences whether the microbiome returns to its original state or changes permanently.
- Microbial diversity refers to the variety of different microbial species living in the gut. High diversity supports a balanced ecosystem that aids digestion, immune function, and disease resistance. Loss of diversity can weaken these functions, making the gut more vulnerable to infections and chronic diseases. It also reduces the microbiome’s ability to recover from disturbances like antibiotics or poor diet.
- In the gut microbiome, "microbial species going extinct" means certain types of bacteria or microbes completely disappear from the gut environment. This loss reduces the diversity of microbes, which can weaken the mi ...
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Strategies For Maintaining or Restoring a Healthy Microbiome
Experts discuss how dietary changes and lifestyle adjustments can significantly impact the health and diversity of the gut microbiome.
High-Fiber, Plant-Rich Diet Diversifies Gut Microbiome
Fiber Fuels Gut Microbes' Growth and Activity
Studies on mice and humans show that a hito a low fiber diet.gh-fiber, plant-rich diet plays a critical role in nourishing the gut microbiota. The gut microbiota, in turn, produces short-chain fatty acids like butyrate from these fibers, which fuel colonocytes, reinforce the gut barrier, reduce inflammation, and regulate the immune system and metabolism. For example, when mice returned to a nutrient-rich diet high in dietary fibers after a low-fiber diet, many lost gut microbes were recovered. Participants in a human study were instructed to increase their plant-based fiber from whole grains, legumes, vegetables, and nuts to over 40 grams per day. As a result, participants reported improved energy, clearer thinking, better sleep, improved complexion, and better bowel movements, all of which could be tied to a healthier gut microbiome.
Diverse Fiber Sources Better Than Supplements
Justin Sonnenburg notes that people with a diverse microbiota capable of degrading various dietary fibers are more likely to benefit from a high-fiber diet. He warns that many in the industrialized world might have a gut microbiota so depleted they can't degrade fiber properly, even if they switch to a high-fiber diet. Studies on prebiotics show mixed results, sometimes leading to decreased microbiota diversity if the fibers foster the growth of only a few types of bacteria. A variety of plants with their diverse fibers is generally better for promoting microbiota diversity than purified fibers.
Fermented Foods Boost Microbial Diversity and Reduce Inflammation
Fermented Foods Offer Beneficial Gut Microbes
Participants in a study increased their consumption of fermented foods to an average of six servings daily. They were advised to eat naturally fermented foods containing live microbes, such as yogurt, kefir, sauerkraut, and kimchi. The study found that over six weeks, an increase in microbiota diversity occurred, which is linked to better health outcomes. Additionally, a ...
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Strategies For Maintaining or Restoring a Healthy Microbiome
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Counterarguments
- While a high-fiber diet is beneficial for many, individuals with certain digestive conditions, such as irritable bowel syndrome (IBS) or inflammatory bowel diseases (IBD), may experience exacerbation of symptoms with high fiber intake, particularly from certain types of fibers.
- The restoration of lost gut microbes through diet alone may not be possible for all species of microbes, especially if they have been absent for a prolonged period or if an individual has taken broad-spectrum antibiotics that have significantly altered their gut microbiome.
- The recommendation of over 40 grams of fiber per day may not be suitable for everyone, as dietary needs can vary greatly depending on age, sex, physical activity level, and overall health.
- The benefits of a diverse gut microbiota are well-documented, but genetic factors and long-term dietary patterns can also significantly influence an individual's ability to degrade various dietary fibers, not just the current state of their microbiome.
- The efficacy of prebiotic fiber supplements can vary, and while some may not be as effective as whole foods, others may be beneficial for individuals who struggle to consume a sufficient variety of fibers through diet alone.
- Fermented foods are generally beneficial, but the recommendation to consume six servings daily may not be practical or necessary for everyone to achieve health benefits, and overconsumption could potentially lead to an imbalance in the gut microbiome. ...
Actionables
- You can diversify your dietary fiber sources by creating a "Fiber Bingo" card with different plant foods in each square, aiming to complete a row each week. This game-like approach encourages you to incorporate a variety of whole grains, legumes, vegetables, and nuts into your meals, ensuring you consume a wide range of fibers that can nourish different gut microbes. For example, one row might include quinoa, lentils, broccoli, almonds, and apples, challenging you to find creative ways to include these in your diet.
- Start a "Fermentation Exploration" journal to track your homemade fermented food experiments and their effects on your well-being. By documenting your process of making foods like yogurt, kefir, or sauerkraut, and noting any changes in your energy levels, cognitive function, or digestion, you can identify which fermented foods have the most positive impact on your health. For instance, you might note that homemade kefir incorporated into your breakfast smoothie improves your digestion throughout the day.
- Implement a "Microbial Mindfulness" routine by adjusting your hygiene practices based on your daily activities. Create a simple chart that outl ...
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