Culture and the Gut Microbiome: Exploring the Health Paradigms of Indigenous Societies

Introduction

What is the gut microbiome and how is it significant to human health?

The human gut microbiome is made up of fungi, viruses and bacteria that reside in the gastrointestinal tract. These microorganisms are increasingly recognized as an integral component of human health (Li et al., 2016). A healthy gut microbiome supports essential bodily processes from digestion to immunity and facilitates greater overall health (Jandhyala, 2015). Moreover, elevated levels of microbial diversity have been associated with greater microbial health and stability (Prakash et al., 2022). Microbial diversity allows the microbiome to adapt to a wider range of conditions, expands its functional capacity, and improves resistance to pathogens (Prakash et al., 2022).

An imbalance in the gut microbiome, on the other hand, has been linked to infectious diseases, neurodegenerative disorders, and mental health conditions (Bashir et al., 2022). Antibiotic use or other drug interventions can reduce microbial diversity, and promote resistance to the administered drugs (Newcombe et al., 2018). This disruption, or dysbiosis, can also affect the metabolites being sent to the brain, which in turn impacts the production of inflammatory biomarkers (Chaudhry et al., 2023). An excess of inflammatory biomarkers in the brain prevents the repair of neuronal connections and suppresses the production of new hippocampal neurons. Neurotransmitters are responsible for the regulation of mood and emotion, so the impairment of their production leads to chronic stress, depression, and anxiety (Xiong et al., 2019).

What factors influence the gut microbiome?

The gut microbiome is shaped by factors such as diet, lifestyle, and environmental interaction (Lozupone et al., 2012). For example, diets made up of fermented, high fiber, and unprocessed foods, as well as regular exercise can increase microbial diversity (Campbell & Wisniewski, 2017). Spending more time in contact with nature also leads to a greater exposure to diverse microbial communities. Yet, these health-promoting behaviors are becoming increasingly inaccessible in industrialized societies (Zheng et al., 2024). Specifically, Western approaches to health often overlook the impact of environmental interactions, and default to lifestyles that tend to be urbanized and high in processed food consumption.

Traditionally, Western biomedicine has been guided by the concept of the “biological individual,” which views a person as an autonomous unit with distinct biological processes working independently to support the whole (Ibeneme et al., 2017). As a result, much of Western health development has emphasized medicalization and institutionalization over a holistic interpretation of health. Industrialization and rapid population growth have, in turn, led to dense living conditions and dependence on processed foods (Crane-Kramer et al., 2023). These factors, coupled with higher rates of antibiotic use, have disrupted the gut microbiome and reduced microbial diversity among many urban Western communities (Zheng et al., 2024)

However, a surge in microbiome research now challenges some of the core beliefs within Western health paradigms by highlighting the critical role of gut microbiome diversity (Wiertsema et al., 2021). Because the gut microbiome changes in response to everyday cultural and social norms, these norms can either enhance or erode microbial diversity. Thus, culture itself, defined as a system of “people, places, and practices” that informs behavior and development within a context of power, plays a vital role in microbial health (Raeff et al., 2020). Examining societies whose traditional practices maintain high levels of microbial diversity can offer insights into preserving or restoring a balanced gut microbiome. Building on these insights, this review explores how cultural conceptions of health inform both healthcare systems and lifestyle practices, which in turn shape gut microbiome diversity in both explicit and implicit ways.

Specifically, this review focuses on Indigenous societies, many of which maintain health practices and environmental connections that have traditionally supported high levels of microbial diversity. The following results section considers the differences in the microbial profiles of non industrialized indigenous societies and Western industrialized societies, examining how healthcare approaches, cultural ideologies and spiritual practices, and historical factors such as colonization have shaped microbiome profiles. Finally, this analysis explores the role of indigenous knowledge and agency in future microbiome research.

Results

This literature review analysed 10 articles published between 2010 to 2025. 5 articles were randomized controlled trials investigating indigenous microbiome diversity, 4 articles were medical/evolutionary anthropology focusing on microbiome diversity and traditional health practices in indigenous communities, and 1 article reviewed the misapplication of race in microbiome research. The results section below is divided into three key sections: 1) The microbial profiles of indigenous groups, 2) cultural health ideologies of indigenous societies, and 3) Indigenous microbial depletion and misrepresentation in western biomedical research. As literature was reviewed from a range of disciplines, a variety of words and definitions were used to represent indigenous communities and their lifestyles. For simplicity and clarity, the term “indigenous” is used as an umbrella term to refer to groups who have historically lived on given land prior to colonization. However, we acknowledge that indigenous communities exist globally and encompass diverse cultures, histories and identities. Secondly, the results section uses the terms “Western” and “industrial” to represent groups whose lifestyles are shaped by common practices such as biomedical care systems, processed food consumption and urbanization. Of course, not all Western industrialized societies live in accordance with the values that are denoted as “Western” in this review. However, a generalization of the Western paradigm was necessary for comparisons between cultural conceptions of health and health practices in western vs. indigenous societies as they relate to the gut microbiome.

Microbial profiles of indigenous groups

Indigenous communities traditionally practice lifestyles that develop diverse microbial profiles (Warbrick et al., 2023). A study conducted by Clemente et al., aimed to characterize the microbiomes of the Yanomami population living in the Amazon rainforest (2015). They collected fecal, oral, and skin samples to compare with samples from Malawi, Guahibo, and American groups (2015). The Yanomami are unique in that their geographic isolation in the Amazon rainforest has allowed them to preserve their specific cultural practices through a limited interaction with the globalized world (2015). The Yanomami displayed the highest microbial diversity ever reported in any human group (2015). Oral diversity was more similar between populations than skin and fecal samples (2015). Fecal diversity of Yanomami was greater than in Guahibo Amerindians and Malawians (2015). The Yanomami also lacked antibiotic resistant strains of bacteria (2015).

The unique microbial profiles of the Yanomami population can be largely attributed to lifestyle differences (Clemente et al., 2015). The Yanomami people have had no exposure to antibiotics, spend a majority of their time outside, eat frequent but small meals consisting of ingredients from their surroundings, and wear garments that allow their skin to have more physical contact with the environment than most Westernized clothing (2015). These cultural health practices all foster a greater connection to the environment, highlighting the interplay between the microbiome and the surrounding ecosystems.

Similar to the Yanomami, many other indigenous societies have diets composed of whole foods accessible to them via the environment. A study conducted by Hauptman et al. looked at the microbiota present in non-industrial animal-sourced foods consumed by the Inuit tribe in Greenland. The dependence of Inuit communities on caribou and raw meat challenges Western perspectives on what constitutes a healthy diet. In Western societies, plant-based eating is often seen as the best mechanism by which to diversify the microbiome (Sidhu et al., 2023). However, the emphasis on plant-based eating may serve as a gateway to transition from processed to whole foods, rather than plant based diets being superior for the gut than whole-food animal diets (Clem & Barthel, 2021).

The traditional, non-industrial methods used by the Innuit to prepare these animal-sources foods, rooted in their dependence on the local ecosystems, likely contribute to their distinct microbiome. The Hauptman et al study found that these raw meats hosted a number of edible parasites that have been lost from the modern diet in Greenland (2020). While parasites are now seen as threats to be prevented rather than seen as a source of nutrients, the consumption of raw meat containing a wide range of parasites fostered greater microbial diversity within Innuit microbiomes.

The traditional hunter-gatherer lifestyle within some indigenous societies fostered a greater connection with the environment, and a dependency on natural surroundings for survival. A study done by Fragiadakis et al., compared the microbial profiles of the Hadza hunter-gatherers in Tanzania to other populations worldwide (2019). Their research found that the microbial composition of the Hadza exhibited seasonal variation corresponding to wet and dry seasons (2019). Notably, VANISH taxa, a bacteria that humans co-evolved with and commonly associated with high fiber diets, were prevalent among Hadza microbiomes (2019). Specific VANISH taxa found in the Hadza microbiomes include Prevotellaceae, Succinovibrionaceae, Paraprevotellaceae, and Spirochaetaceae– all bacterias that are diminished or entirely absent from the microbiomes of most industrialized populations (2019).

Unlike elderly populations in industrialized societies, the Hadza microbial compositions diversified with age (Park et al., 2015). Over the course of their lifespan, an individual’s microbiome develops in response to its host’s circumstances: environmental and dietary factors (2015). The fact that microbiome diversity increases with age in the Hadza, but decreases with age in industrialized societies suggests the health implications of each groups’ respective lifestyle. Overall, both diversity of species and prevalence of bacteria was greater in Hadza microbial profiles than that of industrialized individuals (Fragiadakis et al., 2018). The Hazda diet is high in microbiota-accessible carbohydrates from plant based fibers, and they have regular contact with the natural environment, limited antibiotic access, and a lack of many modern sanitation technologies (2019). Collectively, these factors work to foster the high microbial diversity found within the Hadza population.

There is an abundance of literature reviewing the microbial profiles of children in infancy, as well as adults, but little research has been done on the microbial profiles of older children. A study conducted by Sánches-Quinto et al., used fecal samples to compare the microbiome composition of children ages 5-10 in “Westernized” and “non Westernised” communities within Mexico (2020). The Westernized/industrialized population in the study were children living in Mexico City, while the non Westernized/rural population were members of the Me’phaa tribe (2020). They found that the gut microbiomes of Me’phaa children had higher diversity and certain unique phyla of bacteria, while the children from Mexico City had less microbial diversity and higher concentrations of Saccharibacteria which processes sugars (2020).

There were distinct differences observed in the lifestyle of the Me’phaa and Mexico City children that may account for their microbial differences (2020). The Me’phaa resided in communities composed of fifty to eighty families of 5-10 members, while the children in Mexico City lived mostly in single family homes or apartments (2020). Me’Phaa communities live off subsistence farming, resulting in a diet consisting mainly of legumes, corn, wild plants, fruits, vegetables, and meat on special occasions (2020). The children living in Mexico City consumed greater amounts of processed foods and meat (2020). The Me’phaa children also lacked access to many sanitation facilities available in Mexico city including, health services, plumbing, and water treatment (2020).

The greater levels of microbial diversity among indigenous societies reflected in the articles reviewed in results section one stem from differences in lifestyle practices between Western and indigenous societies. The next section explores how underlying belief systems shape the practices that influence microbial composition, highlighting the important role of culture in developing bodily ecosystems.

Cultural health ideologies of indigenous societies

While studies have been conducted on the microbiomes of indigenous societies, fewer take steps to acknowledge the traditions and knowledge guiding the practices that foster microbial diversity. As a result, limited articles could be found that explicitly connect indigenous health ideologies to microbial diversity. However, some work by indigenous scholars presents an opportunity to understand this connection. For example, a study conducted by Silk et al., discusses “Mātauranga Māori”, a form of traditional Māori knowledge that is often discounted in Western research (2024). This knowledge includes sustainable cultivation practices, interaction with diverse flora and fauna, and an understanding of ecological relationships, waterways, astrology, weather, and human and environmental well being, that has been passed down through generations (2024). Māori embrace a holistic perspective on the relationship between health and ecosystems. The elevated microbial diversity of non-industrialized Māori populations, as compared to industrialized Western groups, is likely the result of the impact that Mātauranga Māori has on Māori interactions with the environment, and dietary habits (2024).

Ibeneme et al., examined ethnomedicine as a sociocultural model that views illness as the product of a disturbance in environmental and social interaction (2017). The review establishes that ethnomedicine is rooted in traditional beliefs that connect the spiritual and natural world (2017). In societies practicing ethnomedicine, healing systems fall into two main categories (2017) . Firstly, the personalistic system which attributes illness to supernatural or spiritual disturbances (2017). Secondly, the Naturalistic System which is derived from a view of health as a balance between the elements (2017). Treatment via the Naturalistic system focuses on restoring balance through diet, herbs, and lifestyle changes (2017). Cultural practices that align with the naturalistic system include communal living, seasonal eating, greater time spent outdoors, and natural medicinal interventions, which are observed by the indigenous groups discussed in results section one respectively (2017). For example, within the Navajo Tribe, health complications are viewed as a symptom of an imbalance between an individual, the supernatural world, the environment, and social interaction (2017). In order to achieve balance, or to fulfill the naturalistic conception of health, greater interaction with the environment, spiritual, and social world must be accomplished (2017). Indigenous societies conceptualize health via the naturalistic system, and have a “long-standing connection with the environments that they descend from—a connection that has informed a deep and multifaceted understanding of the relationship between human well-being and the environment” (Warbrick et al., 2023). This understanding gives way to the development of practices involving more physical connection with the environment, likely elevating microbial diversity.

The Maya and the Kuna people of Panama are examples of how microbial diversity is tied to consideration of external and spiritual influences. Healers among the Kuna people range from shamans to herbalists, and are all centered around curing imbalances between external and internal forces that manifest as damage to physical and soul health (Encounters with the Americas | Peabody Museum of Archaeology & Ethnology, 2025). The belief in this balance, while not directly indicative of knowledge of the microbiome, represents age-old understandings among different indigenous communities that people are intertwined with their surroundings. This understanding is reflected in many of the practices of various indigenous cultures that are now being proven to increase microbial diversity, and in turn benefit overall health.

Indigenous microbial depletion & misrepresentation in Western biomedical research

The previous section highlighted the link between microbial diversity and cultural/spiritual practices of indigenous communities, this section will focus on the impact of colonization on indigenous microbiomes. While epistemologically different from Western biomedicine, traditional indigenous practices sustained the well-being of the communities they served for generations (Warbrick et al., 2023). Escalating industrialization and expansion of Western biomedical paradigms are making it increasingly difficult for indigenous communities to preserve these traditional practices (Silk et al., 2024). It is crucial to acknowledge the value and advancement within biomedicine; however, a more comprehensive and equitable approach necessitates the incorporation of diverse perspectives and the acknowledgment of the devastating effects of colonial legacies on indigenous health and microbial diversity.

Indigenous communities that previously experienced colonization continue to experience forms of economic and social marginalization, and pressure to assimilate into the dominant ex-colonial culture (Silk et al., 2024). For example, Silk et al describes the inequities Maori people face in New Zealand within the dominant health system (2024). Additionally, the relative economic disparity between Maori and Pakeha ^[1] in the country has led to Maori communities disproportionately facing urban residential poverty. Both economic and healthcare inequities can deplete microbial diversity (2024).

Similarly, Warbrick et al discuss how colonization has displaced indigenous people from “ancestral lands” severing their connection to a “diverse environmental microbiome” and decreasing their exposure to health-promoting microbiota (2023). Skelly et al, suggest that the worse health outcomes suffered by nearly all indigenous groups globally is a result of colonial disruptions to indigenous ecosystems leading to decreased microbial diversity and functionality (2018). The study ties microbiota dysbiosis in indigenous populations, even those living in remote areas, to the “loss of ancestral land, depletion or dispossession of traditional resources,” and “the overall abandonment of traditional lifestyles, which impacts dietary composition, physical activity, and psycho-emotional health” (2018).

A study by Klaus & Tam showcased how “colonial-era economic reorganisation” in Peru decreased access to traditional dietary food sources for indigenous Andean communities, likely depleting microbial diversity and leading to poor health outcomes such as increased oral disease (2010). It was concluded that forces of colonialism, industrialization, and globalization exposed indigenous communities to economic, health and social marginalization. This led to the depletion of the microbiome through dietary changes, uprooting of traditional cultural and spiritual practices, and integration into deprived urban environments (Skelly et al, 2018).

Discussion

Microbial profiles of indigenous groups

The studies reviewed in results section one demonstrate a significant increase in the microbial diversity of the indigenous communities reviewed, as compared to Western counterparts. This can be attributed to adherence with traditional lifestyle practices such as frequent contact with the environment, whole food diets composed of MACs, a lack of exposure to antibiotics, and an absence of modern sanitation practices. When these factors are considered in conjunction with diversified microbes they suggest the importance of environmental and dietary factors in shaping human microbiomes.

These results are consistent with the accepted theories on diverse and whole food diets, along with outdoor exposure leading to greater microbial diversity and thus better health outcomes (Lozupone et al., 2012). What is interesting, however, is that in a few of the indigenous populations reviewed, greater microbial diversity did not lead to better health than seen in their Western counterparts (Sánchez-Quinto et al., 2020). The Me’phaa tribe for example, has some of the highest morbidity and mortality rates in Mexico despite having greater microbial diversity than their Mexico City counterparts (2020). It is important to also take into account that the Me’phaa tribe has some of the lowest average incomes in the country, as well as no water treatment or healthcare infrastructure (2020). While the tribe’s relatively high microbial diversity is likely good for their general health, the lack of access to other necessary health safety precautions negates its effect in terms of severe health outcomes (2020). This suggests that in order to optimize health the lifestyle factors that diversify the microbiome should be considered, but should not be implemented as replacements to certain life saving technologies that exist in modern Western biomedicine. Instead, the microbially beneficial practices of indigenous societies should be implemented alongside the technological innovation within Western biomedicine.

Research comparing indigenous microbial profiles with those of Western industrialized societies is limited. Consequently, some studies in section one do not meet ethical standards when working with indigenous communities. For example, while Clemente et al. provide extensive data on the Yanomami’s microbiome, they perpetuate racist ideologies by comparing the Yanomami to “our ancestors,” fail to conduct mutually beneficial research, and reduce the Yanomami to mere scientific subjects.

Cultural health ideologies of indigenous societies

Results section one established the clear differences between microbial profiles of indigenous societies and industrial Westernized societies, and highlighted some of the lifestyle practices that may cause those differences. The lifestyles led by industrialized Western societies and indigenous societies are the product of the driving philosophy behind each group’s respective conceptions of health, and how those conceptions have been implemented overtime.

The indigenous societies examined throughout this review all have unique cultural histories that have shaped their health practices. That being said, certain commonalities exist in their overarching conceptions of health. These include a belief in health as something that goes beyond the absence of sickness, but rather encompasses a balance between external and internal systems. These systems include social organization, the environment, physical well being, and spiritual presences. The habits derived from the belief in maintaining harmony between these systems seem to foster greater microbial diversity.

Examining the effect of non Westernized lifestyles on microbial diversity is important to gain an understanding of how to create optimal conditions for microbial health, however, when doing so these microbial differences must not be misconstrued. Microbial differences between non Western and Westernized societies are related to generations of alternate health practices and lifestyle habits, and are not the product of racial or ethnic differences. Understanding this distinction is necessary in the continuation of research, as microbiome science should not be misapplied to support harmful narratives of biological racial divides. Furthermore, Indigenous societies have developed an enduring understanding of interactions between individuals and the environment which should not be dismissed in research. There are limited studies examining the link between spiritual or health ideologies and microbiome diversity, suggesting that more research into this connection is needed. Understanding the ideologies driving beneficial health practices adds context to different health outcomes across races.

Indigenous microbial depletion & misrepresentation in Western biomedical research

The legacy of colonization has led to a systemic and economic oppression of assimilated indigenous groups (Skelly et al, 2018). Due to economic disparities, indigenous groups are often unable to maintain the traditional health practices that have historically preserved their microbial diversity (Silk et al., 2024). Microbial depletion, paired with the restricted access to healthcare and sanitation services that comes with poverty, leads to worse health outcomes in many indigenous communities (Skelly et al, 2018). In light of this, promoting mutually beneficial microbiome research with indigenous communities is imperative.

Indigenous people are frequently misrepresented in Western biomedical research (Benezra, 2020). Communities are often stereotyped, and displayed solely as scientific subjects (2020). The recurrence of this issue, especially within microbiome research, warrants the need for guidelines when it comes to working with indigenous groups. Words that dehumanize or alienate indigenous people should be removed from studies, and research should be fully consensual, adhering to the boundaries set by indigenous communities.

Whether it be because indigenous health practices are often embedded within broader spiritual beliefs, or because of the portrayal of many indigenous societies as “primitive”, research done within the Western biomedical field often fails to seriously consider the contribution of indigenous knowledge (Warbrick et al., 2023). Non-industrialized societies should be looked at to uncover the lifestyle practices that drive greater microbial diversity, not to perpetuate racial discrimination in scientific practices, and not without consideration of how results can be applied to better all communities including the ones being researched.

Research into the intra community microbial differences, accessibility of traditional practices, and the incorporation of indigenous scientific perspectives are all goals that should be strived toward while working with indigenous communities. To move forward from the longstanding history of forced assimilation, a rejection of indigenous culture and beliefs, and generational oppression, Western communities must not only acknowledge indigenous contributions in all fields, beyond just medicine, but also continue to conduct research in a way that incorporates and benefits indigenous communities.

As conveyed in the review conducted by Silk et al., one way to ensure that research is mutually beneficial is research involving indigenous communities being conducted by members of that community (2024). Members of indigenous communities have a greater understanding of the conceptions of health within their respective community, so they are better able to incorporate indigenous perspectives in microbiome research, and to ensure that their research respects the boundaries set by indigenous communities.

Conclusion

This review focuses on elucidating the difference in health ideologies and practices between indigenous and Western industrialized societies, and consequently how these disparate lifestyles have influenced their respective microbial expression. A belief in the interconnectedness of environments and the conceptualization of health as a state of equilibrium within these environments has led to the establishment of health and lifestyle practices that foster greater microbial diversity among many indigenous societies. Exploration into this topic has revealed great disparities in the research into indigenous communities’ microbial profiles, both in terms of a lack of comprehensive data, and a pattern of exploitation among the comprehensive research that exists.

Recognizing the considerable potential of microbiome science to revolutionize healthcare paradigms, this review posits that the future of this research must incorporate the knowledge and perspective of societies beyond those that practice Western biomedicine. The habits and practices that seem to be fostering greater microbial diversity among indigenous communities should be both utilized to improve current understandings of how to achieve health, and seen as a wakeup call to recognize the knowledge that Western biomedicine is cut off from by a refusal to accept alternate health narratives. Western biomedicine has led to miraculous inventions that save lives in dire situations, however there is still room for improving overall well-being in Westernized societies. If healthcare systems can continue to advance medical technology while also incorporating ideas of holistic wellness then human health and wellbeing can be greatly enhanced, and made more accessible for everyone.

Limitations

This Literature Review was conducted by one person in a set time frame, limiting the scope of the studies that could be included. Moreover, microbiome research is an emerging field, and the cultural health ideologies in indigenous societies are not thoroughly researched. As these topics were central to the literature review, the scarcity of studies pertaining to them created additional barriers to the extent of material that could be reviewed.