This study employed an integrative review methodology to systematically synthesize ethnographic, historical, biochemical, and ethnobiological literature on indigenous Latin American biotechnologies. Given the interdisciplinary nature of this research, we adopted a structured, non-systematic literature review strategy informed by best practices in ethnobiology and historical analyses.

Search strategy

A comprehensive literature search was performed using academic databases, including PubMed, Scopus, Web of Science, Google Scholar, and specialized anthropological and ethnobiological databases. The search utilized Boolean operators to enhance specificity and comprehensiveness. The principal search strings included combinations such as: ("indigenous biotechnology" OR "traditional biotechnology" OR "ethnobiology") AND ("Latin America" OR "Mesoamerica" OR "Andes" OR "Amazonia"), ("microbial fermentation" OR "fermented beverages" OR "traditional fermentation") AND ("cassava" OR "maize" OR "agave" OR "pulque" OR "pozol"), ("terra preta" OR "Amazonian dark earth") AND ("sustainability" OR "agriculture"), and ("ethnopharmacology" OR "medicinal plants") AND ("indigenous knowledge" OR "traditional ecological knowledge").

Inclusion and exclusion criteria

Publications were included if they explicitly addressed traditional biotechnological practices, indigenous knowledge systems, microbial fermentations, ethnobiological or ethnopharmacological relevance, and cultural-historical significance within Latin American contexts. We excluded publications lacking empirical data, reviews without clear methodological rigor, and those unrelated to Latin American indigenous practices.

Data extraction and analysis

Articles selected were assessed for methodological rigor, historical accuracy, biochemical validation, and cultural context. Extracted data included indigenous communities involved, biochemical processes described, identified compounds and microbial species, historical and ethnographic insights, and contemporary relevance or application potential. A standardized data extraction form ensured consistency across reviewed publications.

Synthesis and integration

Data synthesis employed an integrative analytical framework that combined perspectives from ethnobiology, anthropology, microbiology, chemistry, and history. Patterns and themes across indigenous biotechnologies were identified and analyzed, emphasizing historically marginalized practices and their scientific validity, cultural importance, and potential for innovation.

Interpretation and contextualization

The findings were contextualized within broader discourses of epistemic justice, cultural resilience, sustainable agriculture, and contemporary biotechnology. Comparative analyses were performed with analogous global practices to underscore their global relevance and applicability to sustainability initiatives.

Cultural and historical context

Traditional narratives of scientific history have long positioned Latin America primarily as a recipient rather than a creator of knowledge, reinforcing European-centric models of science diffusion. Recent scholarship, however, emphasizes that colonial Latin America was a vibrant site of original knowledge production deeply rooted in unique cultural relationships with nature and human health. Ethnohistorical perspectives highlight how indigenous societies possessed sophisticated ecological and medicinal knowledge systems, intimately connected to their cultural worldviews, spiritual beliefs, and social practices. Iberian colonial science systematically appropriated selected indigenous knowledge, such as quinine-bearing bark, yet broadly dismissed other traditions as mere superstition or idolatry. This selective process led not only to epistemic losses but also to profound disruptions in cultural identity, local health systems, and the transmission of traditional ecological knowledge within indigenous communities [1].

By critically reexamining these indigenous biotechnologies from an ethnobiological and ethnomedical viewpoint, this study engages directly with current discussions in cultural anthropology and ethnobiology, addressing the cultural consequences of marginalizing indigenous knowledge. Scholars such as Kapil Raj (2007) and Warwick Anderson (2009) advocate recognizing the Global South as a dynamic, albeit historically marginalized, participant in global knowledge production. Applying this perspective, our work demonstrates how indigenous Latin American communities developed culturally embedded practices such as fermented probiotic beverages and natural encapsulation methods, which embody their culturally specific interactions with nature, health, and social well-being. By recovering these marginalized indigenous practices, this article not only enriches ethnobiological understanding but also reframes Latin America's historical role from a culturally passive recipient to an active contributor with unique, culturally grounded knowledge traditions [16, 17].

The following sections explore concrete examples of these indigenous biotechnologies, beginning with microbial fermentation systems. These culturally significant examples provide compelling evidence that indigenous Latin American knowledge systems were integral to broader historical and cultural processes that shaped scientific and ethnomedical innovation, despite their systematic exclusion from formal scientific and cultural narratives.

Indigenous microbial fermentation systems

Premodern Latin America fostered diverse fermentation traditions that harnessed native microbes for food, drink, and preservation. These indigenous systems, ranging from Amazonian cassava beers to Mesoamerican maize brews, were sophisticated bioprocesses that yielded nutritional and medicinal benefits. Beyond mere nutrition, these fermentation practices carried profound cultural, symbolic, and social meanings, forming integral parts of identity, community cohesion, and ritualized interactions with the natural world. Yet colonial and postcolonial paradigms often dismissed such practices as unscientific or unsanitary, leading to their marginalization in recorded science.

1.

Cassava Fermentation (Amazonia).

Masato de yuca, a traditional fermented cassava beverage from the Peruvian Amazon, exemplifies the complexity of indigenous brewing practices. Recent microbiological studies have revealed that masato fermentation is driven by consortia of lactic acid bacteria (LAB). In one traditional chicha variant, all identified strains belonged exclusively to Lactiplantibacillus plantarum. In contrast, Masato contained a more diverse microbial community, including Lactiplantibacillus plantarum, Limosilactobacillus fermentum, Pediococcus acidilactici, and Weissella confusa [18]. These microbes ferment cassava starch into mild alcohol and organic acids. For instance, a related Amazonian chicha (bacaba fruit beer) was found to generate 2.69 g/L succinic acid, 0.9 g/L acetic acid, 0.52 g/L ethanol, and other metabolites [19]. Such fermentations enhanced the caloric content, safety, and shelf life. Anthropologically, masato embodies communal relationships, as its preparation, consumption, and ritual sharing reinforce social ties, status, and group identity. Masato preparation involves clearly defined gender roles, with women primarily responsible for fermentation, a culturally significant practice essential for the daily diet and social activities among Amazonian Indigenous communities. Moreover, masato presents lower microbial contamination compared to local untreated water sources, reinforcing its importance as a culturally accepted method for improving water safety [20]. Historically, however, European colonizers largely ignored or suppressed these beverages, preferring European alcohol and deeming indigenous techniques “uncivilized.” The rich cultural meanings and ethnobiological expertise encoded in cassava fermentation, including the deliberate selection of wild microbial strains, remained largely undocumented within formal science for centuries [21, 22].

On the other hand, parakari is a traditional cassava beer of the Wapisiana Amerindians in Guyana, produced by an unusual two-step fermentation involving an amylolytic mold and a subsequent yeast-driven ethanol fermentation [23]. In the first stage, grated cassava (Manihot esculenta) roots are detoxified and baked into cassava bread, which is then inoculated with a domesticated Rhizopus mold and allowed to undergo solid-state saccharification (starch hydrolysis) under carefully controlled conditions [23]. The Wapisiana maintain the mold “starter” on dried plant leaves (e.g., Trema micrantha and locally bishawad) and wrap the fermenting cassava mass in leaves (such as Heliconia) to create a warm, humid incubation environment that encourages fungal growth [24]. After several days of mold activity, the now-sweetened cassava mash crumbled into water to initiate the second stage: a natural fermentation by wild yeasts that produce alcoholic beverages. Henkel’s field studies documented roughly thirty distinct steps in the parakari-making process, demonstrating a high degree of sophistication; for example, Wapisiana brewers selectively use certain cassava varieties, regulate the incubation temperature, and even add extra starch to boost Rhizopus growth and enzyme production during saccharification [25]. As a result, parakari stands out as the only known indigenous New World fermented beverage that employs an amylolytic mold—essentially paralleling Asian koji-based dual fermentation (as in sake or tapé) yet developed independently in Amazonia; this rare integration of mold saccharification and yeast fermentation exemplifies an advanced form of traditional Amazonian biotechnology, underscoring the ingenuity of Wapisiana fermentation practices [23, 25].

Recent findings have highlighted the broader scope of indigenous Amazonian practices, from fermentation techniques to soil management. For instance, Barghini’s studies (2020, 2022) reveal that the two-step “double fermentation” process (involving an initial mold-based saccharification followed by yeast fermentation) was far more widespread in northern Amazonia than previously recognized, extending from the upper Amazon and Guianas to the Orinoco region [24] and even reaching Central American/Caribbean groups (e.g., the Miskito and Bribri) [26]. Most documented cases involve cassava as the fermented substrate, but a few utilize maize, and at least one example uses plantains [24]. On the other hand, the phenomenon of terra preta (Amazonian Dark Earth) exemplifies an advanced pre-Columbian strategy for enhancing soil fertility. While prior works like Factura et al. (2010) and De Gisi et al. (2014) focused on terra preta’s utility in ecological sanitation, comprehensive studies show that its significance is much broader. Terra preta soils are anthropogenic, highly fertile black earths characterized by elevated nutrient levels and stable soil organic matter, which have supported sustainable agriculture in otherwise nutrient-poor tropical soils [27]. These soils were deliberately created through long-term incorporation of charcoal (biochar) and organic waste (e.g., food residues, manure, fish bone, and excreta) into the soil, followed by microbial decomposition and humification that stabilized nutrients and carbon. Authoritative reviews by Glaser & Birk (2012) provide detailed accounts of terra preta genesis, properties, and functioning, elucidating how these ancient engineered soils maintain their enhanced fertility and act as a model for sustainable land use [27].

In conclusion, indigenous Amazonian fermentation practices, such as masato and parakari, represent sophisticated traditional biotechnologies, utilizing deliberate microbial management to enhance nutritional quality, food safety, and social cohesion. The broader geographical distribution of double fermentation across northern Amazonia and the Caribbean highlights its widespread cultural importance. Additionally, terra preta exemplifies advanced pre-Columbian ecological engineering, enhancing soil fertility and sustainability through intentional biochar incorporation and organic matter recycling, thus offering valuable insights for contemporary agriculture.

2.

Maize Fermentation (Pozol, Mesoamerica)

In southern Mexico, Maya communities developed pozol, a fermented drink made from nixtamalized maize dough. This probiotic gruel sustained laborers in tropical climates and possesses remarkable microbial diversity. Metagenomic analysis of pozol identified a core community comprising 25 or more bacterial genera, dominated by fermentative Streptococcus species. During fermentation, genes for starch and fiber degradation are highly expressed alongside pathways for amino acid and vitamin B synthesis [28,29,30]. Beyond its biological role, pozol holds significant cultural symbolism, marking collective identities, territorial belonging, and ritual significance among Maya communities. Its preparation and consumption create and reinforce social bonds, illustrating deep cultural perceptions linking maize, nourishment, and communal health [31]. Nonetheless, Spanish colonial records often derided fermented maize dough as a food of the lower classes, failing to recognize the ethnobiological sophistication required to sustain a safe, nutrient-rich staple without modern preservation techniques. Consequently, pozol and similar indigenous fermentations were historically under-researched in mainstream food science.

3.

3. Agave Fermentation (Pulque, Central Mexico)

Pulque, the traditional Nahua fermented beverage made from agave sap, exemplifies an advanced microbial ecosystem that was stigmatized under colonial rule. Pulque’s spontaneous fermentation yields a tart, nutrient-rich beverage about as alcoholic as beer. Modern microbiological profiling indicates that pulque typically contains ~ 4–7% ethanol, primarily produced by Zymomonas mobilis bacteria and wild Saccharomyces yeasts.

Concurrently, lactic acid bacteria, especially species of Lactobacillus, Lactococcus, and Leuconostoc, generate lactic and acetic acids, lowering the pH to approximately 3.5–4.2 [32]. These microbial processes naturally preserve pulque and confer probiotic properties. Culturally, the agave plant, despite superficial resemblance, is botanically distinct from cacti and belongs to a separate family (Asparagaceae). In Nahua cosmology, pulque was regarded as "nectar of the gods" and played crucial roles in rituals, social ceremonies, and indigenous medicine. Despite its complexity and cultural significance, colonial authorities stigmatized pulque consumption due to associations with indigenous spirituality and perceived social disorder. By the seventeenth century, Spanish officials actively sought to prohibit pulque, labeling its use as a pagan practice linked to indigenous resistance [33]. This historical stigmatization deeply impacted indigenous identity, disrupted traditional practices, and delayed scientific recognition of pulque’s nutritional and therapeutic merits. Only recently have scientific studies begun to characterize pulque’s microbial complexity thoroughly, vindicating indigenous knowledge systems long dismissed as culturally inferior.

Ethnographic insights into natural encapsulation and geophagy

The ancestral practices of natural encapsulation and geophagy among Indigenous Andean peoples, such as the Quechua and Aymara, exemplify sophisticated food and medicinal technologies rooted in deep ecological knowledge. From an ethnographic perspective, these are not merely survival strategies or superstitions but deliberate, empirically informed responses to the environmental challenges of high-altitude living. The ingestion of specific edible clays to neutralize toxins in wild potatoes, particularly glycoalkaloids like tomatine, demonstrates a pharmacological understanding of detoxification. Modern chemical analyses have confirmed that Andean clays can adsorb and sequester such toxins in the gastrointestinal tract, effectively preventing their absorption and enabling the safe consumption of otherwise inedible tubers [34]. Consequently, this early form of oral detoxification technology was excluded from mainstream scientific discourse until modern analyses confirmed its efficacy [35]. Archaeological and ethnobotanical studies show that this practice, known as geophagy, has been part of Andean lifeways for at least 2,500 years [36].

Anthropologically, such practices reveal Indigenous technological agency that was historically obscured by colonial epistemologies. European chroniclers often interpreted geophagy as irrational or pathological “dirt-eating,” failing to recognize its rational pharmacological basis. This mischaracterization reflects a broader pattern of scientific marginalization, where Indigenous knowledge systems were excluded from formal science under colonial rule [37]. The Andean use of natural materials, such as clays, starches, and plant fibers, as encapsulants for drug or nutrient delivery anticipated principles now central to pharmaceutical science. Thus, what Western science once dismissed as folklore is increasingly being recognized as a complex, context-specific form of biomedicine grounded in ecological intelligence.

Alkaline processing (nixtamalization and coca chewing)

Mesoamerican and Andean cultures developed culturally embedded technologies that utilized empirical knowledge of alkaline substances to enhance the nutritional and medicinal properties of plants. In Mesoamerica, the process of nixtamalization, soaking maize in lime (calcium hydroxide), was not only a culinary technique but also a ritualized and socially transmitted form of food science. This treatment releases bound niacin (vitamin B₃) and essential amino acids, such as tryptophan and lysine, from corn [38]. Without it, maize-based diets risk niacin deficiency and pellagra, a problem tragically evident in Europe, where maize was adopted without the corresponding Indigenous processing knowledge [39]. Meanwhile, in the Andes, the application of alkali to coca leaves (Erythroxylum spp.), which are chewed with a pinch of lime or ash, was a pharmacological innovation deeply embedded in daily cultural practice. The base raises oral pH, converting coca alkaloids into their free-base form, thus enhancing mucosal absorption and therapeutic efficacy [38]. This allowed high-altitude Andean populations to mitigate hunger, fatigue, and hypoxia, functioning as a form of ethnopharmacology closely linked to the demands of their ecological niche [40]. Anthropologically, these practices reflect a deep integration of medicinal chemistry within environmental and social systems, contradicting colonial narratives that viewed them as superstition or vice. Spanish colonizers misunderstood or deliberately suppressed such knowledge: nixtamalization was not adopted in Europe, causing preventable disease, while coca-leaf chewing was demonized as idolatrous and criminalized [38]. This reflects a broader pattern of epistemic violence wherein Indigenous technological systems were marginalized under colonial rule, despite their demonstrable biochemical sophistication. In effect, these are early examples of biotechnological traditions that combine nutrition, pharmacology, and cultural meaning, well before the emergence of formal Western science.

Plant mucilages and natural polymers

Indigenous healers often leveraged the gel-forming fibers and mucilages of local plants to encapsulate remedies or soothe tissues. This practice embodies an ethnopharmacological logic deeply rooted in ecological observation and cultural transmission. This technique is functionally analogous to modern hydrogel-based drug delivery, yet it was embedded in the ritual, medical, and environmental practices of Latin American Indigenous communities. For instance, the use of prickly pear cactus (Opuntia spp.) mucilage in traditional medicine across arid regions extended beyond water clarification and wound care; it also carried symbolic associations with healing, fertility, and resilience, reinforcing its role in both practical and ceremonial domains.

Contemporary research has confirmed that Opuntia mucilage is a bioactive polymer with wound healing, hypolipidemic, antioxidant, and antimicrobial properties. It forms a viscous coating that acts much like a slow-release matrix for active compounds in the gastrointestinal tract or on dermal tissue [41, 42]. A recent study demonstrated that Opuntia robusta mucilage, when combined with alginate, effectively encapsulates probiotics such as Lactiplantibacillus plantarum, thereby enhancing their viability and stability [43, 44].

Anthropologically, the marginalization of these practices reflects the broader colonial erasure of Indigenous biomedical systems. Colonial-era physicians prioritized imported remedies, such as flaxseed and plantain from Europe, while dismissing Native American botanical materials. Despite widespread local use and demonstrated efficacy, plant mucilages were rarely documented in colonial pharmacopeias. Their sophisticated application as carriers and stabilizers for medicinal agents was thus excluded from formal science until modern biochemical studies began to "rediscover" their value. This rediscovery reveals that Indigenous technologies were not rudimentary but rather represent nuanced, place-based strategies for health and survival, now inspiring contemporary biotechnological innovations in edible films and encapsulants [6].

Ancestral preservation and biomedical potential

Traditional food preservation methods in Latin America were far more than pragmatic survival strategies—they were culturally embedded technologies interwoven with Indigenous epistemologies, environmental cycles, and health beliefs. Through empirical observation, intergenerational knowledge, and symbolic significance, Indigenous peoples developed preserved foods that not only extended shelf life but also produced antimicrobial agents and medicinal by-products [45]. Yet, these ancestral biotechnologies, precursors to modern pharmacology and food science, were long dismissed as “malodorous” or “primitive” under colonial and postcolonial frameworks. Such epistemic marginalization led to the exclusion of preserved Indigenous foods from scientific legitimacy, a pattern widely recognized in the anthropological literature on food heritage and power structures [46].

1.

Tocosh: The Andean Fermented Antibiotic

In the high Andes, the practice of preparing tocosh, fermented potato or maize left in anaerobic aquatic pits, reflects not just ingenuity but also a cosmopolitical engagement with microbiomes, water, and soil. Among Quechua-speaking communities, tocosh is regarded as both food and medicine, imbued with sacred and ancestral value, used to treat gastrointestinal and respiratory ailments. Scientific studies have corroborated these claims: tocosh fermentation enhances thiamine and riboflavin content, liberates bioavailable nutrients, and fosters microbial consortia that produce natural antibiotics [47, 48]. Dominant bacterial species, such as Lactobacillus sakei and Leuconostoc mesenteroides, have demonstrated potent antimicrobial activity, while others synthesize B vitamins and degrade antinutrients [47, 49, 50].

From an ethnographic viewpoint, the neglect of tocosh by colonial science reveals the dynamics of scientific exclusion tied to race, smell, and perceived “cleanliness”. Tocosh’s pungent odor and Indigenous origin contributed to its dismissal as an unworthy folk remedy. Yet within Andean worldviews, fermentation signifies transformation and renewal, and tocosh’s efficacy was never in doubt. As anthropologist Les Field argues, recognizing such practices requires reassessing Indigenous knowledge as technologically and ecologically valid [51].

2.

Bacteriocins and Bio-Protection in Fermented Foods

The antimicrobial properties of Latin America's fermented foods, such as pulque, pozol, and chicha, are not merely a biochemical phenomenon—they reflect deeply embedded Indigenous food ontologies and microbial stewardship practices. Traditional fermentation was not only about taste or preservation, but also served as a form of cultural pharmacology, a means to regulate health, maintain microbial balance, and convey ritual meaning. Within these complex food systems, lactic acid bacteria (LAB) play a central role—not only acidifying and stabilizing the food matrix, but also producing bacteriocins. These small antimicrobial peptides actively inhibit pathogens such as Escherichia coli.

In fermented maize beverages, such as pozol and chicha, strains like Lactobacillus plantarum release bacteriocins with both probiotic and antimicrobial effects, serving as bio-preservatives and potential therapeutic agents [52]. Studies have shown that LAB from pulque produce selective peptides that inhibit gut pathogens while sparing beneficial microbes, suggesting that ancestral fermentation practices prefigured modern microbiome-based therapies [53]. These endogenous antimicrobial agents allowed communities to create self-stabilizing, health-promoting foods long before the discovery of antibiotics.

However, colonial narratives often framed Indigenous fermented foods as sources of disease, dirt, or moral decline. For instance, the association of chicha with "chichismo" or moral laxity obscures their biochemical sophistication [54]. This ethnocentric framing delayed recognition of their probiotic potential and devalued Indigenous microbial knowledge systems. Only with the recent surge in interest around probiotics and functional foods has serious scientific attention returned to these bioactive peptides [55, 56]. From an anthropological perspective, these fermented products must be seen as living biocultural technologies, maintained through oral tradition, communal labor, and sensory knowledge. Their survival and efficacy underscore not only microbial ecology but also cultural resilience and biochemical ingenuity. As ethnographic studies on food heritagization argue, integrating these fermented systems into contemporary health and research frameworks requires respectful engagement with Indigenous epistemologies [57].

3.

Freeze-Drying Preservation (Chuño)

The practice of producing chuño, the Andean freeze-dried potato, is more than an ancient food preservation method—it is a biocultural adaptation to high-altitude ecologies and a clear case of Indigenous food engineering. Developed millennia before industrial lyophilization, chuño was created by Andean civilizations, such as the Inca, through cycles of night freezing and day drying, followed by trampling and leaching, which transformed perishable tubers into shelf-stable, lightweight, and nutritionally concentrated staples [58]. From an ethnographic perspective, chuño was not simply a technique, it was part of a broader system of ecological knowledge and communal labor embedded in Andean cosmology. It allowed Indigenous peoples to detoxify glycoalkaloids in bitter potatoes, thereby expanding the food base of high-altitude populations [59]. Chuño production involved not only practical knowledge of freeze–thaw dynamics but also ritual and calendrical rhythms that structured when and how chuño was made. It exemplifies how Andean societies fused environmental mastery with social and spiritual cohesion.

Despite its efficacy, colonial regimes viewed chuño through the lens of utility, adopting it to feed mine laborers and slaves without investigating the science behind it. As a result, chuño’s detoxifying properties and biochemical logic were ignored, a typical pattern of epistemic erasure under colonial science [46]. Only recently has chuño been recognized in modern food science as an early form of controlled sublimation and enzymatic detoxification, a natural precedent to today’s freeze-drying technologies [60].

In this light, chuño should not be studied merely as a “primitive precursor” to industrial methods, but rather as a sophisticated Indigenous food technology. Its survival across centuries demonstrates the value of ethnoengineering, technological systems that emerge not in labs but in dialog with climate, ecology, and collective knowledge.

4.

Enzyme-Rich Ferments (Bromelain in Tepache)

Traditional fermentation practices in Mesoamerica often acted as biochemical mediators, not only preserving foods but enhancing their medicinal potential. A compelling case is tepache, a lightly fermented pineapple beverage consumed widely in Mexico. Pineapple is naturally rich in bromelain, a mixture of proteolytic enzymes with anti-inflammatory and digestive properties. Remarkably, this enzyme complex survives and even transforms during fermentation: microbial action breaks down bromelain into bioactive peptide fragments, some of which exhibit enhanced medicinal properties [56]. From an ethnographic standpoint, the knowledge encoded in tepache production reflects a deep, if non-verbalized, understanding of functional biochemistry. Traditional consumers may not have used scientific terminology. Still, they recognized tepache as a digestive, refreshing, and curative drink, with its consumption deeply embedded in daily life, rituals, and seasonal rhythms [61]. Anthropological research on Indigenous healing traditions in central Mexico further confirms that fermented and plant-based beverages occupy liminal roles, bridging the realms of sustenance, medicine, and spirituality.

The acidic and low-alcohol environment of tepache (pH ~ 3.8–4.2) not only supports the preservation of bromelain but also selects for bromelain-tolerant probiotic strains, creating a complex enzyme-microbiota symbiosis in a single cup. However, postcolonial perspectives relegated tepache to the realm of rustic or “p