By Josh Windsor
Senior Caves Manager, Murray’s Cheese

July 17, 2026
From the Summer 2026 Issue of Culture Cheese Magazine

(Image: A close-up, artistic shot of milk in a vat or a cheese wheel, perhaps with subtle hints of microbial activity like a developing rind. Credit: Adobe Stock_Guys Who Shoot)

The world of cheese is a realm of profound sensory delight, a complex interplay of flavors, aromas, and textures that tantalize the palate. Yet, the true architects of this gastronomic marvel remain largely unseen: the microscopic communities of bacteria, yeasts, and molds that orchestrate every stage of cheesemaking. From the udder of the dairy animal to the aging caves of an affineur, these microbial populations dictate not only the unique identity of each cheese but also its fundamental safety. This intricate microbial journey, particularly the pivotal role of heat treatment like pasteurization, is a subject of ongoing fascination, scientific inquiry, and passionate debate within the cheese world.

Josh Windsor, an esteemed affineur and Senior Caves Manager at Murray’s Cheese, delves into the nuances of this microbial universe, breaking down the critical distinctions that shape the cheese on our plates. His insights reveal that while pasteurization is a significant intervention, it is but one thread in the vast, interconnected tapestry of factors that determine a cheese’s character.

The Unseen Architects of Flavor: Understanding Cheese Microbiology

At its core, cheese is a fermented food, and like all fermented products, its essence is defined by microbial activity. These microscopic organisms are not merely passengers in the milk; they are the active agents that transform a simple liquid into a product of astounding complexity. The specific diversity and activity of the microbiota inhabiting the milk are the bedrock upon which a cheese’s identity, its safety profile, and its ultimate sensory appeal are built.

A Microscopic Ecosystem: From Udder to Curd

The journey of milk, and thus its microbial cargo, begins long before it reaches the cheesemaking vat. It starts within the udder of the dairy animal, an environment teeming with its own unique biome. This initial microbial community, composed of various bacteria including many functional Lactobacilli strains crucial for cheesemaking, is naturally transferred to the milk during milking. As milk progresses through collection, cooling, and processing, it encounters new environments, each presenting an ecological niche that selectively favors certain microbial species while inhibiting others. This dynamic process of selection and transformation continually shapes the microbial diversity and, consequently, the evolving character of the dairy product.

The Dual Nature of Microbes: Flavor Creators and Potential Pathogens

The microbial world within milk and cheese is a double-edged sword. On one side, beneficial microbes are indispensable for developing the desirable attributes of cheese. They break down lactose, produce lactic acid, contribute enzymes that ripen proteins and fats, and generate a vast array of volatile compounds responsible for aroma and flavor. Without them, cheese would simply not exist in its recognizable form. On the other side, milk can also harbor pathogenic microorganisms—bacteria, viruses, and parasites—that pose a risk to human health. These pathogens, such as E. coli, Listeria monocytogenes, and Salmonella, can cause serious foodborne illnesses. The challenge for cheesemakers, and indeed for regulatory bodies, lies in harnessing the beneficial aspects of microbial activity while effectively mitigating the risks posed by harmful strains. This delicate balance forms the crux of many debates surrounding milk processing and cheese safety.

A Journey Through Transformation: The Chronology of Milk’s Microbial Life

Understanding the microbial life cycle of milk requires a chronological approach, tracing its path from its origin to its final form as aged cheese. Each stage presents unique conditions that profoundly influence the microbial populations present.

The Udder Biome: Milk’s First Microbial Endowment

Like human skin, the udder of a dairy animal hosts a diverse array of microbes, both those present from birth and those acquired throughout the animal’s life. This "udder biome" is influenced by numerous factors, including the animal’s diet, overall health, breed, and environmental conditions such in bedding, feed, manure, dust, and soil. These environmental microbes are constantly introduced to the teat surface. During the milking process, a portion of this existing udder microbiome, along with environmental contaminants, is inevitably transferred into the freshly drawn milk. This initial microbial load is critical, as it provides the foundational "seed" for the subsequent microbial developments in the milk. Optimal milking hygiene, including proper cleaning of the udder and milking equipment, is paramount in minimizing the transfer of undesirable microorganisms while preserving the beneficial ones.

From Farm to Vat: Cooling and the Rise of Psychrotrophs

Immediately after leaving the udder, milk begins to cool. Modern dairy practices accelerate this cooling process through refrigeration, primarily to reduce the rate of spoilage caused by mesophilic bacteria (those thriving at moderate temperatures). However, this cooling, while essential for preservation, introduces another layer of microbial dynamics. Prolonged storage at colder temperatures, typically between 2°C and 7°C, allows for the proliferation of psychrotrophic (cool-loving) bacteria. While many of the functional lactic acid bacteria beneficial for cheesemaking survive these conditions, they often enter a dormant state, their activity suppressed by the low temperatures. Psychrotrophs, however, remain active and can produce enzymes that, over time, can lead to off-flavors and textures in milk, even before visible spoilage. This highlights the delicate balance between preserving milk and managing the evolving microbial landscape within it.

The Crossroads of Heat Treatment: Raw, Pasteurized, and Thermized

The decision to apply heat treatment to milk marks a significant crossroads in its microbial journey. This step fundamentally alters the microbial community, setting the stage for the cheese’s subsequent development. In the United States, two primary legal classifications exist based on heat treatment: raw milk and pasteurized milk.

Raw Milk: Tradition, Terroir, and Regulatory Debates

Raw milk is legally defined as any milk that has not undergone pasteurization, meaning it has not been heated to the specific temperature and held for the duration required to destroy significant populations of microorganisms. Advocates for raw milk cheeses often emphasize the concept of "terroir" – the unique environmental factors, including microbial ones, that contribute to a cheese’s distinctive flavor profile. They argue that the natural enzymes and diverse indigenous microbiota present in raw milk contribute to a more complex, nuanced, and authentic flavor development that cannot be fully replicated in pasteurized milk. Historically, all cheese was made from raw milk, and many traditional European cheeses still rely on raw milk for their protected designation of origin (PDO) status.

However, raw milk carries an inherent public health risk due to the potential presence of pathogens. This tension between culinary tradition, unique flavor, and food safety forms the core of ongoing regulatory debates globally. While many raw milk cheeses are safely consumed, the potential for contamination from the farm environment or during handling means stringent hygiene practices are non-negotiable for raw milk producers.

Pasteurization: A Public Health Imperative and its Microbial Aftermath

Pasteurization, named after Louis Pasteur who developed the process in the mid-19th century, is a heat treatment designed to significantly reduce the number of viable microorganisms in milk, particularly pathogenic ones, to a level where they are unlikely to cause disease. The most common methods include High-Temperature Short-Time (HTST), where milk is heated to at least 72°C (161°F) for 15 seconds, and Low-Temperature Long-Time (LTLT), involving heating to 63°C (145°F) for 30 minutes.

While highly effective in ensuring food safety, pasteurization is a broad-spectrum process. It destroys not only dangerous pathogens but also many of the technically functional, beneficial microbes and enzymes naturally present in raw milk that contribute to flavor and texture development. This results in a "mostly sterile" canvas for cheesemakers. After pasteurization, cheesemakers must actively repopulate the milk with specific "starter cultures" – carefully selected strains of bacteria (e.g., Lactococcus, Streptococcus) – to initiate fermentation and guide the cheesemaking process. While these cultures provide consistency and control, some argue they can lead to a more standardized, less complex flavor profile compared to cheeses made with the full, diverse microbiome of raw milk.

Thermization: A Delicate Balance

Thermization represents a middle ground between raw milk and full pasteurization. It involves heating milk to temperatures below standard pasteurization levels, typically between 57°C (135°F) and 68°C (154°F) for a shorter duration (e.g., 15-20 seconds). In the US, thermized milk is still classified as raw milk, as it does not meet pasteurization requirements.

The goal of thermization is to reduce the overall microbial load and extend the shelf life of raw milk without completely sterilizing it or destroying all of its indigenous microflora and enzymes. This process can effectively destroy some dangerous strains, such as E. coli, and significantly reduce psychrotrophic spoilage bacteria. However, thermization is generally not hot enough or held long enough to kill more heat-resistant pathogens like Listeria monocytogenes. Cheesemakers might choose thermization to retain some of the unique microbial characteristics of raw milk while enhancing the safety margin and ensuring greater consistency in their cheesemaking process, particularly for cheeses that undergo a long aging period.

Post-Treatment Rebirth: The Creamery’s Influence and Aging Process

Regardless of the initial heat treatment, the microbial journey of cheese continues long after the milk leaves the vat. For pasteurized milk, the "mostly sterile" liquid is intentionally repopulated with carefully chosen starter cultures. These cultures, along with environmental microorganisms present in the creamery itself – on equipment, walls, and even in the air – begin to colonize the developing cheese. The creamery environment, often a stable microbial ecosystem in its own right, plays a crucial role in contributing secondary flora that further develops the cheese’s character.

As the cheese is formed, salted, and moved to aging caves (a process known as affinage), its internal and external environments continue to change. Moisture content, salt concentration, pH levels, and temperature fluctuations in the aging room create new ecological niches, favoring certain microbial populations over others. Surface molds, yeasts, and bacteria on the rind, for example, contribute immensely to the cheese’s final flavor, aroma, and texture, often producing compounds that penetrate deep into the paste. This continuous microbial evolution throughout the life of the cheese ensures that its character is not static but a dynamic reflection of its entire journey.

Evidence and Expertise: Supporting Data and Scientific Insights

Modern scientific research continues to unveil the profound impact of microbial diversity on cheese quality, aesthetics, and safety. Through advanced techniques like DNA sequencing, microbiologists can map the complex communities within different cheeses, offering empirical support for long-held artisanal beliefs.

The Science of Microbial Diversity and Flavor Compounds

Numerous studies have demonstrated a clear correlation between microbial diversity and the complexity of flavor profiles in cheese. For instance, research comparing raw milk cheeses to their pasteurized counterparts often reveals a broader range of volatile organic compounds (VOCs) in raw milk cheeses, which contribute to more nuanced and layered aromas and tastes. The indigenous non-starter lactic acid bacteria (NSLAB) in raw milk, for example, are known to produce a wider array of enzymes that break down proteins and fats into diverse flavor precursors, leading to notes like nutty, fruity, grassy, or earthy, that are less pronounced in cheeses made with a limited starter culture. This scientific evidence underscores the artisanal argument for the unique contributions of raw milk’s natural flora.

Case Studies: Raw Milk Cheeses and Their Unique Profiles

Consider iconic raw milk cheeses like Parmigiano-Reggiano, Gruyère, or Roquefort. Their protected designation of origin (PDO) status often mandates the use of raw milk, recognizing that the local microflora is integral to their specific characteristics. For Roquefort, the distinctive blue veins come from Penicillium roqueforti, a mold that thrives in the caves of Combalou, but its interaction with the indigenous raw sheep’s milk flora is what creates its inimitable pungent, salty, and sweet balance. Similarly, the deep, nutty flavors of aged Gruyère are attributed not just to the specific starter cultures but also to the diverse bacterial populations introduced with the raw milk and fostered in the cheese’s traditional aging environment. These examples serve as powerful case studies illustrating the irreplaceable role of microbial diversity, often originating from raw milk, in shaping world-renowned cheeses.

The Role of Enzymes in Ripening

Beyond live microbial activity, enzymes produced by these microorganisms play a critical, often understated, role in cheese ripening. Both bacterial and native milk enzymes (which are largely destroyed by pasteurization) catalyze biochemical reactions that break down milk components—proteins (proteolysis), fats (lipolysis), and lactose (glycolysis). Proteolysis, for instance, generates peptides and amino acids that contribute to savory flavors and the breakdown of the cheese matrix, influencing texture. Lipolysis releases free fatty acids that are precursors to a wide range of aromatic compounds, from fruity to rancid notes, depending on their concentration and type. The combined enzymatic activity, particularly the broader enzymatic palette found in raw milk, contributes significantly to the depth and evolution of flavor over the aging period.

Navigating the Regulatory Landscape: Official Responses and Industry Standards

The inherent microbial risks associated with raw milk have led to diverse regulatory frameworks worldwide, reflecting varying approaches to balancing public health and culinary tradition.

US Regulations: The 60-Day Rule and Beyond

In the United States, the Food and Drug Administration (FDA) imposes a strict regulation known as the "60-day rule." This rule mandates that any cheese made from raw milk must be aged for a minimum of 60 days at a temperature of at least 35°F (1.7°C) before it can be sold. The scientific rationale behind this rule is that the combined effects of salt, acidity, and time during the aging process are sufficient to significantly reduce or eliminate most common pathogens, making the cheese safe for consumption. However, this rule effectively limits the types of raw milk cheeses that can be legally produced and sold in the US, excluding fresh or soft-ripened raw milk cheeses which might not survive a 60-day aging period or whose character would be fundamentally altered. This regulation has been a point of contention for many artisanal cheesemakers who wish to produce a wider range of traditional raw milk products.

European Approaches: PDO and the Valorization of Raw Milk Cheeses

In stark contrast to the US, many European countries, particularly France, Italy, and Switzerland, have a long-standing tradition of raw milk cheesemaking, often protected by stringent designation of origin systems like PDO (Protected Designation of Origin) or AOC (Appellation d’Origine Contrôlée). These regulations often require the use of raw milk for certain cheeses, recognizing its integral role in their unique character and cultural heritage. Examples include Comté, Roquefort, and Parmigiano-Reggiano. European regulators often emphasize a holistic approach to food safety, focusing on robust hygiene throughout the entire production chain—from farm to finished product—rather than solely relying on heat treatment. This often involves strict controls over animal health, milking practices, and creamery sanitation, alongside the natural pathogen-reducing effects of fermentation and aging.

Public Health Perspectives and Industry Best Practices

Public health organizations, such as the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO), consistently highlight the potential risks of consuming raw milk products due to the possibility of pathogen contamination. Their recommendations generally favor pasteurization as the most effective method for ensuring milk safety.

However, the cheese industry has responded with a commitment to best practices. For raw milk cheesemakers, this involves rigorous testing of milk, environmental swabbing, adherence to Hazard Analysis and Critical Control Points (HACCP) plans, and meticulous hygiene. For pasteurized milk cheesemakers, the focus is on maintaining sterility post-pasteurization, controlling starter cultures, and preventing cross-contamination. The ongoing dialogue between public health officials, regulators, scientists, and cheesemakers aims to strike a balance between ensuring consumer safety and preserving the rich diversity and cultural heritage of cheesemaking.

The Future of Fromage: Implications for Cheesemakers and Consumers

The intricate dance between microbes and milk has profound implications for everyone involved in the cheese ecosystem, from the farmer to the consumer.

The Cheesemaker’s Craft: Balancing Art, Science, and Safety

For cheesemakers, understanding microbial diversity is not just a scientific pursuit; it’s an essential part of their craft. They must act as microbial managers, carefully orchestrating conditions to favor beneficial organisms while suppressing harmful ones. This involves a deep knowledge of milk chemistry, microbiology, and environmental control. Whether working with raw milk to embrace its natural variability and terroir, or with pasteurized milk to carefully select and manage starter cultures, the cheesemaker’s skill lies in manipulating these unseen forces. The decision to pasteurize, thermize, or use raw milk is a complex one, influenced by tradition, desired flavor profile, market demands, and regulatory constraints. Innovation in this space involves exploring new starter cultures, understanding the nuances of creamery microbiomes, and leveraging scientific tools to enhance both safety and flavor complexity.

Consumer Choices: Informed Palates and Responsible Consumption

For consumers, an appreciation of microbial diversity fosters a deeper understanding and enjoyment of cheese. Recognizing that the variations in flavor, aroma, and texture are largely the result of microscopic life allows for a more informed and adventurous palate. Understanding the distinctions between raw, pasteurized, and thermized milk cheeses empowers consumers to make choices aligned with their preferences for flavor complexity, perceived health benefits, and risk tolerance. It encourages a responsible approach to consumption, recognizing that while raw milk cheeses offer unique characteristics, they also come with a different risk profile that necessitates confidence in the producer’s practices.

Innovation and Research: Unlocking New Terroirs

The future of cheesemaking is bright with possibilities stemming from ongoing microbial research. Scientists are increasingly exploring the potential of "precision fermentation" – using specific, identified microbial strains to create novel flavor profiles or enhance existing ones. The study of the cheese rind microbiome, for instance, is revealing new insights into how surface cultures contribute to unique characteristics and can even protect against spoilage. Advancements in metagenomics and metabolomics allow for a detailed mapping of microbial communities and their metabolic outputs, potentially leading to the development of new, bespoke starter cultures or even methods to cultivate specific "terroir" microbes in a controlled environment. This scientific frontier promises to unlock new dimensions of flavor and texture, further enriching the diverse world of cheese.

When we consider the profound impact of microbial diversity on the quality, aesthetics, and safety of cheese, it becomes abundantly clear that no single factor is solely responsible for the final outcome. Rather, cheese is the product of an interconnected biological system, shaped by every step of its journey. While pasteurization significantly alters the microbial composition of milk, it is not the only influence. Refrigeration, storage time, farming practices, milking techniques, creamery sanitation, and the very environment of the aging cave are all equally critical in determining a cheese’s character. The appreciation of cheese, therefore, is an appreciation of a delicate, dynamic microbial ecosystem—a testament to the unseen architects who continuously craft our favorite dairy delights.

About the Author:

(Image: Josh Windsor Head Shot)

Josh Windsor is an affineur and the Senior Caves Manager at Murray’s Cheese in New York City, where he actively nurtures and ages the Cave Aged line of specialty cheeses. His work includes overseeing the development of award-winning cheeses such as the 2019 American Cheese Society (ACS) “Best in Show” winner Stockinghall Clothbound Cheddar and the 2022 World Cheese Awards “Best American Cheese” winner Greensward. Always curious about how cheese ages, Josh is an active member of the community biology lab, Genspace, where he explores the microbial world of cheese rinds. Josh shares his love of all things dairy by teaching cheese appreciation, science, and history at Murray’s Cheese and sensory evaluation at Cornell University’s cheese short courses.