By Josh Windsor (Senior Caves Manager, Murray’s Cheese)
Published: July 17, 2026, from the Summer 2026 Issue of Culture Cheese Magazine

New York, NY – In the intricate world of cheesemaking, an invisible army of microorganisms orchestrates a complex symphony of flavors, aromas, and textures that define every wedge we savor. From the humble beginnings within a dairy animal’s udder to the sophisticated environment of an aging cave, microbes are the unsung heroes, shaping not just the sensory experience but also the fundamental safety of our beloved cheeses. Josh Windsor, a distinguished affineur and Senior Caves Manager at Murray’s Cheese, delves into this microscopic universe, unraveling the crucial distinctions between raw and pasteurized milk and illuminating the myriad factors that contribute to a cheese’s unique identity.

Main Facts: The Microbial Foundation of Cheese

At its core, cheesemaking is a controlled fermentation, a delicate dance between milk, enzymes, and an incredibly diverse microbial community. This article explores how the specific composition and activity of these microorganisms are paramount to developing the characteristic attributes—the pungent bite, the creamy texture, the earthy aroma—that distinguish one cheese from another. Josh Windsor, a leading expert from Murray’s Cheese, emphasizes that understanding this microbial journey is key to appreciating both the artistry and science behind cheese.

The central distinction often revolves around the heat treatment of milk: raw versus pasteurized. Pasteurization, a process designed to eliminate pathogenic bacteria, significantly alters the milk’s initial microbial profile. Raw milk, conversely, retains its native flora, presenting both opportunities for unique flavor development and specific safety considerations. However, Windsor’s insights extend beyond this binary, revealing that the ultimate character and safety of cheese are products of an interconnected system, influenced by everything from farm practices and milking hygiene to refrigeration, storage, and the microclimate of the aging facility. No single factor, not even pasteurization, solely determines the outcome of a cheese; rather, it is the cumulative impact of these elements that shapes its distinct biome.

The Microbial Symphony: A Chronological Journey

The transformation of milk into cheese is a chronological progression, with each stage offering an ecological niche that selects for certain microbial species, progressively refining the dairy’s character.

From Udder to Vat: The Genesis of Microbes

The microbial journey begins long before milk even reaches the cheesemaker’s vat—it starts within the dairy animal itself. The udder, much like human skin, hosts a complex and dynamic biome, a diverse community of microorganisms present from birth and continuously augmented by the animal’s environment. During milking, a significant portion of this udder biome, including many of the technically functional Lactobacilli vital for cheesemaking, is naturally transferred into the milk.

This initial microbial load is incredibly rich and varied. Newcomers arrive constantly from a multitude of sources within the farm environment: bedding straw, nutrient-rich feed, manure, airborne dust particles, and contact with other animals in the herd. These environmental microbes, along with those residing on the teat surface, find opportunities to survive and multiply if conditions such as ambient temperature and time are favorable. This foundational microbial community, often referred to as the "terroir" of the milk, sets the stage for the subsequent microbial transformations that will define the cheese. The health of the animal, its diet, and the overall cleanliness of the milking parlor all play critical roles in determining the initial microbial diversity and quality of the milk.

Cooling and Dormancy: Shaping Early Populations

Immediately after leaving the warmth of the udder, milk begins to cool. Modern dairy practices universally employ rapid refrigeration to mitigate spoilage and extend shelf life. While this cooling is essential for safety and preservation, it also profoundly influences the microbial populations present. As temperatures drop, the growth of many mesophilic (moderate-temperature loving) bacteria slows significantly.

However, colder temperatures favor the proliferation of psychrotrophic (cool-loving) bacteria. These microbes, though not always directly involved in cheese flavor development, can produce enzymes that degrade milk proteins and fats, potentially affecting the cheese’s texture and yield later in the process. Crucially, while some microbes thrive in the cold, many of the beneficial functional bacteria, such as Lactobacilli, do not die but rather enter a dormant state. This dormancy means they are preserved but their active metabolic processes are temporarily halted, awaiting more favorable conditions to resume their flavor-producing work. The duration and temperature of this initial cooling and storage period are therefore critical in shaping the latent microbial potential of the milk.

Heat Treatment: Defining Raw vs. Pasteurized

The next major intervention in the microbial life of milk involves heat treatment, a process that fundamentally alters its microflora and defines its legal classification in many regions, including the United States.

Pasteurization: The Sterilization Standard

Pasteurization is a precise heat treatment designed to significantly reduce the number of viable microorganisms in milk, particularly pathogenic bacteria that can cause illness. Named after Louis Pasteur, who developed the process in the 19th century, it involves heating milk to a specific temperature for a defined period. The most common methods include High-Temperature Short-Time (HTST) pasteurization (e.g., 161°F for 15 seconds) and Low-Temperature Long-Time (LTLT) pasteurization (e.g., 145°F for 30 minutes). The primary goal is to achieve a log reduction in specific pathogens, effectively rendering the milk safe for consumption. However, this process is non-selective; it destroys a large percentage of all microorganisms present, including both harmful pathogens and many of the technically functional microbes that contribute to unique flavors and aromas in raw milk cheeses. The result is a largely sterile canvas, which cheesemakers then "repopulate" with carefully selected starter cultures.

Raw Milk: The Unfiltered Biome

In contrast, raw milk is defined in the US as any milk that has not undergone pasteurization or met its specific heat treatment requirements. It retains its full, native microbial diversity, encompassing a complex ecosystem of bacteria, yeasts, and molds derived from the udder and the farm environment. This inherent microbial richness is often lauded by proponents of raw milk cheese for its potential to develop more complex, nuanced, and "terroir-driven" flavors. However, the presence of this diverse, unfiltered biome also carries a higher potential risk of containing pathogenic bacteria, necessitating stringent hygiene practices and, for raw milk cheeses, often an aging period (e.g., 60 days in the US) to further reduce pathogen risk.

Thermization: A Gentle Compromise

Thermization represents a middle ground, a milder heat treatment below pasteurization standards. Typically involving heating milk to temperatures around 135-155°F for 15-20 seconds, thermization is not hot enough to meet pasteurization requirements and thus milk treated this way is still legally considered raw milk in the US. Its purpose is to reduce the overall microbial load, particularly spoilage organisms and some heat-sensitive pathogens like E. Coli, thereby extending the milk’s shelf life and providing a more consistent starting point for cheesemakers. Crucially, while thermization can reduce certain risks, it is generally not hot enough to eliminate more heat-resistant pathogens like Listeria monocytogenes, which remains a concern and requires additional controls in subsequent cheesemaking and aging. Thermization aims to preserve a significant portion of the beneficial microflora, allowing for more complex flavor development than fully pasteurized milk, while offering a degree of microbial control.

Post-Treatment and Cheesemaking: Rebuilding the Ecosystem

Regardless of whether the milk is raw, thermized, or pasteurized, the journey of microbial transformation continues once it enters the creamery and the cheesemaking process begins.

For pasteurized milk, the largely sterile liquid is intentionally repopulated. Cheesemakers introduce specific "starter cultures"—carefully selected strains of lactic acid bacteria—to initiate fermentation. These cultures are responsible for converting lactose into lactic acid, a critical step that lowers pH, coagulates milk proteins, and sets the stage for flavor development. Additionally, microorganisms present in the creamery environment itself, including yeasts and molds that might colonize walls, shelves, and equipment, can inoculate the cheese, especially during the aging phase.

In both raw and pasteurized milk cheesemaking, as the cheese is made—through processes like acidification, renneting, cutting the curd, salting, and pressing—the environmental conditions within the nascent cheese change dramatically. These shifting conditions, such as decreasing moisture content, increasing salt concentration, and dropping pH, create new ecological niches. This continuous transformation favors the growth of certain microbial populations while inhibiting others. For example, specific yeasts and molds might thrive on the surface of a developing rind, breaking down proteins and fats to create distinctive aromas and textures. This dynamic interplay continues throughout the entire life of the cheese, from its initial formation in the vat to its maturation in the aging cave, with each stage contributing to the final character.

Supporting Data and Scientific Insights

The profound impact of microbial diversity on cheese quality, aesthetics, and safety is not merely anecdotal; it is supported by a growing body of scientific research into the cheese microbiome.

The Science of Terroir in Cheese

The concept of "terroir," traditionally associated with wine, is increasingly applied to cheese. It posits that the unique characteristics of a cheese are influenced by its specific geographical origin, encompassing factors like the local climate, soil composition, pasture flora, animal breeds, and, critically, the indigenous microbial populations. Scientific studies using advanced genetic sequencing techniques have revealed distinct microbial signatures in cheeses produced in different regions, even when using similar recipes. For instance, the microbial communities found in traditional Alpine cheeses differ significantly from those in artisanal French blues, reflecting the unique environmental bacteria, yeasts, and molds present in those specific dairies and aging caves. This microbial "fingerprint" contributes directly to the distinctive flavors and textures associated with specific Protected Designation of Origin (PDO) cheeses.

Microbial Contributions to Flavor and Aroma

The flavor and aroma complexity of cheese are direct results of microbial metabolic activity. Lactic acid bacteria (LAB) are primary drivers, converting lactose into lactic acid, which imparts a tangy taste and helps form the curd. As the cheese ages, other microbes take over. Proteolytic enzymes, produced by bacteria, yeasts, and molds, break down milk proteins into peptides and amino acids, contributing nutty, meaty, or savory notes. Lipolytic enzymes, also from microbes, break down milk fats into fatty acids, yielding buttery, fruity, or pungent aromas. For example, Penicillium roqueforti gives blue cheeses their characteristic piquancy, while Brevibacterium linens is responsible for the strong, pungent aroma of washed-rind cheeses like Limburger or Époisses. These intricate biochemical pathways, orchestrated by diverse microbial communities, are what create the vast spectrum of cheese flavors.

Safety Considerations and Risk Management

The dual nature of microbes—as both beneficial flavor producers and potential pathogens—is central to the debate surrounding raw versus pasteurized milk cheese. Pasteurization provides a broad public health safety net, effectively eliminating common foodborne pathogens like E. Coli O157:H7, Salmonella, and Listeria monocytogenes. This makes pasteurized milk cheese a lower-risk option for general consumption.

For raw milk cheese, safety relies heavily on stringent controls. Regulatory bodies like the FDA in the US often mandate a minimum aging period (e.g., 60 days at 35°F or higher) for raw milk cheeses to allow the natural acidification and drying processes, along with the competitive exclusion by beneficial flora, to reduce pathogen levels to safe limits. Responsible raw milk cheesemakers implement rigorous Hazard Analysis and Critical Control Points (HACCP) plans, including regular microbial testing of milk and cheese, immaculate creamery hygiene, and strict control over aging conditions. While raw milk cheese can carry a higher intrinsic risk, these comprehensive risk management strategies, combined with deep microbiological understanding, allow for the safe production of these complex and cherished cheeses.

Beyond Pasteurization: Other Influential Factors

As Josh Windsor aptly notes, pasteurization is but one piece of a much larger puzzle. Numerous other factors significantly influence the microbial composition and, consequently, the character of cheese:

• Refrigeration and Storage Time: The initial cooling and subsequent storage duration of milk prior to cheesemaking directly impact the growth of psychrotrophic bacteria and the dormancy of beneficial flora. Longer storage times, even at cold temperatures, can alter the enzymatic potential of the milk.
• Farming Practices: Animal health, diet (e.g., pasture-fed vs. grain-fed), and overall farm hygiene (cleanliness of barns, milking parlors, and equipment) dictate the initial microbial load and diversity entering the milk. A healthy herd and clean environment lead to milk with a lower initial pathogen count and a more desirable microbial profile.
• Milking Techniques: Proper udder preparation, sterile milking equipment, and efficient milking procedures minimize external microbial contamination and ensure the quality of the milk harvested.
• Creamery Sanitation: The cleanliness of the cheesemaking facility itself plays a crucial role. The air, surfaces, and equipment in the creamery harbor their own microbial communities, which can inoculate the cheese during production and aging. A well-managed creamery fosters beneficial "house" cultures, while poor sanitation can introduce undesirable microbes or pathogens.

These interconnected elements collectively shape the unique biome of each cheese, underscoring that cheesemaking is an ecosystem management endeavor, not just a simple recipe following.

Official Responses and Regulatory Landscape

The regulation of milk and cheese production, particularly concerning raw milk, is a critical aspect of public health policy and an ongoing area of discussion among producers, consumers, and government agencies.

FDA and State Regulations

In the United States, the Food and Drug Administration (FDA) sets federal standards for milk and dairy products. A key regulation for raw milk cheese dictates that it must be aged for a minimum of 60 days at a temperature no less than 35°F (1.7°C). This aging period is intended to reduce the risk of pathogens, as the low pH, reduced moisture, and competitive microbial environment during aging are believed to create conditions unfavorable for their survival. While raw fluid milk sales are largely prohibited across state lines and heavily regulated within states, raw milk cheese, subject to the 60-day rule, is permitted for interstate commerce. State-level regulations can vary, with some states having stricter rules or outright bans on raw milk sales. These regulations reflect a balance between promoting public health and accommodating traditional foodways and consumer preferences.

Industry Perspectives

The dairy and cheesemaking industries hold varied perspectives on raw versus pasteurized milk. Large-scale industrial producers overwhelmingly rely on pasteurized milk for consistency, extended shelf life, and guaranteed safety, aligning with mass market demands and regulatory ease. For artisanal and small-scale cheesemakers, particularly those focused on traditional or "terroir-driven" products, raw milk is often seen as indispensable for achieving unique flavor profiles and expressing regional identity. They argue that pasteurization, while ensuring safety, strips milk of beneficial enzymes and a complex microbial population vital for character development. These producers often invest heavily in robust quality control, hygiene protocols, and third-party testing to ensure the safety of their raw milk products, advocating for informed consumer choice rather than blanket bans.

Consumer Demand and Education

There is a growing consumer interest in raw milk and raw milk cheeses, driven by perceptions of superior flavor, nutritional benefits, and a desire for less processed foods. This demand highlights the importance of consumer education regarding the distinctions, benefits, and inherent risks associated with raw versus pasteurized products. Organizations and experts like Josh Windsor play a crucial role in providing accurate information, demystifying the science, and empowering consumers to make informed decisions about the cheeses they choose to enjoy.

Implications for the Future of Cheesemaking

The deepening understanding of the cheese microbiome holds profound implications for the future of cheesemaking, spanning innovation, sustainability, and consumer appreciation.

Innovation in Microbial Management

Future advancements will likely see increasingly sophisticated approaches to microbial management. Researchers are actively mapping the genomes of beneficial cheese microbes, identifying specific strains responsible for desirable flavors or pathogen inhibition. This knowledge could lead to the development of novel starter cultures tailored for specific cheese styles, capable of producing more complex flavors, enhancing safety, or accelerating aging processes. It may also lead to improved methods for monitoring and controlling the microbial environment of aging caves, allowing for greater consistency and quality. The integration of microbial science with cheesemaking craft promises a new era of precision cheesemaking.

Sustainability and Traditional Practices

There is a growing global effort to balance modern food safety standards with the preservation of traditional cheesemaking practices, many of which inherently rely on raw milk and ambient microbial inoculation. Future efforts will likely focus on developing sustainable models that integrate stringent hygiene and testing protocols with traditional methods, ensuring both safety and the continuation of cultural heritage. This involves understanding how traditional practices, such as specific aging conditions or the use of wooden equipment, contribute to the unique microbial ecosystems that define these historic cheeses.

The Evolving Palate: Appreciation of Microbial Complexity

As scientific understanding of the cheese microbiome becomes more accessible, it can foster a deeper appreciation among consumers for the nuanced flavors and textures derived from complex microbial ecosystems. Educational initiatives, like those led by Josh Windsor at Murray’s Cheese and Cornell University, are vital in helping consumers understand the invisible forces at play in their food. This evolving palate, informed by scientific insight, can drive demand for diverse, artisan-produced cheeses that showcase the full spectrum of microbial contributions.

Josh Windsor’s Role and Murray’s Cheese’s Contribution

Josh Windsor, with his background as an affineur and his active involvement in community biology labs like Genspace, exemplifies the bridging of traditional craft with modern scientific inquiry. His work at Murray’s Cheese, nurturing award-winning Cave Aged lines, demonstrates a commitment to both the art of aging and the science of microbial management. By exploring the microbial world of cheese rinds and teaching about cheese appreciation and science, Windsor and Murray’s Cheese are at the forefront of educating the industry and public, ensuring that the intricate dance between microbes and milk continues to produce extraordinary cheeses for generations to come. The future of cheese lies in this harmonious blend of tradition, innovation, and a profound respect for the microscopic life that gives cheese its very soul.