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2025-06-03T16:56:30.449Z
Home & Heart/Food & Rituals

Milk Boosts Gut Biodiversity, Cheese Does the Opposite.

New research reveals how dairy choices directly impact your microbiome

Maya Ellis

3 June 2025

A groundbreaking study from Baylor College of Medicine has uncovered the distinct ways dairy products influence our gut bacteria. While milk consumption increases beneficial microbes like Faecalibacterium and Akkermansia that reduce inflammation and support metabolic health, cheese appears to decrease certain important bacteria including Bacteroides. The findings suggest that not all dairy products affect our microbiome equally, potentially requiring more personalized nutritional recommendations beyond simply counting dairy servings.

Summary

  • Dairy products may influence gut microbiome health beyond providing calcium and protein, with effects varying based on product type and individual lactose tolerance.
  • Lactose tolerance varies widely across ethnic groups, complicating standard dietary guidelines that recommend three cups of dairy daily for all adults.
  • Options for those with lactose intolerance include lactose-free milk, aged cheeses, cultured dairy products, and plant-based alternatives that respect cultural food traditions.
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Your glass of milk might be doing more than strengthening your bones—it could be reshaping the complex ecosystem of bacteria living in your digestive tract. While previous nutritional focus centered on dairy's calcium and protein content, current research suggests our dairy choices may influence gut health in important ways. This connection between dairy consumption and gut bacteria appears particularly significant given the wide variation in lactose tolerance across diverse populations, potentially changing how we think about daily nutrition in America's multi-ethnic landscape.

The Dairy-Gut Connection: How Milk Influences Your Microbiome

Your digestive system houses trillions of microorganisms collectively known as the gut microbiome—a living community that helps break down nutrients, supports immune function, and increasingly appears connected to overall health. Researchers have begun investigating how different dairy products might influence this internal ecosystem. Some studies suggest associations between dairy consumption and microbiome composition, though causation hasn't been firmly established.

Scientists believe milk's effects likely relate to its carbohydrate content, particularly lactose, which serves as fuel for certain bacteria. When these microbes metabolize lactose, they produce compounds that may help maintain gut barrier integrity and reduce inflammation—processes essential for digestive health.

Beyond the Glass: How Different Dairy Products Affect Gut Health

What's particularly interesting is how various dairy products appear to affect gut bacteria differently. While milk might enhance certain bacteria, cheese consumption may influence other bacterial populations. These differing effects likely stem from cheese's unique nutritional profile—it contains less lactose than milk due to the fermentation process but includes different proteins and fats that interact with gut bacteria in distinct ways.

This distinction may be particularly relevant for people who cannot tolerate fresh milk but can consume certain cheeses. Traditional Hispanic cheeses like queso fresco, queso blanco, and cotija often contain lower lactose levels than milk, potentially offering microbiome benefits with fewer digestive side effects for those with lactose sensitivity.

Yogurt: Probiotic Powerhouse or Overstated Benefit?

Despite yogurt's reputation as a probiotic powerhouse, research hasn't always established clear connections between yogurt consumption and specific microbiome changes. This surprising result often stems from limited yogurt intake among study participants or variations in yogurt types consumed.

Fermented dairy products like yogurt and kefir typically contain live cultures that can temporarily populate the gut, but their long-term effects on resident bacteria may depend on consumption patterns, the specific strains present, and individual gut environments.

Genetic Diversity: How Lactose Tolerance Varies Across Populations

These emerging findings add important nuance to American dietary guidelines, which currently recommend about three cups of dairy daily for adults—an amount many Americans don't reach. According to the USDA Dietary Guidelines for Americans (2020-2025), adults between 19-50 years should consume 3 cup-equivalents of dairy daily, with the same amount recommended for those 51 and older.

But these one-size-fits-all recommendations become complicated when considering genetic differences in lactose tolerance. Approximately 70-80% of African Americans, 50-80% of Hispanic/Latino Americans, and 80-100% of Native Americans experience some degree of lactose intolerance, compared to just 20-30% of Americans with Northern European ancestry.

These differences stem from a genetic trait called lactase persistence—the continued production of lactase (the enzyme that breaks down lactose) into adulthood. This trait evolved primarily in populations with long histories of dairy consumption, particularly in Northern Europe, where lactase persistence is more common.

Finding Your Dairy Balance: Cultural and Digestive Considerations

For individuals with lactose intolerance who still want potential microbiome benefits, several options exist:

  • Lactose-free milk: Contains the same nutrients as regular milk but with lactose already broken down
  • Aged cheeses: Like manchego or cotija, which naturally contain less than 0.5g lactose per serving (compared to about 12g in a cup of milk)
  • Cultured dairy products: Such as kefir or certain yogurts, which contain bacteria that help digest lactose
  • Plant-based alternatives: Including coconut milk, almond milk, oat milk, and soy milk (with soy providing protein content most similar to cow's milk at 7-8 grams per 8oz serving)

Many plant-based milks are fortified with calcium to match or exceed dairy milk's 300 milligrams per serving, though bioavailability may differ. When considering alternatives, it's essential to respect cultural food traditions rather than simply suggesting unfamiliar options.

The Research Landscape: What We Know and What We're Still Learning

The current research on dairy and gut health comes with important caveats. Many studies include relatively small, homogeneous participant groups, often older and predominantly male. Self-reported dairy intake through food frequency questionnaires introduces potential inaccuracies, and most research captures only a snapshot rather than long-term microbiome changes.

Regional variations in milk consumption across the US—higher in the Midwest and lower in urban areas and the West Coast—further complicate the picture. Additionally, dairy consumption studies often don't account for the wide variation in lactose tolerance across different ethnic groups.

For truly comprehensive understanding, researchers need to expand investigations to include more diverse populations and examine long-term changes in gut microbiota following dairy consumption patterns that reflect America's multicultural reality.

Embracing Diversity: Cultural Perspectives on Dairy Consumption

When considering dairy's potential benefits, it's important to acknowledge barriers to consumption in many communities. Beyond lactose intolerance, factors such as limited access to fresh dairy products, socioeconomic challenges, and lack of culturally relevant dietary education can all influence consumption patterns.

As our understanding of gut health evolves, dietary recommendations must honor both biological diversity and cultural food traditions that have sustained communities for generations.

Dietitians increasingly emphasize cultural sensitivity in food recommendations, understanding that traditional foods and cooking methods vary widely. For example, while dairy may be less prominent in some African American cuisines due to higher rates of lactose intolerance, foods like buttermilk (used in cornbread or fried chicken), cream (in sweet potato pie), and cheese (in macaroni and cheese) remain culturally significant in many communities.

As our understanding of the gut microbiome evolves, we may see more personalized dietary recommendations that consider not just what foods to eat, but which options best support your unique microbiome based on your genetic background, cultural preferences, and individual digestive traits. For now, the research offers compelling evidence that your dairy choices—whether traditional milk, alternative products, or culturally specific options—might be shaping your gut health in ways more significant than previously understood.

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