The Summer Shift: Why Heat Increases Disease Risk in Dairy Cows

• May 29, 2026
• News

By Samanta Fensterseifer, DVM, MSc, Staff Research Scientist and Amy Lange, Microbiologist III

As temperatures rise across the northern hemisphere, dairy cows face more than just heat stress. Warm weather creates ideal environmental conditions for microbial pathogens growth while also triggering physiological changes in the cow that can weaken immune function and disrupt the gastrointestinal (GI) microbiome.

Together, these shifts create the perfect storm for enteric pathogens to thrive.

Warm Weather Supports Pathogen Survival

Heat and humidity promote the survival of opportunistic pathogens in manure, bedding, drinking water, and on barn surfaces. Bacteria from fecal matter survive longer outside the cow during periods of high environmental temperature, and E. coli populations in manure have been shown to peak during summer months.³

Pathogens that spread through the fecal-oral route, including E. coli and Salmonella, may persist at higher levels during warm seasons. This increases environmental pathogen pressure at the same time that cows are becoming more vulnerable to microbial challenges.

The Two-Fold Impact of Heat Stress

Even with use of heat abatement strategies like shade, fans, and sprinkler systems, heat stress still negatively impacts milk production, reproduction, and overall health in dairy herds.

Namely, heat stress suppresses immune function in dairy cows,¹ increasing susceptibility to disease. During hot months, producers commonly observe:

• Increased mastitis incidence
• Higher somatic cell counts (SCC)
• Greater risk of metritis
• Increased displaced abomasum and respiratory disease in dry cows

At the same time, heat stress alters feeding behavior and rumen function. Reduced feed intake and changes in rumination can contribute to rumen pH instability and impaired fermentation. In cases of subacute ruminal acidosis (SARA), low rumen pH and elevated lactate levels can disrupt the microbial balance of the rumen and hindgut.

This disturbance of the normal microbial community, commonly referred to as dysbiosis, creates an environment in which beneficial fiber-digesting bacteria decline, while opportunistic Gram-negative pathogens thrive. As inflammation in the rumen and lower GI tract increases, energy balance and performance can also be negatively affected.²

Coinfection Potential in Summer Conditions

When dysbiosis and immune suppression occur at the same time, cows become increasingly vulnerable to enteric pathogens. In fact, our US dairy surveillance data has shown that, during warm seasons, Gram-negative pathogens such as E. coli and Salmonella exhibit population shifts that align closely with periods of heat stress.

These seasonal upticks in pathogen load may raise the likelihood of coinfections—the presence of multiple pathogens in the same animal at the same time. Coinfections can increase disease severity and make recovery more difficult, especially when the animal is under environmental and physiological stress.

This suggests that seasonal environmental conditions may directly influence microbial dynamics in the GI tract.

Data Deep-Dive: PathKinex™ Surveillance of Key Microbial Virulence Genes

PathKinex™ data from 4,049 dairy cows and heifers enrolled in the UAH dairy surveillance program between 2017 and 2025 was evaluated for seasonal trends in microbial carriage.

Microbial gene quantities were compared across:

• Spring (March–May)
• Summer (June–August)
• Autumn (September–November)
• Winter (December–February)

The results revealed clear seasonal shifts in several important enteric pathogens and virulence genes:

E. coli and Related Virulence Genes

Dairy cows and heifers showed significantly higher quantities of total E. coli markers during summer months, with the lowest levels observed during winter. Several pathogenic E. coli markers and toxin genes also followed similar seasonal patterns:

• Marker genes associated with enterohemorrhagic E. coli (EHEC), including O157, Shiga toxin 1 (stx1), Shiga toxin 2 (stx2), and the attachment gene eaeA, were significantly elevated during summer months
• Genes associated with enterotoxigenic E. coli (ETEC), including the heat-stable toxin gene STa, also increased during warmer periods
• The enteroaggregative heat-stable toxin gene EAST1 showed similar seasonal increases during June, July, and August, with the lowest levels consistently observed during winter months

Figure 1. E. coli virulence markers and toxin genes detected in rectal swabs samples from cows and heifers enrolled in the UAH dairy surveillance PathKinex™ program (n= 4049 individual animals sampled from 2017 to 2025). Different superscript letters denote significant differences among seasons (P < 0.05).

Other Important Pathogens

Not all pathogens followed the same seasonal trend, however. Key observations included:

• Clostridium perfringens levels were significantly higher in winter compared to warmer seasons
• Clostridium difficile was highest during winter and spring and lowest during summer and fall
• Salmonella levels remained elevated during spring, summer, and fall compared to winter
• Eimeria bovis (coccidia) was most prevalent during spring and summer. This increase may contribute to polymicrobial challenges alongside pathogens such as E. coli, Salmonella, and C. perfringens

Figure 2. Virulence markers and toxin genes for Clostridium perfringens, Clostridium difficile, Salmonella, Aspergillus flavus and Eimeria bovis detected in rectal swabs samples from cows and heifers enrolled in the UAH dairy surveillance PathKinex™ program (n= 4049 individual animals sampled from 2017 to 2025). Different superscript letters denote significant differences among seasons (P < 0.05).

Manage Seasonal Enteric Challenges Proactively

Although microbial pathogens are present year-round, elevated summer pathogen pressure from E. coli and Salmonella may contribute to heat-related increases in disease and other potential setbacks. Management and feeding strategies that help reduce pathogen burden in the gut and environment may support cow health during periods of heat stress, mitigating negative impacts to production. This includes:

• Maintaining clean bedding and water sources
• Supporting rumen stability and feed intake
• Reducing environmental pathogen load
• Supporting gut microbial balance and immune function

Bacillus-based direct-fed microbials (DFMs) are one possible element of a comprehensive heat stress management strategy. By helping support microbial balance and reduce pathogen pressure, these types of tools could improve resilience during seasonal stress periods.⁴

Learn more about multi-layer approaches to dairy health and pathogen management. 

References

1. Dahl, G. E., Tao, S., & Laporta, J. (2020). Heat stress impacts immune status in cows across the life cycle. Frontiers in Veterinary Science, 7:116. https://doi.org/10.3389/fvets.2020.00116
2. Zhao, S., Min, L., Zheng, N., & Wang, J. (2019). Effect of heat stress on bacterial composition and metabolism in the rumen of lactating dairy cows. Animals, 9(11), 925. https://doi.org/10.3390/ani9110925
3. Oliver D., & Page, T. (2016). Effects of seasonal meteorological variables on E. coli persistence in livestock faeces and implications for environmental and human health. Scientific Reports, 6, Article No. 37101. https://doi.org/10.1038/srep37101
4. Lange, A. M., Galbraith, E. A., Son, S., Arias, R. P., Peter, C. M., & King M. R. (2019, June 23–26). Microbial virulence gene abundance in rectal swabs from US dairy cows with or without gastrointestinal disease symptoms [Abstract]. American Dairy Science Association Annual Meeting, Cincinnati, OH, United States.