Why is the microbiota so important in dairy calves?
The gastrointestinal microbiota plays a crucial role in dairy calf health, influencing digestion, immunity, and disease resistance from birth. Calves are born with a nearly sterile gastrointestinal tract, and rapid microbial colonization occurs through exposure to the dam, colostrum, and the environment [1]. This microbiota contributes to host health in multiple ways: it synthesizes essential vitamins and energy [2], supports gut tissue and immune system development [3], modulates inflammatory responses both locally and systemically [4, and helps protect against pathogens by competing for nutrients and attachment sites on the gut epithelium [5]. Additionally, microbial fermentation of dietary components generates short-chain fatty acids, such as acetate, propionate, and butyrate, which serve as key energy sources for gut epithelial cells and play a role in intestinal development [1]. Given its critical role in digestion, immunity, and disease resistance, understanding how the microbiota develops and how it can be modulated is essential for optimizing calf health.
Microbiota colonization and development
Initial microbial exposure
Microbial colonization in calves is a dynamic process, shaped by a sequential succession of microbial species influenced by physiological state, diet, and environmental factors [1,6]. The birth environment plays a critical role in early inoculation, with exposure to the dam’s vaginal, skin, and colostrum microbiota initiating microbial colonization. Early colonizers, such as Streptococcus and Enterococcus, utilize available oxygen in the gut, creating an anaerobic environment that facilitates the growth of beneficial bacteria, including Bacteroides and Bifidobacterium [7].
Role of colostrum in microbiota establishment
Colostrum plays a pivotal role in shaping the neonatal gut microbiota, not only by providing immunoglobulins but also by delivering beneficial microbes and prebiotics that support microbial establishment. The timing of colostrum intake is critical as delaying feeding to 12 hours after birth, rather than providing it immediately, disrupts the early colonization of mucosa-associated bacteria in the ileum and colon and slows microbial succession in the intestine [9, 10]. Beyond timing, heat treatment of colostrum has been shown to promote Bifidobacterium colonization while reducing Escherichia coli prevalence [8]. Additionally, extending colostrum feeding beyond the first 12 hours further enhances gut integrity and encourages the development of mucosa-associated bacteria, which play a key role in immune modulation [11]. These effects are likely driven by the high concentration of prebiotics in colostrum and transition milk, particularly oligosaccharides, which selectively stimulate the growth of beneficial bacteria such as Bifidobacterium and Lactobacillus [12]. Through its combined effects on passive immunity, microbial colonization, and gut integrity, colostrum serves as a foundation for a robust and resilient gastrointestinal microbiota in dairy calves.
Other factors influencing microbiota establishment
Beyond colostrum, diet and antimicrobial exposure play key roles in shaping the calf gut microbiota. The transition from colostrum to whole milk supports the growth of milk-utilizing and fibrolytic bacteria [13,14], improving nutrient digestion. Early access to drinking water has also been shown to enhance beneficial gut microbes, potentially leading to improved fiber digestion, growth, and feed efficiency [15,16]. In contrast, antimicrobial exposure, whether through medicated milk replacers, waste milk, or disease treatments, can disrupt microbial balance, promote antimicrobial-resistant strains, and alter gut function [17,6]. Ensuring optimal feeding practices and limiting unnecessary antibiotic use can help maintain a more stable and beneficial microbiota in young calves.
Figure 1. Summary of key factors influencing microbiota development in calves.
Microbiota and gastrointestinal disease in dairy calves
Gut dysbiosis is a major contributor to neonatal calf diarrhea, a leading cause of morbidity and mortality [18]. Diarrheic calves experience significant disruptions in their microbiota, characterized by reduced microbial diversity and increased populations of Escherichia coli, Streptococcus, Fusobacterium, and Lactobacillus [9,18]. Conversely, beneficial bacteria such as Faecalibacterium prausnitzii, Lachnospiraceae, and Ruminococcaceae decline during diarrheal episodes [18], weakening the gut’s natural defense mechanisms. Notably, some microbial shifts may precede clinical signs of diarrhea. Increased Lactobacillus, Clostridium, and Collinsella populations have been detected days before symptom onset, suggesting a potential role in disease progression [19]. This highlights the importance of a well-balanced microbiota in mitigating pathogen colonization and supporting gut health.
Microbiota management strategies for disease prevention
Maintaining a balanced microbiota is key to preventing calf diarrhea. Proper colostrum management is the first step, ensuring passive immunity and early microbial colonization. Probiotics (live beneficial bacteria) and prebiotics (substrates that promote beneficial microbes) are increasingly used to enhance gut health. Specifically, multi-strain probiotics containing Lactobacillus, Bifidobacterium, Bacillus, and Enterococcus, as well as yeast species like Saccharomyces cerevisiae, have been shown to improve microbial diversity and reduce diarrhea risk [18, 20]. Prebiotics, such as oligosaccharides, selectively support beneficial bacteria growth and, in some cases, reduce diarrhea incidence [20].
Although not commonly used in dairy calves, fecal microbiota transplantation (FMT), the transfer of gut bacteria from a healthy donor to a diarrheic animal, is an emerging approach. FMT has been successfully used in humans to treat Clostridium difficile infections [21], in dogs for parvoviral diarrhea resolution [22], and in pigs for necrotizing enterocolitis [23]. In calves, a single study found that FMT can restore microbial balance and accelerate diarrhea recovery [24]. While further research is needed, microbiota-targeted interventions hold promise for improving calf health and reducing reliance on antimicrobial treatments.
Take home messages
- The gut microbiota plays a critical role in digestion, immune function, and disease resistance in dairy calves.
- Early microbial colonization is influenced by colostrum intake, diet, and environmental exposures.
- Dysbiosis is a major risk factor for neonatal diarrhea, highlighting the need to maintain microbial balance.
- Strategies such as proper colostrum management, probiotic and prebiotic supplementation, and limiting unnecessary antimicrobial use can support a healthier microbiota.
- Emerging approaches like fecal microbiota transplantation may offer future solutions for microbiota modulation and disease prevention.
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