Abstract
Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4–21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli. Species of the genus Lactobacillus, such as an unclassified Lactobacillus, Lactobacillus reuteri, and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta, Bifidobacterium longum, and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E. coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.
Highlights
Neonatal calf gastrointestinal (GI) disease, often diagnosed as diarrhea, is considered one of the major health challenges in the dairy industry
The National Animal Health Monitoring System (NAHMS) reported that diarrhea is the most common disease affecting pre-weaned heifers: 21% of pre-weaned heifers were diagnosed with GI problems, and 76% of these calves were treated with antibiotics [2]
Differences were most evident in calves with or without GI disease rather than between breeds
Summary
Neonatal calf gastrointestinal (GI) disease, often diagnosed as diarrhea, is considered one of the major health challenges in the dairy industry. This disorder has a considerable economic impact on dairy farm operations and is responsible for causing substantial economic losses in cattle herds worldwide [1]. On-farm calf caretakers and even veterinary personnel may lack the knowledge and on-farm tools to correctly identify phenotypes and different gradients of severity This disease can manifest clinically as loose feces without other obvious clinical symptoms, it often presents a constellation of clinical signs including variable degrees of dehydration, electrolyte imbalance, and metabolic acidosis [7]. Accurate and specific diagnoses that help in the understanding of these physiological and microbial changes can direct dairy producers and veterinarians to precisely administer therapies and implement practices that prevent new cases from occurring [9,10]
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