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.

Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Therefore, effective strategies to manipulate the microbiome of dairy calves under commercial dairy operations are of great importance to improve animal health and reduce antimicrobial usage. The objective of this study was to develop a farm-specific FMT product and to investigate its effects on clinical outcomes and fecal microbial composition of dairy calves. The FMT product was derived from feces from healthy donors (5–24 days of age) raised in the same calf ranch facility as the FMT recipients. Healthy and diarrheic calves were randomly enrolled to a control (n = 115) or FMT (n = 112) treatment group (~36 g of processed fecal matter once daily for 3 days). Fecal samples were collected at enrollment and again 9 days later after the first FMT dose. Although the FMT product was rich in organisms typically known for their beneficial probiotic properties, the FMT therapy did not prevent or ameliorate GI disease in dairy calves. In fact, calves that received FMT were less likely to recover from GI disease, and more likely to die due to GI disease complications. Fecal microbial community analysis revealed an increase in the alpha-diversity in FMT calves; however, no major differences across treatment groups were observed in the beta-diversity analysis. Calves that received FMT had higher relative abundance of an uncultured organism of the genus Lactobacillus and Lactobacillus reuteri on day 10. Moreover, FMT calves had lower relative abundance of Clostridium nexile and Bacteroides vulgatus on day 10. Our results indicate the need to have an established protocol when developing FMT products, based on rigorous inclusion and exclusion criteria for the selection of FMT donors free of potential pathogens, no history of disease or antibiotic treatment.

Currently, little is known regarding fecal microbial populations and their associations with methanogenic archaea in pasture-based dairy cattle. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. We hypothesized that the fecal methanogenic community, as well as co-occurrence patterns with bacteria, change across diets. To test these hypotheses, we analyzed TMR and pasture samples, as well as the V3-V4 region of 16S rRNA of fecal samples collected over the course of a one-year study period from 209 cows located on an organic dairy in Northwest Washington. The inherent variability in pasture quality, quantity, availability, and animal preference can lead to diverse dietary intakes. Therefore, we conducted a k-means clustering analysis to identify samples from cows that were associated with either a pasture-based diet or a solely TMR diet. A total of 4 clusters were identified. Clusters 1 and 3 were mainly associated with samples primarily collected from cows with access to pasture of varying quality and TMR, cluster 2 was formed by samples from cows receiving only TMR, and cluster 4 was a mix of samples from cows receiving high-quality pasture and TMR or TMR only. Interestingly, we found little difference in the relative abundance of methanogens between the community clusters. There was evidence of differences in diversity between pasture associated bacterial communities and those associated with TMR. Cluster 4 had higher diversity and a less robust co-occurrence network based on Spearman correlations than communities representing TMR only or lower-quality pasture samples. These findings indicate that varied bacterial communities are correlated with the metabolic characteristics of different diets. The overall good pasture and TMR quality in this study, combined with the organic allowance for feeding high levels of TMR even during the grazing season, might have contributed to the lack of differences in the fecal archaeal community from samples associated with a mixed pasture and TMR diet, and a TMR only diet. Mitigation strategies to decrease methane emissions such as increasing concentrate to forage ratio, decreasing pasture maturity and adopting grazing systems targeting high quality pasture have been shown to be efficient for pasture-based systems. However, the allowance for organic dairy producers to provide up to an average of 70% of a ruminant’s dry matter demand from dry matter fed (e.g., TMR), suggests that reducing enteric methane emissions may require the development of novel dietary strategies independent of pasture management.

This study aimed to evaluate performance, gut health and metabolic changes in dairy calves receiving milk replacer supplemented with lysine and methionine with 0.6% or 1% AminoGut (10% Glutamate and 10% Glutamine). Forty-five Holstein calves were blocked and distributed in the treatments: (1) Control: no supplementation; (2) Lys, Met, AminoGut 0.6%; (3) Lys, Met, AminoGut 1%. Animals were individually housed, with free access to water and concentrate. Milk replacer (6 L/d) was fed until the eighth week of life. Feed intake and faecal score were monitored daily. Calves were weighted and measured weekly. Blood samples were collected every other week to determine metabolites. Supplementation did not affect the performance nor the metabolism of calves. There was no effect of supplementation for faecal score. An age effect was observed for most of the variables, mainly as a response of starter intake and consequent shift from a pre to a functional ruminant metabolism. The supplementation of the milk replacer with lysine and methionine in association with 0.6% or 1% AminoGut had no effect on performance, gut health nor metabolism of dairy calves. More important than the fine adjustment of amino acid requirements is the adoption of practices to improve starter intake.

Regardless of the causative agent, diarrhea results in large loss of water and electrolytes, which leads to reduced performance and dead. The aim of this study was to evaluate oral rehydration solutions in order to determine the most effective in restoring electrolytes and water while maintaining animal performance. Forty two calves (14 per treatment) were distributed in one of three treatments (1) Common electrolytes solution (dextrose, sodium bicarbonate and sodium chloride; 507±2 mOsm), (2) Glutellac® (sodium acetate, glucose and sodium and potassium chloride; 665±1 mOsm); and (3) Common electrolytes solution + Aminogut® (glutamate and glutamine; 575±2 mOsm). Treatments were administered when fecal score ≥3, in a scale of 1 to 5. During diarrhea daily water intake was registered and blood sample was taken for metabolites, electrolytes and gases determination. Animals did not differ in days in diarrhea, fecal score or hematocrit. Calves receiving Glutellac® presented higher voluntary water intake. There was no effect of treatment for animal performance and starter feed intake. Concentrations of Na+ and HCO3 tended to be higher for animals rehydrated with Glutellac®. While there was an increase in HCO3 from the first to the second day, K+ and glucose decreased. The increased voluntary water intake in animals rehydrated with Glutellac®, which shows greater simplicity of use, are the main advantages of this solution.

Fungal-bacterial interactions are widespread phenomena that are currently gaining attention across diverse research fields. But what are interactions, how do we identify them, and why should we adopt ecological theory when studying them? While microbial interactions are often conceptualized and characterized as static properties, these relationships are dynamic and complex. They are shaped by the interplay of numerous variables, which themselves fluctuate over space and time, that scale from molecules to ecosystems. In this perspective, we discuss the theoretical and practical challenges of studying the interactions between these two ubiquitous and diverse groups of microorganisms and propose a framework grounded on mechanistic and systems approaches rather than relying on correlations or fragmented practices. We hope to inspire efforts to build and integrate a more comprehensive understanding of this fascinating and quickly growing subdiscipline of microbial ecology.