Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery

Introduction

Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery.

Methods

Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing.

Results

The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD.

Discussion

This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.

Effects of feeding Saccharomyces cerevisiae fermentation postbiotic on the fecal microbial community of Holstein dairy calves

BACKGROUND

The livestock industry is striving to identify antibiotic alternatives to reduce the need to use antibiotics. Postbiotics, such as Saccharomyces cerevisiae fermentation product (SCFP), have been studied and proposed as potential non-antibiotic growth promoters due to their effects on animal growth and the rumen microbiome; however, little is known of their effects on the hind-gut microbiome during the early life of calves. The objective of this study was to measure the effect of in-feed SCFP on the fecal microbiome of Holstein bull calves through 4 months of age. Calves (n = 60) were separated into two treatments: CON (no SCFP added) or SCFP (SmartCare®, Diamond V, Cedar Rapids, IA, in milk replacer and NutriTek®, Diamond V, Cedar Rapids, IA, incorporated into feed), and were blocked by body weight and serum total protein. Fecal samples were collected on d 0, 28, 56, 84, and 112 of the study to characterize the fecal microbiome community. Data were analyzed as a completely randomized block design with repeated measures when applicable. A random-forest regression method was implemented to more fully understand community succession in the calf fecal microbiome of the two treatment groups.

RESULTS

Richness and evenness of the fecal microbiota increased over time (P < 0.001), and SCFP calves tended to increase the evenness of the community (P = 0.06). Based on random-forest regression, calf age as predicted by microbiome composition was significantly correlated with the calf physiological age (R² = 0.927, P < 1 × 10^-15). Twenty-two "age-discriminatory" ASVs (amplicon sequence variants) were identified in the fecal microbiome that were shared between the two treatment groups. Of these, 6 ASVs (Dorea-ASV308, Lachnospiraceae-ASV288, Oscillospira-ASV311, Roseburia-ASV228, Ruminococcaceae-ASV89 and Ruminoccocaceae-ASV13) in the SCFP group reached their highest abundance in the third month, but they reached their highest abundance in the fourth month in the CON group. All other shared ASVs reached their highest abundance at the same timepoint in both treatment groups.

CONCLUSIONS

Supplementation of SCFP altered the abundance dynamics of age discriminatory ASVs, suggesting a faster maturation of some members of the fecal microbiota in SCFP calves compared to CON calves. These results demonstrate the value of analyzing microbial community succession as a continuous variable to identify the effects of a dietary treatment.

Relationship of cow and calf circulating lipidomes with colostrum lipid composition and metabolic status of the cow

Newborn calves rely on lipids in colostrum for energy and immune function. The lipid concentration in colostrum, however, is highly variable, and little is known about its composition and maternal factors that influence its composition. The first objective was to measure plasma lipid composition of multiparous cows at 35 d before calving (BC; 35 ± 3 d; ± standard deviation) and 7 d BC (7 ± 2 d), their colostrum, and serum lipid composition of calves (24 h after birth) using multiple reaction monitoring profiling, which is an exploratory and highly sensitive lipidomic analysis method that screens lipids based on chemical functionality. Second, data were analyzed to determine if there were relationships between circulating lipids in the cow, colostrum lipids, and calf serum lipids. Third, relationships between markers of metabolic status of the cows and circulating and colostrum lipids were analyzed with correlation analysis. Blood was sampled and plasma prepared from multiparous cows (n = 16) at 35 and 7 d BC. Within 3 h of parturition, colostrum was collected from cows and fed to her calf. Calves received another feeding of colostrum within 12 h after birth and a serum sample was collected from each calf 24 h after the first feeding of colostrum. The metabolic status of cows was evaluated using insulin, glucose, and nonesterified fatty acid area under the curve in response to an intravenous glucose tolerance test performed at 3 wk BC. Lipids were extracted from plasma, colostrum, and calf serum and were analyzed using multiple reaction monitoring profiling. Concentration of lipids were calculated using spiked in standards and expressed as percent of lipids identified. Data were uploaded into MetaboAnalyst 5.0 for multivariate and univariate analysis. Principal component analysis indicated that circulating lipids in the cow and calf were distinct from lipids in colostrum. Phosphatidylglycerol (PG) concentration was greater in colostrum and calf serum than in cow plasma, with 23 of the 24 PG found in colostrum also found in calf serum. In response to intravenous glucose tolerance test in late gestation, nonesterified fatty acid area under the curve was positively related to total triacylglycerols lipids in 7 d BC plasma (r = 0.63) but negatively related to total membrane lipids in colostrum (r = -0.55). Thus, the metabolic status of the dam influences circulating lipids and colostrum lipid content. Moreover, the circulating lipidome of the cow and calf are similar to one another and distinct from the colostrum lipidome, except for PG, where it appears that colostrum serves as the source for PG in the calf's circulation.

Effects of feeding Saccharomyces cerevisiae fermentation products on the health of Holstein dairy calves following a lipopolysaccharide challenge

Before weaning, dairy calves are at high risk for illness, especially respiratory and digestive diseases, which reduces average daily gain, age at first calving, and first-lactation milk production. Although these illnesses are commonly treated with antibiotics, efforts are being made to reduce antibiotic use, due to concerns about antibiotic-resistant bacteria. The objective was to evaluate the effects of Saccharomyces cerevisiae fermentation products (SCFP) on the immune status of calves, following a lipopolysaccharide (LPS) challenge administered just before weaning. Thirty Holstein bull calves were blocked based on initial body weight and then assigned to 1 of 2 study treatments. The control group (CON) was fed a 24% crude protein:17% fat milk replacer (MR) and calf starter with no SCFP added. The SCFP treatment was fed the same 24% crude protein:17% fat MR with 1 g/d of SmartCare (Diamond V) and calf starter with 0.8% NutriTek (Diamond V). SmartCare and NutriTek are both produced from anaerobic fermentation of S. cerevisiae. Calves were offered 2.84 L (12.5% solids) of MR twice daily at 0630 and 1630 h through d 51; from d 52 to 56, calves were fed MR once daily at 0630 h; and calves were weaned on d 57. Calves also received ad libitum access to a texturized calf starter and water. On d 50, a subset of calves (n = 20, 10 calves per treatment) were enrolled in an LPS challenge. At -1.5, -0.5, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5, 6, 7, 8, and 24 h relative to dosing with LPS, 20 mL of blood was collected, and rectal temperature and respiration rate were measured for each calf. Blood serum samples were analyzed for interleukin 6, TNF-α (tumor necrosis factor-α), interferon-gamma, haptoglobin, serum amyloid-A, fibrinogen, nonesterified fatty acid, cortisol, and glucose. This study observed increased concentrations of TNF-α at 1 h and 1.5 h and glucose at 0.5 h after dosing with LPS in SCFP calves compared with CON. Calves supplemented with SCFP also had an increase in respiration rate 0.5 h after dosing with LPS and reduced feed intake the day of the challenge compared with CON calves. These results suggest that dairy calves supplemented with SCFP exhibit an increased acute immune response, as observed by increased TNF-α, glucose, and respiration rate immediately after dosing with LPS, compared with CON calves.

Meta-analysis of the relationship between milk trans-10 C18:1, milk fatty acids <16 C, and milk fat production

The economic value of milk fat and its responsiveness to management strategies provides strong interest in maximizing milk fat production by minimizing occurrence of biohydrogenation-induced milk fat depression (BH-MFD) and maximizing de novo synthesized fatty acids (FA). Tools that allow a timely diagnosis of BH-MFD would improve nutritional management. Specific milk FA or FA categories correlate to milk fat concentration and are of interest for diagnosing the cause of changes in milk fat concentration. The objective of the current study was to characterize the relationship between milk fat concentration and trans-10 C18:1, a proxy for BH-MFD, and FA <16 carbons that originate solely from de novo lipogenesis using a meta-analysis approach that used data from the literature and unpublished Penn State experiments. Prior to the meta-analysis, the effect of FA methylation method on milk FA profile was tested to determine potential bias between papers. There was no difference between sodium methoxide, acid, and acid-base methylation methods on trans-10 C18:1 concentration, but acid methods resulted in loss of short-chain FA. The relationship between trans-10 C18:1 and milk fat percentage was investigated using a 2-component model, where one component described the fraction unresponsive to BH-MFD and the other described a responsive fraction that is exponentially related to trans-10 C18:1. The 2 fractions where characterized utilizing a Bayesian hierarchical model accounting for between-study variability. The model was defined by the function f(x, θ1, θ2, θ3) = θ1 + θ2exp(θ3), where the unresponsive θ1 fraction was 2.15 ± 0.09%, the responsive θ2 fraction was 1.55 ± 0.08%, and the exponential term θ3 was -0.503 ± 0.07 (posterior mean ± posterior standard deviation from the Bayesian hierarchical model). A Lin's concordance correlation coefficient of 0.67 suggested good agreement between observations and predictions from the Bayesian hierarchical model, computed only with the model's mean population parameters. There was a linear relationship between milk fat concentration and FA <16 C as a percentage of total FA (intercept = 2.68 ± 0.237 and slope = 0.043 ± 0.011; coefficient of determination = 0.31). The relationship between milk FA <16 C and milk fat concentration is weaker than what has been published, likely because multiple factors can reduce de novo FA without reducing milk fat and the broad range of diets present in the literature.

Postweaning response on growth and nutrient digestion to using different weaning strategies when feeding moderate and high amounts of milk replacer to Holstein calves

Many changes occur in the rumen as calves transition from consuming a liquid diet to a completely solid diet. These changes can influence growth and calf health, being greatly affected by preweaning diet as well as the transitional steps used to wean calves. A 2 × 2 factorial design of moderate [MOD; 0.66 kg of dry matter (DM)] or high (HI; up to 1.1 kg of DM) feeding rates of milk replacer (MR) and abrupt (AB; 7-d step-down) or gradual weaning (GR; 21-d step-down) was used to study how preweaning program affects calf performance from 2 to 4 mo of age. Calves (n = 50) were randomly assigned to 1 of the 4 preweaning treatments. For the following 56-d grower portion of the experiment, calves were grouped into 12 pens based on MR program, with 4 to 5 calves per pen. Data were analyzed as a completely randomized design, with repeated measures when applicable, by PROC MIXED in SAS (version 9.4; SAS Institute Inc., Cary, NC). All calves received ad libitum access to water and a textured starter [42% starch and 20% crude protein (CP)] blended with 5% chopped grass hay. Overall, apparent digestibility coefficients (dC) of DM, neutral detergent fiber, and acid detergent fiber were greater for MOD compared with HI, and apparent dC of DM and ADF were greater for GR than for AB. No significant differences were detected between organic matter, CP, fat, starch, or sugar dC based on treatment, and no interactions were observed. However, by d 56 only starch dC differed by treatment. Weaning body weight (BW), hip width (HW), and hip height (HH) were greater for HI compared with MOD calves. Weaning HH was greater for AB than for GR calves. However, final BW, HW, HH, and body condition score, as well as average daily gain, did not differ among treatments. An interaction occurred where feed efficiency (gain/feed) was reduced with GR weaning in MOD, whereas the opposite occurred in the HI group. When feeding calves a moderate level of MR, a several-step gradual weaning is not necessary to ensure growth and development; however, calves should be gradually weaned when offered a high level of MR.

Exposure to chronic light-dark phase shifts during the prepartum nonlactating period attenuates circadian rhythms, decreases blood glucose, and increases milk yield in the subsequent lactation

Maintaining metabolic balance is a key factor in the health of dairy cattle during the transition from pregnancy to lactation. Little is known regarding the role of the circadian timing system in the regulation of physiological changes during the transition period. We hypothesized that disruption of the cow's circadian timing system by exposure to chronic light-dark phase shifts during the prepartum period would negatively affect the regulation of homeostasis and cause metabolic disturbances, leading to reduced milk production in the subsequent lactation. The objective was to determine the effect of exposure to chronic light-dark phase shift during the last 5 wk prepartum of the nonlactating dry period on core body temperature, melatonin, blood glucose, β-hydroxybutyric acid (BHB) and nonesterified fatty acid (NEFA) concentrations, and milk production. Multiparous cows were moved to tiestalls at 5 wk before expected calving and assigned to control (CTR; n = 16) or phase-shifted (PS; n = 16) treatments. Control cows were exposed to 16 h of light and 8 h of dark. Phase-shifted cows were exposed to the same photoperiod; however, the light-dark cycle was shifted 6 h every 3 d until parturition. Resting behavior and feed intake were recorded daily. Core body temperature was recorded vaginally for 48 h at 23 and 9 d before expected calving using calibrated data loggers. Blood concentrations of melatonin, glucose, BHB, and NEFA were measured during the pre- and postpartum periods. Milk yield and composition were measured through 60 DIM. Treatment did not affect feed intake or body condition. Cosine fit analysis of 24-h core body temperature and circulating melatonin indicated attenuation of circadian rhythms in the PS treatment compared with the CTR treatment. Phase-shifted cows had lower rest consolidation, as indicated by more total resting time, but shorter resting period durations. Phase-shifted cows had lower blood glucose concentration compared with CTR cows (4 mg/mL decrease), but BHB and NEFA concentrations were similar between PS and CTR cows. Milk yield and milk fat yield were greater in PS compared with CTR cows (2.8 kg/d increase). Thus, exposure to chronic light-dark phase shifts during the prepartum period attenuated circadian rhythms of core body temperature, melatonin, and rest-activity behavior and was associated with increased milk fat and milk yield in the postpartum period despite decreased blood glucose pre- and postpartum. Therefore, less variation in central circadian rhythms may create a more constant milieu that supports the onset of lactogenesis.

Effects of feeding different amounts of milk replacer on growth performance and nutrient digestibility in Holstein calves to 2 months of age using different weaning strategies

Growth and the digestibility of nutrients can be greatly affected by diet preweaning and the rate at which calves are weaned. A 2 × 2 factorial design [moderate (MOD) or high (HI) milk replacer (MR) feeding rates and abrupt (AB) or gradual (GR) weaning] was used to compare these effects. Calves (n = 50) were randomly assigned to 1 of 4 treatments: MOD-AB, MOD-GR, HI-AB, and HI-GR. Calves assigned to MOD-AB were fed 0.66 kg of MR for the first 42 d and then 0.33 kg for the last 7 d; those assigned to MOD-GR were fed 0.66 kg of MR for 28 d, 0.33 kg for 14 d, and 0.17 kg for the last 7 d; those assigned to HI-AB were fed 0.66 kg of MR for 7 d, 0.82 kg for 7 d, 1.1 kg for 28 d, and 0.66 kg for the last 7 d; and those assigned to HI-GR were fed 0.66 kg of MR for 7 d, 0.82 kg for 7 d, 1.1 kg for 14 d, 0.66 kg for 14 d, and 0.33 kg for the last 7 d. All calves received the same MR [25% crude protein (CP), 17% fat; dry matter (DM) basis] and were given ad libitum access to water and a textured starter (42% starch and 20% CP). On d 26 to 30 and d 45 to 49, a fecal sample was taken from 5 calves in each treatment via the rectum to estimate apparent digestibility coefficients (dC). Apparent dC of DM, organic matter, and fat were greater for HI versus MOD calves. Apparent dC of neutral detergent fiber, acid detergent fiber, and sugar were greater for MOD versus HI calves. Apparent dC of DM was greater for AB versus GR calves [90.9, 89.0 ± 0.5384 (standard error)], and the apparent dC of acid detergent fiber was greater for GR versus AB calves (39.5, 32.3 ± 1.67). Feed efficiency was greater for HI versus MOD and AB versus GR. There were no significant differences between CP or starch dC based on treatment, and no interactions were observed. Starter consumption was greater for MOD calves compared with HI calves, and GR calves consumed more than AB calves. These results suggest that providing calves high amounts of MR preweaning enhanced readily available nutrient dC, but providing moderate amounts of MR resulted in increased fibrous fraction dC. Accordingly, the AB weaning strategy had higher dC for DM and organic matter, but there was a depression in fiber dC.

Effects of gradual and later weaning ages when feeding high milk replacer rates on growth, textured starter digestibility, and behavior in Holstein calves from 0 to 4 months of age

The objectives of this study were to evaluate calf performance, diet digestibility, and behaviors when feeding 4 milk replacer (MR) programs with different MR rates, weaning ages, and MR reduction steps. Male Holstein calves (n = 96; 40 ± 1 kg of body weight; 1 to 2 d of age) were housed in individual pens for 56 d. Feeding programs for MR were 0.66 kg for 35 d; then 0.33 kg for 7 d fed only in the a.m. (0.6 kg); 0.66 kg for 7 d, 0.82 kg for 35 d, 0.33 kg for 4 d in a.m. only, and 0.22 kg for 3 d in a.m. only (0.8 kg); 0.66 kg for 7 d, 0.82 kg for 7 d, 1.1 kg for 21 d, 0.82 kg for 7 d, 0.33 kg for 4 d in a.m. only, and 0.22 kg for 3 d in a.m. only (1.1 kg); and ad libitum allowance for 35 d, 0.82 kg for 7 d, 0.44 kg for 4 d in a.m. only, and 0.22 kg for 3 d in a.m. only (ad lib). Calves were fed a common MR [25% crude protein, 17% fat, dry matter (DM) basis]. A textured calf starter with whole corn and oats (20% crude protein and 39% starch, DM basis) and water were fed for ad libitum intake during the nursery trial. Daily behavior duration (rumination, eating, and activity) was continuously recorded from d 1 to 55 for 4 calves/treatment using ear tag accelerometers (CowManager SensOor; Agis, Harmelen, the Netherlands). All calves were moved into groups by MR program (4 calves/pen) at 56 d and fed the same starter blended with 5% grass hay. Fecal samples were collected from individual calves between d 52 to 56 and from pen floors on d 66 to 70 to estimate total-tract digestibility. Data were analyzed as a randomized complete block design with repeated measures when appropriate. Intake of MR averaged 25.3, 35.3, 40.9, and 46.5 kg of DM per calf for 0.6 kg, 0.8 kg, 1.1 kg, and ad lib treatments, respectively. Starter intake was greatest for 0.6 kg compared with others and average daily gain (ADG) differed among all 4 programs with 0.6 kg < 0.8 kg < 1.1 kg < ad lib during d 0 to 56. Intake of MR for ad lib was highly variable and was reflected in ADG. Daily rumination, eating, and activity durations did not differ among treatments from d 1 to 55 of the nursery trial. Digestibility of DM, organic matter, acid and neutral detergent fiber, and sugar at d 52 to 56 were greater for 0.6 kg versus ad lib. Digestibility of DM at d 66 to 70 differed for all treatments with 0.6 kg > 0.8 kg > 1.1 kg > ad lib and was mostly influenced by fiber digestibility. During the grower trial (d 56 to 112), ADG was greater for 0.6 kg versus 1.1 kg and ad lib. Hip width change was greater for 0.6 kg versus other treatments. Feeding more than 0.6 kg/d of MR increased ADG preweaning, but reduced diet digestibility postweaning resulted in similar calf BW and frame size by 4 mo of age among MR feeding programs.