Graduate Student Literature Review: Developmental adaptations of immune function in calves and the influence of the intestinal microbiota in health and disease.

This graduate student literature review provides an examination of the ontological adaptations of the calf's immune system and how the intestinal microbiota influences calf immune function in health and disease. Within dairy rearing systems, various nutritional and management factors have emerged as critical determinants of development influencing multiple physiological axes in the calf. Furthermore, we discuss how multiple pre- and postnatal maternal factors influence the trajectory of immune development in favor of establishing regulatory networks to successfully cope with the new environment, while providing early immune protection via immune passive transfer from colostrum. Additionally, our review provides insights into the current understanding of how the intestinal microbiota contributes to the development of the intestinal and systemic immune system in calves. Lastly, we address potential concerns related to the use of prophylactic antimicrobials and waste milk, specifically examining their adverse effects on intestinal health and metabolic function. By examining these factors, we aim to better understand the intricate relationship between current management practices and their long-term effect on animal health.

Dynamics of oxidative stress and immune responses in neonatal calves during diarrhea.

Oxidative stress is the imbalanced redox status between oxidant production and their scavengers leading to intestinal physiological dysfunction. However, the role of systemic and local oxidative status during neonatal calf diarrhea is not known. This study assessed systemic (serum) and local (fecal) oxidative status when calves either naturally developed diarrhea or naturally recovered. Healthy calves were enrolled in the study at d 18 of age, and their health status was monitored from the enrollment. Based on their enteric health status on d 21 and 28, calves were grouped as continuous diarrhea from d 21 to 28 (n = 14), diarrhea at d 21 but recovered at d 28 (DH group, n = 19), healthy at d 21 but developed diarrhea at d 28 (HD group, n = 15), and healthy throughout the study (HH group, n = 16). Serum and fecal samples were collected at d 21 and 28 from all calves in the morning 2 h after feeding. Dynamics of oxidative stress indicators including reactive oxygen species (ROS), malondialdehyde (MDA), H2O2, 8-hydroxy-2'-deoxyguanosine (8-OHDG), glutathione peroxidase, superoxide dismutase, catalase (CAT), and total antioxidant capacity and inflammatory indicators TNF-α, IL-1ß, IL-4, IL-6, IL-10, and IFN-γ were evaluated using serum samples. In addition, fecal oxidative stress indicators ROS and MDA were measured. Serum ROS, MDA, 8-OHDG, as well as fecal ROS and MDA, were higher, whereas serum CAT and H2O2 were lower in diarrheic calves than those of healthy calves. Serum ROS, MDA, and 8OHDG and fecal ROS and MDA increased in the HD group from d 21 to 28 as they developed diarrhea. In contrast, all these oxidative stress markers decreased in the DH group from d 21 to 28 as they recovered. However, serum H2O2 had an opposite changing trend, which became lower in the HD group and higher in the DH group at d 28. In conclusion, both systemic and local oxidative stress markers and cytokine profiles altered as calves moved from being healthy to having diarrhea or vice versa. Serum ROS, MDA, and 8-OHDG can be used to develop biomarkers to screen calves prone to enteric infections during the preweaning period.

[Clinical research progress in non-invasive positive pressure ventilation in 2023].

Non-invasive positive pressure ventilation (NPPV) is a widely used method of providing respiratory support in a variety of clinical settings, including emergency departments, general wards, and intensive care units. The relevant research articles on NPPV published between 1st October 2022 and 30th September 2023 were retrieved from Medline and reviewed. In the management of acute respiratory failure (ARF) associated with COVID-19, studies have highlighted the significant influence of regional economic status on the choice of respiratory support strategies. It has been observed that NPPV is more suitable for patients with mild to moderate acute respiratory distress syndrome (ARDS) than for those with severe ARDS, as the latter group has an increased risk of delayed intubation. In addition, patients with severe dyspnea tended to benefit more from NPPV compared with high flow nasal cannula (HFNC) and conventional oxygen therapy, with a reduced risk of self-induced lung injury. For non-COVID-19-related ARF, research shows no significant differences in mortality and intubation rates between HFNC and NPPV in patients with hypercapnic ARF. The updated HACOR score and ROX score have been validated to have a high predictive value for clinical outcomes in patients receiving NPPV for hypoxemic ARF. With regard to weaning from invasive mechanical ventilation, immediate application of NPPV after extubation showed a lower mortality rate compared to continued invasive weaning. Moreover, NPPV with active humidification significantly decreased the reintubation rate within 7 days after extubation compared with HFNC. The choice between using NPPV and HFNC should be based on the specific etiology of the patient's condition. The potential effect of noninvasive high-frequency oscillatory ventilation on CO2 clearance was also investigated.

Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves.

Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.

[Clinical update in non-invasive positive pressure ventilation for respiratory failure in 2022].

In this article, we searched the research literatures related to clinical investigation of non-invasive positive pressure ventilation (NPPV) in acute respiratory failure(ARF)/chronic respiratory failure(CRF) between 1st October 2021 and 30th September 2022 through Medline, and reviewed the important advances. Three prospective randomized controlled studies related to the efficacy and safety of NPPV and/or high-flow nasal cannula oxygen therapy (HFNC) on patients with COVID-19 with ARF were reported, showing that NPPV (including continuous positive airway pressure and bilevel positive airway pressure) was able to reduce the intubation rate, but the efficacy of HFNC was contradictory. In addition, progress has been made in outcome prediction models for ARF treated with NPPV, NPPV-related cardiac arrest, and the impact of human-machine interface on NPPV treatment outcomes. The effects of NPPV as preoxygenation method before intubation was reported to be able to reduce severe desaturation during intubation, especially in obese population. The use of NPPV in extubated patients resulting in reduced reintubation rate was also studied. With regard to long-term home application of NPPV, five indicators of successful initiation were proposed, but the success rate was low in clinical practice. Some reports showed that psychological support could improve the adherence to NPPV. The results of these studies contributed to the rational selection and optimal application of NPPV in clinical practice.

Invited review: Effect of subacute ruminal acidosis on gut health of dairy cows.

Subacute ruminal acidosis (SARA) is assumed to be a common disease in high-yielding dairy cows. Despite this, the epidemiological evidence is limited by the lack of survey data. The prevalence of SARA has mainly been determined by measuring the pH of ruminal fluid collected using rumenocentesis. This may not be sufficiently accurate, because the symptoms of SARA are not solely due to ruminal pH depression, and ruminal pH varies among sites in the rumen, throughout a 24-h period, and among days. The impact of SARA has mainly been studied by conducting SARA challenges in cows, sheep, and goats based on a combination of feed restriction and high-grain feeding. The methodologies of these challenges vary considerably among studies. Variations include differences in the duration and amount of grain feeding, type of grain, amount and duration of feed restriction, number of experimental cows, and sensitivity of cows to SARA challenges. Grain-based SARA challenges affect gut health. These effects include depressing the pH in, and increasing the toxin content of, digesta. They also include altering the taxonomic composition of microbiota, reducing the functionality of the epithelia throughout the gastrointestinal tract (GIT), and a moderate inflammatory response. The effects on the epithelia include a reduction in its barrier function. Effects on microbiota include reductions in their richness and diversity, which may reduce their functionality and reflect dysbiosis. Changes in the taxonomic composition of gut microbiota throughout the GIT are evident at the phylum level, but less evident and more variable at the genus level. Effects at the phylum level include an increase in the Firmicutes to Bacteroidetes ratio. More studies on the effects of a SARA challenge on the functionality of gut microbiota are needed. The inflammatory response resulting from grain-based SARA challenges is innate and moderate and mainly consists of an acute phase response. This response is likely a combination of systemic inflammation and inflammation of the epithelia of the GIT. The systemic inflammation is assumed to be caused by translocation of immunogenic compounds, including bacterial endotoxins and bioamines, through the epithelia into the interior circulation. This translocation is increased by the increase in concentrations of toxins in digesta and a reduction of the barrier function of epithelia. Severe SARA can cause rumenitis, but moderate SARA may activate an immune response in the epithelia of the GIT. Cows grazing highly fermentable pastures with high sugar contents can also have a low ruminal pH indicative of SARA. This is not accompanied by an inflammatory response but may affect milk production and gut microbiota. Grain-based SARA affects several aspects of gut health, but SARA resulting from grazing high-digestible pastures and insufficient coarse fiber less so. We need to determine which method for inducing SARA is the most representative of on-farm conditions.

[Clinical research progress in non-invasive positive pressure ventilation from 2020 to 2021].

Non-invasive positive pressure ventilation (NPPV), an essential respiratory support method, is widely used in acute/chronic respiratory failure and assisting rehabilitation in patients with chronic obstructive pulmonary disease (COPD). We searched the relevant research articles about NPPV published from 1st October 2020 to 30th September 2021 through Medline. Researches focusing on the clinical application and viral transmission protection during high-flow nasal cannula oxygen and NPPV in COVID-19, were mainly retrospective and of small sample size. It demonstrated that high-flow nasal cannula oxygen and NPPV might reduce intubation rates when treating patients with mild-to-moderate respiratory failure, but the risk of delayed intubation should draw particular precaution. When using NPPV in non-COVID-19-related de novo acute respiratory failure, diaphragm thickening fraction and tidal change of esophageal pressure were validated to predict the treatment outcome. In addition, some studies explored the compliance and related influencing factors associated with the treatment effects of early NPPV initiation on amyotrophic lateral sclerosis patients and the effects of NPPV on dynamic hyperinflation during exercise in COPD patients. Furthermore, the effectiveness of neurally adjusted ventilatory assist ventilation and a novel communication device optimizing the use of NPPV were also investigated and outlined.

Preweaning to postweaning rumen papillae structural growth, ruminal fermentation characteristics, and acute-phase proteins in calves.

This study evaluated pre- to postweaning ruminal structural development, fermentation characteristics, and acute-phase protein levels in calves with a high milk replacer (MR) feeding rate prior to weaning. Six ruminally cannulated Holstein bull calves were fed MR (150 g/L) at 15% of body weight (BW) in 2 equal volumes daily. Volumes were adjusted weekly based on BW. Calves were weaned using a 1-step weaning method, with MR decreased by 50% at the end of wk 5 and full weaning at the end of wk 6. Calf starter, chopped straw, and water were offered ad libitum. Intake was recorded daily, and BW was recorded weekly. From wk 5 to 12, ruminal pH was continuously measured using a ruminal pH bolus. Ruminal fluid was collected weekly from wk 5 to 12 for measurement of short-chain fatty acid concentrations and quantification of total bacteria and protozoa. Rumen papillae were obtained at wk 5, 6, 7, 8, and 12 for histological analysis. Serum amyloid A and lipopolysaccharide-binding protein were measured weekly. Data were analyzed using GLIMMIX procedure of SAS (SAS Institute Inc., Cary, NC), with week as a fixed effect and calf as a random effect. During the weaning step-down, starter intake was 3-fold higher and continued to increase until wk 12. Body weight increased from birth to wk 12; however, BW did not change during wk 6, 7, and 8, possibly due to low metabolizable energy intake caused by the weaning strategy. Preweaning ruminal pH was below 5.8 for approximately 936.3 ± 125.99 min/d, implying ruminal acidosis. Furthermore, ruminal pH below 5.8 reached a peak at wk 8 with 1,203.9 ± 227.65 min/d below pH 5.8 and slowly decreased to 388.1 ± 189.82 min/d below pH 5.8 at wk 12. Papillae surface area, length, and width increased during wk 12 compared with wk 5. Corneum thickness increased by week, whereas spinosum/basale thickness only increased during wk 8 compared with wk 5. The acute-phase protein concentration was highest at wk 1 and then decreased and remained constant until wk 12. In conclusion, even before step-down weaning, calves experienced ruminal acidosis despite low starter intake. Further, the observed prolonged ruminal pH depression suggests that dietary rumen adaptation after weaning can take several weeks in calves with a high MR feeding rate preweaning. The prolonged depressed ruminal pH did not affect acute-phase proteins and this finding, along with the other results, suggests that rumen epithelium barrier integrity is not compromised during weaning.

Longitudinal assessment revealed the shifts in rumen and colon mucosal-attached microbiota of dairy calves during weaning transition.

The objectives of this study were to investigate the shifts in rumen and colon mucosa-associated microbiota in dairy calves fed a high milk replacer feeding rate before and after weaning and to determine whether such shifts are associated with tissue physiological measures. Longitudinal biopsy was performed to collect rumen and colon mucosal tissues of 4 ruminally cannulated Holstein dairy bull calves (weaned at 6 wk of age) at the end of wk 5 (before weaning), 7 (weaning adaptation) and 12 (after weaning), and were used to assess mucosa-associated microbiota and their changes using amplicon sequencing. Both rumen and colon mucosa-associated bacterial communities shifted during the weaning process, as evidenced by their clear separation among 3 different weaning periods and increased α diversity (Shannon and Chao1 indices) during weaning transition. Among the 3 dominant bacterial phyla identified (relative abundance >1.0%), the relative abundance of Proteobacteria and Bacteroidetes decreased in the rumen mucosa, whereas the relative abundance of Firmicutes increased in both rumen and colon mucosa during weaning transition. In the rumen mucosa, Campylobacter (0.6-22.1%) gradually became prevalent during weaning transition, whereas Succinivibrio (6.2-10.3%) and Prevotella 1 (4.7-10.5%) were dominant regardless of weaning transition. In the colon mucosa, Bacteroides (12.8-25.4%) was dominant during weaning transition, although its relative abundance decreased after weaning. In the meantime, relative abundance of uncultured Lachnospiraceae increased from 2.2% to 25.7% during this period. In addition, genera Pyramidobacter (in the rumen mucosa) and Lachnoclostridium (in the colon mucosa) were positively correlated with rumen papilla surface area and colon mucosal thickness, respectively. Moreover, genera Ruminococcaceae UCG-005 and Sharpea in the rumen mucosa were positively correlated with the molar proportion of propionate and butyrate, respectively. Overall, our findings revealed that rumen and colon mucosa-associated bacterial communities altered in response to the weaning transition, and some bacterial taxa in these communities may have positive effects on rumen and colon mucosa development during this period.

Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding.

The aim of this study was to explore the effect of colostrum feeding time on the ileal microbiome of neonatal calves. In this study, 22 male Holstein calves were randomly assigned to different colostrum feeding time treatments: after birth (at 45 min, n = 7); at 6 h after birth (n = 8); and at 12 h after birth (TRT12h; n = 7). At 51 h after birth, calves were killed and ileum digesta was collected for microbiome analysis using shotgun metagenomic sequencing. Bacteria, archaea, eukaryotes, and viruses were identified from the ileum microbiome. For the bacteriome, Firmicutes and Proteobacteria were the predominant phyla, and Escherichia, Streptococcus, Lactobacillus were the 3 most abundant genera. For the archaeal community, Euryarchaeota and Crenarchaeota were the 2 major phyla, and Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the 3 most abundant genera. In total, 116 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified from the ileal microbiome, with "biosynthesis of vancomycin group antibiotics," "biosynthesis of ansamycins," "valine, leucine, and isoleucine biosynthesis," "ribosome," and "d-alanine metabolism" as the top 5 functions. When the ileal microbiomes were compared among the 3 treatments, the relative abundance of Enterococcus was higher in TRT12h calves, suggesting that calves may have a higher abundance of opportunistic pathogens when the feeding of colostrum is delayed for 12 h. Moreover, among all KEGG pathways, the enriched "taurine and hypotaurine metabolism" (KO00430) pathway was identified in the ileal microbiome of TRT12h calves; however, future studies are needed to understand the effect on the host. Additionally, 2 distinct ileal microbial profiles were identified across all samples, indicating that that host factors may play a significant role in driving varied microbiome changes in response to colostrum feeding time. Whether such microbiome shifts affect long-term gut function and calf performance warrants future studies.

The effect of neomycin inclusion in milk replacer on the health, growth, and performance of male Holstein calves during preweaning.

The prophylactic use of oral antimicrobials, such as neomycin, in milk replacer (MR) or whole milk is a common practice in calf-rearing that is thought to aid in preventing disease. Heavy reliance on antimicrobials is of concern not only because of the development of antimicrobial resistance, but also because of the potentially negative effects on health. The objective of this study was to investigate the effects of neomycin on calf health and growth performance. One hundred and sixty calves (approximately 3-10 d of age), distributed across 2 experimental periods, were stratified by body weight (BW) and serum total protein, and assigned to 1 of 3 treatments: control (CON; nonmedicated MR, n = 60), short-term antibiotic (ST; neomycin mixed in MR from d 1-14, n = 50), or long-term antibiotic (LT; neomycin in ​MR from d 1-28, n = 50). Arrival BW (47.69 ± 0.87 kg) and serum total protein (5.67 ± 0.09 g/dL) were not different between treatment groups. Neomycin in ST and LT was dosed in MR at a rate of 20 mg/kg of BW and was adjusted weekly according to BW. Calf BW was measured weekly for 49 d, and health indicators (fecal score, attitude score, respiratory score, and rectal temperature), MR intake, starter intake, and the use of additional electrolytes and antimicrobials were recorded daily. Calves in the CON group experienced a higher proportion of days with diarrhea (20.32 ± 0.02%) compared with ST (14.70 ± 0.02%) or LT (13.80 ± 0.02%) calves, as well as longer bouts of diarrhea (7.45 ± 0.38 d, 5.69 ± 0.46 d, and 5.62 ± 0.45 d for CON, ST, and LT calves, respectively). Calves in the CON group also experienced higher fecal scores (score of 0.64 ± 0.04) than ST (score of 0.53 ± 0.04) or LT (score of 0.49 ± 0.04) calves, especially at d 7. However, no differences were observed in other health-related measures. The time to reach first diarrhea and first respiratory illness was not different between treatments, nor was the time to recover from respiratory illness. The time to intervention with additional electrolytes or antimicrobials was not different between treatment groups. Furthermore, growth performance, feed intake, and feed conversion ratio were not different. No differences were found when comparing ST and LT, except in the defined daily dose of total antimicrobials received. Calves in the LT group received a higher overall dose than ST calves, and both ST and LT calves received a higher dose than CON calves, which received no prophylactic antimicrobials. Given that there were no differences in performance variables and no additional health benefits aside from reduced fecal scores in calves fed neomycin, current practices involving the use of antimicrobials on dairy and veal operations need to be considered more prudently.

Rumen microbiota and its relation to fermentation in lactose-fed calves.

In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present study as a follow-up study to identify the shift in rumen microbiota and its relation to rumen fermentation when calves are fed a lactose-containing starter. Thirty Holstein bull calves were divided into 2 calf starter treatment groups: texturized calf starter (i.e., control; n = 15) or calf starter in which starch was replaced with lactose at 10% (i.e., LAC10; n = 15) on a dry matter basis. All calves were fed their respective treatment calf starter ad libitum from d 7, and kleingrass hay from d 35. Rumen digesta were collected on d 80 (i.e., 3 wk after weaning) and used to analyze rumen microbiota and fermentation products. There was no apparent effect of lactose feeding on the α-diversity and overall composition of rumen microbiota. Amplicon sequencing and real-time PCR quantification of the 16S rRNA gene confirmed that the abundance of butyrate-producing bacteria (i.e., Butyrivibrio group and Megasphaera elsdenii) did not differ between the control and LAC10 groups. Conversely, the relative abundance of Mitsuokella spp., which produce lactate, succinate, and acetate, was significantly higher in the rumen of calves that were fed lactose, whereas the lactate concentration did not differ between the control and LAC10 groups. These findings suggest that the lactate production can be elevated by an increase of Mitsuokella spp. and then converted into butyrate, not propionate, since the proportion of propionate was lower in lactose-fed calves. In addition, we observed a higher abundance of Coriobacteriaceae and Pseudoramibacter-Eubacterium in the LAC10 group. Both these bacterial taxa include acetate-producing bacteria, and a positive correlation between the acetate-to-propionate ratio and the abundance of Pseudoramibacter-Eubacterium was observed. Therefore, the higher abundance of Coriobacteriaceae, Mitsuokella spp., and Pseudoramibacter-Eubacterium in the rumen of lactose-fed calves partially explains the increase in the proportion of rumen acetate that was observed in our previous study.

Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing.

The identification of functional genetic variants and associated candidate genes linked to feed efficiency may help improve selection for feed efficiency in dairy cattle, providing economic and environmental benefits for the dairy industry. This study used RNA-sequencing data obtained from liver tissue from 9 Holstein cows [n = 5 low residual feed intake (RFI), n = 4 high RFI] and 10 Jersey cows (n = 5 low RFI, n = 5 high RFI), which were selected from a single population of 200 animals. Using RNA-sequencing, 3 analyses were performed to identify: (1) variants within low or high RFI Holstein cattle; (2) variants within low or high RFI Jersey cattle; and (3) variants within low or high RFI groups, which are common across both Holstein and Jersey cattle breeds. From each analysis, all variants were filtered for moderate, modifier, or high functional effect, and co-localized quantitative trait loci (QTL) classes, enriched biological processes, and co-localized genes related to these variants, were identified. The overlapping of the resulting genes co-localized with functional SNP from each analysis in both breeds for low or high RFI groups were compared. For the first two analyses, the total number of candidate genes associated with moderate, modifier, or high functional effect variants fixed within low or high RFI groups were 2,810 and 3,390 for Holstein and Jersey breeds, respectively. The major QTL classes co-localized with these variants included milk and reproduction QTL for the Holstein breed, and milk, production, and reproduction QTL for the Jersey breed. For the third analysis, the common variants across both Holstein and Jersey breeds, uniquely fixed within low or high RFI groups were identified, revealing a total of 86,209 and 111,126 functional variants in low and high RFI groups, respectively. Across all 3 analyses for low and high RFI cattle, 12 and 31 co-localized genes were overlapping, respectively. Among the overlapping genes across breeds, 9 were commonly detected in both the low and high RFI groups (INSRR, CSK, DYNC1H1, GAB1, KAT2B, RXRA, SHC1, TRRAP, PIK3CB), which are known to play a key role in the regulation of biological processes that have high metabolic demand and are related to cell growth and regeneration, metabolism, and immune function. The genes identified and their associated functional variants may serve as candidate genetic markers and can be implemented into breeding programs to help improve the selection for feed efficiency in dairy cattle.

Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle.

BACKGROUND: Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. RESULTS: On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. CONCLUSION: The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.

Feeding colostrum or a 1:1 colostrum:whole milk mixture for 3 days after birth increases serum immunoglobulin G and apparent immunoglobulin G persistency in Holstein bulls.

Conflicting reports exist on whether prolonged IgG consumption can further increase serum IgG in neonatal calves. Given that higher serum IgG in neonates has lifelong benefits, our objective was to determine whether serum IgG can be increased by providing multiple meals containing IgG to neonatal calves. Twenty-seven Holstein bulls were all fed 1 colostrum meal (7.5% body weight; 62 g of IgG/L) at 2 h after birth and randomly assigned to be fed (5% body weight) colostrum (COL; n = 9), whole milk (WM; n = 9), or a 1:1 colostrum:whole milk mixture (MX; n = 9) every 12 h from 12 to 72 h. Serum IgG was measured at 1, 2, 3, 6, 9, 11, and 12 h after birth. After the 12-h meal, IgG was determined at 0.5-h intervals until 16 h and then at 1-h intervals from 16 to 24 h. Serum IgG was then measured at 27 h, then every 6 h from 30 to 60 h. From 60 to 64 h, IgG was measured every 0.5 h, then at 65 and 66 h, and then every 2 h until 72 h. Serum IgG increased rapidly between 2 and 12 h for all calves. A treatment × time interaction occurred as serum IgG began to diverge between treatments after they were fed at 12 h; the interaction was greatest over the entire period for COL compared with both MX and WM and was greater for MX than for WM. Maximum IgG concentrations (Cmax) were 30.4 ± 0.8, 27.2 ± 0.8, and 23.9 ± 0.8 g/L for COL, MX, and WM, respectively. Although MX Cmax was equivalent to both COL and WM Cmax, COL Cmax was greater than WM Cmax. Feeding COL and MX also prolonged the time to reach Cmax. Respectively, these calves achieved Cmax at 29.5 and 27.0 ± 3.4 h, whereas WM IgG peaked at 13.4 ± 3.4 h. No differences were observed for apparent efficiency of absorption between treatments from 0 to 12 h and 0 to 24 h. Immunoglobulin G area under the curve (AUC) was the same for COL and MX calves over the entire experimental period and from when treatments were fed. The IgG AUC for 0 to 72 h for WM calves was 27.4% lesser than that for COL calves but not different from MX calves. However, the IgG AUC for 12 to 72 h for WM calves differed relative to that for both COL (30.8% less) and MX (19.6% less) calves. Serum IgG concentrations were more persistent when COL (88.2 ± 2.4%) and MX (91.2 ± 2.4%) were fed rather than WM (75.3 ± 2.4%). Prolonged IgG consumption increased serum IgG concentrations, corresponding to the mass of IgG fed, and improved apparent IgG persistency in Holstein bulls. Neonatal calves should be fed at least 62 g of IgG at 12 h after birth to further increase serum IgG concentrations.

Short communication: Effect of delaying the first colostrum feeding on small intestinal histomorphology and serum insulin-like growth factor-1 concentrations in neonatal male Holstein calves.

The primary objective of this study was to determine the effect of delaying the first colostrum feeding on small intestinal histomorphology and serum insulin-like growth factor-1 (IGF-1) concentrations, and the secondary objective was to characterize the ultrastructure of the small intestine of neonatal calves at 51 h of life. Twenty-seven male Holstein calves were fed pooled, pasteurized colostrum (7.5% of birth body weight; 62 g of IgG/L) at 45 min (0H, n = 9), 6 h (6H, n = 9), or 12 h (12H, n = 9) after birth. At 12 h after their respective colostrum feeding, calves were fed milk replacer at 2.5% of birth body weight per meal and every 6 h thereafter. Blood samples were collected every 6 h using a jugular catheter and analyzed for serum IGF-1 concentrations using an automated solid-phase chemiluminescent immunoassay. At 51 h of life, calves were euthanized to facilitate collection of the duodenum, proximal and distal jejunum, and ileum. All segments of the small intestine were assessed for histomorphology, whereas scanning electron and transmission electron microscopy analyses were conducted only for the proximal jejunum and ileum. The results revealed that there was no overall effect of colostrum feeding time on serum IGF-1 concentrations; however, serum IGF-1 concentrations were influenced by time. Specifically, concentrations of serum IGF-1 at 48 h were 29% greater than concentrations at 0 h of life (312.8 ± 14.85 vs. 241.9 ± 14.06 ng/mL). Although there was no overall effect of colostrum feeding time on all histomorphological measures assessed, treatment × segment interactions were observed. Villi height was 1.4 times greater in the distal jejunum of 0H calves than in 6H and 12H calves, and 0H calves tended to have 1.2 times greater ileal villus height than 12H calves. In addition, 0H calves had 1.2 and 1.3 times greater ileal crypt depth than 6H and 12H calves, respectively, and 1.3 times greater surface area index than 12H calves in the distal jejunum. Qualitative ultrastructural evaluation of small intestinal enterocytes conducted irrespective of colostrum treatment revealed the presence of large vacuoles of electron-dense material, apical mitochondria, and apical canalicular systems in the jejunum and ileum. These results indicate that the calf intestine at 51 h of life contains unique enterocyte characteristics similar to fetal enterocytes and that delaying colostrum feeding may negatively influence intestinal growth and development.

Feeding colostrum or a 1:1 colostrum:milk mixture for 3 days postnatal increases small intestinal development and minimally influences plasma glucagon-like peptide-2 and serum insulin-like growth factor-1 concentrations in Holstein bull calves.

This study evaluated how feeding colostrum- or a colostrum-milk mixture for 3 d postnatal affects plasma glucagon-like peptide-2 (GLP-2), serum insulin-like growth factor-1 (IGF-1), and small intestinal histomorphology in calves. Holstein bulls (n = 24) were fed colostrum at 2 h postnatal and randomly assigned to receive either colostrum (COL), whole milk (WM), or a 1:1 COL:WM mixture (MIX) every 12 h from 12 to 72 h. A jugular venous catheter was placed at 1 h postnatal to sample blood frequently for the duration of the experiment. Samples were collected at 1, 2, 3, 6, 9, 11, and 12 h. Following the 12-h meal, blood was collected at half-hour intervals until 16 h and then at 1-h intervals from 16 to 24 h. A 27-h sample was taken, then blood was sampled every 6 h from 30 to 60 h. Again, blood was taken at half-intervals from 60 to 64 h, then at 65 and 66 h, following which, a 2-h sampling interval was used until 72 h. Plasma GLP-2 (all time points) and serum IGF-1 (at time points: 1, 6, 12, 18, 24, 36, 48, and 72 h) were both analyzed. Duodenal, jejunal, and ileal tissues were collected at 75 h of age to assess histomorphology and cellular proliferation. Feeding COL, rather than WM, increased plasma GLP-2 by 60% for 2 h and tended to increase GLP-2 by 49.4% for 4 h after the 60-h meal. Insulin-like growth factor-1 area under the curve (from 12 to 72 h) tended to be 27% greater for COL than WM calves but was otherwise unaffected by treatment. Ileal crypts tended to proliferate more with MIX than WM, whereas ileal crypt proliferation did not differ for COL compared with MIX or WM and was not different between treatments in the proximal jejunum. Villi height was increased 1.8 and 1.5× (COL and MIX vs. WM) in the proximal and distal jejunum, respectively, whereas MIX duodenal and ileal villi height tended to be 1.5 and 1.4× that of WM. Crypt depth did not differ in any region. Surface area of the gastrointestinal tract was reduced for WM by 60 and 58% (proximal jejunum) and 38 and 52% (ileum) relative to COL and MIX and was 54% less than MIX in the distal jejunum. Overall, extended COL feeding minimally increased plasma GLP-2 and serum IGF-1 compared with WM feeding. As COL and MIX similarly promoted small intestinal maturation, feeding calves transition milk to promote intestinal development could be a strategy for producers.

Early supplementation of Saccharomyces cerevisiae boulardii CNCM I-1079 in newborn dairy calves increases IgA production in the intestine at 1 week of age.

The early development of immunity and microbiota in the gut of newborn calves can have life-long consequences. Gut microbiota and the intestinal barrier interplay after birth, establishing a homeostatic state whereby mucosal cells cohabit with microorganisms to develop a healthy gut. We hypothesized that postnatal codevelopment of gut immunity and microbiota could be influenced by early-life supplementation with live yeast. Starting from birth, calves either received a daily supplementation of Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB, 10 × 109 cfu/d, n = 10) in the morning meal for 7 d or no supplementation (n = 10). Each animal received 2 adequate colostrum replacer meals at 2 and 12 h of life (expected total IgG fed = 300 g) before being fed milk replacer twice a day. Passive transfer of immunity (total protein, IgG, and IgA) through colostrum was evaluated and endogenous production of IgA was investigated by measuring IgA-producing plasma cells, IgA relative gene expression (PIGR and CD79A), and secretory IgA concentration in the gut. The concentration of targeted microbial groups was evaluated with quantitative PCR in the gut digesta collected at d 7 of life. Early SCB supplementation did not impair immunoglobulin absorption and all calves had successful passive transfer of immunity (serum IgG concentration >15 mg/mL at d 1 and d 7 of age). Although the expression of IgA relative gene expression (PIGR and CD79A) was not different, SCB calves had higher secretory IgA concentrations in the ileum (1.98 ± 0.12 mg/g of dry matter; DM) and colon (1.45 ± 0.12 mg/g of DM) digesta compared with control animals (1.18 and 0.59 ± 0.12 mg/g of DM, respectively). In addition, the number of IgA-producing plasma cells were greater in both ileum (2.55 ± 0.40 cells/mm2) and colon (3.03 ± 0.40 cells/mm2) tissues for SCB calves compared with control (respectively 1.00 ± 0.40 and 0.60 ± 0.42 cells/mm2). Endogenous IgA production in the gut of SCB calves was enhanced, which could make them less prone to pathogen intrusion. In addition, SCB calves had higher Lactobacillus and tended to have higher Faecalibacterium prausnitzii in the jejunum compared with control calves, which suggests that SCB supplementation during early-life gut colonization may have a positive effect in newborn calves. Direct SCB supplementation or the cross-talk between SCB and bacteria may be responsible for stimulating IgA production and may play a key role in shaping early colonization in the gut of newborn calves.

Effect of amount of milk replacer fed and the processing of corn in starter on growth performance, nutrient digestibility, and rumen and fecal fibrolytic bacteria of dairy calves.

The aim of this study was to evaluate effects of milk replacer (MR) feeding rate and processing of corn in calf starter (CS) on growth performance, nutrient digestibility, and rumen and fecal fibrolytic bacteria in dairy calves. Holstein male calves (n = 48, 2-3 d of age) were randomly assigned to 1 of 4 treatments with a 2 × 2 factorial arrangement of MR level of 0.749 kg of MR/d (LO) or up to 1.498 kg of MR/d (HI); and whole corn or flaked corn in textured CS. Calves were weaned by reducing MR offered by 50% during wk 6. Intakes of MR and CS were recorded daily, whereas body weight (BW) was measured weekly. Rumen fluid and fecal matter were collected at wk 5 and 8 to quantify fibrolytic bacteria and nutrient digestibility. Data were analyzed as a completely randomized design using mixed model ANOVA. Repeated measures were used as appropriate. Calves fed HI had greater average daily gain than calves fed LO at wk 2, 3, 4, and 5, yet at wk 7 calves fed HI had lower average daily gain compared with calves fed LO. Starter intake was greater for calves fed LO compared with HI at wk 4, 5, 6, and 7. During wk 5 and 8, calves fed LO had increased ADF and NDF digestibility compared with calves fed HI. During wk 5, dry matter and organic matter digestibility were lower for LO-fed calves compared with HI-fed calves, but during wk 8 the opposite was observed, with HI-fed calves having lower dry matter and organic matter digestibility than LO-fed calves. At wk 5, Clostridium cluster IV and Butyrivibrio fibrisolvens proportions in rumen fluid tended to be higher and Clostridium cluster IV, Fecalibacterium sp., and Prevotella sp. proportions in fecal matter were higher in calves fed LO compared with HI. From wk 8 to 16, dry matter intake was unaffected by treatment; however, energy efficiency was greater in calves fed LO, causing LO calves to have higher BW gain during this period. Greater starter digestibility was observed for calves fed LO versus HI in concert with increased fibrolytic bacteria proportions (wk 5) in fecal and rumen samples, which resulted in greater postweaning BW gain and similar BW and frame measurements by 16 wk of age. Overall the results show that rate of MR feeding has a larger effect than the processing of corn in CS on performance, fiber digestibility, and rumen and fecal fibrolytic bacterial communities.

Short communication: Relationship of blood DNA methylation rate and milk performance in dairy cows.

The objective of this study was to investigate the global methylation rate in blood DNA and its relationship with lactation performance. A total of 196 mid-lactation dairy cows were fed the same diet under the same management. Milk yield was recorded and blood samples were collected from the jugular vein before morning feeding. The blood global DNA methylation rates were quantified using a methylation quantification kit. Overall, the average blood global DNA methylation rate of all cows was 12.4%. When DNA methylation rates were compared between cows with high (n = 40; 37.0 to 42.0 kg/d) and low (n = 33; 24.0 to 30.0 kg/d) milk yield, DNA methylation rates in the lower-yield cows (14.1 ± 0.7%) were significantly higher than those in the higher-yield animals (11.6 ± 0.7%). Our results indicated an association of milk and protein yields with global DNA methylation rates in lactating dairy cows. However, further research is needed to determine whether this association reflects the true influence of epigenetic mechanisms on yield or whether other factors, such as different proportions of blood cell types in high- and low-yielding cows, affect apparent global DNA methylation levels.