Metataxonomic and metabolomic profiling revealed Pinus koraiensis cone essential oil reduced methane emission through affecting ruminal microbial interactions and host-microbial metabolism.

BACKGROUND: Pinus koraiensis cone essential oil (PEO) contains functional compounds such as monoterpene hydrocarbons, and the administration of PEO reduced methane (CH4) emissions during growing phase of goats. However, the mode of action of PEO driven CH4 reduction is not known, especially how the administration of PEO can affect rumen microbiota and host metabolism in goats during the fattening phase. This study aimed to elucidate the potential microbial and host responses PEO supplementation in goats using metataxonomics (prokaryotes and protozoa) and metabolomics (rumen fluid and serum). RESULTS: Ten fattening Korean native goats were divided into two dietary groups: control (CON; basal diet without additives) and PEO (basal diet + 1.5 g/d of PEO) with a 2 × 2 crossover design and the treatment lasted for 11 weeks. Administration of PEO reduced CH4 concentrations in the exhaled gas from eructation by 12.0-13.6% (P < 0.05). Although the microbial composition of prokaryotes (bacteria and archaea) and protozoa in the rumen was not altered after PEO administration. MaAsLin2 analysis revealed that the abundance of Selenomonas, Christensenellaceae R-7 group, and Anaerovibrio were enriched in the rumen of PEO supplemented goats (Q < 0.1). Co-occurrence network analysis revealed that Lachnospiraceae AC2044 group and Anaerovibrio were the keystone taxa in the CON and PEO groups, respectively. Methane metabolism (P < 0.05) was enriched in the CON group, whereas metabolism of sulfur (P < 0.001) and propionate (P < 0.1) were enriched in the PEO group based on microbial predicted functions. After PEO administration, the abundance of 11 rumen and 4 serum metabolites increased, whereas that of 25 rumen and 14 serum metabolites decreased (P < 0.1). Random forest analysis identified eight ruminal metabolites that were altered after PEO administration, among which four were associated with propionate production, with predictive accuracy ranging from 0.75 to 0.88. Additionally, we found that serum sarcosine (serum metabolite) was positively correlated with CH4 emission parameters and abundance of Methanobrevibacter in the rumen (|r|≥ 0.5, P < 0.05). CONCLUSIONS: This study revealed that PEO administration reduced CH4 emission from of fattening goats with altered microbial interactions and metabolites in the rumen and host. Importantly, PEO administration affected utilizes various mechanisms such as formate, sulfur, methylated amines metabolism, and propionate production, collectively leading to CH4 reduction. The knowledge is important for future management strategies to maintain animal production and health while mitigate CH4 emission.

High deoxynivalenol and ergot alkaloid levels in wheat grain: effects on growth performance, carcass traits, rumen fermentation, and blood parameters of feedlot cattle.

This study was designed to assess the impacts of a mixture of deoxynivalenol (DON) and ergot alkaloids (EAs) on growth performance, rumen function, blood parameters, and carcass traits of feedlot cattle. Forty steers (450 ± 6.0 kg) were stratified by weight and randomly allocated to 1 of 4 treatments; control-low (CON-L), control-high (CON-H) which contained low or high wheat screenings that lacked mycotoxins at the same level as the mycotoxin-low (MYC-L; 5.0 mg/kg DON, 2.1 mg/kg EA), and mycotoxin-high (MYC-H: 10 mg/kg DON, 4.2 mg/kg EA) diets that included wheat screening with mycotoxins. Steers were housed in individual pens for a 112-day finishing trial. Intake was 24.8% lower (P < 0.001) for MYC steers compared to CON steers. As a result, average daily gains of MYC steers were 42.1% lower (P < 0.001) than CON steers. Gain to feed ratio was also lower (P < 0.001) for MYC steers compared to CON steers. Platelets, alanine aminotransferase, globulins, and blood urea nitrogen were lower (P ≤ 0.008), and lymphocytes, glutathione peroxidase activity (GPx), and interleukin-10 (IL-10) were elevated (P ≤ 0.002) in MYC steers compared to CON steers. Hot carcass weights and backfat thickness were reduced (P < 0.001) in MYC steers, resulting in leaner (P < 0.001) carcasses and higher (P < 0.007) meat yield compared to CON steers. Results suggest that a mixture of DON and EAs negatively impacted health, performance, and carcass traits of feedlot steers, with the majority of this response likely attributable to EAs. However, more research is needed to distinguish the relative contribution of each mycotoxin to the specific responses observed.

[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.

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.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency.

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

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.

Assessment of microRNA profiles in small extracellular vesicles isolated from bovine colostrum with different immunoglobulin G concentrations.

The consumption of bovine colostrum by newborn calves during the first days of life is essential to ensure the transfer of passive immunity. In addition to critical IgG, colostrum also contains non-IgG biomolecules, including microRNA (miRNA). The present study investigated the profiles of miRNA in small extracellular vesicles (sEV) isolated from bovine colostrum with high (256.5 ± 5.7 mg/mL, mean ± standard deviation, n = 4) and low (62.8 ± 3.6 mg/mL, n = 4) concentrations of IgG. Different combination of sEV extraction methods and bioinformatic pipelines (miRDeep2 and sRNAbench) for miRNA analysis were evaluated. Results showed that miRCURY exosome Cell/Urine/CSF and miRNeasy Mini kits yielded the highest RNA concentration. The miRNA-seq data analysis showed miRDeep2 yielded more comprehensive miRNAome compared with sRNAbench (527 versus 392 unique miRNA), whereas 389 shared miRNA were identified using both approaches. The profiles of top 50 miRNA were the same using both approaches, and their abundance contributed to 91.7% and 94.3% of total abundance of miRNA using miRDeep2 and sRNAbennch, respectively. These core miRNA were predicted to target 2,655 genes, which regulate 78 KEGG (Kyoto Encyclopedia of Genes and Genomes) level-3 pathways including PI3K-Akt and MAPK signaling pathway, axon guidance, and focal adhesion. The expression profiles of sEV-associated miRNA were similar between high- and low-IgG colostrum samples, despite the fact that the abundance of miR-27a-3p was higher in colostrum with high concentrations of IgG. In conclusion, a core miRNAome in bovine colostrum may play a role in regulating health and developmental stages in neonatal calves, independent of IgG concentration.

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.

Effects of medium-chain fatty acid supplementation on performance and rumen fermentation of lactating Holstein dairy cows.

Medium-chain fatty acids (MCFAs) have antimicrobial properties and cause negative or positive effects on animal performance depending on its dosage. We hypothesized that MCFA supplementation at a lower dose (i.e., 0.05-0.2% of dietary DM) would increase rumen pH and milk production without decreasing nutrient digestibility which is typically observed with the higher inclusion rates (i.e., >1% of dietary DM). The objective of this study was to evaluate the effects of MCFA supplementation at a lower dose on productivity, plasma energy metabolite concentrations, apparent total tract nutrient digestibility, rumen fermentation, and rumen microbial profile of lactating dairy cows. Thirty (n = 8 primiparous, n = 22 multiparous) Holstein cows in mid-lactation (637 ± 68.5 kg of initial BW, 98.5 ± 27.4 d in milk; mean ± standard deviation) were used in a crossover design with two 28-d periods. The MCFA supplement, consisted of 25% MCFA (containing 32% C8:0, 21% C10:0, 47% C12:0 on DM basis) and 75% carrier ingredients, was fed at 0.25% of dietary DM replacing dry ground corn in control (CON). Total inclusion of MCFA was 0.063% of dietary DM. No differences were observed in DM intake, apparent total tract nutrient digestibility and BW change between MCFA and CON. Milk and milk component yields did not differ between treatment groups. The MCFA supplementation tended to have higher minimum rumen pH (5.66 vs. 5.54), and decreased daily fluctuation range of rumen pH (1.17 vs. 1.40) compared to CON. However, the duration of acidosis (pH < 5.8, min/d) did not differ between treatment groups and ruminal total volatile fatty acid concentration and its profile did not differ between treatment groups. For rumen microbiota, the Chao1 index of bacterial community tended to be lower (10.9 vs. 11.6) whereas the Shannon index did not differ (0.91 vs. 0.93) in MCFA compared to CON, and both indices did not differ for archaeal and protozoan communities between treatment groups. The relative abundance of Methanobrevibacter gottschalkii increased when supplemented with MCFA (5.14 vs. 4.92%). These results suggest that supplementation of MCFA at 0.063% dietary DM may not affect overall animal performance or total tract nutrient digestibility, but decrease the daily range of pH and the bacterial richness in the rumen.

[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.

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.

Association between fecal methanogen species with methane production and grazed forage intake of beef heifers classified for residual feed intake under drylot conditions.

Reduction in greenhouse gas emission from beef production is essential to the survival of the beef industry from environmental and social-economic perspectives. There are different systems available to measure methane from animals, but they are expensive, not easily accessible, and not suitable for large-scale methane measurements on the farm. Therefore exploring indicator traits, which are easy to measure, cost-effective, and suitable for large-scale measurement, are recommended. The objectives of this study were to examine the diversity of fecal methanogen profile among efficient and inefficient beef heifers on pasture and investigate methanogen profile as a possible proxy to predict methane emission in beef cattle consuming a forage diet. Forty pregnant (1st trimester) heifers previously classified for postweaning residual feed intake adjusted for off-test back fat (RFIfat; 20 high and 20 low) were included in this study. To determine individual pasture grazing intake, heifers were dosed with 1 kg of C32 labeled pellets once per day from Day 0 to Day 12, and fecal samples were collected twice daily from Day 8 to Day 15. Fecal samples from Days 8, 10, and 12 were analyzed for their methanogen profile. Animals were monitored individually for methane and carbon dioxide production using a GreenFeed Emissions Monitoring system. Total methanogen population and methanogenic community diversity of fecal samples were not different (P > 0.1) between low and high RFIfat groups, as measured by quantitative PCR and α- and ß-diversity indices. However, both groups had a different methanogen profile; the relative abundance of Methanobrevibacter wolinii and relatives were higher (P < 0.002), while that of Methanosphaera species ISO3-F5 was lower (P < 0.01) in low RFIfat cattle compared to the high RFIfat group. We also demonstrated that fecal methanogen profiles may be a useful proxy in predicting daily methane and carbon dioxide emissions with an adjusted R2 of 0.53 and 0.33, respectively, for low RFIfat heifers and 0.46 and 0.57, respectively, for the high RFIfat group.

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.

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.

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.

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.