Different milk diets have substantial effects on the jejunal mucosal immune system of pre-weaning calves, as demonstrated by whole transcriptome sequencing

Using the conditioned place preference paradigm to assess hunger in dairy calves: Preliminary results and methodological issues

Dairy calves are typically fed restricted amounts of milk. Although feed restrictions are predicted to result in negative affective states, the relative aversiveness of 'hunger' remains largely unexplored in this species. Here, we investigated whether the conditioned place preference paradigm can be used to explore how calves feel when experiencing different levels of satiation. This paradigm provides insight into what animals remember from past experiences, the assumption being that individuals will prefer places associated with more pleasant or less unpleasant experiences. Sixteen Holstein calves were either fed a restricted (3 L per meal totalling 6 L per day) or 'enhanced' milk allowance (ad libitum up to 6 L per meal totalling up to 12 L per day) in their home-pen. Calves were then placed in a conditioning pen for 4 h immediately after being fed their morning meal to allow them to develop an association between the pen and their state of post-prandial satiation. Calves were conditioned across four days with their satiation state alternating between days to allow them to develop an association between pen and satiation levels. On the 5th day, calves were individually allowed to roam freely between the two pens for 30 min. We expected that calves would prefer the pen where they previously experienced higher levels of satiation, but our results show no to limited effects of treatment. However, some methodological issues (colour and side bias) prevent us from drawing strong conclusions. We discuss reasons for these issues and potential solutions to avoid these in future studies.

Dairy farmer and farm staff attitudes and perceptions regarding daily milk allowance to calves

The benefits of feeding calves more milk are increasingly being recognized by dairy farmers. However, most producers have still not implemented higher feeding plans. The aim of the present study was to gain a deeper understanding of farmer and farm staff attitudes, and the perceptions and factors considered in their decision-making regarding daily milk allowances. We collected data through focus group interviews with dairy farmers, farm managers, and calf-care workers who were selected using purposive and snowball sampling. In total, 40 persons (24 women and 16 men) joined a focus group interview (6 in all, each with 5-8 participants). Interviews were recorded, and recordings were transcribed and analyzed thematically. Participants had contrasting opinions about the minimum, maximum, and recommended daily milk allowances to their calves. Their suggested lowest daily milk allowance to sustain animal welfare ranged from 4 to 8-10 L and the maximum allowance from 6 to 15 L. We found that farmers' and farm staff's choices and recommendations of milk-feeding protocols were influenced by a large number of factors that could be grouped into 4 themes: (1) Life beyond work, (2) Farm facilities and equipment, (3) Care of the calves, and (4) Profitability and production. Participants' considerations were similar and aimed to maximize daily milk allowance based on farm conditions. However, the allowances they described as optimal for their calves often differed from what they considered practically feasible. We found that the care of the calves and the well-being of the owners and the staff was central in the participants' decision-making, but that this care perspective was challenged by the social and economic sustainability of the farm. Most participants fed their calves twice daily and did not think that increasing that number would be practically feasible. Our results indicate that the participants' viewpoints regarding calves were important for their decision-making about milk allowances. We suggest that a more holistic perspective should be used when advising farmers about milk allowances, putting particular emphasis on the caring and social sustainability aspects of the individual farm.

Effect of ad libitum feeding of Holstein Friesian calves on immunological parameters and molecular stress on a transcriptional level

Our aim was to compare the health and performance of ad libitum (ADLIB) and restrictedly fed Holstein Friesian heifer calves. Calves were selected to ADLIB (n = 13) and control (n = 13) groups randomly. The period of ADLIB feeding lasted for 3 weeks after colostrum supplementation. The calves in the control group received the same milk replacer, which was supplied according to the restrained feeding schedule of the farm. There was no difference between the two groups in weight, weight gain or movement activity, furthermore in the values of glucose, albumin, total protein, BHB, AST, oxidant and antioxidant status incl. dROM, PAT and OSI. The IL8 gene had higher levels (non significant, p > 0.05) of expression in the ADLIB group during the first 20 days of life, which indicates that ADLIB feeding might potentiate a stronger immune response to environmental stress. The IGF1 gene showed increased expression in the ADLIB fed group at almost all time points, however the difference was already detected on the first day of the study, indicating the importance of individual differences even within the same breed. During the first 10 days INS expression was higher in the restricted group, followed by a shift by day 20 and after, when the ADLIB group showed a higher relative expression level. The observed values describe a trend that, although not significant (p > 0.05), would seem to indicate that ADLIB feeding might potentiate a stronger immune response to environmental stress.

Effects of rumen cannulation combined with different pre-weaning feeding intensities on the intestinal, splenic and thymic immune system in heifer calves several month after surgery

Fistulation is a helpful procedure in animal nutritional research and also common practise in human medicine. However, there are indications that alterations in the upper gastrointestinal tract contribute to intestinal immune modulations. The present study aimed to investigate effects of a rumen cannulation in week 3 of life on the intestinal and tissue specific immune system of 34-week old heifers. Nutrition influences the development of the neonatal intestinal immune system to a high extent. Therefore, rumen cannulation was investigated in combination with different pre-weaning milk feeding intensities (20% (20MR) vs. 10% milk replacer feeding (10MR). Heifers of 20MR without rumen cannula (NRC) showed higher cluster of differentiation (CD)8⁺ T cell subsets in mesenteric lymph nodes (MSL) compared to heifers with rumen cannula (RC) and 10MRNRC heifers. CD4⁺ T cell subsets in jejunal intraepithelial lymphocytes (IELs) were higher in 10MRNRC heifers compared to 10MRRC heifers. CD4⁺ T cell subsets in ileal IELs were lower and CD21⁺ B cell subsets were higher in NRC heifers compared to RC heifers. CD8⁺ T cell subsets in spleen tended to be lower in 20MRNRC heifers compared to all other groups. Splenic CD21⁺ B cell subsets were higher in 20MRNRC heifers compared to RC heifers. Splenic toll like receptor (TLR) 6 expression was increased and IL4 expression tended to be increased in RC heifers than NRC heifers. Splenic TLR2, 3 and 10 gene expression was higher in 20MR compared to 10MR heifers. Jejunal prostaglandin endoperoxide synthase 2 expression was higher in RC heifers than NRC heifers, and MUC2 expression tended to increase in 20MR heifers compared to 10MR heifers. In conclusion, rumen cannulation modulated T and B cell subsets in the down streaming gastrointestinal tract and spleen. Pre-weaning feeding intensity seemed to affect intestinal mucin secretion and T and B cell subsets in MSL, spleen and thymus until several month later. Interestingly, in MSL, spleen and thymus the 10MR feeding regime evoked similar modulations of T and B cell subsets like rumen cannulation.

Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion

The insertion of an endogenous retroviral long terminal repeat (LTR) sequence into the bovine apolipoprotein B (APOB) gene is causal to the inherited genetic defect cholesterol deficiency (CD) observed in neonatal and young calves. Affected calves suffer from developmental abnormalities, symptoms of incurable diarrhoea and often die within weeks to a few months after birth. Neither the detailed effects of the LTR insertion on APOB expression profile nor the specific mode of inheritance nor detailed phenotypic consequences of the mutation are undisputed. In our study, we analysed German Holstein dairy heifers at the peak of hepatic metabolic load and exposed to an additional pathogen challenge for clinical, metabolic and hepatic transcriptome differences between wild type (CDF) and heterozygote carriers of the mutation (CDC). Our data revealed that a divergent allele-biased expression pattern of the APOB gene in heterozygous CDC animals leads to a tenfold higher expression of exons upstream and a decreased expression of exons downstream of the LTR insertion compared to expression levels of CDF animals. This expression pattern could be a result of enhancer activity induced by the LTR insertion, in addition to a previously reported artificial polyadenylation signal. Thus, our data support a regulatory potential of mobile element insertions. With regard to the phenotype generated by the LTR insertion, heterozygote CDC carriers display significantly differential hepatic expression of genes involved in cholesterol biosynthesis and lipid metabolism. Phenotypically, CDC carriers show a significantly affected lipomobilization compared to wild type animals. These results reject a completely recessive mode of inheritance for the CD defect, which should be considered for selection decisions in the affected population. Exemplarily, our results illustrate the regulatory impact of mobile element insertions not only on specific host target gene expression but also on global transcriptome profiles with subsequent biological, functional and phenotypic consequences in a natural in-vivo model of a non-model mammalian organism.

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.

Dynamic progression of the calf's microbiome and its influence on host health

The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.

Review: Importance of colostrum supply and milk feeding intensity on gastrointestinal and systemic development in calves

Feeding management of the postnatal and preweaning calf has an important impact on calf growth and development during this critical period and affects the health and well-being of the calves. After birth, an immediate and sufficient colostrum supply is a prerequisite for successful calf rearing. Colostrum provides high amounts of nutrient as well as non-nutrient factors that promote the immune system and intestinal maturation of the calf. The maturation and function of the neonatal intestine enable the calf to digest and absorb the nutrients provided by colostrum and milk. Therefore, colostrum intake supports the start of anabolic processes in several tissues, stimulating postnatal body growth and organ development. After the colostrum feeding period, an intensive milk feeding protocol, that is, at least 20% of BW milk intake/day, is required to realise the calf potential for growth and organ development during the preweaning period. Insufficient milk intake delays postnatal growth and may have detrimental effects on organ development, for example, the intestine and the mammary gland. The somatotropic axis as the main postnatal endocrine regulatory system for body growth is stimulated by the intake of high amounts of colostrum and milk and indicates the promotion of anabolic metabolism in calves. The development of the forestomach is an important issue during the preweaning period in calves, and forestomach maturation is best achieved by solid feed intake. Unfortunately, intensive milk-feeding programmes compromise solid feed intake during the first weeks of life. In the more natural situation for beef calves, when milk and solid feed intake occurs at the same time, calves benefit from the high milk intake as evidenced by enhanced body growth and organ maturation without impaired forestomach development during weaning. To realise an intensive milk-feeding programme, it is recommended that the weaning process should not start too early and that solid feed intake should be at a high extent despite intensive milk feeding. A feeding concept based on intensive milk feeding prevents hunger and abnormal behaviour of the calves and fits the principles of animal welfare during preweaning calf rearing. Studies on milk performance in dairy cows indicate that feeding management during early calf rearing influences lifetime performance. Therefore, an intensive milk-feeding programme affects immediate as well as long-term performance, probably by programming metabolic pathways during the preweaning period.

Effects of ad libitum milk replacer feeding and butyrate supplementation on the epithelial growth and development of the gastrointestinal tract in Holstein calves

Intensive milk feeding and butyrate supplementation in calves stimulate body growth and affect gastrointestinal development. The aim of the present study was to investigate the synergistic effects of ad libitum milk replacer (MR) feeding and butyrate supplementation of MR on rumen and small intestinal growth and on gene expression in the small intestine related to growth and energy metabolism at weaning. Male Holstein calves (n = 32) received colostrum from birth to d 3 of age and MR either ad libitum (Adl) or restrictively (Res; 6 L of MR/d; 12.5% solids) with (AdlB+, ResB+) or without (AdlB-, ResB-) 0.24% butyrate from d 4 until wk 8 of age. From wk 9 to 10, all calves were weaned and were fed 2 L/d until the end of the trial. Concentrate, hay, and water were freely available. At d 80, calves were slaughtered, volatile fatty acids were measured in rumen fluid, and rumen and small intestine samples were taken for histomorphometric measurements. The expression of mRNA associated with the local insulin-like growth factor (IGF) system and glucose metabolism as well as lactase and maltase activities were measured in the intestinal mucosa. The small intestine was 3 m longer in Adl than in Res. In the atrium ruminis, papilla width was greater in Res than in Adl. Villus circumference, cut surface, and height in the duodenum, proximal jejunum, and ileum were greater in Adl than in Res and in the proximal, mid, and distal jejunum and ileum were greater in calves treated with butyrate. Crypt depth in the duodenum and proximal jejunum was greater in Adl than in Res and in the ileum was smaller in calves treated with butyrate. The villus height:crypt depth ratio was greatest in AdlB+ calves. In the proximal and mid jejunum, IGF1 mRNA abundance was lower in calves treated with butyrate. In the proximal jejunum, INSR mRNA abundance was greater in Res than in Adl. The abundance of PCK2 mRNA was greater in Res than in Adl in the duodenum and was greatest in ResB- in the mid jejunum. Lactase activity tended to be greater in Res than in Adl and after butyrate treatment in the proximal jejunum. The results indicated an elevated growth of the small intestinal mucosa at weaning due to intensive milk feeding and butyrate supplementation, and the local IGF system was involved in intestinal growth regulation. Rumen development was not affected by butyrate supplementation of MR and was slightly delayed due to ad libitum MR feeding.

Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue

Background

In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global transcriptome analyses. Therefore, the aim of this study was to develop and evaluate a method to deplete extremely highly expressed transcripts in mRNA from lactating mammary gland tissue.

Results

Selective RNA depletion was performed by hybridization of antisense oligonucleotides targeting genes encoding the caseins (CSN1S1, CSN1S2, CSN2 and CSN3) and whey proteins (LALBA and PAEP) within total RNA followed by RNase H-mediated elimination of the respective transcripts. The effect of the RNA depletion procedure was monitored by RNA sequencing analysis comparing depleted and non-depleted RNA samples from Escherichia coli (E. coli) challenged and non-challenged udder tissue of lactating cows in a proof of principle experiment. Using RNase H-mediated RNA depletion, the ratio of highly abundant milk protein gene transcripts was reduced in all depleted samples by an average of more than 50% compared to the non-depleted samples. Furthermore, the sensitivity for discovering transcripts with marginal expression levels and transcripts not yet annotated was improved. Finally, the sensitivity to detect significantly differentially expressed transcripts between non-challenged and challenged udder tissue was increased without leading to an inadvertent bias in the pathogen challenge-associated biological signaling pathway patterns.

Conclusions

The implementation of selective RNase H-mediated RNA depletion of milk protein gene transcripts from the mammary gland transcriptome of lactating cows will be highly beneficial to establish comprehensive transcript catalogues of the tissue that better reflects its transcriptome complexity.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5781-3) contains supplementary material, which is available to authorized users.

Heat stress directly impairs gut integrity and recruits distinct immune cell populations into the bovine intestine

Consequences of heat stress, particularly for the immune system and the intestinal health of mammals, are a topic of increasing global relevance due to rising temperatures and potential health impairments. Specific climate effects, however, are often difficult to discriminate from indirect consequences, e.g. reduced feed intake. Our study in dairy cattle, which are particularly sensitive to heat, identifies the infiltration of the small intestinal epithelium by a previously unobserved distinct cell population with macrophage-like phenotype in response to moderate heat stress. By using a pair-feeding design, we attributed these effects as direct consequences of heat stress via impaired intestinal barrier function. Therefore, an appropriate gut function is an important component in combating the negative consequences of heat stress.

High ambient temperature has multiple potential effects on the organism such as hyperthermia, endotoxemia, and/or systemic inflammation. However, it is often difficult to discriminate between cause and consequence of phenotypic effects, such as the indirect influence of heat stress via reduced food intake. Lactating dairy cows are a particularly sensitive model to examine the effects of heat stress due to their intensive metabolic heat production and small surface:volume ratio. Results from this model show heat stress directly induced a so-far unknown infiltration of yet uncategorized cells into the mucosa and submucosa of the jejunum. Due to a pair-feeding design, we can exclude this effect being a consequence of the concurrent heat-induced reduction in feed intake. Isolation and characterization of the infiltrating cells using laser capture microdissection and RNA sequencing indicated a myeloic origin and macrophage-like phenotype. Furthermore, targeted transcriptome analyses provided evidence of activated immune- and phagocytosis-related pathways with LPS and cytokines as upstream regulators directly associated with heat stress. Finally, we obtained indication that heat stress may directly alter jejunal tight junction proteins suggesting an impaired intestinal barrier. The penetration of toxic and bacterial compounds during heat stress may have triggered a modulated immune repertoire and induced an antioxidative defense mechanism to maintain homeostasis between commensal bacteria and the jejunal immune system. Our bovine model indicates direct effects of heat stress on the jejunum of mammals already at moderately elevated ambient temperature. These results need to be considered when developing concepts to combat the negative consequences of heat stress.

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression

One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterization of transcription of the entire gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 164 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Using network cluster analysis we illustrate how the complexity of the GI tract is reflected in tissue- and developmental stage-specific differences in gene expression. The most significant transcriptional differences between neonatal and adult sheep were observed in the rumen complex. Comparative analysis of gene expression in three GI tract tissues from age-matched sheep and goats revealed species-specific differences in genes involved in immunity and metabolism. This study improves our understanding of the transcriptomic mechanisms involved in the transition from pre-ruminant to ruminant by identifying key genes involved in immunity, microbe recognition and metabolism. The results form a basis for future studies linking gene expression with microbial colonization of the developing GI tract and provide a foundation to improve ruminant efficiency and productivity through identifying potential targets for novel therapeutics and gene editing.

Nutrient supply alters transcriptome regulation in adipose tissue of pre-weaning Holstein calves

Performance of dairy cows can be influenced by early life nutrient supply. Adipose tissue is diet sensitive and an important component in that process as it is involved in the regulation of energetic, reproductive and immunological functions. However, it is not clear how early life nutrition alters the molecular regulation of adipose tissue in calves and potentially adult individuals. This study aimed at determining how differences in pre-weaning nutrient supply alter gene expression profiles and physiology in omental adipose tissue. A total of 12 female Holstein calves were fed two levels of milk replacer supply: a restricted amount of 11.72 MJ of metabolizable energy (ME) intake per day (n = 6) or an enhanced amount of 1.26 MJ ME intake per kg of metabolic body weight (BW^0.75), resulting in supply from 17.58 to 35.17 MJ ME intake per day (n = 6). All calves had ad libitum access to a commercial calf starter and water. Analysis of the transcriptome profiles at 54 ± 2 days of age revealed that a total of 396 out of 19,968 genes were differentially expressed (DE) between groups (p < 0.001, FDR < 0.1). The directional expression of DE genes through Ingenuity Pathway Analysis showed that an enhanced nutrient supply alters adipose tissue physiology of pre-weaned calves. Several biological functions were increased (Z-score > +2), including Lipid Metabolism (Fatty Acid Metabolism), Cell Cycle (Entry into Interphase, Interphase, Mitosis and Cell Cycle Progression), Cellular Assembly and Organization (Cytoskeleton Formation and Cytoplasm Development) and Molecular Transport (Transport of Carboxylic Acid). These changes were potentially orchestrated by the activation/inhibition of 17 upstream regulators genes. Our findings indicate that adipose tissue of calves under an enhanced nutrient supply is physiologically distinct from restricted calves due to an increased development/expansion rate and also a higher metabolic activity through increased fatty acid metabolism.

Molecular characterisation and risk factor analysis of Cryptosporidium spp. in calves from Italy

To provide up-to-date information on the occurrence of Cryptosporidium in pre-weaned calves from Sardinia (Italy), the species implicated and their zoonotic potential, 147 faecal samples from 22 cattle herds were microscopically examined for Cryptosporidium oocysts; positive isolates were molecularly characterised. A questionnaire was developed to identify risk factors for Cryptosporidium infection. Overall, the percentage of positive calves and farms was 38.8 and 68.2%, respectively. The SSU rRNA-based PCR identified two Cryptosporidium species, Cryptosporidium parvum (95.8%) and C. bovis (4.2%). Sequence analyses of the glycoprotein (gp60) gene revealed that all C. parvum isolates belonged to the subtype family IIa (IIaA15G2R1 and IIaA16G3R1), with the exception of three isolates that belonged to the subtype family IId (IIdA20G1b and IIdA20). Mixed logistic regression results indicated that calves aged 15-21 days were more likely to be Cryptosporidium-positive. The risk of being positive was also significantly higher in herds from Central Sardinia and in farms using non-slatted flooring. In addition, the application of disinfectants and milk replacers was significantly associated with higher Cryptosporidium prevalence. In contrast, the risk of being positive was significantly reduced in halofuginone-treated calves. Our results reveal that a significant percentage of suckling calves are carriers of zoonotic subtypes of C. parvum. Thus, both healthy and diarrhoeic calves younger than 1 month may represent a risk for the transmission of cryptosporidiosis in humans and animals.

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets

Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome.

Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves’ intestinal mucosa.

Nine lncRNA loci were differentially expressed (DE lncRNAs) between both calf groups. To elucidate their biological function, we applied a systems biology approach that combines weighted gene co-expression network analysis with functional enrichment and biological pathway analysis. Four DE lncRNAs were found to be strongly correlated with a gene network module (GNM) enriched for genes from canonical pathways of remodeling of epithelial adherens junction, tight junction and integrin signaling. Another DE lncRNA was strongly correlated with a GNM enriched for genes associated with energy metabolism and maintaining of cellular homeostasis with a focus on mitochondrial processes.

Our data suggest that these DE lncRNAs may play potential regulatory roles in modulating biological processes associated with energy metabolism pathways and cellular signaling processes affecting the barrier function of intestinal epithelial cells of calves in response to different feeding regimens in the pre-weaning period.