Milk microbiome in the first month of lactation and at weaning from ewes supplemented with zinc pre- and postpartum.

Mastitis is an important disease with economic and welfare implications in both clinical and subclinical states. The aim of this research was to sequence the hypervariable V4 region of the 16S rRNA gene to describe the microbial diversity and taxonomy of milk from clinically healthy ewes (Rambouillet, WF = 9; Hampshire, BF = 5). Experimental ewes represented a subset of a larger study assessing the impacts of divergent dietary zinc (Zn) concentrations [1 × National Academics of Sciences, Engineering, and Medicine (NASEM) recommendations = CON or 3 × NASEM recommendations = ZnTRT] throughout late gestation and lactation. Milk was collected at four periods during early lactation (18 to 24 h, 7 d, 14 d, and 21 d postpartum) and at weaning (84 ±â€…14 d postpartum). Somatic cell counts (SCC) were quantified, averaged, and classed (low: < 500 × 103; medium: 500 × 103 - 100 × 104; high: > 100 × 104 cells/mL). Milk samples (n = 67) were sequenced to identify bacteria and archaea; the most abundant phyla were Actinobacteria, Bacteroidetes, Cyanobacteria, Euryarchaeota, Firmicutes, Fusobacteria, Lentisphaerae, Proteobacteria, Spirochaetes, Tenericutes, Saccharibacteria TM7, and Verrucomicrobia. Mastitis pathogens were among the most relatively abundant genera, including Staphylococcus, Mannheimia, Corynebacterium, and Pseudomonas. Effects of breed, dietary Zn concentration, SCC class, and their two-way interactions on milk microbiome diversity and taxonomy were assessed within early lactation (using a repeated measures model) and weaning samples. Alpha-diversity metrics included Pielou's evenness, Faith's phylogenetic diversity, and Shannon's entropy indices. The main and interactive effects between Zn treatment, breed, SCC class, and period were variable in early lactation and not evident in weaning samples. Milk from BF ewes had increased Faith's phylogenetic diversity and Shannon's entropy, and differed in unweighted UniFrac composition (P ≤ 0.10). Milk from CON ewes had a reduced rate of composition change through early lactation (P = 0.02) indicating greater microbiome stability than ZnTRT ewe milk. These results support that milk is not sterile, and breed, dietary Zn concentration, and SCC class variably affect the milk microbiome. Findings from the current study provide important foundational insights into the effects of increased dietary Zn supplementation on longitudinal changes in the milk microbiome and associations with mammary gland health and mastitis.

Mastitis is an important disease with economic and welfare implications in both clinical and subclinical states. This research described the microbial diversity and taxonomy of milk collected from clinically healthy Rambouillet (WF; n = 9) and Hampshire (BF; n = 5) primiparous ewes in a longitudinal study involving differing dietary zinc concentrations [1 × National Academics of Sciences, Engineering, and Medicine (NASEM) recommendations, CON; 3 × NASEM recommendations, ZnTRT]. Milk was collected weekly during the first 3 wk of lactation and at weaning, and somatic cell counts (SCC) were classed (low, medium, high). Mastitis pathogens were among the most relatively abundant via amplicon sequencing, including Staphylococcus, Mannheimia, Corynebacterium, and Pseudomonas. Breed, zinc treatment, and SCC class effects on milk microbiome α-diversity and ß-diversity changes and taxonomy were assessed. These effects and their two-way interactions were limited but variable in early lactation samples and not evident in weaning samples. Notably, BF ewe milk samples had increased Faith's phylogenetic diversity and increased Shannon's entropy during early lactation, and CON ewe milk samples had a reduced rate of compositional change than ZnTRT samples. These results support the existence of a milk microbiome that is variably affected by breed, increased dietary zinc concentrations, and SCC class.

Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake.

The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 (n = 16) were selected for high and low RFI. Jejunum mucosal tissue was obtained for RNA-seq. Thirty-two genes were differentially expressed (PFDR≤0.15), and five were over-represented in pathways including inflammatory mediator, cholecystokinin receptor (CCKR) signaling, and p38 MAPK pathways. Several differentially expressed genes (ALOX12, ALPI, FABP6, FABP7, FLT1, GSTA2, MEF2B, PDK4, SPP1, and TTF2) have been previously associated with RFI in other studies. Real-time qPCR was used to validate nine differentially expressed genes in the Year 1 steers used for RNA-seq, and in the Year 2 validation cohort. Six genes were validated as differentially expressed (P < 0.1) using RT-qPCR in the Year 1 population. In the Year 2 population, five genes displayed the same direction of expression as the Year 1 population and 3 were differentially expressed (P < 0.1). The CCKR pathway is involved in digestion, appetite control, and regulation of body weight making it a compelling candidate for feed efficiency in cattle, and the validation of these genes in a second population of cattle is suggestive of a role in feed efficiency.

Calf rumen microbiome from birth to weaning and shared microbial properties to the maternal rumen microbiome.

Optimization of host performance in cattle may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that there exists a shared microbial profile between the cow and calf rumen microbiomes from birth through weaning. Specifically, our objective was to relate the calf's meconium and rumen fluid microbiomes in early life to that of the cow rumen fluid prior to parturition and at weaning. Rumen fluid was collected from multiparous Angus crossbred cows (n = 10) prior to parturition and at weaning. Immediately following the parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again from the calf on day 2, day 28, and at weaning. The rumen fluid microbial profile and subsequent volatile fatty acid (VFA) profile were characterized using 16S rRNA sequencing and gas liquid chromatography, respectively. Microbial data was analyzed using QIIME2 and the GLM procedure of SAS was used to analyze the VFA profile. Alpha diversity was similar in the early gut microbiome (meconium, rumen fluid at birth and day 2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition, determined by beta diversity, differed in the early rumen microbiome (rumen fluid at birth, day 2, and day 28; q ≤ 0.04), and VFA profiles complimented these results. There were similarities in composition between meconium, rumen fluid at birth, and rumen fluid from the cow at weaning (q ≥ 0.09). These data indicate successive development of the rumen microbiome and stabilization over time. Similarities between meconium and rumen fluid at birth potentially indicates in utero colonization of the calf gastrointestinal tract. Similarities in composition between the early calf rumen microbiome and the cow at weaning prompt an interesting comparison and area for future consideration in terms of identifying at what stage of gestation might colonization begin. Overall, this study provides insight into similarities between the cow and calf microbiomes and may be helpful in developing hypotheses for the pathway of colonization and programming potential in the early gut.

Developmental programming has highlighted important influences of maternal factors on offspring development. Recent research indicates a programming potential of the rumen microbiome and understanding this role as well as how inoculation occurs may allow beef producers to optimize management practices of gestating cows such that offspring performance is improved via the rumen microbiome. To investigate this, rumen fluid samples were collected from mature cows immediately prior to calving, from their calf immediately after calving with a meconium sample, day 2, and day 28 as well as collected from both dam and calf at weaning. The rumen and meconium microbiome of the newborn calf were similar to each other as well as to the cow rumen microbiome at weaning, although not to the cow rumen microbiome immediately prior to calving. The shared microbiome of the early calf gut highlight a common source of inoculation. The similarities with the cow rumen at weaning could indicate initiation of colonization occurs early in gestation. Results indicate there are shared microbial properties between the cow and calf rumen microbiome. This further supports the opportunity to alter the calf rumen microbiome to improve productivity through the management of the cow during gestation.

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers.

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging. The purpose of this study was to perform a meta-analysis of the ruminal transcriptome of two unrelated populations of animals to identify genes that are involved in feed efficiency across populations. RNA-seq data from animals with high and low residual feed intake (RFI) from a United States population of cattle (eight high and eight low RFI) and a Canadian population of cattle (nine high and nine low RFI) were analyzed for differences in gene expression. A total of 83 differentially expressed genes were identified. Some of these genes have been previously identified in other feed efficiency studies. These genes included ATP6AP1, BAG6, RHOG, and YPEL3. Differentially expressed genes involved in the Notch signaling pathway and in protein turnover were also identified. This study, combining two unrelated populations of cattle in a meta-analysis, produced several candidate genes for feed efficiency that may be more robust indicators of feed efficiency than those identified from single populations of animals.

Effects of management strategies during early lactation and weaning on etiological agents of ovine subclinical mastitis and antimicrobial susceptibility of milk-derived bacterial isolates.

Subclinical mastitis is a common intramammary disease in sheep production systems. Expenses associated with compromised animal performance, therapeutic interventions, and decreased ewe longevity make efforts to minimize its prevalence worthwhile. The objectives of this study were to 1) quantify the prevalence of subclinical mastitis throughout lactation, 2) evaluate the impact of bedding treatments on subclinical mastitis during early lactation, 3) evaluate the efficacy of prophylaxis and feed restriction during weaning on subclinical mastitis cure rates, and 4) identify levels and types of antimicrobial resistance in milk-derived bacteria. Ewe milk samples were collected at days 1, 2, and 28 post-partum, weaning, and 3-d post-weaning for bacterial identification via culture-based methods. Staphylococcus spp. and Streptococcus spp. isolates were subjected to in vitro antimicrobial susceptibility testing. The overall prevalence of subclinical mastitis defined by culture growth ranged between 22% and 66% and differences were observed between post-weaning and days 1 and 28 milk samples. Commonly isolated bacteria include coagulase-negative staphylococci (CoNS; 59%), Bacillus spp. (35%), Mannheimia haemolytica (10%), Staphylococcus aureus (8%), Streptococcus spp. (5%), and Corynebacterium spp. (5%). Early milk samples (days 1 and 2) were compared between jug bedding treatment: jugs were recently vacated, cleaned, and dusted with barn lime before adding fresh straw (CLEAN) or jugs were previously vacated and fresh straw was added atop soiled bedding (SOILED). Jug bedding treatment did not affect the prevalence of subclinical mastitis, though CoNS had greater sulfadimethoxine resistance in SOILED isolates than CLEAN isolates (P = 0.03). Three different weaning treatments were used: ewes were injected with penicillin at weaning (PENN), ewes had restricted feed access 48 h prior to and 72 h post-weaning (FAST), or a combination of these treatments (COMBO). Weaning treatment did not affect the prevalence of subclinical mastitis or cure rate from weaning to 3-d post-weaning, though all PENN and no FAST milk S. aureus isolates were resistant against tetracycline (P = 0.08). Subclinical mastitis prevalence tended to decrease from weaning to post-weaning (P = 0.08). These data show that subclinical mastitis is common throughout lactation and the levels of antimicrobial resistance of bacteria isolated from ewe milk are generally low against commonly used antimicrobials.

Subclinical mastitis is a common intramammary disease in livestock. Expenses associated with compromised animal performance, therapeutic interventions, and decreased ewe longevity make minimizing its prevalence worthwhile. The objectives of this study were to quantify the prevalence of subclinical mastitis, evaluate the impact of bedding treatments on subclinical mastitis, evaluate the efficacy of weaning treatments, and identify levels of antimicrobial resistance in milk-derived bacteria. The overall prevalence of subclinical mastitis was 45%. Common bacteria included coagulase-negative staphylococci (CoNS), Bacillus spp., Mannheimia haemolytica, Staphylococcus aureus, Corynebacterium spp., and Streptococcus spp. Early lactation milk samples were compared between jug bedding treatments: jugs were cleaned before adding fresh straw (CLEAN) or jugs had fresh straw added atop soiled bedding (SOILED). Jug bedding treatment did not affect the prevalence of subclinical mastitis, though did affect CoNS resistance to sulfadimethoxine. Three different weaning treatments were used: ewes were administered penicillin at weaning, ewes had restricted feed access at weaning, or a combination of the two treatments. Weaning treatment did not affect the prevalence of subclinical mastitis, though subclinical mastitis prevalence decreased post-weaning. Our data show that subclinical mastitis is generally prevalent throughout lactation, and the levels of antimicrobial resistance of bacteria isolated from ewe milk are generally low.

Comparing the maternal-fetal microbiome of humans and cattle: a translational assessment of the reproductive, placental, and fetal gut microbiomes.

Despite differences in gut physiology and morphology, both humans and cattle require a functional gut microbiome in early life. Evidence suggests that both species acquire gut microbes prior to birth, likely from a maternal source, indicating the use of similar mechanisms and timing for fetal gut colonization. Unlike mouse models, cattle share a similar gestation length, parity, and placental microbiome characteristics to humans. The large size of calves allow for contamination-protected sampling of the gut, vagina, and uterus, which would typically require invasive procedures in human cohorts. The ruminant placenta also exhibits a larger degree of separation between maternal and fetal physiology, necessitating a direct and explicit route by which microbes may access the fetal gut. These and other features permit cattle to act as a translational model for early gut colonization. However, cattle do not share similar placental morphology, gut function, or early immune system interactions with humans, creating barriers to their use as a biomedical model. Identifying similarities and differences between humans and cattle may outline the most important functions of the placental and fetal gut microbiomes, indicate the source of these microbes, and highlight the role of maternal or environmental influences upon fetal health across species.

Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation.

OBJECTIVE: Realimentation can compensate for weight loss from poor-quality feedstuffs or drought. Mature cows fluctuate in body weight throughout the year due to nutrient availability. The objective of this study was to determine whether cows that differ in weight gain during realimentation also differ in the abundance of transcripts for enzymes associated with energy utilization in skeletal muscle. Mature cows were subjected to feed restriction followed by ad libitum feed. Skeletal muscle transcriptome expression differences during the two feeding periods were determined from cows with greater (n = 6) and less (n = 6) weight gain during the ad libitum feeding period. RESULTS: A total of 567 differentially expressed genes (408 up- and 159 down-regulated) were identified for the comparison of restriction and ad libitum periods (PBonferroni < 0.05). These genes were over-represented in lysosome, aminoacyl-tRNA biosynthesis, and glutathione metabolism pathways. Validation of the expression of five of the genes was performed and four were confirmed. These data suggest that realimentation weight gain for all cows is partially controlled by protein turnover, but oxidative stress and cellular signaling pathways are also involved in the muscle tissue. This dataset provides insight into molecular mechanisms utilized by mature cows during realimentation after a period of low abundance feed.

Gene expression signatures in motor neurone disease fibroblasts reveal dysregulation of metabolism, hypoxia-response and RNA processing functions.

AIMS: Amyotrophic lateral sclerosis (ALS) and primary lateral sclerosis (PLS) are two syndromic variants within the motor neurone disease spectrum. As PLS and most ALS cases are sporadic (SALS), this limits the availability of cellular models for investigating pathogenic mechanisms and therapeutic targets. The aim of this study was to use gene expression profiling to evaluate fibroblasts as cellular models for SALS and PLS, to establish whether dysregulated biological processes recapitulate those seen in the central nervous system and to elucidate pathways that distinguish the clinically defined variants of SALS and PLS. METHODS: Microarray analysis was performed on fibroblast RNA and differentially expressed genes identified. Genes in enriched biological pathways were validated by quantitative PCR and functional assays performed to establish the effect of altered RNA levels on the cellular processes. RESULTS: Gene expression profiling demonstrated that whilst there were many differentially expressed genes in common between SALS and PLS fibroblasts, there were many more expressed specifically in the SALS fibroblasts, including those involved in RNA processing and the stress response. Functional analysis of the fibroblasts confirmed a significant decrease in miRNA production and a reduced response to hypoxia in SALS fibroblasts. Furthermore, metabolic gene changes seen in SALS, many of which were also evident in PLS fibroblasts, resulted in dysfunctional cellular respiration. CONCLUSIONS: The data demonstrate that fibroblasts can act as cellular models for ALS and PLS, by establishing the transcriptional changes in known pathogenic pathways that confer subsequent functional effects and potentially highlight targets for therapeutic intervention.

Novel FUS/TLS mutations and pathology in familial and sporadic amyotrophic lateral sclerosis.

OBJECTIVE: To determine the frequency of and clinicopathologic phenotypes associated with FUS/TLS mutations in a large cohort of amyotrophic lateral sclerosis (ALS) cases from the north of England. DESIGN: Genetic screening project with neuropathologic examination of postmortem tissue in selected cases. The clinical details of selected cases are also presented. SETTING: Neurology departments of 2 university teaching hospitals in the north of England. PARTICIPANTS: The 15 exons of FUS/TLS were sequenced in an initial cohort of 42 familial ALS (FALS) and 117 sporadic ALS (SALS) cases. Exons 14 and 15 were subsequently screened in a larger cohort of 431 SALS cases. Regions mutated in ALS cases were also screened in 293 controls. MAIN OUTCOME MEASURE: Evaluation of gene-sequencing chromatographs and detailed histopathologic analysis of the central nervous system. RESULTS: Four heterozygous mutations, 1 of which is novel, were identified in 6 patients with ALS (4 with FALS and 2 with SALS). Two of the substitutions were not found to be present in controls, and neuropathology in these cases revealed neuronal and/or glial cytoplasmic inclusions positive for the FUS/TLS protein. One of these cases is also the first reported SALS case with an FUS/TLS mutation. The other 2 substitutions identified were also identified in control cases. Neuropathology in these cases revealed typical SALS pathology, suggesting that they are likely to represent benign polymorphisms. CONCLUSIONS: FUS/TLS mutations represented approximately 5% of FALS cases screened. A FUS/TLS mutation was also identified in a single SALS case. Subsequent screening of this region in a larger cohort of SALS cases, however, did not reveal any additional mutations.

Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS).

BACKGROUND: Amyotrophic lateral sclerosis (ALS), a common late-onset neurodegenerative disease, is associated with fronto-temporal dementia (FTD) in 3-10% of patients. A mutation in CHMP2B was recently identified in a Danish pedigree with autosomal dominant FTD. Subsequently, two unrelated patients with familial ALS, one of whom also showed features of FTD, were shown to carry missense mutations in CHMP2B. The initial aim of this study was to determine whether mutations in CHMP2B contribute more broadly to ALS pathogenesis. METHODOLOGY/PRINCIPAL FINDINGS: Sequencing of CHMP2B in 433 ALS cases from the North of England identified 4 cases carrying 3 missense mutations, including one novel mutation, p.Thr104Asn, none of which were present in 500 neurologically normal controls. Analysis of clinical and neuropathological data of these 4 cases showed a phenotype consistent with the lower motor neuron predominant (progressive muscular atrophy (PMA)) variant of ALS. Only one had a recognised family history of ALS and none had clinically apparent dementia. Microarray analysis of motor neurons from CHMP2B cases, compared to controls, showed a distinct gene expression signature with significant differential expression predicting disassembly of cell structure; increased calcium concentration in the ER lumen; decrease in the availability of ATP; down-regulation of the classical and p38 MAPK signalling pathways, reduction in autophagy initiation and a global repression of translation. Transfection of mutant CHMP2B into HEK-293 and COS-7 cells resulted in the formation of large cytoplasmic vacuoles, aberrant lysosomal localisation demonstrated by CD63 staining and impairment of autophagy indicated by increased levels of LC3-II protein. These changes were absent in control cells transfected with wild-type CHMP2B. CONCLUSIONS/SIGNIFICANCE: We conclude that in a population drawn from North of England pathogenic CHMP2B mutations are found in approximately 1% of cases of ALS and 10% of those with lower motor neuron predominant ALS. We provide a body of evidence indicating the likely pathogenicity of the reported gene alterations. However, absolute confirmation of pathogenicity requires further evidence, including documentation of familial transmission in ALS pedigrees which might be most fruitfully explored in cases with a LMN predominant phenotype.

Broad clinical phenotypes associated with TAR-DNA binding protein (TARDBP) mutations in amyotrophic lateral sclerosis.

The finding of TDP-43 as a major component of ubiquitinated protein inclusions in amyotrophic lateral sclerosis (ALS) has led to the identification of 30 mutations in the transactive response-DNA binding protein (TARDBP) gene, encoding TDP-43. All but one are in exon 6, which encodes the glycine-rich domain. The aim of this study was to determine the frequency of TARDBP mutations in a large cohort of motor neurone disease patients from Northern England (42 non-superoxide dismutase 1 (SOD1) familial ALS (FALS), nine ALS-frontotemporal dementia, 474 sporadic ALS (SALS), 45 progressive muscular atrophy cases). We identified four mutations, two of which were novel, in two familial (FALS) and two sporadic (SALS) cases, giving a frequency of TARDBP mutations in non-SOD1 FALS of 5% and SALS of 0.4%. Analysis of clinical data identified that patients had typical ALS, with limb or bulbar onset, and showed considerable variation in age of onset and rapidity of disease course. However, all cases had an absence of clinically overt cognitive dysfunction.