Effect of Post-extraction Algal Residue Supplementation on the Therumen Microbiome of Steers Consuming Low-quality Forage

The rumen microbiome is a dynamic environment consisting of bacteria, protist, and fungi responsible for fiber degradation. Advances in molecular techniques have enabled description of bacterial microbiome via pyrosequencing. Cattle consuming low-quality forage are often supplemented with protein to increase forage intake and digestion, but effect on the rumen bacterial community is unknown. Thus, increasing post-extraction algal residue (PEAR) and cottonseed meal (CSM) supplementation was provided to steers consuming oat straw to observe the rumen microbiome within the liquid and solid fraction. Weighted UniFrac analysis indicated different fraction-associated communities with greater similarity across treatments in the solid fraction. Bacteroidetes was the predominant phyla detected in all samples (>65%). Within Bacteroidetes, Prevotella was the most abundant genus. In the liquid fraction, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae increased with PEAR provision (P < 0.05). Similar proportions of bacteria between unsupplemented control and CSM supplemented steers indicate factors other than N supply may impact ruminal bacteria populations. A second experiment evaluated the effect of supplemental CSM or dried distillers’ grain (DDG) for Brahman steers consuming rice straw. Total digestible OM intake and total tract OM digestion increased linearly with additional CSM and DDG provision (P < 0.01). Provision of CSM increased ruminal ammonia linearly (P < 0.01), but DDG supplementation resulted in a quadratic response (P = 0.02). Overall, protein supplementation may increase LQF utilization via changes in the rumen microbiome

Influence of nutrition on the muscle transcriptome and ruminal microbiome in cattle

Beef cattle nutrition research has historically focused on formulating diets to address nutrient requirements of cattle for given level of animal performance. While predictive models account for many factors that may affect nutrient requirements, additional physiological effects can alter the animal's ability to utilize dietary nutrients. Several of these factors include the ruminal microbiome composition and epithelial tissue function, and nutrient provision in utero. The objective of this dissertation was to evaluate the effects of nutrition on these physiological effects to determine their potential to influence nutrient utilization. Supplemental sources of fat, such as condensed distillers solubles (CDS), are often added to the diets of growing cattle to increase the energy density of the diet, but these products may negatively impact rumen bacteria at high inclusion levels. Five ruminally-fistulated steers were used in a 5 × 5 Latin square design to determine the effects of increasing dietary fat and sulfur from (CDS) on the ruminal microbiome. Alpha-diversity and species richness decreased (linear; P 0.10) of feeding increasing dietary fat from CDS on fibroylytic phyla Fibrobacteres in either fraction. Rapid consumption of a highly digestible diet causes rapid fermentation and may lead to the onset of subacute ruminal acidosis (SARA), a condition that negatively impacts the dairy industry by decreasing dry matter intake, milk production, and profitability. Six ruminallyfistulated, lactating Holstein cows were used in a replicated incomplete Latin square design to determine the effects of SARA induction on the ruminal microbiome and epithelium using a SARA induction model. Ruminal contents and epithelial biopsies were collected on d 1 and 6 of each period prior to feeding. Principal coordinate analysis of beta-diversity indicated samples within the liquid fraction separated by day and coincided with an increased relative abundance of genera Prevotella, Ruminococcus, Streptococcus, and Lactobacillus on d 6 (P < 0.06). Phylum Bacteroidetes increased on d 6 (P < 0.01) for SARA cows driven by greater genera Prevotella and YRC22 (P < 0.01). Streptococcus bovis and Succinivibrio dextrinosolvens populations tended to increase on d 6 but were not affected by the severity of acidotic bout. In ruminal epithelium, CLDN1 and CLDN4 expression increased on d 6 (P < 0.03) 24 h after SARA induction, but overall effects on ruminal epithelium were modest. Maternal nutrition provided during mid-gestation may influence skeletal muscle development and long-term metabolism. Three planes of nutrition were provided to cows to address 70% (70%REQ), 100% (REQ), and 130% NRC energy and protein requirements (130%REQ) during mid-gestation. All calf progeny were managed as a single contemporary group and longissimus muscles biopsies were taken on 99, 197, and 392 d of age. The skeletal muscle transcriptome analysis at d 392 indicated over 2,000 co-expressed genes were downregulated in progeny born to 130%REQ-fed compared with REQ-fed dams. These genes were annotated to many lipid-associated pathways including steroid and steroid hormone biosynthesis, sulfur metabolism, retinol metabolism, ketone synthesis and degradation, fat digestion and absorption, and PPAR signaling pathways. Another set of genes (342) was activated in progeny born to 130%REQ-fed compared with 70%REQ-fed dams and correlated negatively with marbling score. These genes were annotated to pathways centered on glycolysis/gluconeogenesis, energy metabolism, and calcium signaling to support increased glycolytic muscle fibers (type 2x) in progeny born to 130%REQ-fed dams. Skeletal muscle miRNA were tightly regulated over time suggesting various roles in postnatal hypertrophy. Maternal plane of nutrition effects (P < 0.1) were observed for miR-376d and miR-381. Results indicate that maternal plane of nutrition has a long-term impact on the skeletal muscle transcriptome and may be linked to effects on meat quality

Polyclonal antibodies inhibit growth of key cellulolytic rumen bacterial species

Antibodies targeting specific bacterial species could allow for modification of the rumen microbial population to enhance rumen fermentation. However, there is limited knowledge of targeted antibody effects on rumen bacteria. Therefore, our objective was to develop efficacious polyclonal antibodies to inhibit the growth of targeted cellulolytic bacteria from the rumen. Egg-derived, polyclonal antibodies were developed against pure cultures of Ruminococcus albus 7 (anti-RA7), Ruminococcus albus 8 (anti-RA8), and Fibrobacter succinogenes S85 (anti-FS85). Antibodies were added to a cellobiose-containing growth medium for each of the three targeted species. Antibody efficacy was determined via inoculation time (0 h and 4 h) and dose response. Antibody doses included: 0 (CON), 1.3 × 10−4 (LO), 0.013 (MD), and 1.3 (HI) mg antibody per ml of medium. Each targeted species inoculated at 0 h with HI of their respective antibody had decreased (P &lt; 0.01) final optical density and total acetate concentration after a 52 h growth period when compared with CON or LO. Live/dead stains of R. albus 7 and F. succinogenes S85 dosed at 0 h with HI of their respective antibody indicated a decrease (≥ 96%; P &lt; 0.05) in live bacterial cells during the mid-log phase compared with CON or LO. Addition of HI of anti-FS85 at 0 h in F. succinogenes S85 cultures reduced (P &lt; 0.01) total substrate disappearance over 52 h by at least 48% when compared with CON or LO. Cross-reactivity was assessed by adding HI at 0 h to non-targeted bacterial species. Addition of anti-RA8 or anti-RA7 to F. succinogenes S85 cultures did not affect (P ≥ 0.45) total acetate accumulation after 52 h incubation, indicating that antibodies have less of an inhibitory effect on non-target strains. Addition of anti-FS85 to non-cellulolytic strains did not affect (P ≥ 0.89) OD, substrate disappearance, or total VFA concentrations, providing further evidence of specificity against fiber-degrading bacteria. Western blotting with anti-FS85 indicated selective binding to F. succinogenes S85 proteins. Identification by LC-MS/MS of 8 selected protein spots indicated 7 were outer membrane proteins. Overall, polyclonal antibodies were more efficacious at inhibiting the growth of targeted cellulolytic bacteria than non-targeted bacteria. Validated polyclonal antibodies could serve as an effective approach to modify rumen bacterial populations

Analysis of the Rumen Microbiota of Beef Calves Supplemented During the Suckling Phase

A study was conducted to examine the effects of supplementing beef calves during their suckling phase (popularly known as creep feeding) with supplements that contained or did not contain the enzyme xylanase. Forty-two cow-calf pairs were divided into three groups and assigned to one of three treatments for a period of 105 days, as follows: (1) No supplemental feed for calves (control; CON); (2) Corn and soybean meal-based supplement feed for calves (positive control; PCON); and (3) Same feed regimen as PCON with xylanase added to the supplement (enzyme; ENZ). After 105 days, out of the 42 calves participating in the study, 25 male calves were randomly selected (8 from CON, 9 from PCON, and 8 from ENZ) and samples of their forestomach were collected by esophageal tubing. Immediately after this procedure, all calves were weaned, commingled, and placed in a common post-weaning diet for 4 weeks. At the end of this period, ruminal fluid was once again collected from the same 25 calves. All samples were subjected to DNA extraction and 16S rRNA gene sequencing. At weaning, most of the alpha diversity indexes were greater in CON; however, no differences (P ≥ 0.23) in alpha diversity were observed in samples collected 4 weeks after weaning. Regardless of treatment, 2 phyla – Bacteroidetes and Firmicutes – comprised approximately 80% of the total bacterial abundance of samples collected on both days. At the genus level, an effect of diet (P = 0.02) was observed for Prevotella in the samples collected at weaning; however, no differences were detected in the samples collected 4 weeks after weaning. Calf average daily gain (ADG) during the 105-day creep feeding trial tended (P = 0.09) to be greater in the groups that received supplementation, with the greatest numerical value observed in ENZ. Moreover, there was a positive correlation (ρ = 0.43; P = 0.03) between ADG and abundance of Prevotella, indicating the importance of this bacterial group for ruminants. In summary, most of the significant differences found in this study were detected at weaning, and the majority of them disappeared 4 weeks after the calves were weaned and commingled

GABAergic and inflammatory changes in the frontal cortex following neonatal PCP plus isolation rearing, as a dual-hit neurodevelopmental model for schizophrenia

The pathogenesis of schizophrenia begins in early neurodevelopment and leads to excitatory-inhibitory imbalance. It is therefore essential that preclinical models used to understand disease, select drug targets and evaluate novel therapeutics encompass similar neurochemical deficits. One approach to improved preclinical modelling incorporates dual-hit neurodevelopmental insults, like neonatal administration of phencyclidine (PCP, to disrupt development of glutamatergic circuitry) then post-weaning isolation (Iso, to mimic adolescent social stress). We recently showed that male Lister-hooded rats exposed to PCP-Iso exhibit reduced hippocampal expression of the GABA interneuron marker calbindin. The current study expanded on this by investigating changes to additional populations of GABAergic interneurons in frontal cortical and hippocampal tissue from the same animals (by immunohistochemistry) as well as levels of GABA itself (via ELISA). Because inflammatory changes are also implicated in schizophrenia, we performed additional immunohistochemical evaluations of Iba-1 positive microglia as well as ELISA analysis of IL-6 in the same brain regions. Single-hit isolation-reared and dual-hit PCP-Iso rats both showed reduced parvalbumin immunoreactivity in the prelimbic/infralimbic region of the frontal cortex. However, this was more widespread in PCP-Iso, extending to the medial/ventral and lateral/dorsolateral orbitofrontal cortices. Loss of GABAergic markers was accompanied by increased microglial activation in the medial/ventral orbitofrontal cortices of PCP-Iso, together with frontal cortical IL-6 elevations not seen following single-hit isolation rearing. These findings enhance the face validity of PCP-Iso, and we advocate the use of this preclinical model for future evaluation of novel therapeutics—especially those designed to normalise excitatory-inhibitory imbalance or reduce neuroinflammation

“Did I bring it on myself?” An exploratory study of the beliefs that adolescents referred to mental health services have about the causes of their depression

Background: The causal beliefs which adults have regarding their mental health difficulties have been linked to help-seeking behaviour, treatment preferences and the outcome of therapy; yet the topic remains a relatively unexplored one in the adolescent literature. Aims: This exploratory study aims to explore the causal beliefs regarding depression among a sample of clinically referred adolescents. Design: 77 adolescents, aged between 11 and 17, all diagnosed with moderate to severe depression, were interviewed using a semi-structured interview schedule, at the beginning of their participation in a randomised controlled trial. Data were analysed qualitatively using Framework Analysis. Findings: The study identified three themes related to causal beliefs: 1) Bewilderment about why they were depressed; 2) Depression as a result of rejection, victimisation and stress; and 3) Something inside is to blame. Conclusion: Although some adolescents struggled to identify the causes of their depression, many identified stressful life experiences as the cause of their current depression. They also tended to emphasise their own negative ways of interpreting those events, and some believed that their depression was caused by something inside them. Adolescents’ causal beliefs are likely to have implications for the way they seek help and engage in treatment, making it important to understand how adolescents understand their difficulties

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.

BACKGROUND: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. METHODS: We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hr following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020. RESULTS: We analysed data from 326 HOCIs. Among HOCIs with time from admission ≥8 days, the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time from admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%). CONCLUSIONS: The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period. FUNDING: COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute

Implementable Deep Learning for Multi-sequence Proton MRI Lung Segmentation:A Multi-center, Multi-vendor, and Multi-disease Study

Background: Recently, deep learning via convolutional neural networks (CNNs) has largely superseded conventional methods for proton (1H)-MRI lung segmentation. However, previous deep learning studies have utilized single-center data and limited acquisition parameters.Purpose: Develop a generalizable CNN for lung segmentation in 1H-MRI, robust to pathology, acquisition protocol, vendor, and center.Study type: Retrospective.Population: A total of 809 1H-MRI scans from 258 participants with various pulmonary pathologies (median age (range): 57 (6–85); 42% females) and 31 healthy participants (median age (range): 34 (23–76); 34% females) that were split into training (593 scans (74%); 157 participants (55%)), testing (50 scans (6%); 50 participants (17%)) and external validation (164 scans (20%); 82 participants (28%)) sets.Field Strength/Sequence: 1.5-T and 3-T/3D spoiled-gradient recalled and ultrashort echo-time 1H-MRI.Assessment: 2D and 3D CNNs, trained on single-center, multi-sequence data, and the conventional spatial fuzzy c-means (SFCM) method were compared to manually delineated expert segmentations. Each method was validated on external data originating from several centers. Dice similarity coefficient (DSC), average boundary Hausdorff distance (Average HD), and relative error (XOR) metrics to assess segmentation performance.Statistical Tests: Kruskal–Wallis tests assessed significances of differences between acquisitions in the testing set. Friedman tests with post hoc multiple comparisons assessed differences between the 2D CNN, 3D CNN, and SFCM. Bland–Altman analyses assessed agreement with manually derived lung volumes. A P value of &lt;0.05 was considered statistically significant.Results: The 3D CNN significantly outperformed its 2D analog and SFCM, yielding a median (range) DSC of 0.961 (0.880–0.987), Average HD of 1.63 mm (0.65–5.45) and XOR of 0.079 (0.025–0.240) on the testing set and a DSC of 0.973 (0.866–0.987), Average HD of 1.11 mm (0.47–8.13) and XOR of 0.054 (0.026–0.255) on external validation data.Data Conclusion: The 3D CNN generated accurate 1H-MRI lung segmentations on a heterogenous dataset, demonstrating robustness to disease pathology, sequence, vendor, and center.Evidence Level: 4.Technical Efficacy: Stage 1.</p