Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits.

BACKGROUND: Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits. RESULTS: Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance. CONCLUSIONS: This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.

Disclosing the obvious: Psychosocial implications of (not) explaining facial differences.

Although the disclosure of invisible stigmatized identities has been frequently researched, little work has examined disclosure of facial differences (FD), in which stigma is often highly visible. People with FD are frequently expected by others to disclose or explain their condition. Qualitative work indicates that people with FD have a range of disclosure approaches from agentic disclosure (feeling obliged to disclose), autonomous nondisclosure (choosing not to disclose or to disclose only to certain people), and autonomous disclosure (choosing to openly disclose). The purpose of the present study was to validate these disclosure approaches in a large international sample, examine their frequency of use, and test their relationship to psychosocial outcomes using validated measures. English-speaking participants (n = 288) with 33 different types of FD completed an online survey of disclosure approaches and psychosocial outcomes (i.e. anxiety, depression, self-esteem, stigma, job satisfaction, and relationship self-concept). Participants disclosed to 59 % of the people they knew. Selective and indiscriminate disclosure were the most frequently used and recommended approaches. As predicted, autonomous disclosure was associated with more positive psychosocial outcomes than agentic (non)disclosure and autonomous nondisclosure. Findings from this study can support disclosure autonomy, and thus positive psychosocial outcomes, among people with FD.

Enacted Stigma Experiences and Identity Noticeability of LGBQ+ Women with Rare Diseases.

Lesbian, gay, bisexual, and queer (LGBQ+) people and those with rare diseases (RDs) experience considerable enacted stigma due to their sexual identity and disability/RD status. The frequency, severity, and type of enacted stigma is often influenced by identity noticeability. Although research has shown the challenging impacts of compounded oppression on multiply marginalized individuals, there has been no empirical research to date on the experiences of LGBQ+ women with RDs. This mixed methods study used survey and interview methods to explore enacted stigma experiences and identity noticeability of 29 LGBQ+ women with RDs. We found that RD visibility had a significant positive correlation to RD stigma. Additionally, age had a significant negative correlation to RD stigma and RD visibility. Common concerns for participants included healthcare stigma, sexual identity erasure, RD and/or LGBQ+ community exclusion, and heteropatriarchal expectations and norms. Increased research and support are needed for LGBQ+ women with RDs.

Impact of breeding for reduced methane emissions in New Zealand sheep on maternal and health traits.

Enteric methane emissions from ruminants account for ∼35% of New Zealand's greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal and Nematodirus egg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 years. Sheep were fed on a restricted diet calculated as approximately twice the maintenance. Methane measures were converted to absolute daily emissions of methane measured in g per day (CH4/day). Two measures of methane yield were recorded: the ratio of CH4 to dry matter intake (g CH4/kg DMI; CH4/DMI) and the ratio of CH4 to total gas emissions (CH4/(CH4 + CO2)). Ewes were maintained in the flocks for at least two parities. Non-methane trait data from over 8,000 female relatives were collated to estimate genetic correlations. Results suggest that breeding for low CH4/DMI is unlikely to negatively affect faecal egg counts, adult ewe fertility and litter survival traits, with no evidence for significant genetic correlations. Fleece weight was unfavourably (favourably) correlated with CH4/DMI (rg = -0.21 ± 0.09). Live weight (rg = 0.3 ± 0.1) and body condition score (rg = 0.2 ± 0.1) were positively correlated with methane yield. Comparing the two estimates of methane yield, CH4/DMI had lower heritability and repeatability. However, correlations of both measures with adult ewe traits were similar. This suggests that breeding is a suitable mitigation strategy for lowering methane yield, but wool, live weight and fat deposition traits may be affected over time and should be monitored.

Genetic parameters for residual feed intake, methane emissions, and body composition in New Zealand maternal sheep.

There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducing methane (CH4) emissions. The relationship (genetic and phenotypic) between feed efficiency (characterized as residual feed intake: RFI) and greenhouse gases [methane (CH4) and carbon dioxide (CO2)] traits in New Zealand (NZ) maternal sheep has not previously been investigated, nor has their relationship with detailed estimates of body composition. To investigate these relationships in NZ maternal sheep, a feed intake facility was established at AgResearch Invermay, Mosgiel, NZ in 2015, comprising automated feeders that record individual feeding events. Individual measures of feed intake, feeding behavior (length and duration of eating events), and gas emissions (estimated using portable accumulation chambers) were generated on 986 growing maternal ewe lambs sourced from three pedigree recorded flocks registered in the Sheep Improvement Limited database (www.sil.co.nz). Additional data were generated from a subset of 591 animals for body composition (estimated using ultrasound and computed tomography scanning). The heritability estimates for RFI, CH4, and CH4/(CH4+CO2) were 0.42 ± 0.09, 0.32 ± 0.08, and 0.29 ± 0.06, respectively. The heritability estimates for the body composition traits were high for carcass lean and fat traits; for example, the heritability for visceral fat (adjusted for body weight) was 0.93 ± 0.19. The relationship between RFI and CH4 emissions was complex, and although less feed eaten will lead to a lowered absolute amount of CH4 emitted, there was a negative phenotypic and genetic correlation between RFI and CH4/(CH4+CO2) of -0.13 ± 0.03 and -0.41 ± 0.15, respectively. There were also genetic correlations, that were different from zero, between both RFI and CH4 traits with body composition including a negative correlation between the proportion of visceral fat in the body and RFI (-0.52 ± 0.16) and a positive correlation between the proportion of lean in the body and CH4 (0.54 ± 0.12). Together the results provide the first accurate estimates of the genetic correlations between RFI, CH4 emissions, and the body composition (lean and fat) in sheep. These correlations will need to be accounted for in genetic improvement programs.

Navigating the unknown: A content analysis of the unique challenges faced by adults with rare diseases.

Living with a rare disease can present unique challenges not shared by individuals with common diseases. A content analysis explored which challenges, in participants' own words, are most prevalent across a sample of individuals (n = 1157) with diverse rare diseases in the United States. Symptoms, activity limitations, treatments, uncertainty, and companionship support were mentioned most. Differences across the most frequently mentioned codes were found among disease types, gender, income, years since diagnosis, and symptom duration. Results suggest a need for improved medical care to reduce activity limitations, increased awareness, social support, and access to information for people with rare diseases.

Social support, stress, and life satisfaction among adults with rare diseases.

OBJECTIVE: The goal of this study was to examine the role of stress and four different types of social support in satisfaction with life (SWL) among adults with rare diseases (RDs). We examined whether support is directly related to SWL (main effects model) or related through moderating the inverse relationship between stress and SWL (stress-buffering hypothesis). METHOD: Data came from a cross-sectional survey of adults living in the United States diagnosed with any RD. Participants (n = 1,203) filled out measures of stress, four short-form scales of social support (emotional, informational, tangible, companionship), and SWL. Hierarchical multiple regression was used to test both the main effects model and stress-buffering hypothesis. RESULTS: Controlling for age, gender, years since diagnosis, and symptom severity, emotional support, but not informational or tangible support, positively predicted SWL. Companionship support was related to SWL over and above other factors. Stress negatively predicted SWL, but none of the types of support moderated this relationship. CONCLUSION: Results suggest companionship and emotional support are beneficial to individuals with RDs regardless of their stress levels. Intervention research should focus on ways to foster more companionship and emotional support to improve SWL in this underserved population. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

Genetic parameters of methane emissions determined using portable accumulation chambers in lambs and ewes grazing pasture and genetic correlations with emissions determined in respiration chambers.

Methane (CH4) emission traits were previously found to be heritable and repeatable in sheep fed alfalfa pellets in respiration chambers (RC). More rapid screening methods are, however, required to increase genetic progress and to provide a cost-effective method to the farming industry for maintaining the generation of breeding values in the future. The objective of the current study was to determine CH4 and carbon dioxide (CO2) emissions using several 1-h portable accumulation chamber (PAC) measurements from lambs and again as ewes while grazing ryegrass-based pasture. Many animals with PAC measurements were also measured in RC while fed alfalfa pellets at 2.0 × maintenance metabolizable energy requirements (MEm). Heritability estimates from mixed models for CH4 and CO2 production (g/d) were 0.19 and 0.16, respectively, when measured using PAC with lambs; 0.20 and 0.27, respectively, when measured using PAC with ewes; and 0.23 and 0.34, respectively, when measured using RC with lambs. For measured gas traits, repeatabilities of measurements collected 14 d apart ranged from 0.33 to 0.55 for PAC (combined lambs and ewes) and were greater at 0.65 to 0.76 for the same traits measured using RC. Genetic correlations (rg) between PAC in lambs and ewes were 0.99 for CH4, 0.93 for CH4 + CO2, and 0.85 for CH4/(CH4 + CO2), suggesting that CH4 emissions in lambs and ewes are the same trait. Genetic correlations between PAC and RC measurements were lower, at 0.62 to 0.67 for CH4 and 0.41 to 0.42 for CH4 + CO2, likely reflecting different environmental conditions associated with the protocols used with the 2 measurement methods. The CH4/(CH4 + CO2) ratio was the most similar genetic trait measured using PAC (both lambs and ewes, 63% and 66% selection efficiency, respectively) compared with CH4 yield (g/kg DMI) measured using RC. These results suggest that PAC measurements have considerable value as a rapid low-cost method to estimate breeding values for CH4 emissions in sheep.