Asthma has striking disparities across ancestral groups, but the molecular underpinning of these differences is poorly understood and minimally studied. A goal of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to understand multi-omic signatures of asthma focusing on populations of African ancestry. RNASeq and DNA methylation data are generated from nasal epithelium including cases (current asthma, N = 253) and controls (never-asthma, N = 283) from 7 different geographic sites to identify differentially expressed genes (DEGs) and gene networks.
View Article and Find Full Text PDFMotivation: The identification of differentially expressed genes (DEGs) from transcriptomic datasets is a major avenue of research across diverse disciplines. However, current bioinformatic tools do not support covariance matrices in DEG modeling. Here, we introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling including covariates, weights, random effects, covariance matrices, and fit metrics.
View Article and Find Full Text PDFIntroduction: The composition of the nasal microbiota in surgical patients in the context of general anesthesia and nasal povidone-iodine decolonization is unknown. The purpose of this quality improvement study was to determine: (i) if general anesthesia is associated with changes in the nasal microbiota of surgery patients and (ii) if preoperative intranasal povidone-iodine decolonization is associated with changes in the nasal microbiota of surgery patients.
Materials And Methods: One hundred and fifty-one ambulatory patients presenting for surgery were enrolled in a quality improvement study by convenience sampling.
A major goal for the dairy industry is to improve overall milk production efficiency (MPE). With the advent of next-generation sequencing and advanced methods for characterizing microbial communities, efforts are underway to improve MPE by manipulating the rumen microbiome. Our previous work demonstrated that a near-total exchange of whole rumen contents between pairs of lactating Holstein dairy cows of disparate MPE resulted in a reversal of MPE status for ∼10 days: historically high-efficiency cows decreased in MPE, and historically low-efficiency cows increased in MPE.
View Article and Find Full Text PDFThis study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), = 4), or sterilized rumen content (Con, = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing.
View Article and Find Full Text PDFAnalysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows.
View Article and Find Full Text PDFDevelopment of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk.
View Article and Find Full Text PDFA correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
View Article and Find Full Text PDFEarly gut microbial colonization is important for postnatal metabolic and immune development. However, little is known about the effects of different feeding modes (suckling versus bottle-feeding) or microbial sources on this process in farm animals. We found that suckled and bottle-fed newborn lambs had their own distinct gut microbiota.
View Article and Find Full Text PDFIn mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome.
View Article and Find Full Text PDFThe objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) before exchange and over time postexchange. Three pairs of ruminally cannulated, third-lactation cows were selected whose MPE (energy-corrected milk per unit of dry matter intake) differed over their first 2 lactations. Approximately 95% of ruminal contents were exchanged between cows within each pair.
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