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"Watts, Stephen"
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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Klebsiella pneumoniae
is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of
K. pneumoniae
genome data. Here we introduce Kleborate, a tool for analysing genomes of
K. pneumoniae
and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available
Klebsiella
genomes, including clinical isolates from a pan-European study of carbapenemase-producing
Klebsiella
, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type
K. pneumoniae
from gut metagenomes.
Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.
Journal Article
The effects of dietary saturated fat source on weight gain and adiposity are influenced by both sex and total dietary lipid intake in zebrafish
The effects of saturated fat intake on obesity and cardiovascular health remain inconclusive, likely due in part to their varied nature and interactions with other nutrients. Investigating the synergistic effects of different saturated fat sources with other dietary lipid components will help establish more accurate nutritional guidelines for dietary fat intake. Over the past two decades, zebrafish ( Danio rerio ) have been established as an attractive model system to address questions regarding contributions of dietary lipid intake to diet-induced obesity in humans. The goal of the present study was to assess interactions of three different saturated fat sources (milk fat, palm oil, and coconut oil) with sex and total dietary lipid intake on weight gain and body composition in adult zebrafish. Larvae were raised on live feeds until 28 days post fertilization, and then fed a formulated maintenance diet until three months of age. An eight-week feeding trial was then initiated, in which zebrafish were fed nine experimental low- and high-fat diets varying in saturated fatty acid and long-chain polyunsaturated fatty acid content, in addition to a low-fat and high-fat control diet. At termination of the feeding trial, each treatment was evaluated according to body mass, moisture content, and adiposity. Sex and diet significantly interacted in their effects on body mass ( P = 0.026), moisture content ( P = 0.044), and adiposity ( P = 0.035). The influence of saturated fat source on body mass was observed to be dependent on intake of total dietary lipid. In females, all three saturated fat sources had similar effects on adiposity. From these observations, we hypothesize that impacts of saturated fat intake on energy allocation and obesity-related phenotypes are influenced by both sex and intake of other dietary lipid components. Our results suggest that current nutritional guidelines for saturated fat intake may need to be re-evaluated and take sex-specific recommendations into consideration.
Journal Article
Root density distribution and biomass allocation of co-occurring woody plants on contrasting soils in a subtropical savanna parkland
Background and aims
Root niche partitioning among trees/shrubs and grasses facilitates their coexistence in savannas, but little is known regarding root distribution patterns of co-occurring woody plants, and how they might differ on contrasting soils.
Methods
We quantified root distributions of co-occurring shrubs to 2 m on argillic and non-argillic soils.
Results
Root biomass in the two shrub communities was 3- to 5- fold greater than that in the grassland community.
Prosopis glandulosa
, the dominant overstory species was deep-rooted, while the dominant understory shrub,
Zanthoxylum fagara
, was shallow-rooted (47% vs. 25% of root density at depths >0.4 m). Shrubs on argillic soils had less aboveground and greater belowground mass than those on non-argillic soils. Root biomass and density on argillic soils was elevated at shallow (< 0.4 m) depths, whereas root density of the same species on non-argillic soils were skewed to depths >0.4 m. Root density decreased exponentially with increasing distance from woody patch perimeters.
Conclusions
Belowground biomass (carbon) pools increased markedly with grassland-to-shrubland state change. The presence/absence of a restrictive barrier had substantial effects on root distributions and above- vs. belowground biomass allocation. Differences in root distribution patterns of co-occurring woody species would facilitate their co-existence.
Journal Article
Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome
Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome-rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as lipids, by intestinal epithelial cells. However, whether protein absorption is also affected by the gut microbiome is poorly understood. Here, we investigate connections between protein absorption and microbes in the zebrafish gut. Using live microscopy-based quantitative assays, we find that microbes slow the pace of protein uptake and degradation in LREs. While microbes do not affect the number of absorbing LRE cells, microbes lower the expression of endocytic and protein digestion machinery in LREs. Using transgene-assisted cell isolation and single cell RNA-sequencing, we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria-sensing and metabolic pathways in LREs, and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs. Using custom-formulated diets, we investigated the influence of diet and LRE activity on the gut microbiome. Impaired protein uptake activity in LREs, along with a protein-deficient diet, alters the microbial community and leads to an increased abundance of bacterial genera that have the capacity to reduce protein uptake in LREs. Together, these results reveal that diet-dependent reciprocal interactions between LREs and the gut microbiome regulate protein absorption.
Journal Article
Current basis and future directions of zebrafish nutrigenomics
This review investigates the current state of nutrigenomics in the zebrafish animal models. The zebrafish animal model has been used extensively in the study of disease onset and progression and associated molecular changes. In this review, we provide a synopsis of nutrigenomics using the zebrafish animal model. Obesity and dyslipidemia studies describe the genomics of dietary-induced obesity in relation to high-fat/high-calorie diets. Inflammation and cardiovascular studies describe dietary effects on the expression of acute inflammatory markers and resulting chronic inflammatory issues including atherosclerosis. We also evaluated the genomic response to bioactive dietary compounds associated with metabolic disorders. Carbohydrate metabolism and β-cell function studies describe the impacts of high-carbohydrate dietary challenges on nutritional programming. We also report tumorigenesis in relation to dietary carcinogen exposure studies that can result in permanent genomic changes. Vitamin and mineral deficiency studies demonstrate transgenerational genomic impacts of micronutrients in the diet and temporal expression changes. Circadian rhythm studies describe the relation between metabolism and natural temporal cycles of gene expression that impacts health. Bone formation studies describe the role of dietary composition that influences bone reabsorption regulation. Finally, this review provides future directions in the use of the zebrafish model for nutrigenomic and nutrigenetic research.
Journal Article
The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles
In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray–Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described.
This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico.
Graphical Abstract Figure.
This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico.
Journal Article
The Kids Aren’t Alright: School Attachment, Depressive Symptoms, and Gun Carrying at School
Social science has frequently examined the relationships between school environment and delinquency, mental health and delinquency, and school environment and mental health. However, little to no research to date has examined the interrelationship between these variables simultaneously, especially at it relates specifically to delinquent acts committed at school. The current study uses data from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to look at the interrelationship between these variables. What is found in this data is that the relationship between negative mental health states and delinquency at school, specifically measured as depressive symptoms and gun carrying at school, respectively, is possibly a spurious one, wherein both of these variables are partly shaped by school attachment, which accounts for their correlation. Implications for theory and policy are discussed.
Journal Article
Trajectories of Offending: Comparing US Born and Non-US Born Respondents in the Add Health
Immigration is sometimes associated with crime and delinquency in the mind of the public, and it is often assumed that individuals not born in the U.S. engage in more crime and delinquency than do the native born. However, not enough research to date has looked at offending across the life-course and compared trajectories between U.S. born and non-U.S. born populations. Guided by life-course perspectives and utilizing group-based trajectory modeling (GBTM), this article uses four waves of National Longitudinal Study of Adolescent to Adult Health (Add Health) data to describe and contrast longitudinal variations in offending behavior between US born and non-US born individuals. The analyses show that there are fewer offending trajectory groups among the non-U.S. born, and that they generally offend at lower levels across the life-course than do the U.S. born. Further analysis also shows differences between the two groups in factors that shape trajectory group membership.
Journal Article