Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts

The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for 5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts

Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients

A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease

Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) show a large overlap in clinical presentation, which presents diagnostic challenges. As a consequence, invasive and burdensome endoscopies are often used to distinguish between IBD and IBS. Here, we aimed to develop a noninvasive fecal test that can distinguish between IBD and IBS and reduce the number of endoscopies. We used shotgun metagenomic sequencing to analyze the composition and function of gut microbiota of 169 IBS patients, 447 IBD patients and 1044 population controls and measured fecal Calprotectin (FCal), human beta defensin 2 (HBD2), and chromogranin A (CgA) in these samples. These measurements were used to construct training sets (75% of data) for logistic regression and machine learning models to differentiate IBS from IBD and inactive from active IBD. The results were replicated on test sets (remaining 25% of the data) and microbiome data obtained using 16S sequencing. Fecal HBD2 showed high sensitivity and specificity for differentiating between IBD and IBS (sensitivity = 0.89, specificity = 0.76), while the inclusion of microbiome data with biomarkers (HBD2 and FCal) showed a potential for improvement in predictive power (optimal sensitivity = 0.87, specificity = 0.93). Shotgun sequencing-based models produced comparable results using 16S-sequencing data. HBD2 and FCal were found to have predictive power for IBD disease activity (AUC approximate to 0.7). HBD2 is a novel biomarker for IBD in patients with gastro-intestinal complaints, especially when used in combination with FCal and potentially in combination with gut microbiome data

Dinámica de las tierras irrigadas en el centro-oeste de Argentina durante el período 1986-2018: análisis a partir de la anomalía del índice de vegetación mejorado

Los cambios en las áreas de riego de zonas áridas tienen fuertes implicancias para la producción de alimentos, la demanda de agua, la sustentabilidad de los cultivos y los acuíferos subterráneos. Los oasis del Centro-Oeste de Argentina constituyen una de las mayores áreas de riego en zonas áridas de Sudamérica. El objetivo del presente trabajo es estudiar la dinámica espacial y temporal de las áreas irrigadas del Centro-Oeste de Argentina en el período 1986-2018, su relación con la evolución del sistema agrícola-productivo y los factores impulsores de cambio en los usos de la tierra. Para el análisis de las áreas de riego se utilizó un modelo empírico que permite estimar las anomalías de evapotranspiración a partir del índice EVI, implementado en la plataforma Google Earth Engine. El área irrigada se incrementó un 17%, impulsada por el crecimiento en las cuencas de los ríos Tunuyán Superior (36%), San Juan (19%) y Mendoza (10,4%). El crecimiento de las áreas irrigadas comprende, principalmente, la expansión hacia el pedemonte mediante el aprovechamiento de aguas subterráneas y nuevas zonas de reúso de efluentes cloacales. El abandono de sitios de riego se asocia al avance urbano sobre áreas irrigadas y el abandono en áreas marginales, donde se produce una profunda transformación en el uso de la tierra y del agua. Los resultados encontrados sugieren un aporte sostenido de agua de riego en sitios abandonados para la producción agrícola y una disminución del área irrigada y cultivada durante la última década. Las transformaciones encontradas en los patrones de riego, tipo de cultivos y el área irrigada total tienen fuertes implicancias para los balances hídricos, por lo que deben ser consideradas para la planificación territorial y la gestión sustentable del agua en las cuencas del Centro-Oeste de Argentina.Irrigated cropland changes in arid regions have strong implications for food production, water demand, crop and groundwater sustainability. The oases of Central-Western Argentina constitute one of the largest irrigated areas across South America. The aim of this paper is to study the spatial and temporal dynamics of the irrigated lands in Central-Western Argentina in the period 1986-2018, their relationship with the evolution of the agricultural-productive system and the drivers of land use change. For the analysis of irrigated areas, an empirical model was used to estimate evapotranspiration anomalies based on the EVI index, implemented in the Google Earth Engine cloud-computing platform. The irrigated area increased by 17%, driven by growth in the Upper Tunuyán (36%), San Juan (19%) and Mendoza (10.4%) river basins. The growth of irrigated areas mainly includes expansion into the foothills through the use of groundwater and new sewage effluent reuse areas. The abandonment of irrigated plots is associated with urban sprawling over irrigated croplands and abandonment in marginal areas, where a deep transformation in land and water use occurs. The results suggest an irrigation water supply sustained in plots abandoned for agricultural production and a decrease in irrigated and cultivated area during the last decade. The transformations found in irrigation patterns, crop choices and total irrigated area have strong implications for water balances and should be considered for territorial planning and sustainable water management in the Central-Western Argentina basins.Asociación Argentina de Geofísicos y Geodesta

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease

The impact of black carbon (BC) on mode-specific galvanic skin response (GSR) as a measure of stress in urban environments

Previous research has shown that walking and cycling could help alleviate stress in cities, however there is poor knowledge on how specific microenvironmental conditions encountered during daily journeys may lead to varying degrees of stress experienced at that moment. We use objectively measured data and a robust causal inference framework to address this gap. Using a Bayesian Doubly Robust (BDR) approach, we find that black carbon exposure statistically significantly increases stress, as measured by Galvanic Skin Response (GSR), while cycling and while walking. Augmented Outcome Regression (AOR) models indicate that greenspace exposure and the presence of walking or cycling infrastructure could reduce stress. None of these effects are statistically significant for people in motorized transport. These findings add to a growing evidence-base on health benefits of policies aimed at decreasing air pollution, improving active travel infrastructure and increasing greenspace in cities

Oleic acid variation and marker-assisted detection of Pervenets mutation in high- and low-oleic sunflower cross

High-oleic sunflower oil is in high demand on the market due to its heart-healthy properties and richness in monounsaturated fatty acids that makes it more stable in processing than standard sunflower oil. Consequently, one of sunflower breeder's tasks is to develop stable high-oleic sunflower genotypes that will produce high quality oil. We analyzed variability and inheritance of oleic acid content (OAC) in sunflower, developed at the Institute of Field and Vegetable Crops, by analyzing F-1 and F-2 progeny obtained by crossing a standard linoleic and high-oleic inbred line. F-2 individuals were classified in two groups: low-oleic with OAC of 15.24-31.28% and high-oleic with OAC of 62.49-93.82%. Monogenic dominant inheritance was observed. Additionally, several molecular markers were tested for the use in marker-assisted selection in order to shorten the period of detecting high-oleic genotypes. Marker F4-R1 was proven to be the most efficient in detection of genotypes with Pervenets (high-oleic acid) mutation

Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus

OBJECTIVE: Alterations in the microbiota composition of the gastro-intestinal tract are suspected to be involved in the etiopathogenesis of two closely related systemic inflammatory autoimmune diseases: primary Sjögren's syndrome (pSS) and systemic lupus erythematosus (SLE). Our objective was to assess whether alterations in gut and oral microbiota compositions are specific for pSS and SLE. METHODS: 16S ribosomal RNA gene sequencing was performed on fecal samples from 39 pSS patients, 30 SLE patients and 965 individuals from the general population, as well as on buccal swab and oral washing samples from the same pSS and SLE patients. Alpha-diversity, beta-diversity and relative abundance of individual bacteria were used as outcome measures. Multivariate analyses were performed to test associations between individual bacteria and disease phenotype, taking age, sex, body-mass index, proton-pump inhibitor use and sequencing-depth into account as possible confounding factors. RESULTS: Fecal microbiota composition from pSS and SLE patients differed significantly from population controls, but not between pSS and SLE. pSS and SLE patients were characterized by lower bacterial richness, lower Firmicutes/Bacteroidetes ratio and higher relative abundance of Bacteroides species in fecal samples compared with population controls. Oral microbiota composition differed significantly between pSS patients and SLE patients, which could partially be explained by oral dryness in pSS patients. CONCLUSIONS: pSS and SLE patients share similar alterations in gut microbiota composition, distinguishing patients from individuals in the general population, while oral microbiota composition shows disease-specific differences between pSS and SLE patients

The 1000IBD project:multi-omics data of 1000 inflammatory bowel disease patients; data release 1

BackgroundInflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.Construction and contentWe initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.Utility and discussionAll molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org, accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.ConclusionsWe report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets