High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

Harnessing root-soil-microbiota interactions for drought-resilient cereals.

Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.

The biodiversity effect of reduced tillage on soil microbiota.

The conversion of natural habitats into farmland has been a leading cause of species loss worldwide. Here, we investigated to what extent less intensive soil disturbance can mitigate this loss. Specifically, we examined whether reduced soil disturbance by tillage in agricultural fields could contribute to soil microbial biodiversity by providing a habitat for species that are limited by conventional tillage. To do so, we studied the diversity of soil biotas from three agricultural practices representing conventional tillage, reduced tillage and no tillage. Study fields were sampled by taking a bulk soil sample at the centre and edge of each field. The soil communities were recorded with environmental DNA metabarcoding using three molecular markers targeting bacteria, fungi and eukaryotes. While these three markers represent the vast majority of biotic variation in the soil, they will inevitably be dominated by the megadiverse microbiota of bacteria, microfungi and protists. We found a significant differentiation in community composition related to the intensity of tillage. Richness was weakly correlated to tillage, and more influenced by whether the sample was taken in the center or the edge of the field. Despite the significant effect of tillage on composition, comparisons with natural ecosystems revealed that all 30 study fields were much more similar in composition to other rotational fields than to more natural habitats, oldfields and leys. Despite a slightly higher similarity to oldfields and semi-natural grasslands, the contribution of no-till soil communities to biodiversity conservation is negligible, and our results indicate that restoration on set aside land may contribute more to conservation.

Universal Dermal Microbiome in Human Skin.

Human skin microbiota has been described as a "microbial fingerprint" due to observed differences between individuals. Current understanding of the cutaneous microbiota is based on sampling the outermost layers of the epidermis, while the microbiota in the remaining skin layers has not yet been fully characterized. Environmental conditions can vary drastically between the cutaneous compartments and give rise to unique communities. We demonstrate that the dermal microbiota is surprisingly similar among individuals and contains a specific subset of the epidermal microbiota. Variability in bacterial community composition decreased significantly from the epidermal to the dermal compartment but was similar among anatomic locations (hip and knee). The composition of the epidermal microbiota was more strongly affected by environmental factors than that of the dermal community. These results indicate a well-conserved dermal community that is functionally distinct from the epidermal community, challenging the current dogma. Future studies in cutaneous disorders and chronic infections may benefit by focusing on the dermal microbiota as a persistent microbial community.IMPORTANCE Human skin microbiota is thought to be unique according to the individual's lifestyle and genetic predisposition. This is true for the epidermal microbiota, while our findings demonstrate that the dermal microbiota is universal between healthy individuals. The preserved dermal microbial community is compositionally unique and functionally distinct to the specific environment in the depth of human skin. It is expected to have direct contact with the immune response of the human host, and research in the communication between host and microbiota should be targeted to this cutaneous compartment. This novel insight into specific microbial adaptation can be used advantageously in the research of chronic disorders and infections of the skin. It can enlighten the alteration between health and disease to the benefit of patients suffering from long-lasting socioeconomic illnesses.

Hundred Fifty Years of Herbarium Collections Provide a Reliable Resource of Volatile Terpenoid Profiles Showing Strong Species Effect in Four Medicinal Species of Salvia Across the Mediterranean.

Herbarium samples are increasingly being recognized for their potential in answering a wide range of research questions. However, the suitability of herbarium samples for chemical analysis is largely unexplored as they are thought to be too degraded. The aim of this study was to explore terpenoid profiles across time and geographic space for four medicinal species of Salvia across the Mediterranean to assess the suitability of using herbarium specimens in chemical analyses. Herbarium samples of Salvia aethiopis, S. multicaulis, S. officinalis, and S. sclarea collected over 150 years across the Mediterranean were compared to modern samples using both targeted and untargeted gas chromatography-mass spectrometry analysis of terpene profiles. There was no effect of collection year on chemical composition, although the total concentration of the 20 assessed standards and two individual standards significantly decreased over time. Instead, chemical profiles were defined by species, with strong species effects identified on both the targeted and untargeted chemical composition. Geographic variation was a factor in regulating the untargeted chemical compositions, suggesting some underlying environmental effects. However, there was no effect of sample altitude on either the targeted or untargeted chemical compositions. Chemical composition of four Salvia species are predominantly defined by species, and there was a substantially smaller effect of year of sampling. Given these results herbarium collections may well represent a considerably underused resource for chemical analyses that can benefit biodiversity and other studies.