How new generation techniques are shaping the future of environmental sciences

This perspective highlights the role of new-generation analytical techniques in future applications in environmental sciences since the shift to the One Health research paradigm. It reviews the interactions between the compartments of One Health and indicates the current challenges in traditional environmental research. The term One Health was first used at the beginning of the 20th century, yet much is still needed for the cross-disciplinary research collaboration required in this approach

Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach

Variation of gut microbiota in metabolic diseases seems to be related to dysbiosis induced by exposure to multiple substances called Microbiota Disrupting Chemicals (MDCs), which are present as environmental and dietary contaminants. Some recent studies have focused on elucidating the alterations of gut microbiota taxa and their metabolites as a consequence of xenobiotic exposures to find possible key targets involved in the severity of the host disease triggered. Compilation of data supporting the triad of xenobiotic-microbiota-metabolic diseases would subsequently allow such health misbalances to be prevented or treated by identifying beneficial microbe taxa that could be Next Generation Probiotics (NGPs) with metabolic enzymes for MDC neutralisation and mitigation strategies. In this review, we aim to compile the available information and reports focused on variations of the main gut microbiota taxa in metabolic diseases associated with xenobiotic exposure and related microbial metabolite profiles impacting the host health status. We performed an extensive literature search using SCOPUS, Web of Science, and PubMed databases. The data retrieval and thorough analyses highlight the need for more combined metagenomic and metabolomic studies revealing signatures for xenobiotics and triggered metabolic diseases. Moreover, metabolome and microbiome compositional taxa analyses allow further exploration of how to target beneficial NGP candidates according to their alleged variability abundance and potential therapeutic significance. Furthermore, this holistic approach has identified limitations and the need of future directions to expand and integrate key knowledge to design appropriate clinical and interventional studies with NGPs. Apart from human health, the beneficial microbes and metabolites identified could also be proposed for various applications under One Health, such as probiotics for animals, plants and environmental bioremediation.FEDER Project Infrastructure IE_2019-198Instituto de Salud Carlos IIIEuropean Commission PI20/01278FIBAO EU-FORA Programme (2020/2021

Microbiota analysis for risk assessment of xenobiotics: cumulative xenobiotic exposure and impact on human gut microbiota under One Health approach

Abstract Human gut microbiota is the microbial community that, through the constant bidirectional communication with its host, plays the critical role of maintaining the state of eubiosis and health balance, contributing to food digestion, detoxification, and proper endocrine, neurological, immunological and potentially reproductive health. To this extent, gut microbiota is called the ‘second brain’ as well as the ‘second liver’. Xenobiotics, including environmental pollutants, are widely spread in the environment and easily accessible in food, cosmetics, personal care products, drugs and medicinal products. Thus, the gut microbiota can be exposed to these xenobiotics, which in turn might alter its composition and metabolism that can trigger dysbiosis, and they seem associated with disorders and diseases in the host. A specific group of xenobiotics, called endocrine‐disrupting chemicals, is particularly important due to relevant adverse health effects. A considerable challenge in risk assessment is the combined exposure to xenobiotics, for which the integrated approaches, including the One Health concept, are still under development. Nevertheless, recent research advancements focus on molecular data in the search for elucidating crucial microbiome biomarkers, associated with physiopathology and specific dysfunctions triggered by xenobiotic exposure. In this context, the application of meta‐omics and integration of genomics, metagenomics, metabolomics, metatranscriptomics, proteomics and multidisciplinary approaches are particularly important

Microbiota analysis for risk assessment of xenobiotics: toxicomicrobiomics, incorporating the gut microbiome in the risk assessment of xenobiotics and identifying beneficial components for One Health

Abstract This work explores three areas of relevance to the gut microbiome in the context of One Health; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and specifically, in the context of antimicrobial resistance. We conclude that, although challenging, focusing on the microbiota resilience, function and active components, are critical for advancing the incorporation of the gut microbiome in the risk assessment of xenobiotics. Moreover, research technologies, such as toxicomicrobiomics, culturomics and genomics, especially in combination, have revealed that the human microbiota may be a promising source of beneficial taxa or other components, with the potential to metabolise and biodegrade xenobiotics. These may have possible applications in several health areas, including in animals or plants for detoxification or in the environment for bioremediation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, we propose that the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation in the pursuit of holistically elucidating their involvement in the balance between health and disease

An Embedded Multiple-Case Study on OSS Design Quality Assessment across Domains

Context: Investing on Open Source Software (OSS) as a “code reuser”, involves certain risks, such as the difficulty in understanding the level of OSS design quality Aim: We investigate the levels of design quality of OSS projects, across different application domains. Method: We conducted a case study, which is the most fitting research method for observing a phenomenon in its real context, which is active for a long period of time, and for which variables cannot be controlled. Results: We present the values for seven design quality metrics of 546 OSS projects, as well as the statistically significant differences across application domains. Conclusions: The results of the study suggest that OSS application domains correlate with several design quality characteristics, in the sense that projects within one application domain appear to have similar levels of design quality. In addition to that, the results reveal application domains with high and low levels of design quality.

A methodology on extracting reusable software candidate components from open source games

Component-Based Software Engineering (CBSE) focuses on thedevelopment of reusable components in order to enable their reusein more systems, rather than only to be used to the original onesfor which they have been implemented in the first place (i.e.development for reuse) and the development of new systems withreusable components (i.e. development with reuse). This paperaims at introducing a methodology for the extraction of candidatereusable software components from open source games. Theextracted components have been empirically evaluated through acase study. Additionally, the component candidates that have beenextracted are available for reuse through a web service

CODE reuse in practice:Benefiting or harming technical debt

During the last years the TD community is striving to offer methods and tools for reducing the amount of TD, but also understand the underlying concepts. One popular practice that still has not been investigated in the context of TD, is software reuse. The aim of this paper is to investigate the relation between white-box code reuse and TD principal and interest. In particular, we target at unveiling if the reuse of code can lead to software with better levels of TD. To achieve this goal, we performed a case study on approximately 400 OSS systems, comprised of 897 thousand classes, and compare the levels of TD for reused and natively-written classes. The results of the study suggest that reused code usually has less TD interest; however, the amount of principal in them is higher. A synthesized view of the aforementioned results suggest that software engineers shall opt to reuse code when necessary, since apart from the established reuse benefits (i.e., cost savings, increased productivity, etc.) are also getting benefits in terms of maintenance. Apart from understanding the phenomenon per se, the results of this study provide various implications to research and practice

Identifying Extract Method Refactoring Opportunities Based on Functional Relevance

`Extract Method' is considered one of the most frequently applied and beneficial refactorings, since the corresponding Long Method smell is among the most common and persistent ones. Although Long Method is conceptually related to the implementation of diverse functionalities within a method, until now, this relationship has not been utilized while identifying refactoring opportunities. In this paper we introduce an approach (accompanied by a tool) that aims at identifying source code chunks that collaborate to provide a specific functionality, and propose their extraction as separate methods. The accuracy of the proposed approach has been empirically validated both in an industrial and an open-source setting. In the former case, the approach was capable of identifying functionally related statements within two industrial long methods (approx. 500 LoC each), with a recall rate of 93 percent. In the latter case, based on a comparative study on open-source data, our approach ranks better compared to two well-known techniques of the literature. To assist software engineers in the prioritization of the suggested refactoring opportunities the approach ranks them based on an estimate of their fitness for extraction. The provided ranking has been validated in both settings and proved to be strongly correlated with experts' opinion