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Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.

Infectious agents, both standard and emerging or engineered, might initiate outbreaks with global impact and/or existential- level threat potential. Such agents might infect human, livestock, exploitable plant cultures or the environment at large. Instead of responding by sampling teams which may also carry out prolonged surveillance, a more effective concept is to pre-process the samples, possibly to nucleic acid extract so as to transport them without biological risks by standard channels, or to process them up to a point and return the results, leaving the samples which only need specialized tests and dedicated equipment. In this context a portable device, allowing multiple routine and crisis -management applications due to its inherent flexibility, is scrutinized against alternatives and possible needs so as to develop a novel standard of surveillance and intervention, meant to facilitate containment by providing faster much more reliable laboratory results at a fraction of older generation mobile nucleic acids analyzers. Additional steps, such as agarose in pills and buffers pre-packaged in expendable syringes with pistons locked by improvised safety features may improve the Complexity Level of the whole system so as to make it appealing to intervention/crisis management personnel, while the instrument proper may double as backup for respective benchtop devices.

The advances made by microbiome research call for new vocabulary and expansion of our thinking in microbiology. For example, the life-forms presenting in both unicellular and multicellular formats invite us to rethink microbial existence, organization, growth, pathogenicity, and therapeutics in the 21st century. A view of such populations as parts of single organisms with a loose, distributed multicellular organization, introduced here as a germ-ganism, rather than communities, might open up interesting prospects for diagnostics and therapeutics innovation. This study tested and further contextualized the concept of germ-ganism using solid cultures of bacteria and fungi. Based on our findings and the literature reviewed herein, we propose that germ-ganism has synergy with a systems medicine approach by broadening host-environment interactions from cells and microorganisms to a scale of biological ecosystems. Germ-ganism also brings about the possibility of studying the multilevel impacts of novel therapeutic agents within and across networks of microbial ecosystems. The germ-ganism would lend itself, in the long term, to a veritable biocybernetics system, while in the mid-term, we anticipate it will contribute to new diagnostics and therapeutics. Biosecurity applications would be immensely affected by germ-ganism. Industrial applications of germ-ganism are of interest as a more sustainable alternative to costly solutions such as tampered strains/microorganisms. In conclusion, germ-ganism is informed by lessons from microbiome research and invites rethinking microbial existence, organization, and growth as an organism. Germ-ganism has vast ramifications for understanding pathogenicity, and clinical, biosecurity, and biotechnology applications in the current historical moment of the COVID-19 pandemic and beyond.

Entomopathogenic fungi are essential participants in ecosystems that help regulate arthropod communities. Many of them have a symbiotic-endophytic relationship with plants, endowing them with insecticidal or insect-repellent traits, which could be exploited for insect control in agriculture. Among insects, aphids are one of the most harmful taxa; they damage plants directly by sucking plant sap or indirectly by transmitting economically important viruses. Plant infestation by aphids depends on prefeeding activities related to host identification, particularly leaf walking and short probing. Although several aspects of aphid prefeeding activities have been studied in different hosts, this behavior has not been examined on plants colonized by entomopathogenic fungi. Here, we studied the effects of three strawberry endophytic entomopathogenic fungi, namely, Beauveria bassiana, Isaria fumosorosea and Metarhizium anisopliae var. robertsii, on the prefeeding activity of the aphid Myzus persicae by monitoring aphids feeding on leaves of fungus colonized and uncolonized plants. Our analysis revealed that the endophytes significantly affected aphid prefeeding behavior, which was typified by a reduction of the expected mean number of short probes, an avoidance to make a second probe, and a high propensity for abandoning the leaf. We discuss possible mechanisms of fungal interference with aphid activity.

Modern microbiology and drug development are in a watershed moment with the advent of electroceuticals. In addition to genomics, electrical impulses in an organism are believed to contribute to tissue and cellular plasticity. Hence, electroceuticals or bioelectronics offers the promise to identify innovative approaches to treat human diseases. However, applications toward electromicrobiology are still limited and rare, despite the high potential to innovate the fields of both microbiology and therapeutics. For example, electric modalities for manipulating microbial growth are highly sustainable; can be combined with biopharmaceuticals, probiotics, and pharmacobiotics; and, thus, are well poised for use in medicine, public health, and ecology and diverse industries. We report here the introduction of a new research framework and technology platform for electroculturomics, by coupling standard solid-state mycological cultures with conductive treatment using a conformite Europeene (CE-)-certified medical ionophoresis device. We share our experience with a diverse range of fungi that have been treated with the electroculturomics approach reported herein. We suggest that this line of inquiry can be extended to electrotranscriptomics and electrometabolomics by deploying electroculturomics in tandem with multi-omics approaches in the future. This article makes a specific contribution to fungal microbiology, and a broader contribution to advance the theory and practice of the field of electroculturomics emerging in 21st-century microbiology and ecology research.

Serological methods serve as a direct or indirect means of pathogen infection diagnosis in plant and animal species, including humans. Dot-ELISA (DE) is an inexpensive and sensitive, solid-state version of the microplate enzyme-linked immunosorbent assay, with a broad range of applications in epidemiology. Yet, its applicability is limited by uncertainties in the qualitative output of the assay due to overlapping dot colorations of positive and negative samples, stemming mainly from the inherent color discrimination thresholds of the human eye. Here, we report a novel approach for unambiguous DE output evaluation by applying machine learning-based pattern recognition of image pixels of the blot using an impartial predictive model rather than human judgment. Supervised machine learning was used to train a classifier algorithm through a built multivariate logistic regression model based on the RGB (“Red”, “Green”, “Blue”) pixel attributes of a scanned DE output of samples of known infection status to a model pathogen (Lettuce big-vein associated virus). Based on the trained and cross-validated algorithm, pixel probabilities of unknown samples could be predicted in scanned DE output images which would then be reconstituted by pixels having probabilities above a cutoff that may be selected at will to yield desirable false positive and false negative rates depending on the question at hand, thus allowing for proper dot classification of positive and negative samples and, hence, accurate diagnosis. Potential improvements and diagnostic applications of the proposed versatile method that translates unique pathogen antigens to the universal basic color language are discussed.

There are many factors determining the strawberry organoleptic profile and they are difficult to define. In this study, the sensory, physical, and chemical quality characteristics, the antioxidant properties as examined using ferric reducing antioxidant power (FRAP) and 1-diphenyl-2-picrylhydrazyl (DPPH) assays, the lactone concentration, and the FaFAD1 expression of ripe strawberries (cv. Camarosa, Florida Fortuna, and Sabrina) from Greece were evaluated and their interrelationships were investigated.; Results: 'Camarosa' had the highest antioxidant capacity and polyphenol content, although significant intra-cultivar variations of sugars, solid soluble content/titratable acidity (SSC/TA), red color intensity, sweetness, and hardness were recorded. In 'Sabrina' there was a constant lactone presence and FaFAD1 expression; it also had the lowest ascorbic acid content, the highest pH, SSC/TA index, firmness, and sweetness. 'Fortuna' showed the lowest sweetness and aroma indices, whereas 'Camarosa' had intermediate ones. Overall, firmness was correlated with hardness, while pH and SSC/TA index correlated with juiciness and sweetness. Both γ-decalactone and γ-dodecalactone concentrations were correlated with FaFAD1 expression and pH, but they did not solely determine the aroma sensory perception. In total, FRAP values were positively correlated with ascorbic acid and polyphenol content, and negatively with pH.; Conclusions: Significant inter- and intra-cultivar variation was recorded, revealing the impact of the genotype and underlining the effect of microenvironmental and cultivation conditions on quality and sensory perception. © 2018 Society of Chemical Industry.; © 2018 Society of Chemical Industry.

Photosynthesis in host plants is significantly reduced by many virus families. The early detection of viral infection before the onset of visual symptoms in both directly and systemically infected leaves is critical in crop protection. Viral pathogens cause a variety of symptoms through modifications of chloroplast structure and function and the response of the photochemistry process is immediate. Therefore, chlorophyll fluorescence monitoring has been extensively investigated the last two decades as a tool for timely assessment of pathogenic threats. Alternatively, the analysis of Chla fluorescence transients offers several interlinked parameters which describe the fate of excitation energy round and through the photosystems. Additionally, OJIP fluorescence transients and leaf reflectance spectra methodologies serve for rapid screening of large number of samples. The objective of the present study was to achieve early detection of viral infection, integrating the multiparametric information of the Chla fluorescence transients and of the leaf reflectance spectra into one photochemical performance index. Infection decreased the maximum quantum yield of PSII (FV/FM), the effective quantum yield of PSII (ΦPSII), the CO2 assimilation rate (A) and the stomatal conductance (gs) in the studied TMV-pepper plant pathosystem, while non-photochemical quenching (NPQ) increased. Some parameters from the OJIP transients and the leaf reflectance spectra were significantly affected 24 h after infection, while others modified three to five days later. Similar results were obtained from systemically infected leaves but with one to three days hysteresis compared to inoculated leaves. Differences between healthy and infected leaves were marginal during the first 24 h post infection. The Integrated Biomarker Response tool was used to create a photochemical infection index (PINFI) which integrates the partial effects of infection on each fluorescence and reflectance index. The PINFI, which to the best of our knowledge is the first photochemical infection index created by the IBR method, discriminated reliably between the infected and healthy leaves of pepper plants from the first 24 h after infection with the TMV.

Global Catastrophic Biological Risks (GCBRs) refer to biological events-natural, deliberate, and accidental-of a global and lasting impact. This challenges the life scientists to raise their game on two hitherto neglected innovation frontiers: a veritable "futures" thinking to "think the unthinkable," and "systems thinking" so as to see both the trees and the forest when it comes to GCBRs. This innovation analysis article outlines the promise of Omics systems science biotechnologies, for example, to deploy rapid fire diagnostics for health security crises at GCBR level, possibly involving neopathogens and/or incurring epidemics (e.g., severe acute respiratory syndrome [SARS] and Ebola) that collectively threaten the lives of global society and interdependent biological ecosystems. Moreover, Omics encourages thinking beyond immediacy and in long-term strategies for biopreparedness and response innovation when the timelines are aggressive and compressed in response to crises such as GCBRs, but also to non-global but surging, multiple threats occurring as successive, overlapping, or distinct events, rather than as distinct entities-a prospect enforcing a reboot in Bioresilience. We define Next-Generation Bioresilience as "a systems approach against natural, accidental and perpetrated GCBRs using Omics technologies, and a shift in mentality, whereby the systems approach is expanded to include multiple plausible futures and expose unchecked assumptions attendant to risks, beyond technological determinism." In sum, it is time to think about the realistic potential of Omics biotechnologies beyond clinical practice and precision medicine so as to harness the opportunities and address the uncertainties associated not only with GCBRs but also with other emerging Omics applications in health and society.

This chapter focuses on the intrinsic nature of the interactions of the viral components of the microbiome that collectively form “the virome” and its differences from other microbiomatic entities. To tackle this profoundly complex problem and analyze the host–virus interactome, we applied a cutting-edge exploratory approach, network analysis. Contrary to the traditional tree representation of phylogenetics that stresses the entities’ evolution ex unibus plurum, the network representation that uses graphs to analyze microbial complexity and evolution, emphasizes how entities evolve ex pluribus unum. Since double-stranded DNA (dsDNA) viruses represent the most prevalent Baltimore class and DNA is the molecule of (cellular) life, we constructed the network of dsDNA virus–host interactions and use it as a paradigm of how networks may serve as roadmaps for probing the interactome of the entire virome, revealing, inter alia, details of the continuum of interactions among microbiota and their components.

The current challenge in public-health monitoring is the extended spectrum of agents that become pathogenic and virulent due to a number of diverse reasons: the climate change altering the ambient temperature and humidity; the deterioration of health and health care, for any and all applicable reason(s), allowing aggressive communicable patterns; advances in synthetic biology increasing the danger of custom-engineered microbiota for legitimate and nefarious purposes; and massive migration/travel and transportation movements dispersing microbiota and reshuffling local microbiomes in receiving countries. Thus new microbiota has to be processed on a regular basis so as to be included in monitoring and surveillance practice. The latter is challenged with an unprecedented range of pathogens and more aggressive outbreaks. A fast turnover is at a premium of a specification list, which also contains, without being limited to, operational flexibility, technical adaptability, reasonable cost, and straightforward applications, preferably decentralized and transdisciplinary application in the monitoring of plant, animal, and human pathogen, as a result of pathogens breaking through the species’ or kingdoms’ barriers much easier than thought. Common but adaptable platforms using genomic and postgenomic technological breakthroughs, such as portable instrumentation and very long–read sequencing, pave the way for adaptive, massive testing with limited up-front costs.

Global governance of pathogens such as Ebola virus and infectious diseases is central to global health, and to innovation in systems medicine. Worrisomely, the gaps in human immunity and healthcare services combined with novel pathogens emerging by travel, biotechnological advances, or the rupture of the host-species barrier challenge infectious diseases' global governance. Such biorisks and biothreats may scale up to global catastrophic biological risks (GCBRs) spatiotemporally, either as individual or as collective risks. The scale and intensity of such threats challenge current thinking on surveillance, and calls for a move toward pan-biosurveillance. New multilayered, cross-sectoral, and adaptable strategies of prevention and intervention on GCBRs should be developed, considering human hosts in entirety, and in close relationship with other hosts (plants and animals). This also calls for the "Humanome," which we introduce in this study as the totality of human subjects plus any directly dependent biological or nonbiological entities (products, constructs, and interventions). Surveillance networks should be implemented by integrating communications, diagnostics, and robotics/aeronautics technologies. Suppression of pathogens must be enforced both before and during an epidemic outbreak, the former allowing more drastic measures before the pathogens harbor the host. We propose in this expert review that microbiome-level intervention might particularly prove as an effective solution in medical and environmental scales against traditional, currently emerging, and future infectious threats. We conclude with a discussion on the ways in which the humanome and microbiome contest and cooperate, and how this knowledge might usefully inform in addressing the GCBRs, bioterrorism, and associated threats in the pursuit of pan-biosurveillance.

Agrigenomics is one of the emerging focus areas for omics sciences. Yet, agrigenomics differs from medical omics applications such as pharmacogenomics and precision medicine, by virtue of vastly distributed geography of applications at the intersection of agriculture, nutrition, and genomics research streams. Crucially, agrigenomics can address diagnostics and safety surveillance needs in remote and rural farming communities or decentralized food, crop, and environmental monitoring programs for prompt, selective, and differential identification of pathogens. A case in point is the potato crop that serves as a fundamental nutritional source worldwide. Decentralized potato crop and plant protection facilities are pivotal to minimize unnecessary, preemptive use of broad-spectrum fungicides, thus helping to curtail the costs, environmental burden, and the development of resistance in opportunistic human pathogenic fungi. We report here a polymerase chain reaction-restriction fragment length polymorphism approach that is sensitive and adaptable in detection and broad identification of fungal pathogens in potato crops, with a view to future decentralized agrigenomic surveillance programs. Notably, the fingerprinting patterns obtained by the method fully differentiated 12 fungal species examined in silico, with 10 of them also tested in vitro. The method can be scaled up through improvements in electrophoresis and enzyme panel for adaption to other crops and/or pathogens. We suggest that decentralized and integrated agrosurveillance programs and translational agrigenomic programs can inform future innovations in multidomain biosecurity, particularly across omics applications from agriculture and nutrition to clinical medicine and environmental biosafety.

Common bean (Phaseolus vulgaris) is a traditional vegetable in Bulgaria. The area grown in for 2013 was estimated to be 344 ha which increased gradually to reach 708 ha in 2016. During the summer of 2013, leaf samples (n=76) with …

There are many factors determining the strawberry organoleptic profile and they are difficult to define. In this study, the sensory, physical, and chemical quality characteristics, the antioxidant properties as examined using ferric reducing antioxidant power (FRAP) and 1-diphenyl-2-picrylhydrazyl (DPPH) assays, the lactone concentration, and the FaFAD1 expression of ripe strawberries (cv. Camarosa, Florida Fortuna, and Sabrina) from Greece were evaluated and their interrelationships were investigated.'Camarosa' had the highest antioxidant capacity and polyphenol content, although significant intra-cultivar variations of sugars, solid soluble content/titratable acidity (SSC/TA), red color intensity, sweetness, and hardness were recorded. In 'Sabrina' there was a constant lactone presence and FaFAD1 expression; it also had the lowest ascorbic acid content, the highest pH, SSC/TA index, firmness, and sweetness. 'Fortuna' showed the lowest sweetness and aroma indices, whereas 'Camarosa' had intermediate ones. Overall, firmness was correlated with hardness, while pH and SSC/TA index correlated with juiciness and sweetness. Both γ-decalactone and γ-dodecalactone concentrations were correlated with FaFAD1 expression and pH, but they did not solely determine the aroma sensory perception. In total, FRAP values were positively correlated with ascorbic acid and polyphenol content, and negatively with pH.Significant inter- and intra-cultivar variation was recorded, revealing the impact of the genotype and underlining the effect of microenvironmental and cultivation conditions on quality and sensory perception. © 2018 Society of Chemical Industry.

Electrostimulation (ES), hitherto successfully employed in wound treatment, has shown potential in antimicrobial applications, suggesting its use as synergistic to or replacement of antibiotics. The differential susceptibility of pathogens and host tissue and organs to various ES modalities might allow selective use against specific infections. The use of ES is cheaper in terms of development/testing, routine application and environmental footprint. If extensive substitution of chemical compounds is achieved, the development of resistance might be reversed through negative selection. A promising setup of ES seems to be the noncontact current transfer, due to low amperage similar to innate bioelectricity, painlessness, simple logistics and low risk for treatment-caused infection.