Maintenance of sterility in SMS packaging in dental environments: concern with biosafety

Healthcare services must be guided by biosafety practices and microbial control. This control is highly influenced by humidity, which directly impacts the maintenance of sterility of the materials used in the appointments. High concentration of moisture, in the form of aerosol, splashes and spills, is caused during dental care. During the COVID-19 times the contamination by aerosol and droplets worries greatly. Considering that it could cause harm to the sterility of an autoclaved material, especially in dental environments, the objective was to evaluate the behavior of SMS sterilization packages (Spunbonded / Meltblown / Spunbonded) against microbial penetration in an aqueous vehicle. SMS of three brands were challenged, equally divided into two groups: virgin and processed (subjected to a single autoclaving cycle). Each specimen was aseptically deposited on Macconkey agar. Subsequently, 5 µL of Escherichia coliATCC 25922 saline solution [108CFU mL-1] was deposited in center of the SMS specimen and the dish incubated at36°C/ 48h. Reading was performed by the presence or absence of bacterial growth typical of the species under the SMS, observed on the back of Petri dish. The lowest penetration rate observed was 60% for one of the brands in the virgin condition, and 75% for two brands in the processed condition. Statistical analysis showed an association between bacterial penetration and the evaluated group, this association being valid only in the virgin condition. The different SMS behave similarly in terms of resistance to bacterial penetration after being processed. The data show that moisture can assist in bacterial transport through sterilized SMS. Therefore, SMS packages are not able to prevent bacterial penetration, and possibly other microorganisms, when in aqueous vehicles, offering a potential risk of breaking the aseptic chain. Thus, care must be taken in routines for handling and storage sterile packaging.

Curating COBRA Models of Microbial Metabolism.

Constraint-based reconstruction and analysis (COBRA) methods have been used for over 20 years to generate genome-scale models of metabolism in biological systems. The COBRA models have been utilized to gain new insights into the biochemical conversions that occur within organisms and allow their survival and proliferation. Using these models, computational biologists can conduct a variety of different analyses such as examining network structures, predicting metabolic capabilities, resolving unexplained experimental observations, generating and testing new hypotheses, assessing the nutritional requirements of a biosystem and approximating its environmental niche, identifying missing enzymatic functions in the annotated genomes, and engineering desired metabolic capabilities in model organisms. This chapter details the protocol for developing curated system-level COBRA models of metabolism in microbes.

Fungal Dysbiosis in Children with Celiac Disease.

BACKGROUND: Although intestinal fungi are known to interact with the immune system, the relationship between intestinal fungi and childhood celiac disease (CeD), an immune-mediated condition, has rarely been reported. AIMS: The aim of this study was to describe gut fungal profiles in a cohort of children with new-onset CeD. METHODS: Mucosal and fecal samples were collected from children with CeD and controls and subjected to metagenomics analysis of fungal microbiota communities. DNA libraries were sequenced using Illumina HiSeq platform 2 × 150 bp. Bioinformatic analysis was performed to quantify the relative abundance of fungi. Shannon alpha diversity metrics and beta diversity principal coordinate (PCo) analyses were calculated, and DESeq tests were performed between celiac and non-celiac groups. RESULTS: Overall more abundant taxa in samples of children with CeD included Tricholomataceae, Saccharomycetaceae, Saccharomycetes Saccharomyces cerevisiae, and Candida, whereas less abundant taxa included Pichiaceae, Pichia kudriavzevii, Pneumocystis, and Pneumocystis jirovecii. Alpha diversity between CeD and control individuals did not differ significantly, and beta diversity PCo analysis showed overlap of samples from CeD and controls for both fecal or mucosal samples; however, there was a clear separation between mucosal and fecal overall samples CONCLUSIONS: We report fungal dysbiosis in children with CeD, suggesting a possible role in the pathogenesis of CeD. Further larger, controlled, prospective and longitudinal studies are needed to verify the results of this study and clarify the functional role of fungi in CeD.

Manual de biossegurança e bioprotecção 2ª edição, 2022 / Biosafety and bioprotection 2nd edition, 2022

A Biossegurança e Bioprotecção em Laboratórios de Saúde Pública, Laboratórios de Análises Clínicas e instituções de pesquisa em saúde são áreas do conhecimento relativamente novas, reguladas em vários países por um conjunto de leis, normas, directrizes e procedimentos específicos. Actualmente, a Biossegurança e a Bioprotecção são vistas como disciplinas científicas que requerem um domínio de conhecimentos, habilidades e atitudes (CHA) multi-disciplinares. A aplicação dos princípios de Biossegurança e Bioprotecção é essencial para conter, prevenir, reduzir e eliminar os riscos de exposição por agentes microbiológicos, químicos, físicos, ergonómicos, acidentais e entre outros perigos que podem ou poderiam causar doenças de âmbito ocupacional. A Biossegurança e a Bioprotecção são também importantes para prevenir a exposição a riscos aos familiares de profissionais de saúde, utentes dos serviços de saúde, e para garantir a protecção do meio ambiente e da vida selvagem

Service-learning in microbiology during the pandemic: A Malaysian perspective

Aims@#During the Covid-19 pandemic, adaptation, flexibility and creativity is paramount in conducting Service-Learning courses. The study aims to evaluate the feasibility of a hybrid mode service-learning in Microbiology course conducted over a semester which involved undergraduate students being strewn all over the country, with highly diversified conditions varying from local movement control laws and availability of facilities such as internet access.@*Methodology and results@#A cohort of undergraduate students conducted the course from the comfort of their own homes to teach underprivileged school students. The undergraduate students engaged school students in the proximity of their location, then conducted STEM activities over the course of a few weeks either via face-to-face, online or hybrid mode. Microbiology activities included microscopy using a Foldscope (paper microscope), isolation and growth of microbes, preparation of microbe-related food and others. Surveys were conducted with school students pre- and postprogramme, parents and the undergraduate students conducting the programme. While the school students benefitted from highly engaging STEM modules, the undergraduate students underwent a steep learning curve, mentoring school students in STEM whilst juggling challenges presented by the pandemic but finally achieved all learning outcomes.@*Conclusion, significance and impact of study@#Service-learning for life sciences subjects can be conducted efficiently during a pandemic when flexibility and freedom is given to students to achieve the learning outcomes.

Methane from microbial hydrogenolysis of sediment organic matter before the Great Oxidation Event.

Methane, along with other short-chain alkanes from some Archean metasedimentary rocks, has unique isotopic signatures that possibly reflect the generation of atmospheric greenhouse gas on early Earth. We find that alkane gases from the Kidd Creek mines in the Canadian Shield are microbial products in a Neoarchean ecosystem. The widely varied hydrogen and relatively uniform carbon isotopic compositions in the alkanes infer that the alkanes result from the biodegradation of sediment organic matter with serpentinization-derived hydrogen gas. This proposed process is supported by published geochemical data on the Kidd Creek gas, including the distribution of alkane abundances, stable isotope variations in alkanes, and CH2D2 signatures in methane. The recognition of Archean microbial methane in this work reveals a biochemical process of greenhouse gas generation before the Great Oxidation Event and improves the understanding of the carbon and hydrogen geochemical cycles.

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.

This research addresses the interactions between the unicellular slime mold Physarum polycephalum and a red yeast in a spatial ecosystem over week-long imaging experiments. An inverse relationship between the growth rates of both species is shown, where P. polycephalum has positive growth when the red yeast has a negative growth rate and vice versa. The data also captures successional and oscillatory dynamics between both species. An advanced image analysis methodology for semantic segmentation is used to quantify population density over time, for all components of the ecosystem. We suggest that P. polycephalum is capable of exhibiting a sustainable feeding strategy by depositing a nutritive slime trail, allowing yeast to serve as a periodic food source. This opens a new direction of P. polycephalum research, where the population dynamics of spatial ecosystems can be readily quantified and complex ecological dynamics can be studied.

Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells.

Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate λ decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in λ we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a "sizer" and an "adder"). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies.

A novel relationship for the maximum specific growth rate of a microbial guild.

One of the major parameters that characterizes the kinetics of microbial processes is the maximum specific growth rate. The maximum specific growth rate for a single microorganism (${\mu _{max}}$) is fairly constant. However, a certain microbial process is typically catalyzed by a group of microorganisms (guild) that have various ${\mu _{max}}$ values. In many occasions, it is not feasible to breakdown a guild into its constituent microorganisms. Therefore, it is a common practice to assume a constant maximum specific growth rate for the guild ($\acute{\mu}_{max}$) and determine its value by fitting experimental data. This assumption is valid for natural environments, where microbial guilds are stabilized and dominated by microorganisms that grow optimally in those environments' conditions. However, a change in an environment's conditions will trigger a community shift by favoring some of the microorganisms. This shift leads to a variable ${\acute{\mu}_{max}}$ as long as substrate availability is significantly higher than substrate affinity constant. In this work, it is illustrated that the assumption of constant ${\acute{\mu}_{max}}$ may underestimate or overestimate microbial growth. To circumvent this, a novel relationship that characterizes changes in ${\acute{\mu}_{max}}$ under abundant nutrient availability is proposed. The proposed relationship is evaluated for various random microbial guilds in batch experiments.

An overview of neonicotinoids: biotransformation and biodegradation by microbiological processes.

Neonicotinoids are a class of pesticides widely used in different phases of agricultural crops. Similar to other classes of pesticides, they can damage human and environmental health if overused, and can be resistent to degradation. This is especially relevant to insect health, pollination, and aquatic biodiversity. Nevertheless, application of pesticides is still crucial for food production and pest control, and should therefore be carefully monitored by the government to control or reduce neonicotinoid contamination reaching human and animal feed. Aware of this problem, studies have been carried out to reduce or eliminate neonicotinoid contamination from the environment. One example of a green protocol is bioremediation. This review discusses the most recent microbial biodegradation and bioremediation processes for neonicotinoids, which employ isolated microorganisms (bacteria and fungi), consortiums of microorganisms, and different types of soils, biobeds, and biomixtures.

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research. We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links.

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.

Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity; extensions allow estimates from 16S rRNA sequences alone as well as weighted community estimates from metagenomes. We compared the growth rates of cultivated and uncultivated organisms to illustrate how culture collections are strongly biased toward organisms capable of rapid growth. Finally, we found that organisms naturally group into two growth classes and observed a bias in growth predictions for extremely slow-growing organisms. These observations ultimately led us to suggest evolutionary definitions of oligotrophy and copiotrophy based on the selective regime an organism occupies. We found that these growth classes are associated with distinct selective regimes and genomic functional potentials.

AMR and Covid-19 on the Frontline: A Call to Rethink War, WASH, and Public Health.

This Viewpoint calls for a greater understanding of the role that water plays in the transmission of anti-microbial resistance and covid-19 in protracted urban armed conflict, in order to develop a 'pathogen-safe' practice. It argues that dealing with the twin threats is difficult enough in the best of circumstances, and is so little understood in war zones that surgeons and water engineers now question if their practice does more harm than good. Experience suggests that the known transmission routes are complicated by a great number of factors, including the entry of heavy metals through bullets in patients' wounds, hospital over-crowding, mutation in treated water or wastewater, and other threats which endure long after the bombing has stopped. The skeleton research agenda proposes greater sewage surveillance, testing of phages and monitoring of treatment designed to dispel or substantiate these assertions.

Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data.

BACKGROUND: Alterations of gut microbiota may play a role in Anorexia Nervosa (AN) through perturbations of the gut-brain axis. Some studies found differences in the gut microbiota of patients with AN compared to healthy controls, but results are heterogeneous. The aim of this work was to systematically review the existing studies comparing gut microbial composition in AN and healthy controls, and to perform a quantitative synthesis of the pooled clinical and microbiological data, when available. METHODS: A comprehensive literature search was performed to identify human studies investigating relationships between AN and gut microbiota. Microbiome datasets from studies were pooled and analysed focusing on alpha and beta-diversity and the relative abundance of microbial species in patients' gut microbiota compared to healthy controls. RESULTS: Nine studies were eligible for the systematic review, of which 4 were included in the quantitative synthesis. Preserved alpha-diversity and decreased beta-diversity in AN emerged from the qualitative synthesis, while a slight increase of alpha-diversity (d < 0.4) and comparable beta-diversity were reported by the quantitative synthesis. Out of the 46 common species compared, three had a large combined effect size (d ≥ 0.9) to differentiate patients from controls, namely Alistipes, Parabacterioides and Roseburia. The latter was also correlated with BMI (ρ = 0.29). CONCLUSIONS: The decrease of butyrate-producing species and the increase of mucine-degrading species may represent hallmarks of the gut microbiota alterations in AN, and therefore potentially interesting therapeutic targets. The heterogeneity of clinical and methodological characteristics hampers the generalizability of the results. Standardized research methods could improve comparability among studies to better identify the alterations of gut microbiota in AN.

Stability of a non-local kinetic model for cell migration with density-dependent speed.

The aim of this article is to study the stability of a non-local kinetic model proposed by Loy & Preziosi (2020a) in which the cell speed is affected by the cell population density non-locally measured and weighted according to a sensing kernel in the direction of polarization and motion. We perform the analysis in a $d$-dimensional setting. We study the dispersion relation in the one-dimensional case and we show that the stability depends on two dimensionless parameters: the first one represents the stiffness of the system related to the cell turning rate, to the mean speed at equilibrium and to the sensing radius, while the second one relates to the derivative of the mean speed with respect to the density evaluated at the equilibrium. It is proved that for Dirac delta sensing kernels centered at a finite distance, corresponding to sensing limited to a given distance from the cell center, the homogeneous configuration is linearly unstable to short waves. On the other hand, for a uniform sensing kernel, corresponding to uniformly weighting the information collected up to a given distance, the most unstable wavelength is identified and consistently matches the numerical solution of the kinetic equation.

Microbiologically Induced Carbonate Precipitation in the Restoration and Conservation of Cultural Heritage Materials.

Microbiologically induced carbonate precipitation (MICP) is a well-known biogeochemical process that allows the formation of calcium carbonate deposits in the extracellular environment. The high concentration of carbonate and calcium ions on the bacterial surface, which serves as nucleation sites, promotes the calcium carbonate precipitation filling and binding deteriorated materials. Historic buildings and artwork, especially those present in open sites, are susceptible to enhanced weathering resulting from environmental agents, interaction with physical-chemical pollutants, and living organisms, among others. In this work, some published variations of a novel and ecological surface treatment of heritage structures based on MICP are presented and compared. This method has shown to be successful as a restoration, consolidation, and conservation tool for improvement of mechanical properties and prevention of unwanted gas and fluid migration from historical materials. The treatment has revealed best results on porous media matrixes; nevertheless, it can also be applied on soil, marble, concrete, clay, rocks, and limestone. MICP is proposed as a potentially safe and powerful procedure for efficient conservation of worldwide heritage structures.

Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes.

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Large Deviation Principle Linking Lineage Statistics to Fitness in Microbial Populations.

In exponentially proliferating populations of microbes, the population doubles at a rate less than the average doubling time of a single-cell due to variability at the single-cell level. It is known that the distribution of generation times obtained from a single lineage is, in general, insufficient to determine a population's growth rate. Is there an explicit relationship between observables obtained from a single lineage and the population growth rate? We show that a population's growth rate can be represented in terms of averages over isolated lineages. This lineage representation is related to a large deviation principle that is a generic feature of exponentially proliferating populations. Due to the large deviation structure of growing populations, the number of lineages needed to obtain an accurate estimate of the growth rate depends exponentially on the duration of the lineages, leading to a nonmonotonic convergence of the estimate, which we verify in both synthetic and experimental data sets.

A review of the nature, role and control of lithobionts on stone cultural heritage: weighing-up and managing biodeterioration and bioprotection.

Lithobionts (rock-dwelling organisms) have been recognized as agents of aesthetic and physico-chemical deterioration of stonework. In consequence, their removal from cultural heritage stone surfaces (CHSS) is widely considered a necessary step in conservation interventions. On the other hand, lithobiontic communities, including microbial biofilms ('biological patinas'), can help integrate CHSS with their environmental setting and enhance biodiversity. Moreover, in some cases bioprotective effects have been reported and even interpreted as potential biotechnological solutions for conservation. This paper reviews the plethora of traditional and innovative methodologies to characterize lithobionts on CHSS in terms of biodiversity, interaction with the stone substrate and impacts on durability. In order to develop the best management and conservation strategies for CHSS, such diagnosis should be acquired on a case-by-case basis, as generalized approaches are unlikely to be suitable for all lithobionts, lithologies, environmental and cultural contexts or types of stonework. Strategies to control biodeteriogenic lithobionts on CHSS should similarly be based on experimental evaluation of their efficacy, including long-term monitoring of the effects on bioreceptivity, and of their environmental safety. This review examines what is known about the efficacy of control methods based on traditional-commercial biocides, as well as those based on innovative application of substances of plant and microbial origin, and physical techniques. A framework for providing a balanced scientific assessment of the role of lithobionts on CHSS and integrating this knowledge into management and conservation decision-making is presented.

From waste to fuel: Energy recovery from household food waste via its bioconversion to energy carriers based on microbiological processes.

In the present study the bioconversion of dried household food waste (FORBI) to energy carriers was investigated aiming to its sustainable management and valorization. FORBI was either directly fermented towards ethanol and hydrogen or was previously subjected to extraction with water resulting to a liquid fraction (extract) rich in sugars and a solid residue, which were then fermented separately. Subsequently, the effluents were assessed as substrates for methane production via anaerobic digestion (AD). Mono-cultures and co-cultures of C5 and C6 yeasts were used for the alcoholic fermentation whereas for the production of hydrogen, mixed acidogenic consortia were used. Taking into account the optimum yields of biofuels, the amount of recoverable energy was estimated based for each different approach. The maximum ethanol yield was 0.16 g ethanol per kg of FORBI and it was achieved for separate fermentation of liquid and solid fractions of the waste. The highest hydrogen yield that was observed was 210.44 L ± 4.02 H2/kg TS FORBI for 1% solids loading and supplementation with cellulolytic enzymes. Direct AD of either the whole FORBI or its individual fractions led to lower overall energy recovery, compared to that obtained when fermentation and subsequent AD were applied. The recoverable energy was estimated for the different exploitation approaches of the waste. The maximum achieved recoverable energy was 21.49 ± 0.57 MJ/kg.