Microbes and us: microbiology literacy in Greece.

Microbes are ubiquitous and provide numerous services to humans and our planet. However, a query arises as to whether these microbial services are valued by the general public especially after unprecedented conditions like the COVID-19 pandemic. In this context a survey was conducted to investigate the concept of microbe in Greece. Thematic analysis of 672 anonymous responses (age range 4-75yo) received for the open-ended prompt "What is the first thing that comes to mind when you hear the word microbe?" revealed five thematic categories: Negative emotions, Fuzzy associations, Biology, Entities and Health. Almost 80% of responses fell under "Biology" and "Health" and the general pattern of answers was the same across all age groups. Microbes took a variety of forms in the minds of respondents, however, the concept of "microbe" seems to be more unshaped at younger ages (4-11yo), as revealed in children's language choices. Overall, the often-negative perception of microorganisms seems to be confirmed in this study. Although this research was limited to participants from Greece, it remains relevant to other countries around the world as well. We discuss the reasons behind this negative perception and offer suggestions for reversing it.

Reflections on the Teaching Symposium at the Microbiology Society Annual Conference 2023.

The Microbiology Society Education and Outreach Network (EON) recently hosted the Teaching Symposium at the Microbiology Society Annual Conference, sponsored by Access Microbiology. The presence of the Symposium as an established parallel session within the wider Annual Conference reflects the importance of high-quality, contemporary microbiology education and outreach delivered in an enthusiastic and inclusive manner. At the 2023 Symposium, a variety of pedagogical research projects in higher education learning, teaching and assessment, as well as public engagement projects, were showcased through invited talks, offered talks, flash talks and posters. The event was attended by up to 70 delegates. Several themes were noted throughout the day: engaging with Gen Z (Generation Z, those born between 1996 and 2010), active learning, art in science and engaging with non-higher education (HE) audiences. Inclusivity was a key driver in the organization of the Symposium; the room was set up to encourage discussion and participants could ask questions using an online platform as well as speaking in the room. We now encourage all speakers to consider publishing their work as a peer-reviewed article for further dissemination and impact.

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions.

Multi-strain probiotics are widely regarded as effective products for improving gut microbiota stability and host health, providing advantages over single-strain probiotics. However, in general, it is unclear to what extent different strains would cooperate or compete for resources, and how the establishment of a common biofilm microenvironment could influence their interactions. In this work, we develop an integrative experimental and computational approach to comprehensively assess the metabolic functionality and interactions of probiotics across growth conditions. Our approach combines co-culture assays with genome-scale modelling of metabolism and multivariate data analysis, thus exploiting complementary data- and knowledge-driven systems biology techniques. To show the advantages of the proposed approach, we apply it to the study of the interactions between two widely used probiotic strains of Lactobacillus reuteri and Saccharomyces boulardii, characterising their production potential for compounds that can be beneficial to human health. Our results show that these strains can establish a mixed cooperative-antagonistic interaction best explained by competition for shared resources, with an increased individual exchange but an often decreased net production of amino acids and short-chain fatty acids. Overall, our work provides a strategy that can be used to explore microbial metabolic fingerprints of biotechnological interest, capable of capturing multifaceted equilibria even in simple microbial consortia.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review.

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

A guide to pedagogical research for scientists from a biological sciences background.

How we teach science and engage with the public, particularly in fast moving subjects such as microbiology, are constantly being reflected upon, improved and innovated. This has led to a significant increase of pedagogy publications by microbiology educators in higher education that have had a positive impact on teaching quality, student retention, progression and course satisfaction as well as how science is communicated with the public. In this paper we describe the different types of pedagogical manuscripts that biological scientists could write and the benefits that derive from doing so. We provide a glossary of terms often seen in educational literature. Project design and qualitative and quantitative research methodologies are discussed, highlighting ethical and General Data Protection Regulation (GDPR) considerations. Suggestions are made regarding how to network with colleagues who are also keen on writing pedagogical papers as well as examples of good practice. Lastly, a handy how-to-start guide aims to help with first steps. We hope that this paper will be a useful survival manual for colleagues who wish to engage in exciting pedagogical research in the field of microbiology and the broader biological sciences.

In Silico Genomic and Metabolic Atlas of Limosilactobacillus reuteri DSM 20016: An Insight into Human Health.

Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful metabolites. The strain was explored using genomic and proteomic tools, manual searches, and databases, including KEGG, STRING, BLAST Sequence Similarity Search, and UniProt. This study located over 200 key genes that were involved in human health benefit pathways. L. reuteri DSM 20016 has metabolic pathways to produce acetate, propionate, and lactate, and there is evidence of a pathway for butanoate production through a FASII mechanism. The bacterium produces histamine through the hdc operon, which may be able to suppress proinflammatory TNF, and the bacterium also has the ability to synthesize folate and riboflavin, although whether they are secreted is yet to be explored. The strain can bind to human Caco2 cells through srtA, mapA/cnb, msrB, and fbpA and can compete against enteric bacteria using reuterin, which is an antimicrobial that induces oxidative stress. The atlas could be used for designing metabolic engineering approaches to improve beneficial metabolite biosynthesis and better probiotic-based cures.

Microbes Against Humanity, a workshop game for horrible students: using a creative card game in higher education microbiology teaching.

Introducing creative workshops in higher education curricula, in addition to formal lectures, is an excellent way of reinforcing knowledge and encouraging creative thinking. In particular, the use of card games as a tool for inducing student engagement and enthusiasm has been reported to be a very effective approach. Here, we report an innovative card game-based workshop for use at the intermediate undergraduate level. The name of the game is Microbes Against Humanity and has been adapted from the widely known party game Cards Against Humanity, which is freely available under a creative commons licence. Overall, 64 students and two academics participated in this 2 h workshop. Our students found the workshop to be very enjoyable, considered it to be helpful for their learning and suggested interesting ideas for further improvement. In conclusion, it was shown that such exciting workshops can trigger students' enthusiasm for microbiology and enhance their learning potential.

Toll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function.

Innate immunity mediated by Toll-like receptors (TLRs), which can recognize pathogen molecular patterns, plays a critical role in type 1 diabetes development. TLR7 is a pattern recognition receptor that senses single-stranded RNAs from viruses and host tissue cells; however, its role in type 1 diabetes development remains unclear. In our study, we discovered that Tlr7-deficient (Tlr7-/-) nonobese diabetic (NOD) mice, a model of human type 1 diabetes, exhibited a significantly delayed onset and reduced incidence of type 1 diabetes compared with Tlr7-sufficient (Tlr7+/+) NOD mice. Mechanistic investigations showed that Tlr7 deficiency significantly altered B-cell differentiation and immunoglobulin production. Moreover, Tlr7-/- NOD B cells were found to suppress diabetogenic CD4+ T-cell responses and protect immunodeficient NOD mice from developing diabetes induced by diabetogenic T cells. In addition, we found that Tlr7 deficiency suppressed the antigen-presenting functions of B cells and inhibited cytotoxic CD8+ T-cell activation by downregulating the expression of both nonclassical and classical MHC class I (MHC-I) molecules on B cells. Our data suggest that TLR7 contributes to type 1 diabetes development by regulating B-cell functions and subsequent interactions with T cells. Therefore, therapeutically targeting TLR7 may prove beneficial for disease protection.

Antibiofilm Activity of Heather and Manuka Honeys and Antivirulence Potential of Some of Their Constituents on the DsbA1 Enzyme of Pseudomonas aeruginosa.

Heather honey was tested for its effect on the formation of biofilms by Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, Salmonella Enteriditis and Acinetobacter baumanii in comparison with Manuka honey. At 0.25 mg/mL, Heather honey inhibited biofilm formation in S. aureus, A. baumanii, E. coli, S. Enteriditis and P. aeruginosa, but promoted the growth of E. faecalis and K. pneumoniae biofilms. Manuka honey inhibited biofilm formation in K. pneumoniae, E. faecalis, and S. Enteriditis, A. baumanii, E. coli and P. aeruginosa, but promoted S. aureus biofilm formation. Molecular docking with Autodock Vina was performed to calculate the predictive binding affinities and ligand efficiencies of Manuka and Heather honey constituents for PaDsbA1, the main enzyme controlling the correct folding of virulence proteins in Pseudomonas aeruginosa. A number of constituents, including benzoic acid and methylglyoxal, present in Heather and/or Manuka honey, revealed high ligand efficiencies for the target enzyme. This helps support, to some extent, the decrease in P. aeruginosa biofilm formation observed for such honeys.

Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.

Methicillin-resistant Staphylococcus aureus (MRSA) strains are important human pathogens and a significant health hazard for hospitals and the food industry. They are resistant to ß-lactam antibiotics including methicillin and extremely difficult to treat. In this study, we show that the Staphylococcus aureus COL (MRSA) strain, with a known complete genome, can easily survive and grow under acidic and alkaline conditions (pH5 and pH9, respectively), both planktonically and as a biofilm. A microarray-based analysis of both planktonic and biofilm cells was performed under acidic and alkaline conditions showing that several genes are up- or down-regulated under different environmental conditions and growth modes. These genes were coding for transcription regulators, ion transporters, cell wall biosynthetic enzymes, autolytic enzymes, adhesion proteins and antibiotic resistance factors, most of which are associated with biofilm formation. These results will facilitate a better understanding of the physiological adjustments occurring in biofilm-associated S. aureus COL cells growing in acidic or alkaline environments, which will enable the development of new efficient treatment or disinfection strategies.

Effect of Rocket (Eruca sativa) Extract on MRSA Growth and Proteome: Metabolic Adjustments in Plant-Based Media.

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) in food has provoked a great concern about the presence of MRSA in associated foodstuff. Although MRSA is often detected in various retailed meat products, it seems that food handlers are more strongly associated with this type of food contamination. Thus, it can be easily postulated that any food could be contaminated with this pathogen in an industrial environment or in household and cause food poisoning. To this direction, the effect of rocket (Eruca sativa) extract on MRSA growth and proteome was examined in the present study. This goal was achieved with the comparative study of the MRSA strain COL proteome, cultivated in rocket extract versus the standard Luria-Bertani growth medium. The obtained results showed that MRSA was able to grow in rocket extract. In addition, proteome analysis using 2-DE method showed that MRSA strain COL is taking advantage of the sugar-, lipid-, and vitamin-rich substrate in the liquid rocket extract, although its growth was delayed in rocket extract compared to Luria-Bertani medium. This work could initiate further research about bacterial metabolism in plant-based media and defense mechanisms against plant-derived antibacterials.

Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2).

BACKGROUND: The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset. FINDINGS: A microarray dataset using samples from two replicate cultures for each nutrient limitation was generated. In this report our analysis has focused on the genes which are significantly differentially expressed, as determined by Rank Products Analysis, between samples from matched time points correlated by growth phase for the three pairs of differently limited culture datasets. With a few exceptions, genes are only significantly differentially expressed between the N6/N7 time points and their corresponding time points in the C and P-limited cultures, with the vast majority of the differentially expressed genes being more highly expressed in the N-limited cultures. Our analysis of these genes indicated expression of several members of the GlnR regulon are induced upon nitrogen limitation, as assayed for by [NH4+] measurements, and we are able to identify several additional genes not present in the GlnR regulon whose expression is induced in response to nitrogen limitation. We also note SCO3327 which encodes a small protein (32 amino acid residues) unusually rich in the basic amino acids lysine (31.25%) and arginine (25%) is significantly differentially expressed in the nitrogen limited cultures. Additionally, we investigate the expression of known members of the GlnR regulon and the relationship between gene organization and expression for the SCO2486-SCO2487 and SCO5583-SCO5585 operons. CONCLUSIONS: We provide a list of genes whose expression is differentially expressed in low nitrogen culture conditions, including a putative nitrogen storage protein encoded by SCO3327. Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. These genes represent likely targets for future studies into the nitrogen starvation response in Streptomyces coelicolor.