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In June 2019, the 12th International Conference on Halophilic Microorganisms - Halophiles 2019, was held in Cluj-Napoca, Romania. This thematic issue of FEMS Microbiology Letters contains papers based on lectures and posters presented at the conference. We here provide a short overview of past research on hypersaline environments in Romania and the microorganisms inhabiting them, and briefly present the papers published in this thematic issue., (© FEMS 2020.)

Microbiology is an area with a high research production, classified in different branches. Thus, it is difficult to identify research trends without many backgrounds. The present paper aims to apply bibliometric methods to identify the highly cited papers that contribute to the Microbiology development. Furthermore, a science mapping analysis allows discovering the main thematic areas covered by those detected papers. From the 572 153 papers (articles and reviews) indexed in the Web of Science Microbiology category (1900-2017), a total of 645 highly cited papers were detected. Concerning the main scientific producers in Microbiology, Applied and Environmental Microbiology as a journal, R. Knight from the University of Colorado (USA) as an author and the USA as a country are the most productive actors. Nevertheless, taking into account the gross domestic product per capita, China and Spain are remarkable countries. Furthermore, according to the relative priority index (RPI), Denmark, Belgium, Spain and The Netherlands are the countries that make a higher scientific effort in this field. About the co-word analysis, several important themes were detected, such as Next Generation Sequencing, Gene, Escherichia Coli or Gene Expression. Concerning these results, this work supposes a framework on which to base future research.

Several Eastern Harris County communities lie near the now enclosed San Jacinto River (SJR) Waste Pit Superfund, a dumping ground for chlorinated dioxins and other paper mill waste products. Currently, no active monitoring of the SJR is conducted for these toxins with the exact concentration and health impact to the area unknown. As such, remediation and monitoring efforts outside of the Superfund itself could be necessary. To better understand the possible environmental fate of these aromatics, here we provide a shotgun metagenomic analysis of the structural and putative functional diversity of the SJR microbiome from two impacted Channelview, Texas communities bordering the Superfund. Results show that the underlying SJR microbiome possesses a core of metabolic enzymes related to the β-ketoadipate and benzoate degradation pathways. This suggests possible endpoints for many aromatics found deposited in the SJR including dioxin-like compounds. However, degradation biomarkers related to the priming and initial cleavage of chlorinated dioxin-like aromatics while present, are poorly concentrated across sampled sites. This may be due in part to decreased coverage of low abundance bacterial species, but also be a contributing factor leading to increased recalcitrance of these compounds in this environment compared to other aromatics. [ABSTRACT FROM AUTHOR]

Sludges from pulp and paper mills represent a major ecological and environmental cost, and anaerobic digestion represents a method of waste reduction and energy recovery for these mills. This study compared methane production potential and microbial communities across 11 primary- and biosludges from five pulp and paper mills using various mill processes. We measured methane production from sludges in anaerobic batch reactor experiments over 64 days. Sludges were incubated with and without added substrate to test for organic substrate limitation versus inhibition of methanogens. Initial microbial communities and changes to community composition were determined using Illumina MiSeq for metabarcoding of bacterial and archaeal 16S rRNA genes. Mean methane production potential varied greatly between sludges (0.002–79 mL CH4 g–1 TS). Among primary sludges, kraft mill sludge produced more methane than other mill types. For these other mills, biosludge produced more methane than primary sludge, which had evidence of methanogen inhibition. Microbial communities and diversity were influenced by the initial community composition, and high methane production was only seen in sludges with high diversity. A number of sludges innately produced substantial methane and may be targets for further modelling and larger scale testing of anaerobic digestion. [ABSTRACT FROM AUTHOR]

Genomic sequencing analysis and previous studies have shown that there are eight genes in Streptomyces coelicolor A3(2) encoding putative cellulases. One of these genes, sco6548, was cloned into the Streptomyces/Escherichia coli shuttle vector pUWL201PW. The recombinant protein was successfully overexpressed in S. lividans TK24 under the control of the strong ermE promoter. Sco6548 was 1740 bp in length, and encoded a 579-amino acid-, 60.8-kDa protein with strong hydrolyzing activity toward Avicel and filter paper, yielding cellobiose as the final product. SCO6548 showed optimal activity at 50°C and pH 5. The Km values of SCO6548 toward Avicel and filter paper were 15.38 and 16.1 mg/mL, respectively. The Vmax values toward Avicel and filter paper were 0.432 and 0.084 μM/min, respectively. EDTA did not affect cellulase activity; however, several divalent cations, including Co(2+), Cu(2+), Ni(2+) and Mn(2+) (at 10 mM) had severe inhibitory effects on enzyme activity. Our analysis showed that SCO6548 is a cellulose 1,4-β-cellobiosidase that hydrolyzes cellulose into cellobiose., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

In June 2019, the 12th International Conference on Halophilic Microorganisms – Halophiles 2019, was held in Cluj-Napoca, Romania. This thematic issue of FEMS Microbiology Letters contains papers based on lectures and posters presented at the conference. We here provide a short overview of past research on hypersaline environments in Romania and the microorganisms inhabiting them, and briefly present the papers published in this thematic issue. [ABSTRACT FROM AUTHOR]

Recent research has shown the potential of yeast-based biosensors (YBBs) for point-of-use detection of pathogens and target molecules in saliva, blood, and urine samples. The choice of output can greatly affect the sensitivity, dynamic range, detection time, and ease-of-use of a sensor. For visual detection without the need for additional reagents or machinery, colorimetric outputs have shown great potential. Here, we evaluated the inducible generation of prodeoxyviolacein and proviolacein as colorimetric YBB outputs and benchmarked these against lycopene. The outputs were induced via the yeast mating pathway and were compared on agar plates, in liquid culture, and on paper slips. We found that all three outputs produced comparable pigment intensity on agar plates, making them applicable for bioengineering settings. In liquid media and on paper slips, lycopene resulted in a higher intensity pigment and a decreased time-of-detection. [ABSTRACT FROM AUTHOR]

In response to the challenges presented by the COVID-19 pandemic, this paper proposes an exam system for STEM students that effectively test higher-order thinking skills, such as the ability to apply, create, evaluate, and analyse. Higher education institutions (HEIs) must incorporate all three strands of democratic STEM pedagogy, namely student voice, shared and transformational authority, and STEM criticality, according to empathy interviews with educators. It is imperative that these strands are reflected in the assessments of students within HEIs. During the pandemic, it became evident that the lack of a suitable proctored online examination system impeded the accurate and fair evaluation of students. This circumstance was in stark contrast to the offline mode of examination, which permitted monitoring and control. Notably, many students struggled to answer questions requiring higher-order thinking, with responses frequently identical in unproctored online examinations or settings with insufficient proctoring mechanisms, especially in contexts with limited resources. Consequently, there is an urgent need to redesign the online proctored test system in accordance with STEM criticality and student voice. To address this need, this paper proposes the creation of OPERHOT, a proctored online exam system integrated with random questions requiring higher-order thinking. This system employs a timed assessment methodology and requires students to keep their cameras on throughout the examination. By implementing OPERHOT, a proper and secure online evaluation of students can be made possible. In addition, this system will strengthen the online education and assessment systems in HEIs, thereby promoting integrity and enhancing the learning experience. In addition, the adoption of OPERHOT will also improve the assessment process and contribute to the enhancement of online education and assessment in HEIs as a whole. This reimagined system will catalyse the development of a robust and inclusive learning environment that encourages students' voices and equips educators to foster the growth of critical thinking and problem-solving skills. This perspective aims to address the pressing need for an updated and effective proctored assessment system in the online educational landscape while promoting STEM critical thinking and student voice. The OPERHOT platform is at the ideation stage, and once developed, it may be tested in a few HEIs. Based on the feedback from educators and other stakeholders, it can be further modified to make it more inclusive and accessible and can be offered to other HEIs for wider piloting. [ABSTRACT FROM AUTHOR]

Nontransgenic New Genomic Techniques (NGTs) have emerged as a promising tool for food industries, allowing food cultures to contribute to an innovative, safe, and more sustainable food system. NGTs have the potential to be applied to microorganisms, delivering on challenging performance traits like texture, flavour, and an increase of nutritional value. This paper brings insights on how nontransgenic NGTs applied to food cultures could be beneficial to the sector, enabling food industries to generate innovative, safe, and sustainable products for European consumers. Microorganisms derived from NGTs have the potentials of becoming an important contribution to achieve the ambitious targets set by the European 'Green Deal' and 'Farm to Fork' policies. To encourage the development of NGT-derived microorganisms, the current EU regulatory framework should be adapted. These technologies allow the introduction of a precise, minimal DNA modification in microbial genomes resulting in optimized products carrying features that could also be achieved by spontaneous natural genetic evolution. The possibility to use NGTs as a tool to improve food safety, sustainability, and quality is the bottleneck in food culture developments, as it currently relies on lengthy natural evolution strategies or on untargeted random mutagenesis. [ABSTRACT FROM AUTHOR]

We all need to adapt constantly in order to thrive in our ever-changing complex world. Thus, education and educators need to empower learners to develop a mindset and skills set of lifelong and lifewide learning. Papers from around the globe, reflecting the current drivers in education, were published in the FEMS Microbiology Letters virtual Thematic Issue 'Empowering learning' in October 2023. Its content is reviewed here to provide the context for further discussions within the professional community. The focus is on being inclusive, on lowering and removing barriers to learning, and fostering a sense of belonging. So learning communities can be established and connected in support of learning with and from each other for societal benefit, and this is discussed. Authentic learning approaches are highlighted with respect to the inherent opportunities for learners to take ownership for their learning, yet learn collaboratively, and develop resilience over time. Supporting learners in becoming self-regulated and realizing their full potential is truly worthwhile. [ABSTRACT FROM AUTHOR]

Koji is made using steamed rice and a koji mold, which plays an essential role in sake brewing. We challenge to build a new sake brewing method using the kuratsuki bacteria that have inhabited each sake brewery. In this paper, effects of the kuratsuki Kocuria strain TGY1127_2 were estimated on sake brewing in different koji conditions. Sake was produced by incubation of a mixture solution of koji , water, and sake yeast (strain K1401) with and without the kuratsuki Kocuria TGY1127_2. The effects of the kuratsuki Kocuria on the taste of the sake differed among different koji. The kuratsuki Kocuria led to an increase in ethanol concentration. Additionally, the sugar content (Brix) and acidity of the sake increased in proportion to the amount of koji. These results strongly suggest that the kuratsuki Kocuria does not adversely affect the fermentation activity of the sake yeast. Thus, the kuratsuki Kocuria had different effects on the taste of sake among different koji but the fermentation activity of the sake yeast was maintained. [ABSTRACT FROM AUTHOR]

Aggression is a complex psychological program that is influenced by genetics, environment, and psychological history. Research has shown that the hormonal levels in the body and the development of the brain can be major predictors of aggression. This review highlights recent studies that have connected the gut microbiome to alterations in hormones and brain development and how this can impact aggression. This paper also provides a systematic review on studies that directly assess the connection between the gut microbiome and aggression and reviews these connections in relation to age. We conclude with future directions that are needed to further determine the link between the microbiome and aggression among adolescents. [ABSTRACT FROM AUTHOR]

This is an invited review/commentary by the first and last authors of a paper that was the most cited in FEMS Microbiology Letters for 1996, presently showing in excess of 150 citations at Web of Science, and over 200 at Google Scholar. It was the first paper in which diffuse reflectance absorbance FT-IR spectroscopy was used with a supervised learning method in the form of artificial neural networks, and showed that this combination could succeed in discriminating a series of closely related, clinically relevant, Gram-positive bacterial strains. [ABSTRACT FROM AUTHOR]

Over the past two decades, there has been a lorry of government papers and policy reports worldwide calling for increased number and diversity of doctoral researchers and a broadening of the curriculum to meet the developing needs of respective national 'knowledge-driven' economies. This has been followed by position papers and best practice examples of employability skills development in boundary-crossing doctoral programmes, especially in response to these initiatives. However, there is a disassociation between this ample literature expounding the new doctorate with its broader remit, inclusivity and production of 'industry-ready' graduates and the comparatively sparse literature on the doctoral candidates' experiences of their programmes and career readiness. Within this review, we briefly outline international government initiatives and examples of the responses by Life Science and Biomedical doctoral programmes to address these various challenges. Furthermore, we explore the recent literature on the lived experience of doctoral researchers by examining their perception of the recent changes to the research context to make recommendations for universities and supervisors on how to better support an ever more diverse doctoral population for a wide range of career opportunities. Examples of how doctoral researchers themselves can make the best of currently available opportunities are also provided. [ABSTRACT FROM AUTHOR]

On 17 September 1683, Antonie van Leeuwenhoek, a Dutch merchant who lacked formal education and fortune, wrote a letter to the Royal Society of London describing for the first time a single-celled organism. As a tribute to this revolutionary discovery, the Portuguese Society of Microbiology with the support of the Federation of European Microbiological Societies in 2017, designated this day as International Microorganism Day (IMD), a day aiming to raise awareness about the wonderful world of microbes. Six years after the establishment of IMD, the knowledge of microbiology outreach around this celebration has expanded greatly, with 5 years of in-person and 2 years of online events. The peak of these commemorations was in 2023, with 63 parallel outreach events and more than 5000 attendees, most of which were children, and young adults. While these in-person events were occurring in the month of September, the #InternationalMicroorganismDay hashtag reached nearly 2.3 million people online, reflecting the number of users who have seen a post containing this hashtag on social media. Using a decentralized model to facilitate 63 grass-roots teams to organize events locally, IMD achieved global representation both online and offline. This paper presents details behind the organization and data on the international impact of the IMD 2022 and 2023 events, outlines plans to expand reach to more countries and audiences, and encourages readers to participate with their own events in future IMD editions so that global impact can be expanded even further. [ABSTRACT FROM AUTHOR]

Oguntola Odunbaku Sapara Williams (born Alexander Johnson Williams, 1861–1935) was a Fellow of the Royal Institute of Public Health. This paper attempts to highlight the effort of an African doctor to fight disease outbreaks during the African colonial era. His uninterrupted 32 years career as a colonial medical officer in one of the British colonies in West Africa, provided superintendence for the eradication of smallpox as a result of this, he was credited with the demystification of metaphysical involvement in the smallpox epidemic and thus eradication of smallpox in the Lagos colony. He also provided leadership for the control of bubonic plague, and tuberculosis epidemics and pioneered initiatives to reduce maternal and infant mortality by vaccination, enactment of public health law, environmental sanitation, and health education in Southwest Nigeria. [ABSTRACT FROM AUTHOR]

When Antoni van Leeuwenhoek began his work with microscopes in the late 17th century, western medicine was mostly based on the work of a Roman doctor called Galen (129–199 ad), theological interpretation, superstition, and folk remedies. During modern discussions of Van Leeuwenhoek's work, a common question from listeners is why it took so long for the link between Van Leeuwenhoek's discoveries and infectious disease to be accepted. Published literature, examples of which are discussed here, shows that many researchers, doctors, and others reported the link, even during Van Leeuwenhoek's lifetime. However, it was frequently not taken seriously by the most influential people. The scientific establishment included a faction of the Royal Society of London who called themselves the 'Mechanical Philosophers'. They ridiculed those reporting animalcule-linked infection, dismissing them as 'Contagionists'. The medical establishment also included many influential people with a lot to lose if they changed their established approaches, and many quack doctors. Most religious ministers were strongly orthodox, some even claiming that helping the sick angered God. A major problem, of course, was that technology and biological understanding also lagged far behind. Despite the fact that the use of vaccination was under active discussion in the Royal Society at the time of Van Leeuwenhoek's death and quarantine was in regular use, a possible microbial connection was apparently not considered. It was not until late in the 19th century, that Robert Koch (1843–1910) isolated Bacillus anthracis , proved that it caused anthrax, and was believed. This paper follows a lecture given during the online Microbe Forum in June 2021, and illustrates the difficulties of establishing the true link between Van Leeuwenhoek's animalcules and infectious disease in humans, animals, and plants. [ABSTRACT FROM AUTHOR]

As a native CoQ10 producer, Rhodobacter sphaeroides has been extensively engineered to enhance CoQ10 production. However, the genetic manipulations using plasmids suffer from risk of plasmid loss during propagation process, biomass impairment due to cellular burden and bio-safety concerns. In this paper, genomic manipulations via Tn7 transposition was conducted to boost the CoQ10 biosynthesis in R. sphaeroides. The titer production and content of CoQ10 were improved by 18.44% and 18.87%, respectively compared to the wild type, when an additional copy of dxs and dxr were integrated into the genome. Further overexpression of idi and ispD by genomic integration created strain RSPCDDII with CoQ10 production and content of 81.23 mg/L and 5.93 mg/g, which were 54.28 and 55.97% higher than those of the wild type. The gene segments were successfully inserted into the att Tn7 site of the R. sphaeroides genome. Meanwhile, the biomass was not affected. Compared to overexpression of genes on plasmids, this strategy could enhance protein expression to a proper level without affecting cell growth, and in a more stable manner. [ABSTRACT FROM AUTHOR]

With more than one academic year into the pandemic, it is timely to consider the lessons we learnt, and how they could shape education in the future. Papers from around the globe, reflecting on the directions we took and could take, were published in the FEMS Microbiology Letters virtual Thematic Issue 'Educating in a pandemic and beyond' in October 2021. Its content is reviewed here to facilitate discussions within the professional community. Online platforms and tools, that allowed a rapid emergency response, are covered, as well as enhancing student engagement, complementing and blending in-person activities with online elements for more flexible and accessible learning opportunities, the need for educator training, and improving science literacy overall and microbiology literacy specifically. As we go forward, in order to benefit from blended and flexible learning, we need to select our approaches based on evidence, and mindful of the potential impact on learners and educators. Education did not only continue during the pandemic, but it evolved, leading us into the future. [ABSTRACT FROM AUTHOR]

Transient modification of the environment involves the expression of specific genes and degradation of mRNAs and proteins. How these events are linked is poorly understood. CCR4-NOT is an evolutionary conserved complex involved in transcription initiation and mRNA degradation. In this paper, we report that the yeast Not4 localizes in cytoplasmic foci after cellular stress. We focused our attention on the functional characterization of the C-terminus of the Not4 protein. Molecular dissection of this region indicates that the removal of the last 120 amino acids, does not affect protein localization and function, in that the protein is still able to suppress the thermosensitivity observed in the not4Δ mutant. In addition, such shortened form of Not4, as well its absence, increases the transcription of stress-responsive genes conferring to the cell high resistance to the oxidative stress. On the contrary, the last C-terminal 211 amino acids are required for proper Not4 localization at cytoplasmic foci after stress. This truncated version of Not4 fails to increase the transcription of the stress genes, is more stable and seems to be toxic to cells undergoing oxidative stress. [ABSTRACT FROM AUTHOR]

Genomic sequencing analysis and previous studies have shown that there are eight genes in Streptomyces coelicolor A3(2) encoding putative cellulases. One of these genes, sco6548, was cloned into the Streptomyces/Escherichia coli shuttle vector pUWL201PW. The recombinant protein was successfully overexpressed in S. lividans TK24 under the control of the strong ermE promoter. Sco6548 was 1740 bp in length, and encoded a 579-amino acid-, 60.8-kDa protein with strong hydrolyzing activity toward Avicel and filter paper, yielding cellobiose as the final product. SCO6548 showed optimal activity at 50°C and pH 5. The Km values of SCO6548 toward Avicel and filter paper were 15.38 and 16.1 mg/mL, respectively. The Vmax values toward Avicel and filter paper were 0.432 and 0.084 μM/min, respectively. EDTA did not affect cellulase activity; however, several divalent cations, including Co2+, Cu2+, Ni2+ and Mn2+ (at 10 mM) had severe inhibitory effects on enzyme activity. Our analysis showed that SCO6548 is a cellulose 1,4-β-cellobiosidase that hydrolyzes cellulose into cellobiose. [ABSTRACT FROM AUTHOR]

During the coronavirus pandemic, second-year students on the B.Sc. molecular biology and genetics degree at Istanbul Technical University sat an open-ended online exam for a microbiology course in which one of the compulsory questions asked how the course had helped them during the first phase of the pandemic (April–July 2020). Fifty of 69 students gave consent for their (anonymous) responses to be analysed in order to discern any key ways in which their knowledge had been applied. The aim of the study was to investigate whether taking an advanced microbiology course increases understanding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic and has a positive impact on student behaviours with respect to public health practices. Findings were divided into four major themes: course content (information), application of course content to behavioural change (practice), professionalism and their 'audience' whilst at home in lockdown (family and friends). Social distancing, wearing face masks, and hand and surface hygiene were described as important behaviours, with this practice informed by their basic microbiology knowledge. This paper describes a scenario where rote assessment can be used to assess wider scientific literacy with respect to application in society, providing students with an opportunity to incorporate and apply their learning into real-life situations, whilst tutors can assess constructivist learning, conceptual understanding and impact on student behaviour. [ABSTRACT FROM AUTHOR]

T-2 is a common mycotoxin contaminating cereal crops. Chronic consumption of food contaminated with T-2 toxin can lead to death, so simple and accurate detection methods in food and feed are necessary. In this paper, we establish a highly sensitive and accurate method for detecting T-2 toxin using AlphaLISA. The system consists of acceptor beads labeled with T-2-bovine serum albumin (BSA), streptavidin-labeled donor beads and biotinylated T-2 antibodies. T-2 in the sample matrix competes with T-2-BSA for antibodies. Adding biotinylated antibodies to the test well followed by T-2 and T-2-BSA acceptor beads yielded a detection range of 0.03–500 ng/mL. The half-maximal inhibitory concentration was 2.28 ng/mL and the coefficient of variation was <10%. In addition, this method had no cross-reaction with other related mycotoxins. This optimized method for extracting T-2 from food and feed samples achieved a recovery rate of approximately 90% in T-2 concentrations as low as 1 ng/mL, better than the performance of a commercial ELISA kit. This competitive AlphaLISA method offers high sensitivity, good specificity, good repeatability and simple operation for detecting T-2 toxin in food and feed. [ABSTRACT FROM AUTHOR]

Previous investigations have indicated that the reservoir of extraintestinal pathogenic Escherichia coli (ExPEC) strains is the intestinal microbiota. Nevertheless, studies focused on the prevalence of potential ExPEC strains among the bowel microbiota in healthy human individuals practically do not exist and a strong bias towards pathogenic strains among the E. coli data set is obvious. To assess the prevalence of potential ExPEC strains among E. coli from the intestinal microbiota of healthy humans, we performed a search for data on the prevalence of virulence-associated genes and pathogenicity islands among fecal E. coli found in published studies, including studies comparing isolates from patients suffering from extraintestinal E. coli infections with E. coli from feces of healthy humans. An extensive literature search, including more than 500 published papers, revealed 24 papers with data on prevalences of =5 virulence-associated genes among 21 E. coli collections including =20 fecal/rectal strains obtained from healthy individuals and 4 papers with prevalences of pathogenicity islands among E. coli collections from healthy humans. The gathered data are presented in this minireview and clearly show that potential ExPEC strains are present among fecal isolates with a prevalence of around =10%. [ABSTRACT FROM AUTHOR]

Aquaculture plays an important role in human nutrition and economic development but is often expanded to the detriment of the natural environment. Several research projects, aimed at cultivating microalgae in aquaculture wastewaters (AWWs) to reduce organic loads and minerals, along with the production of microalgal cell mass and metabolic products, are underway. Microalgal cell mass is of high nutritional value and is regarded as a candidate to replace, partially at least, the fish meal in the fish feed. Also, microalgal cell mass is considered as a feedstock in the bio-fuel manufacture, as well as a source of high-added value metabolic products. The production of these valuable products can be combined with the reuse of AWWs in the light of environmental concerns related with the aquaculture sector. Many research papers published in the last decade demonstrate that plenty of microalgae species are able to efficiently grow in AWWs, mainly derived from fish and shrimp farms, and produce valuable metabolites reducing the AWW pollutant load. We conclude that bio-remediation of AWWs combining with the production of microalgae cell mass and specific metabolites is probably the most convenient and economical solution for AWWs management and can contribute to the sustainable growth of the aquaculture. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) have extensive industrial applications as producers of lactic acid, as probiotics, as biocontrol agents and as biopreservatives. LAB play a large role in food fermentation and in silage processes, where crops such as grass, legumes, cereals or corn are fermented into high-moisture feed that is storable and can be used to feed cattle, sheep or other ruminants. LAB also have great applications within green biorefineries, with simultaneous production of protein-rich feed for monogastric animals, silage or feed pellets for ruminants and production of lactic acid or specific amino acids. In green biorefineries, fresh or ensiled wet biomass is mechanically fractionated into green juice and solid residues (press cake), where the plant juice, for example, can be used for production of lactic acid using LAB. In a process named 'ENLAC', recovery of protein and chlorophyll from silage by simultaneous lactic acid fermentation and enzyme hydrolysis has been developed. Furthermore, a process for protein recovery was recently developed by applying a specific LAB starter culture to green juice from freshly harvested crops. This paper focuses on reviewing LAB for their applications within biorefining of 'green' crops such as clover, alfalfa, grasses and other green plant materials. Applications of lactic acid bacteria within the green biorefinery. [ABSTRACT FROM AUTHOR]

The article "Retraction of: Disruption of the gene (spooA) encoding sporulation transcription factor blocks endospore formation and enterotoxin production in enterotoxigenic Clostridium perfringens type A" from FEMS Microbiology Letters was retracted due to concerns about manipulated images in Figure 2 and Figure 4. The last-named author contacted the journal editor after being alerted to these concerns, leading to the decision to retract the paper. The original laboratory cannot reconstruct the figures or repeat the experiment, prompting the retraction. [Extracted from the article]

Fatty acid and their amide derivatives are natural self-defense agents in plants. They have been observed to be broadly bioactive against a variety of disease agents. The mechanism of action understood so far being their targeting the protein synthesis and causing leakage of the intracellular components. Owing to their broad bioactivity, the fatty acids and their amides as therapeutics can cover a wide range of indications such as cancer, bacterial infections, parasitic infection, inflammations, diabetes and obesity to name a few. The microorganisms residing inside the healthy plant tissues are a unique niche for exploration of novel bioactive compounds. The recent identification of fatty acid amide derivatives as well as prior reports from endophytes have drawn fresh attention to this unique source for their isolation. Hence, they represent an exciting opportunity for the development of new therapeutic agents against existing disease causative agents. In this paper, we will discuss the production of fatty acids and amide derivatives by plants and their associated endophytes. Their reported bioactivities establishing their potential benefit as possible therapeutic agents will also be examined. [ABSTRACT FROM AUTHOR]

Cell differentiation is one of the marks of multicellular organisms. Terminally specialised nitrogen-fixing cells, termed heterocysts, evolved in filamentous cyanobacteria more than 2 Gya. The development of their spacing pattern has been thoroughly investigated in model organisms such as Anabaena sp. PCC 7120. This paper focuses on the more complex, branching cyanobacterium Mastigocladus laminosus (Stigonematales). Contrary to what has been previously published, a heterocyst spacing pattern is present in M. laminosus but it varies with the age of the culture and the morphology of the cells. Heterocysts in young, narrow trichomes were more widely spaced (~14.8 cells) than those in old, wide trichomes (~9.4 cells). Biochemical and transgenic experiments reveal that the heterocyst spacing pattern is affected by the heterocyst inhibitor PatS. Addition of the pentapeptide RGSGR (PatS-5) to the growth medium and overexpression of patS from Anabaena sp. PCC 7120 in M. laminosus resulted in the loss of heterocyst differentiation under nitrogen deprivation. Bioinformatics investigations indicated that putative PatS sequences within cyanobacteria are highly diverse, and fall into two main clades. Both are present in most branching cyanobacteria. Despite its more complex, branching phenotype, M. laminosus appears to use a PatS-based pathway for heterocyst differentiation, a property shared by Anabaena/Nostoc. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria as Lactococcus lactis are used as vector for protein but also DNA delivery into intestinal cells in vitro and in vivo. For the plasmid delivery strategy, the plasmid copy number per bacteria (PCN) is thus of great importance. The aim of this paper is to determine the physiological conditions when PCN is the highest in the bacteria. PCN was characterized by qPCR in five different recombinant Lactococcus lactis strains, containing one (mono-) or two different plasmids (biplasmidic), at exponential or stationary phase. We showed that in all cases but one, PCN is higher at exponential than stationary phase. PCN seems to depend on (i) monoplasmidic or biplasmidic strain; (ii) origin of replication of the plasmid; and (iii) the DNA load of the bacteria. Then we studied plasmid transfer in vitro from recombinant L. lactis to eukaryotic COS-7 cells using culture at exponential or stationary phase. We showed that plasmid transfer can be improved in vitro by using bacteria at exponential phase. [ABSTRACT FROM AUTHOR]

Several early models describing host–pathogen interaction have assumed that each individual host has approximately the same likelihood of becoming infected or of infecting others. More recently, a concept that has been increasingly emphasized in many studies is that for many infectious diseases, transmission is not homogeneous but highly skewed at the level of populations. In what became known as the '20/80 rule', about 20% of the hosts in a population were found to contribute to about 80% of the transmission potential. These heterogeneities have been described for the interaction between many microorganisms and their human or animal hosts. Several epidemiological studies have reported transmission heterogeneities for Escherichia coli by cattle, a phenomenon with far-reaching agricultural, medical and public health implications. Focusing on E. coli as a case study, this paper will describe super-spreading and super-shedding by cattle, review the main factors that shape these transmission heterogeneities and examine the interface with human health. Escherichia coli super-shedding and super-spreading by cattle are shaped by microorganism-specific, cattle-specific and environmental factors. Understanding the factors that shape heterogeneities in E. coli dispersion by cattle and the implications for human health represent key components that are critical for targeted infection control initiatives. Understanding factors that shape Escherichia coli shedding by cattle promises to advance prophylactic and therapeutic interventions and has critical medical and public health implications. [ABSTRACT FROM AUTHOR]

The following paper is reviewing the current trends in research connected to fermentation, highlighting the work carried out in the various research kitchens that have gained a new understanding of fermentation in the recent years. The reflection on the developments made both on microbiological as well on the technological level aims to create pathways within the research fields in order to foster new innovations within the food production system. Fermentation is not just a current trend in gastronomy, but also the steady driver for food Innovation. [ABSTRACT FROM AUTHOR]

Triazophos is a broad-spectrum and highly effective insecticide, and the residues of triazophos have been frequently detected in the environment. A triazophos-degrading bacterium, Burkholderia sp. SZL-1, was isolated from a long-term triazophos-polluted soil. Strain SZL-1 could hydrolyze triazophos to 1-phenyl-3-hydroxy-1,2,4-triazole, which was further utilized as the carbon sources for growth. The triazophos hydrolase gene trhA, cloned from strain SZL-1, was expressed and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. TrhA is 55 kDa and displays maximum activity at 25°C, pH 8.0. This enzyme still has nearly 60% activity at the range of 15°C-50°C for 30 min. TrhA was mutated by sequential error prone PCR and screened for improved activity for triazophos degradation. One purified variant protein (Val89-Gly89) named TrhA-M1 showed up to 3-fold improvement in specific activity against triazophos, and the specificity constants of Kcat and Kcat/Km for TrhA-M1 were improved up to 2.3- and 8.28-fold, respectively, compared to the wild-type enzyme. The results in this paper provided potential material for the contaminated soil remediation and hydrolase genetic structure research. [ABSTRACT FROM AUTHOR]

Bacteriophages play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e. auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phages in diverse environments. [ABSTRACT FROM AUTHOR]

State-of-the-art papers from around the globe addressing current topics in education were published in the FEMS Microbiology Letters virtual Thematic Issue 'Education' in November 2015 (http://femsle.oxfordjournals.org/content/thematicissue- education), which was innovative and well received by microbiologists and other educators. Its unique content is reviewed here to facilitate broader access and further discussions in the professional community. Best practice in supporting school teaching and exposing students to concepts from other disciplines is presented in context of inspiring the next generations, where also historical microbiology can be drawn upon. Technology-enhanced education is discussed including its applications (e.g. lecture podcasts for flipped learning, learning from experts via videoconference). Authentic learning is covered with examples of research-led teaching, water and showerhead biofilm analyses and participation in the International Genetically Engineered Machines competition. Enhancing employability is focussed on, including supporting personal development and work-readiness in general and for the changing nature of the microbiology profession. International mobility develops international awareness but challenges teachers. Teaching training, teaching excellence and dissemination of best practice are reviewed. Times of challenge and change in the Higher Education landscape motivate us to improve educational approaches and frameworks, so that we are prepared for new topics to emerge as current topics in education. [ABSTRACT FROM AUTHOR]