Survivability and long-term preservation of bacteria in water and in phosphate-buffered saline

Bioinspired oriented calcium phosphate nanocrystal arrays with bactericidal and osteogenic properties

The global diffusion of antibiotic resistance poses a severe threat to public health. Addressing antibiotic-resistant infections requires innovative approaches, such as antibacterial nanostructured surfaces (ANSs). These surfaces, featuring ordered arrays of nanostructures, exhibit the ability to kill bacteria upon contact. However, most currently developed ANSs utilize bioinert materials, lacking bioactivity crucial for promoting tissue regeneration, particularly in the context of bone infections. This study introduces ANSs composed of bioactive calcium phosphate nanocrystals. Two distinct ANSs were created through a biomineralization-inspired growth of amorphous calcium phosphate (ACP) precursors. The ANSs demonstrated efficient antibacterial properties against both Gram-negative (P. aeruginosa) and Gram-positive (S. aureus) antibiotic resistant bacteria, with up to 75 % mortality in adhered bacteria after only 4 h of contact. Notably, the ANS featuring thinner and less oriented nano-needles exhibited superior efficacy attributed to simultaneous membrane rupturing and oxidative stress induction. Moreover, the ANSs facilitate the proliferation of mammalian cells, enhancing adhesion, spreading, and reducing oxidative stress. The ANSs displayed also significant bioactivity towards human mesenchymal stem cells, promoting colonization and inducing osteogenic differentiation. Specifically, the ANS with thicker and more ordered nano-needles demonstrated heightened effects. In conclusion, ANSs introduced in this work have the potential to serve as foundation for developing bone graft materials capable of eradicate site infections while concurrently stimulating bone regeneration. STATEMENT OF SIGNIFICANCE: Nanostructured surfaces with antibacterial properties through a mechano-bactericidal mechanism have shown significant potential in fighting antibiotic resistance. However, these surfaces have not been fabricated with bioactive materials necessary for developing devices that are both antibacterial and able to stimulate tissue regeneration. This study demonstrates the feasibility of creating nanostructured surfaces of ordered calcium phosphate nano-needles through a biomineralization-inspired growth. These surfaces exhibit dual functionality, serving as effective bactericidal agents against Gram-negative and Gram-positive antibiotic-resistant bacteria while also promoting the proliferation of mammalian cells and inducing osteogenic differentiation of human mesenchymal stem cells. Consequently, this approach holds promise in the context of bone infections, introducing innovative nanostructured surfaces that could be utilized in the development of antimicrobial and osteogenic grafts.

Efficacy assessment of different cryoprotectants for preserving the viability of Enterobacterales strains at - 20 °C

The preservation of microorganisms is pivotal in microbiological practice. Currently, cryopreservation is assumed to be an effective and inexpensive approach for the storage of microorganisms, including bacteria. The key point of cryopreservation is optimal cryoprotectant selection. In the present study, different cryoprotectant compositions were tested for long-term storage of 15 Enterobacterales bacterial strains at - 20 °C. The survival rates of the bacterial strains were evaluated in four different cryoprotectant solutions containing 70% glycerin only (cryoprotectants 1 and 4), 10% dimethyl sulfoxide (DMSO) with 70% glycerin (cryoprotectant 2), and 10% DMSO (cryoprotectant 3). In addition, cryoprotectants 1 and 2 contained peptone and yeast extract as nutritional supplements. The general survival rates of the bacterial strains were evaluated after 12 months of storage. After 12 months, the survival rates of the different cryoprotectants were as follows: cryoprotectant 1-88.87%; cryoprotectant 2-84.85%; cryoprotectant 3-83.50%; and cryoprotectant 4-44.81%. Thus, the composition of cryoprotectant 1 (70% glycerin with nutrient supplements) was optimal for preserving 15 tested strains of the order Enterobacterales. Despite these findings, the biochemical properties of the tested strains changed after cryopreservation for 12 months in the presence of 1 or 3 cryoprotectants. Alterations in the biochemical profile could be related to changes in environmental conditions and cold adaptation. We assume that the composition of cryoprotectant 1 can be optimal for storing the order Enterobacterales at - 20 °C. However, further investigations are needed to elucidate the problem of cryopreservation and to support our assumption.

Intestinal lysozyme engagement of Salmonella Typhimurium stimulates the release of barrier-impairing InvE and Lpp1

Lysozyme is a β-1,4-glycosidase that hydrolyzes the polysaccharide backbone of bacterial cell walls. With an additional bactericidal function mediated by a separate protein domain, lysozyme is considered a uniquely important antimicrobial molecule contributing to the host's innate immune response to infection. Elevated lysozyme production is found in various inflammatory conditions while patients with genetic risks for inflammatory bowel diseases demonstrate abnormal lysozyme expression, granule packaging, and secretion in Paneth cells. However, it remains unclear how a gain- or loss-of-function in host lysozyme may impact the host inflammatory responses to pathogenic infection. We challenged Lyz1-/- and ectopic Lyz1-expressing (Villin-Lyz1TG) mice with S. Typhimurium and then comprehensively assessed the inflammatory disease progression. We conducted proteomics analysis to identify molecules derived from human lysozyme-mediated processing of live Salmonella. We examined the barrier-impairing effects of these identified molecules in human intestinal epithelial cell monolayer and enteroids. Lyz1-/- mice are protected from infection in terms of morbidity, mortality, and barrier integrity, whereas Villin-Lyz1TG mice demonstrate exacerbated infection and inflammation. The growth and invasion of Salmonella in vitro are not affected by human or chicken lysozyme, whereas lysozyme encountering of live Salmonella stimulates the release of barrier-disrupting factors, InvE-sipC and Lpp1, which directly or indirectly impair the tight junctions. The direct engagement of host intestinal lysozyme with an enteric pathogen such as Salmonella promotes the release of virulence factors that are barrier-impairing and pro-inflammatory. Controlling lysozyme function may help alleviate the inflammatory progression.

The Biologically Active Biopolymer Silk: The Antibacterial Effects of Solubilized Bombyx mori Silk Fibroin with Common Wound Pathogens

Antibacterial properties are desirable in wound dressings. Silks, among many material formats, have been investigated for use in wound care. However, the antibacterial properties of liquid silk are poorly understood. The aim of this study is to investigate the inherent antibacterial properties of a Bombyx mori silk fibroin solution. Silk fibroin solutions containing ≥ 4% w/v silk fibroin do not support the growth of two common wound pathogens, Staphylococcus aureus and Pseudomonas aeruginosa. When liquid silk is added to a wound pad and placed on inoculated culture plates mimicking wound fluid, silk is bacteriostatic. Viability tests of the bacterial cells in the presence of liquid silk show that cells remain intact within the silk but could not be cultured. Liquid silk appears to provide a hostile environment for S. aureus and P. aeruginosa and inhibits growth without disrupting the cell membrane. This effect can be beneficial for wound healing and supports future healthcare applications for silk. This observation also indicates that liquid silk stored prior to processing is unlikely to experience microbial spoilage.

Prospects of probiotics in beekeeping: a review for sustainable approach to boost honeybee health

Honeybees are vital for global crop pollination, making indispensable contributions to agricultural productivity. However, these vital insects are currently facing escalating colony losses on a global scale, primarily attributed to parasitic and pathogenic attacks. The prevalent response to combat these infections may involve the use of antibiotics. Nevertheless, the application of antibiotics raises concerns regarding potential adverse effects such as antibiotic resistance and imbalances in the gut microbiota of bees. In response to these challenges, this study reviews the utilization of a probiotic-supplemented pollen substitute diet to promote honeybee gut health, enhance immunity, and overall well-being. We systematically explore various probiotic strains and their impacts on critical parameters, including survival rate, colony strength, honey and royal jelly production, and the immune response of bees. By doing so, we emphasize the significance of maintaining a balanced gut microbial community in honeybees. The review also scrutinizes the factors influencing the gut microbial communities of bees, elucidates the consequences of dysbiosis, and evaluates the potential of probiotics to mitigate these challenges. Additionally, it delineates different delivery mechanisms for probiotic supplementation and elucidates their positive effects on diverse health parameters of honeybees. Given the alarming decline in honeybee populations and the consequential threat to global food security, this study provides valuable insights into sustainable practices aimed at supporting honeybee populations and enhancing agricultural productivity.

A flow cytometric assay to detect viability and persistence of Salmonella enterica subsp. enterica serotypes in nuclease-free water at 4 and 25°C

Salmonella spp. is one of the most isolated microorganisms reported to be responsible for human foodborne diseases and death. Water constitutes a major reservoir where the Salmonella spp. can persist and go undetected when present in low numbers. In this study, we assessed the viability of 12 serotypes of Salmonella enterica subsp. enterica for 160 days in nuclease-free water at 4 and 25°C using flow cytometry and Tryptic Soy Agar (TSA) plate counts. The results show that all 12 serotypes remain viable after 160 days in distilled water using flow cytometry, whereas traditional plate counts failed to detect ten serotypes incubated at 25°C. Moreover, the findings demonstrate that 4°C constitutes a more favorable environment where Salmonella can remain viable for prolonged periods without nutrients. Under such conditions, however, Salmonella exhibits a higher susceptibility to all tested antibiotics and benzalkonium chloride (BZK). The pre-enrichment with Universal Pre-enrichment Broth (UP) and 1/10 × Tryptic Soy broth (1/10 × TSB) resuscitated all tested serotypes on TSA plates, nevertheless cell size decreased after 160 days. Furthermore, phenotype microarray (PM) analysis of S. Inverness and S. Enteritidis combined with principal component analysis (PCA) revealed an inter-individual variability in serotypes with their phenotype characteristics, and the impact of long-term storage at 4 and 25°C for 160 days in nuclease-free water. This study provides an insight to Salmonella spp. long-term survivability at different temperatures and highlights the need for powerful tools to detect this microorganism to reduce the risk of disease transmission of foodborne pathogens via nuclease-free water.

Germicidal efficacy of continuous and pulsed ultraviolet-C radiation on pathogen models and SARS-CoV-2

Ultraviolet radiation's germicidal efficacy depends on several parameters, including wavelength, radiant exposure, microbial physiology, biological matrices, and surfaces. In this work, several ultraviolet radiation sources (a low-pressure mercury lamp, a KrCl excimer, and four UV LEDs) emitting continuous or pulsed irradiation were compared. The greatest log reductions in E. coli cells and B. subtilis endospores were 4.1 ± 0.2 (18 mJ cm-2) and 4.5 ± 0.1 (42 mJ cm-2) with continuous 222 nm, respectively. The highest MS2 log reduction observed was 2.7 ± 0.1 (277 nm at 3809 mJ cm-2). Log reductions of SARS-CoV-2 with continuous 222 nm and 277 nm were ≥ 3.4 ± 0.7, with 13.3 mJ cm-2 and 60 mJ cm-2, respectively. There was no statistical difference between continuous and pulsed irradiation (0.83-16.7% [222 nm and 277 nm] or 0.83-20% [280 nm] duty rates) on E. coli inactivation. Pulsed 260 nm radiation (0.5% duty rate) at 260 nm yielded significantly greater log reduction for both bacteria than continuous 260 nm radiation. There was no statistical difference in SARS-CoV-2 inactivation between continuous and pulsed 222 nm UV-C radiation and pulsed 277 nm radiation demonstrated greater germicidal efficacy than continuous 277 nm radiation. Greater radiant exposure for all radiation sources was required to inactivate MS2 bacteriophage. Findings demonstrate that pulsed irradiation could be more useful than continuous UV radiation in human-occupied spaces, but threshold limit values should be respected. Pathogen-specific sensitivities, experimental setup, and quantification methods for determining germicidal efficacy remain important factors when optimizing ultraviolet radiation for surface decontamination or other applications.

Thermal Inactivation of Escherichia Phage OSYSP and Host Strain Escherichia coli O157:H7 EDL933: A Comparative Kinetic Analysis

Lytic bacteriophages are promising biocontrol agents against pathogenic bacteria for food and therapeutic applications. Investigating the feasibility of combining phage and physical lethal agents, such as heat, as an effective hurdle combination could lead to beneficial applications. The current research was initiated to compare the thermal inactivation kinetics of a lytic phage (Escherichia phage OSYSP) and its host (Shiga toxin-producing Escherichia coli O157:H7 EDL933), considering they have different critical thermal targets in their structures. To provide a basis for comparison, thermal inactivation kinetics were determined on suspensions of these agents in buffered peptone water using a thermally controlled circulating water bath. Results showed that the bacteriophage virions have a remarkable heat resistance (p < 0.05) compared to their host cells. The D-values of the populations of phage (PFU/mL) and EDL933 strain (CFU/mL) were 166.7 and 7.3 min at 55°C, compared to 44.4 and 0.3 min at 60°C, respectively. Additionally, D-values were significantly (p < 0.05) more influenced by temperature changes in the case of E. coli O157:H7 EDL933 (z-value 3.7°C) compared to that for phage OSYSP (z-value 7.7°C). When the phage suspension was heat-treated in a thermal cycler instead of a water bath, no significant differences between the two treatment procedures (p > 0.05) in estimating virus D- and z-values were observed. Based on these findings, it may be feasible to combine phage OSYSP with mild heat during processing of food to selectively inactivate E. coli O157:H7 EDL933 and subsequently maintain product safety during storage by the surviving phage population; however, the feasibility of this application needs to be investigated. Additionally, the relatively heat-resistant phage OSYSP could qualify as a biological indicator to validate thermal treatments of minimally processed foods in which E. coli O157:H7 EDL933 is the pathogen-of-concern.

Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing

Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.

Delivery mechanism can enhance probiotic activity against honey bee pathogens

Managed honey bee (Apis mellifera) populations play a crucial role in supporting pollination of food crops but are facing unsustainable colony losses, largely due to rampant disease spread within agricultural environments. While mounting evidence suggests that select lactobacilli strains (some being natural symbionts of honey bees) can protect against multiple infections, there has been limited validation at the field-level and few methods exist for applying viable microorganisms to the hive. Here, we compare how two different delivery systems-standard pollen patty infusion and a novel spray-based formulation-affect supplementation of a three-strain lactobacilli consortium (LX3). Hives in a pathogen-dense region of California are supplemented for 4 weeks and then monitored over a 20-week period for health outcomes. Results show both delivery methods facilitate viable uptake of LX3 in adult bees, although the strains do not colonize long-term. Despite this, LX3 treatments induce transcriptional immune responses leading to sustained decreases in many opportunistic bacterial and fungal pathogens, as well as selective enrichment of core symbionts including Bombilactobacillus, Bifidobacterium, Lactobacillus, and Bartonella spp. These changes are ultimately associated with greater brood production and colony growth relative to vehicle controls, and with no apparent trade-offs in ectoparasitic Varroa mite burdens. Furthermore, spray-LX3 exerts potent activities against Ascosphaera apis (a deadly brood pathogen) likely stemming from in-hive dispersal differences, whereas patty-LX3 promotes synergistic brood development via unique nutritional benefits. These findings provide a foundational basis for spray-based probiotic application in apiculture and collectively highlight the importance of considering delivery method in disease management strategies.

An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs

The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.

Influence of Surface Roughness, Nanostructure, and Wetting on Bacterial Adhesion

Bacterial fouling is a persistent problem causing the deterioration and failure of functional surfaces for industrial equipment/components; numerous human, animal, and plant infections/diseases; and energy waste due to the inefficiencies at internal and external geometries of transport systems. This work gains new insights into the effect of surface roughness on bacterial fouling by systematically studying bacterial adhesion on model hydrophobic (methyl-terminated) surfaces with roughness scales spanning from ∼2 nm to ∼390 nm. Additionally, a surface energy integration framework is developed to elucidate the role of surface roughness on the energetics of bacteria and substrate interactions. For a given bacteria type and surface chemistry; the extent of bacterial fouling was found to demonstrate up to a 75-fold variation with surface roughness. For the cases showing hydrophobic wetting behavior, both increased effective surface area with increasing roughness and decreased activation energy with increased surface roughness was concluded to enhance the extent of bacterial adhesion. For the cases of superhydrophobic surfaces, the combination of factors including (i) the surpassing of Laplace pressure force of interstitial air over bacterial adhesive force, (ii) the reduced effective substrate area for bacteria wall due to air gaps to have direct/solid contact, and (iii) the reduction of attractive van der Waals force that holds adhering bacteria on the substrate were summarized to weaken the bacterial adhesion. Overall, this study is significant in the context of designing antifouling coatings and systems as well as explaining variations in bacterial contamination and biofilm formation processes on functional surfaces.

Methods to extract and study the biological effects of murine gut microbiota using Caenorhabditis elegans as a screening host

Gut microbiota has been established as a main regulator of health. However, how changes in gut microbiota are directly associated with physiological and cellular alterations has been difficult to tackle on a large-scale basis, notably because of the cost and labor-extensive resources required for rigorous experiments in mammals. In the present study, we used the nematode Caenorhabditis elegans as a model organism to elucidate microbiota-host interactions. We developed a method to extract gut microbiota (MCB) from murine feces, and tested its potential as food source for and its impact on C. elegans biology compared to the standard bacterial diet Escherichia coli OP50. Although less preferred than OP50, MCB was not avoided but had a lower energy density (triglycerides and glucose). Consistently, MCB-fed worms exhibited smaller body length and size, lower fertility, and lower fat content than OP50-fed worms, but had a longer mean lifespan, which resembles the effects of calorie restriction in mammals. However, these outcomes were altered when bacteria were inactivated, suggesting an important role of symbiosis of MCB beyond nutrient source. Taken together, our findings support the effectiveness of gut MCB processing to test its effects in C. elegans. More work comparing MCB of differently treated mice or humans is required to further validate relevance to mammals before large-scale screening assays.

Investigation of the Influence of Stress on Label-Free Bacterial Surface-Enhanced Raman Spectra

Label-free surface-enhanced Raman spectroscopy (SERS) has been proposed as a promising bacterial detection technique. However, the quality of the collected bacterial spectra can be affected by the time between sample acquisition and the SERS measurement. This study evaluated how storage stress stimuli influence the label-free SERS spectra of Pseudomonas syringae samples stored in phosphate buffered saline. The results indicate that when faced with nutrient limitations and changes in osmatic pressure, samples at room temperature (25 °C) exhibit more significant spectral changes than those stored at cold temperature (4 °C). At higher temperatures, bacterial communities secrete extracellular biomolecules that induce programmed cell death and result in increases in the supernatant SERS signals. Surviving cells consume cellular components to support their metabolism, thus leading to measurable declines in cell SERS intensity. Two-dimensional correlation spectroscopy analysis suggests that cellular component signatures decline sequentially in the following order: proteins, nucleic acids, and lipids. Extracellular nucleic acids, proteins, and carbohydrates are secreted in turn. After subtracting the SERS changes resulting from storage, we evaluated bacterial response to viral infection. P. syringae SERS profile changes enable accurate bacteriophage Phi6 quantification over the range of 10⁴-10¹⁰ PFU/mL. The results indicate that storage conditions impact bacterial label-free SERS signals and that such influences need to be accounted for and if possible avoided when detecting bacteria or evaluating bacterial response to stress stimuli.

Long-term preservation at low temperature of Escherichia coli cells embedded in egg white glass formed by slow drying at room temperature

Sterile homogeneous egg white (EW) is obtained through a three-step process, high-speed homogenization, centrifugation, and ultraviolet radiation. After incorporating 1.056 × 10¹⁰ CFU/g of Escherichia coli, the EW mixture was dehydrated by slow drying to form a brittle, water-soluble, and transparent bacteria-embedded egg white glass (BE-EWG). The BE-EWG stored at -20 °C for 4 months maintains almost all the cell growth functions and proliferation activities of the labeled E. coli, and most of the cell functions and 60 % of the proliferation activities are maintained for up to one year. The BE-EWG exhibits a porous hydrogel membrane structure after heat treatment, and many E. coli cells are accommodated in a grid with a pore size of 2-10 mm. The loss of bacteria-carrying viability after storage at room temperature may be related to the Maillard reaction between protein and glucose in EW, which results in the structural changes caused by protein cross-linking, darkened color and water insolubility of the BE-EWG. Therefore, the method of embedding E. coli cells in EWG as solid form at room temperature to avoid ice crystal formation during cryopreservation is more beneficial for storage, packaging and shipping at -20 °C.

Probiotic Bifidobacteria Mitigate the Deleterious Effects of para-Cresol in a Drosophila melanogaster Toxicity Model

Renal impairment associated with chronic kidney disease (CKD) causes the buildup of uremic toxins that are deleterious to patient health. Current therapies that manage toxin accumulation in CKD offer an incomplete therapeutic effect against toxins such as para-cresol (p-cresol) and p-cresyl sulfate. Probiotic therapies can exploit the wealth of microbial diversity to reduce toxin accumulation. Using in vitro culture techniques, strains of lactobacilli and bifidobacteria from a 24-strain synbiotic were investigated for their ability to remove p-cresol. Four strains of bifidobacteria internalized p-cresol from the extracellular environment. The oral supplementation of these toxin-clearing probiotics was more protective than control strains in a Drosophila melanogaster toxicity model. Bifidobacterial supplementation was also associated with higher abundance of lactobacilli in the gut microbiota of p-cresol-exposed flies. The present findings suggest that these strains might reduce p-cresol in the gut in addition to increasing the prevalence of other beneficial bacteria, such as lactobacilli, and should be tested clinically to normalize the dysbiotic gut microbiota observed in CKD patients. IMPORTANCE Chronic kidney disease (CKD) affects approximately 10% of the global population and has limited treatment options. The accumulation of gut microbiota-derived uremic toxins, such as para-cresol (p-cresol) and p-cresyl sulfate, is associated with the onset of comorbidities (i.e., atherosclerosis and cognitive disorders) in CKD. Unfortunately, dialysis, the gold standard therapy is unable to remove these toxins from the bloodstream due to their highly protein-bound nature. Some strains of Bifidobacterium have metabolic properties that may be useful in managing uremic toxicity. Using a Drosophila model, the present work highlights why dosing with certain probiotic strains may be clinically useful in CKD management.

The Maleth program: Malta's first space mission discoveries on the microbiome of diabetic foot ulcers

The purpose of the Maleth Program, also known as Project Maleth, is Malta's first space program to evaluate human skin tissue microbiome changes in type 2 diabetes mellitus (T2DM) patients afflicted with diabetic foot ulcers (DFU). This was carried out in both ground-based models and spaceflight. The first mission (Maleth I) under this program was carried out to uncover the effects of spaceflight, microgravity and radiation on human skin tissue microbiome samples from six T2DM patients recruited into the study. Each patient human skin tissue sample was split in three, with one section processed immediately for genomic profiling by 16S typing and the rest were processed for longer term ground-control and spaceflight experiments. Ground-control and spaceflight human skin tissue samples were also processed for genomic profiling upon mission re-entry and completion. Maleth I's overall objective was achieved, as human skin tissue samples with their microbiomes travelled to space and back yielding positive results by both standard microbiology techniques and genetic typing using 16S rRNA amplicon sequencing. Preliminary findings of this mission are discussed in light of its innovative approach at DFU microbiome research, and the clinical implications that may emerge from this and other future similar studies.

A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix

Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.

Fecal microbiota transplantation: a review on current formulations in Clostridioides difficile infection and future outlooks

INTRODUCTION

The role of the gut microbiota in health and the pathogenesis of several diseases has been highlighted in recent years. Even though the precise mechanisms involving the microbiome in these ailments are still unclear, microbiota-modulating therapies have been developed. Fecal microbiota transplantation (FMT) has shown significant results against Clostridioides difficile infection (CDI), and its potential has been investigated for other diseases. Unfortunately, the technical aspects of the treatment make it difficult to implement. Pharmaceutical technology approaches to encapsulate microorganisms could play an important role in providing this treatment and render the treatment modalities easier to handle.

AREAS COVERED

After an overview of CDI, this narrative review aims to discuss the current formulations for FMT and specifically addresses the technical aspects of the treatment. This review also distinguishes itself by focusing on the hurdles and emphasizing the possible improvements using pharmaceutical technologies.

EXPERT OPINION

FMT is an efficient treatment for recurrent CDI. However, its standardization is overlooked. The approach of industrial and hospital preparations of FMT are different, but both show promise in their respective methodologies. Novel FMT formulations could enable further research on dysbiotic diseases in the future.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.

Polystyrene shaping effect on the enriched bacterial community from the plastic-eating Alphitobius diaperinus (Insecta: Coleoptera)

Plastic pollution has become a serious issue of global concern, and biodegradation of plastic wastes is representing one attractive environment-friendly alternative to traditional disposal paths. It is known that insects are involved in the plastic polymer degradation process, with reported evidence of tenebrionid beetle larvae capable to degrade polystyrene (PS), one of the most used plastics worldwide. Recently, a ribosomal RNA based survey on the insect gut microbiota of the lesser mealworm Alphitobius diaperinus has revealed differentially abundant microbial taxa between PS-fed larvae and control group. Following these findings, an enrichment bacterial culture was set up in liquid carbon-free basal medium with PS film as sole carbon source using PS-fed larvae of A. diaperinus as inoculum. After two-months the culture was analysed both by molecular and culture-based methods. Isolated bacteria which had become prevalent under the selective enrichment conditions resulted ascribable to three taxonomic groups: Klebsiella, Pseudomonas, and Stenothrophomonas. The predominance of these groups in PS-fed larvae was confirmed by using bacterial 16S rRNA gene amplicon sequencing, and it was consistent with the results of previous reports. Isolated bacteria were able to attach to PS surfaces and SEM observations showed the presence of thin fibrillar structures connecting the bacterial cells to the abiotic surface.

Washed preparation of faecal microbiota changes the transplantation related safety, quantitative method and delivery

The safety, quantitative method and delivery of faecal microbiota transplantation (FMT) vary a lot from different countries in practice. Recently, the improved methodology of FMT based on the automatic filtration, washing process and the related delivery was named as washed microbiota transplantation (WMT). First, this study aimed to describe the methodology development of FMT from manual to washing preparation from 2012 to 2021 in China Microbiota Transplantation System (CMTS), a centralized stool bank for providing a national non‐profit service. The secondary aim is to describe donor screenings, the correlation between faecal weight and treatment doses, incidence of adverse events and delivery decision. The retrospective analysis on the prospectively recorded data was performed. Results showed that the success rate of donor screening was 3.1% (32/1036). The incidence rate of fever decreased significantly from 19.4% (6/31) in manual FMT to 2.7% (24/902) in WMT in patients with ulcerative colitis (UC), which made UC a considerable disease model to reflect the quality control of faecal microbiota preparation. We defined one treatment unit as 10 cm³ microbiota precipitation (1.0 × 10¹³ bacteria) based on enriched microbiota instead of rough faecal weight. For delivering microbiota, colonic transendoscopic enteral tube is a promising way especially for multiple WMTs or frequent colonic administration of drugs combined with WMT. This study should help improve the better practice of FMT for helping more patients in the future.

Implementation of bactericidal topographies on biomimetic calcium phosphates and the potential effect of its reactivity

Since the discovery that nanostructured surfaces were able to kill bacteria, many works have been published focusing on the design of nanopatterned surfaces with antimicrobial properties. Synthetic bone grafts, based on calcium phosphate (CaP) formulations, can greatly benefit from this discovery if adequate nanotopographies can be developed. However, CaP are reactive materials and experience ionic exchanges when placed into aqueous solutions which may in turn affect cell behaviour and complicate the interpretation of the bactericidal results. The present study explores the bactericidal potential of two nanopillared CaP prepared by hydrolysis of two different sizes of α-tricalcium phosphate (α-TCP) powders under biomimetic or hydrothermal conditions. A more lethal bactericidal response toward Pseudomonas aeruginosa (~75% killing efficiency of adhered bacteria) was obtained from the hydrothermally treated CaP which consisted in a more irregular topography in terms of pillar size (radius: 20-60 nm), interpillar distances (100-1500 nm) and pillar distribution (pillar groups forming bouquets) than the biomimetically treated one (radius: 20-40 nm and interpillar distances: 50-200 nm with a homogeneous pillar distribution). The material reactivity was greatly influenced by the type of medium (nutrient-rich versus nutrient-free) and the presence or not of bacteria. A lower reactivity and superior bacterial attachment were observed in the nutrient-free medium while a lower attachment was observed for the nutrient rich medium which was explained by a superior reactivity of the material paired with the lower tendency of planktonic bacteria to adhere on surfaces in the presence of nutrients. Importantly, the ionic exchanges produced by the presence of materials were not toxic to planktonic cells. Thus, we can conclude that topography was the main contributor to mortality in the bacterial adhesion tests.

An influence of dew point temperature on the occurrence of Mycobacterium tuberculosis disease in Chennai, India

Climate factors such as dew point temperature, relative humidity and atmospheric temperature may be crucial for the spread of tuberculosis. This study was conducted for the first time to investigate the relationship of climatic factors with TB occurrence in an Indian setting. Daily tuberculosis notification data during 2008–2015 were generated from the National Treatment Elimination Program, and analogous daily climatic data were obtained from the Regional Meteorological Centre at Chennai city, Tamil Nadu, India. The decomposition method was adopted to split the series into deterministic and non-deterministic components, such as seasonal, non-seasonal, trend and cyclical, and non-deterministic climate factors. A generalized linear model was used to assess the relation independently. TB disease progression from latent stage infection to active was supported by higher dew point temperature and moderate temperature. It had a significant association with TB progression in the summer and monsoon seasons. The relative humidity may be favored in the winter and post-monsoon. The water tiny dew droplets may support the TB bacterium to recuperate in the environment.

Dataset of 16S ribosomal DNA sequences of bacteria isolated from marine red algae Kappaphycus alvarezii

The data provided in the article contains bacterial community profiles present on the surface of red algae (Kappaphycus alvarezii) isolated directly after collection and after 30 days of cultivation in a closed circulation system. The explants of Kappaphycus alvarezii were cultivated in a laboratory setting under controlled growth conditions for 30 days in order to determine bacteria that could adapt to controlled culture conditions. Amplification and sequencing of bacterial 16S rDNA amplicon were performed on bacterial isolates associated with the seedlings. The 16S rDNA gene sequences were analyzed, trimmed, and assembled into contigs using DNA Baser Sequence Assembler (V5) software. Taxonomic identification for the assembled sequences was achieved using the online BLAST (blastn) algorithm, and the construction of a phylogenetic tree was performed using the MEGA7 software. The data reveals a distinct set of microbial variations between day one and day 30. The phylogenetic tree depicts four major clusters, Vibrio, Pseudoalteromonas, Alteromonas, and Bacterioplanes resident on the surface of the K. alvarezii. Comparison between these two bacterial groups provides evidence of the persistent marine bacteria that adapt to the long-term culture in closed circulation systems. Raw data files are available at the GenBank, NCBI database under the accession number of MZ570560 to MZ570580.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety

Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in Mycobacterium tuberculosis H37Rv (Mtb-Rv) and MRA_3031 in M. tuberculosis H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in Escherichia coli. Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing E. coli BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and E. coli IlvCs. The E. coli knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and E. coli IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of E. coli IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.

Danish national guideline for the treatment of Clostridioides difficile infection and use of faecal microbiota transplantation (FMT)

Aim: This Danish national guideline describes the treatment of adult patients with Clostridioides (formerly Clostridium) difficile (CD) infection and the use of faecal microbiota transplantation (FMT). It suggests minimum standard for implementing an FMT service.Method: Four scientific societies appointed members for a working group which conducted a systematic literature review and agreed on the text and recommendations. All clinical recommendations were evalluated for evidence level and grade of recommendation.Results: In CD infection, the use of marketed and experimental antibiotics as well as microbiota-based therapies including FMT are described. An algorithm for evaluating treatment effect is suggested. The organisation of FMT, donor recruitment and screening, laboratory preparation, clinical application and follow-up are described.Conclusion: Updated evidence for the treatment of CD infection and the use of FMT is provided.

Culture-free biphasic approach for sensitive detection of Escherichia coli O157:H7 from beef samples

Foodborne illnesses are a major threat to public health also leading to significant mortality and financial and reputational damage to industry. It is very important to detect pathogen presence in food products early, rapidly, and accurately to avoid potential outbreaks and economic loss. However, "gold standard" culture methods, including enrichment of pathogens, can take up to several days. Moreover, the food matrix often interferes with nucleic acid amplification methods of detection, requiring DNA extraction from the sample for successful molecular detection of pathogens. Here, we introduce a "biphasic" amplification method that can achieve high sensitivity detection with background noise from ground beef food samples without culture or other extraction methods in 2.5 h. Homogenized ground beef is dried resulting in an increase in porosity of the dried food matrix to allowing amplification enzymes and primers to access the target DNA and initiate the reaction within the dried food matrix. Using Loop Mediated Isothermal Amplification, we demonstrate the detection of 1-3 cfu of Escherichia coli bacteria in 30 mg of dried food matrix. Our approach significantly lowers the time to result to less than a few hours and have a pronounced impact on reduction of instrumentation complexity and costs.

Portable Pathogen Diagnostics Using Microfluidic Cartridges Made from Continuous Liquid Interface Production Additive Manufacturing

Biomedical diagnostics based on microfluidic devices have the potential to significantly benefit human health; however, the manufacturing of microfluidic devices is a key limitation to their widespread adoption. Outbreaks of infectious disease continue to demonstrate the need for simple, sensitive, and translatable tests for point-of-care use. Additive manufacturing (AM) is an attractive alternative to conventional approaches for microfluidic device manufacturing based on injection molding; however, there is a need for development and validation of new AM process capabilities and materials that are compatible with microfluidic diagnostics. In this paper, we demonstrate the development and characterization of AM cartridges using continuous liquid interface production (CLIP) and investigate process characteristics and capabilities of the AM microfluidic device manufacturing. We find that CLIP accurately produces microfluidic channels as small as 400 μm and that it is possible to routinely produce fluid channels as small as 100 μm with high repeatability. We also developed a loop-mediated isothermal amplification (LAMP) assay for detection of E. coli from whole blood directly on the CLIP-based AM microfluidic cartridges, with a 50 cfu/μL limit of detection, validating the use of CLIP processes and materials for pathogen detection. The portable diagnostic platform presented in this paper could be used to investigate and validate other AM processes for microfluidic diagnostics and could be an important component of scaling up the diagnostics for current and future infectious diseases and pandemics.

Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs

Ginkgo biloba is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes' role in Ginkgo, and whether genetic exchange happens between Ginkgo and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. A total of 25 endophyte strains were isolated from the Ginkgo root and distributed in 16 genera of 6 phyla. Significant morphological diversities lead to the diversity in the COG functional classification. KEGG mapping revealed that endophytic bacteria and fungi potentially synthesize chalcone, while endophytic fungi might also promote flavonoid derivatization. Both bacteria and fungi may facilitate the lignin synthesis. Aspergillus sp. Gbtc_1 exhibited the feasibility of regulating alcohols to lignans. Although Ginkgo and the endophytes have not observed the critical levopimaradiene synthase in ginkgolides synthesis, the upstream pathways of terpenoid precursors are likely intact. The MVK genes in Ginkgo may have alternative non-homologous copies or be compensated by endophytes in long-term symbiosis. Cellulomonas sp. Gbtc_1 became the only bacteria to harbor both MEP and MVA pathways. Endophytes may perform the mutual transformation of IPP and DMAPP in the root. Ginkgo and bacteria may lead to the synthesis and derivatization of the carotenoid pathway. The isoquinoline alkaloid biosynthesis seemed lost in the Ginkgo root community, but L-dopa is more probably converted into dopamine as an essential signal-transduction substance. So, endophytes may participate in the secondary metabolism of the Ginkgo in a shared or complementary manner. Moreover, a few endophytic sequences predicted as Ty3/Gypsy and Ty1/Copia superfamilies exhibited extremely high similarity to those of Ginkgo. CDSs in such endophytic LTR-RT sequences were also highly homologous to one Ginkgo CDS. Therefore, LTR-RTs may be a rare unit flowing between the Ginkgo host and endophytes to exchange genetic information. Collectively, this research effectively expanded the insight on the symbiotic relationship between the Ginkgo host and the endophytes in the root.

Mitigating the Spread and Translocation of Salmonella Enteritidis in Experimentally Infected Broilers under the Influence of Different Flooring Housing Systems and Feed Particle Sizes

This study aimed to evaluate the influences of different flooring designs and feed particle sizes on the spread of Salmonella (S.) in broiler chickens. Birds (n = 480) were allocated to four different housing systems (fully littered with and without floor heating, partially and fully slatted flooring with sand bath) and two dietary treatments (finely and coarsely ground diets) in 24 boxes. Two broilers per box were experimentally infected with S. Enteritidis (8.00 log10 CFU/bird) at d 17. Salmonella prevalence in caecal contents and the liver was highest in broilers housed on fully slatted floor until d 36/37 (88.1% and 91.5%, respectively), and lowest in litter flooring (caecal content 64.4%) and litter flooring with floor heating (liver 61.7%). In turn, broilers on littered flooring expressed the lowest Salmonella counts in caecal content at d 36/37 (2.21 ± 1.75 log10 CFU/g), partial slatted flooring the highest (3.76 ± 1.46 log10 CFU/g). The mean Salmonella count in the caecal content was significantly lower for birds fed a coarsely ground diet (0.96 and 1.94 log10 CFU/g) than a finely ground diet (5.07 and 3.34 log10 CFU/g) at d 23 and d 36/37, respectively (p < 0.0001). Slatted flooring with a sand bath did not show advantages in terms of Salmonella reduction, whereas the coarsely ground diet markedly reduced the spread of Salmonella.

Development of a rapid method for assessing the efficacy of antibacterial photocatalytic coatings

Visible-light activated photocatalytic coatings may represent an attractive antimicrobial solution in domains such as food, beverage, pharmaceutical, biomedical and wastewater remediation. However, testing methods to determine the antibacterial effects of photocatalytic coatings are limited and require specialist expertise. This paper describes the development of a method that enables rapid screening of coatings for photocatalytic-antibacterial activity. Relying on the ability of viable microorganisms to reduce the dye resazurin from a blue to a pink colour, the method relates the time taken to detect this colour change with number of viable microorganisms. The antibacterial activity of two photocatalytic materials (bismuth oxide and titanium dioxide) were screened against two pathogenic organisms (Escherichia coli and Klebsiella pneumoniae) that represent potential target microorganisms using traditional testing and enumeration techniques (BS ISO 27447:2009) and the novel rapid method. Bismuth oxide showed excellent antibacterial activity under ambient visible light against E. coli, but was less effective against K. pneumoniae. The rapid method showed excellent agreement with existing tests in terms of number of viable cells recovered. Due to advantages such as low cost, high throughput, and less reliance on microbiological expertise, this method is recommended for researchers seeking an inexpensive first-stage screen for putative photocatalytic-antibacterial coatings.

Photo Augmented Copper-based Fenton Disinfection under Visible LED Light and Natural Sunlight Irradiation

Copper-based Fenton disinfection system (Cu(II)/H₂O₂) is an emerging advanced oxidation process (AOP). Previous works have used reducing agents and organic ligands to improve the disinfection efficiency of Cu(II)/H₂O₂ system. Here, we report visible light/Cu(II)/H₂O₂ system showed enhanced disinfection compared to Cu(II)/H₂O₂ system, without the need of reducing chemical agent or organic ligand. Energy-efficient LED array was used as a visible light source in the visible light/Cu(II)/H₂O₂ system. Under the optimized condition, pseudo-first-order inactivation rate constant (k_obs) of E. coli by visible light/Cu(II)/H₂O₂ (0.613 ± 0.005 min^-1) was about ~8 times greater than Cu(II)/H₂O₂ (0.08 ± 0.011 min^-1). Scanning electron microscopy and Baclight Live/Dead assay proved enhanced cell membrane damage by visible light/Cu (II)/H₂O₂ in comparison with Cu(II)/H₂O₂. Based on the bovine serum albumin (BSA) degradation and OH˙ radical measurement by visible light/Cu(II)/H₂O₂, a ligand to metal charge transfer (LMCT) mechanism by Cu(II)-bacterial complex is proposed for enhanced disinfection. Electrical energy efficiency (E _E,1) for a log reduction of E. coli and the total treatment cost of visible light/Cu(II)/H₂O₂ was determined to be 32.64 KWh/m³ and 350 ₹/m³ (3.9 €/m³ or 4.74 $/m³), respectively, indicating its cost-effectiveness. Disinfection efficiency by sunlight/Cu(II)/H₂O₂ system (solar irradiance; 746 ± 138 W/m²) was almost comparable to LED-based visible light/Cu(II)/H₂O₂ system, with total treatment cost estimated to be 80 ₹/m³ (0.9 €/m³ or 1.1 $/m³).

Culture Volume Influences the Dynamics of Adaptation under Long-Term Stationary Phase

Escherichia coli and many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown that E. coli populations adapt genetically under LTSP in an extremely convergent manner. Here, we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment-culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared with lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.

Comparison of Preservation Methods of Staphylococcus aureus and Escherichia coli Bacteria

One of the most important problems faced by microbiologists is to preserve bacterial isolates in the best state to study and further diagnosis. The current study aims to provide a summary of experimental results to maintain two species of bacteria alive after being stored by using some additives. This study found that the best temperature to preserve Staphylococcus aureus was -20°C for a year, while for Escherichia coli it was the same temperature except in using Glycerol (G) 100% and Food oil (FO) methods. The optimum method to preserve S. aureus was by using Normal Saline (NS), while Distilled Water (DW) was the optimum method to preserve E. coli at temperatures (4, 25 and -20)°C for a year, the phenotypic patterns for examining bacteria were maintained except in NS at 4°C for S. aureus after a year ago. Glycerol was used alone at concentrations (100, 50, 30 and 15)%, and another group used G+NS in the same volumes, good results were achieved when it used alone or with NS to preserve bacteria for six months at 4°C except for methods of G100% and (G100% + NS) for examining bacteria. FO has never been used as preservation liquid, it is successful to survive S. aureus at -20°C for a year, and when it was added to NS, E. coli survived for a year at three temperatures (4, 25 and -20)°C, while S. aureus didn’t survive for a year when FO+NS method used at room temperature. The precipitation method was used for bacterial suspension, then added the preserving liquid, but the results were not effective compared to the First method.

Monitoring antibiotic resistomes and bacterial microbiomes in the aerosols from fine, hazy, and dusty weather in Tianjin, China using a developed high-volume tandem liquid impinging sampler

Accurate quantification of the airborne antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is critically important to assess their health risks. However, the currently widely used high-volume filter sampler (HVFS) often causes the desiccation of the sample, interfering with subsequent bacterial culture. To overcome this limitation, a high-volume tandem liquid impinging sampler (HVTLIS) was developed and optimized to investigate the airborne bacterial microbiomes and antibiotic resistomes under different weathers in Tianjin, China. Results revealed that HVTLIS can capture significantly more diverse culturable bacteria, ARB, and ARGs than HVFS. Compared with fine and hazy weathers, dusty weather had significantly more diverse and abundant airborne bacteria, ARGs, and human opportunistic pathogens with the resistance to last-resort antibiotics of carbapenems and polymyxin B, implicating a potential human health threat of dusty bioaerosols. Intriguingly, we represented the first report of Saccharibacteria predominance in the bioaerosol, demonstrating that the potential advantage of HVTLIS in collecting airborne microbes.

Conditionally essential genes for survival during starvation in Enterococcus faecium E745

BACKGROUND

The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients.

RESULTS

We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species.

CONCLUSIONS

We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.

Surface waves control bacterial attachment and formation of biofilms in thin layers

Formation of bacterial biofilms on solid surfaces within a fluid starts when bacteria attach to the substrate. Understanding environmental factors affecting the attachment and the early stages of the biofilm development will help develop methods of controlling the biofilm growth. Here, we show that biofilm formation is strongly affected by the flows in thin layers of bacterial suspensions controlled by surface waves. Deterministic wave patterns promote the growth of patterned biofilms, while wave-driven turbulent motion discourages patterned attachment of bacteria. Strong biofilms form under the wave antinodes, while inactive bacteria and passive particles settle under nodal points. By controlling the wavelength, its amplitude, and horizontal mobility of the wave patterns, one can shape the biofilm and either enhance the growth or discourage the formation of the biofilm. The results suggest that the deterministic wave-driven transport channels, rather than hydrodynamic forces acting on microorganisms, determine the preferred location for the bacterial attachment.

Smart capsule for non-invasive sampling and studying of the gastrointestinal microbiome

Microbes in regions within the gut, which have been inaccessible so far, can now be retrieved and analyzed through a passive sampling mechanism in the form of a 3D printed capsule equipped with a superabsorbent hydrogel.

Quantitative assessment of fecal contamination in multiple environmental sample types in urban communities in Dhaka, Bangladesh using SaniPath microbial approach

Rapid urbanization has led to a growing sanitation crisis in urban areas of Bangladesh and potential exposure to fecal contamination in the urban environment due to inadequate sanitation and poor fecal sludge management. Limited data are available on environmental fecal contamination associated with different exposure pathways in urban Dhaka. We conducted a cross-sectional study to explore the magnitude of fecal contamination in the environment in low-income, high-income, and transient/floating neighborhoods in urban Dhaka. Ten samples were collected from each of 10 environmental compartments in 10 different neighborhoods (4 low-income, 4 high-income and 2 transient/floating neighborhoods). These 1,000 samples were analyzed with the IDEXX-Quanti-Tray technique to determine most-probable-number (MPN) of E. coli. Samples of open drains (6.91 log10 MPN/100 mL), surface water (5.28 log10 MPN/100 mL), floodwater (4.60 log10 MPN/100 mL), produce (3.19 log10 MPN/serving), soil (2.29 log10 MPN/gram), and street food (1.79 log10 MPN/gram) had the highest mean log10 E. coli contamination compared to other samples. The contamination concentrations did not differ between low-income and high-income neighborhoods for shared latrine swabs, open drains, municipal water, produce, and street foodsamples. E. coli contamination levels were significantly higher (p <0.05) in low-income neighborhoods compared to high-income for soil (0.91 log10 MPN/gram, 95% CI, 0.39, 1.43), bathing water (0.98 log10 MPN/100 mL, 95% CI, 0.41, 1.54), non-municipal water (0.64 log10 MPN/100 mL, 95% CI, 0.24, 1.04), surface water (1.92 log10 MPN/100 mL, 95% CI, 1.44, 2.40), and floodwater (0.48 log10 MPN/100 mL, 95% CI, 0.03, 0.92) samples. E. coli contamination were significantly higher (p<0.05) in low-income neighborhoods compared to transient/floating neighborhoods for drain water, bathing water, non-municipal water and surface water. Future studies should examine behavior that brings people into contact with the environment and assess the extent of exposure to fecal contamination in the environment through multiple pathways and associated risks.

Quantifying the Influence of Relative Humidity, Temperature, and Diluent on the Survival and Growth of Enterobacter aerogenes

Survival of bacteria on surfaces plays an important role in the cross-contamination of food. Temperature, relative humidity (RH), surface type, and inoculum diluent can affect bacterial survival. This study was conducted to examine how temperature, RH, and diluent affect the survival of Enterobacter aerogenes on stainless steel, polyvinyl chloride, and ceramic tile. Although surface type had little effect on survival, temperature had a clear effect. E. aerogenes survival was highest at 7°C and 15 and 50% RH on all surfaces. Some diluents allowed growth under high RH conditions. Cell populations in distilled water inoculated onto each surface decreased initially compared with populations in 1% phosphate-buffered saline (PBS) and 0.1% peptone broth. At 15 and 50% RH, cell populations in 1% PBS declined more sharply after 120 h than did those 0.1% peptone, but populations in both diluents had similar declines up to 3 weeks. Cell populations in 0.1% peptone had the greatest growth and reached the highest population density (∼8 log CFU/mL). Cell populations in PBS and distilled water increased by ∼2 log CFU/mL. When cells in 0.1% peptone were inoculated onto stainless steel at 100% RH, populations increased to ∼7 log CFU per coupon, whereas cells in 1% PBS increased to ∼5 log CFU per coupon followed by a decline over 3 weeks. DMFit and GInaFiT software modeled inactivation on surfaces at all conditions other than 100% RH at 21°C. These findings have important implications for experiments in which microorganisms are inoculated onto foods or food contact surfaces because the growth observed may be affected more by the inoculum diluent at high or uncontrolled RH than by the type of inoculated surface.

Optimization of microorganism preservation conditions for the development of an acute toxicity bioassay for biocides

Biocides, also referred to as 'microbicides' or 'inhibitors', are widely used in industrial processes (e.g. utility water in cooling towers) to control and/or eliminate the growth of microorganisms. Because of their inherent toxicity, their presence in various sources (e.g. river sediments, potable water) can negatively affect ecosystems. Currently available biocide detection techniques are not suitable for 'point-of-use' applications since they are tedious, complicated, and often require experienced personnel to operate. To address this concern, we sought to develop a simple-to-use toxicity bioassay based on a model microorganism (E. coli) after short (<30 min) exposure to known biocides that can be stored at room temperature (preferably) or in the fridge. Based on recent work and our expertise in polymer-based preservation of biomolecules, we leveraged this knowledge to improve E. coli preservation for biocide detection purposes. A design-of-experiments strategy was used to evaluate 16 different preservation conditions from 5 process parameters (i.e. 2^5-1 fractional factorial). It was found that pullulan, a sugar-based polymer, improved E. coli culturability by an order of magnitude after three months of storage. Also, it was found that storing E. coli in the fridge in Milli-Q water was favorable for maintaining a high level of culturability. Finally, the toxicity of three common biocides (Cetyltrimethylammonium bromide (CTAB), ProClin™ 300, and Grotan^® BK) was evaluated using a fluorescence-based assay across all 16 preservation conditions. The response of the preserved E. coli was biocide specific and at certain conditions did not vary during the entire three-month storage period.

Transparent Copper-Based Antibacterial Coatings with Enhanced Efficacy against Pseudomonas aeruginosa

Bacterial surface contamination is a major cause of hospital-associated infections. Antibacterial coatings can play an important role in reducing bacterial transmission via inanimate surfaces in healthcare settings. In this work, transparent copper-based antibacterial coatings were fabricated on commercial poly(vinyl fluoride) and stainless steel. Acrylated quaternized chitosan and ethylenediaminetetraacetic acid were covalently grafted on the substrate for complexation with copper ions. The number of viable Staphylococcus aureus in a droplet [containing ∼10⁴ colony forming units (CFU)], deposited on the copper-containing coating decreased by ∼96% within 60 min at 25 °C. With Pseudomonas aeruginosa, one of the most virulent and hardest to kill bacteria, no CFU could be observed within the same time span (killing efficacy >99.8% based on the detection limit). An increase in copper release from the coating was observed in the presence of P. aeruginosa, which was postulated to be due to the proteolytic activity of P. aeruginosa. The higher efficacy of the coating against P. aeruginosa compared to S. aureus is thus attributed to this increased copper release from the coating, which resulted in extensive bacterial membrane damage and death. The copper-containing coating on poly(vinyl fluoride) retained its antibacterial efficacy after 100 wipes with a water-wetted cloth or isopropanol wipes, demonstrating its durability and long-term efficacy. The coating did not exhibit significant cytotoxicity toward mammalian fibroblasts, further demonstrating its potential for mitigating bacterial transmission in a clinical setting.

Biofilm-Forming Capacity of Five Salmonella Strains and Their Fate on Postharvest Mini Cucumbers

Salmonella enterica is one of the pathogens that is frequently identified as the cause of fresh produce-related outbreaks. Biofilm formation is a factor that can contribute to pathogen survival on produce surface. The goal of our current research was to investigate the survival of five S. enterica strains representing different serotypes (i.e., Typhimurium, Enteritidis, Daytona, Poona, and Newport) on whole mini cucumbers stored at refrigeration (4°C) and room temperature (22°C). We also determined the strains survival on glass slides and in phosphate-buffered saline at 4 and 22°C, as well as the ability to form biofilms on a solid-liquid interphase. A rapid decrease in cell density (>4-log reduction over 8 days) of all five tested strains was observed on glass slides, while a slower die-off (<1-log reduction in 8 days) was observed in PBS. No significant difference in the die-off rate was observed among the five strains at 4 or 22°C. The die-off rate on the surface of mini cucumbers at 4°C was significantly slower ( P < 0.02) for Salmonella Enteritidis LMFS-S-JF-005 compared with the remaining four strains. At 22°C, Salmonella Poona S306 was able to grow by more than 1.5 log units on whole mini cucumbers over a period of 8 days, while the cell density of the other four strains remained at the same level compared with day 0. At this temperature, Salmonella Poona S306 was also able to form significantly stronger biofilms on a solid-liquid interphase ( P < 0.01) and was the only strain that presented a red, dry, and rough morphotype on Congo red agar plates, indicating the formation of both curli fimbriae and cellulose. These results revealed that the fate of Salmonella on mini cucumbers is strain specific, which highlighted the need for tailored mitigation strategies, such as the effective control of temperature and moisture for limiting the survival or growth of high-risk Salmonella strains between harvest and consumption of fresh produce.

Fecal microbiota transplant - a new frontier in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic multifactorial disease that affects the gastrointestinal tract and results from an aberrant immune response toward luminal antigens in genetically susceptible people. Most of the current therapies for IBD focus on the management of the inflammation by using corticosteroids, immune modulators, and more recently, monoclonal antibodies (biological therapy). Although these therapies provide benefit in most cases, there are still a significant number of patients who do not respond or become refractory over time, suggesting the need for alternative therapeutic options. In the last decade, it has been recognized that "dysbiosis," an imbalanced gut microbiota, is a key element in IBD suggesting microbiome-based therapies as an attractive approach. Recently, fecal microbiota transplant (FMT) has been successfully used for the treatment of Clostridium difficile infection, and it is now under investigation for the treatment of IBD. Clinical trials data are still poor but strongly support a future introduction of FMT in therapy to manage IBD microbiome. More studies are needed to assess the optimal route of administration and the frequency of FMT, the best matched donor for each patient as well as the risks associated with FMT in IBD.