PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.

The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools are available for this purpose. Hence, we have developed a tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates. This tool consists of an ensemble of machine-learning-based predictors for determining the presence of temperate markers (integrase, Cro/CI repressor, immunity repressor, DNA partitioning protein A, and antirepressor) along with the integration of the ABRicate tool to determine the presence of antibiotic resistance genes and virulence genes. Using the biological features of the temperate markers, we were able to predict the presence of the temperate markers with high MCC scores (>0.70), corresponding to the lifestyle of the phages with an accuracy of 96.5%. Additionally, the screening of 183 lytic phage genomes revealed that six phages were found to contain AMR or virulence genes, showing that not all lytic phages are suitable to be used for therapy. The suite of predictors, PhageLeads, along with the integrated ABRicate tool, can be accessed online for in silico selection of suitable therapeutic phage candidates from single genome or metagenomic contigs.

The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health.

East Asians (EAs) experience worse metabolic health outcomes compared to other ethnic groups at lower body mass indices; however, the potential role of the gut microbiota in contributing to these health disparities remains unknown. We conducted a multi-omic study of 46 lean and obese East Asian and White participants living in the San Francisco Bay Area, revealing marked differences between ethnic groups in bacterial richness and community structure. White individuals were enriched for the mucin-degrading Akkermansia muciniphila. East Asian subjects had increased levels of multiple bacterial phyla, fermentative pathways detected by metagenomics, and the short-chain fatty acid end-products acetate, propionate, and isobutyrate. Differences in the gut microbiota between the East Asian and White subjects could not be explained by dietary intake, were more pronounced in lean individuals, and were associated with current geographical location. Microbiome transplantations into germ-free mice demonstrated stable diet- and host genotype-independent differences between the gut microbiotas of East Asian and White individuals that differentially impact host body composition. Taken together, our findings add to the growing body of literature describing microbiome variations between ethnicities and provide a starting point for defining the mechanisms through which the microbiome may shape disparate health outcomes in East Asians.

The community of microbes living in the human gut varies based on where a person lives, in part because of differences in diets but also due to factors still incompletely understood. In turn, this 'microbiome' may have wide-ranging effects on health and diseases such as obesity and diabetes. Many scientists want to understand how differences in the microbiome emerge between people, and whether this may explain why certain diseases are more common in specific populations. Self-identified race or ethnicity can be a useful tool in that effort, as it can serve as a proxy for cultural habits (such as diets) or genetic information. In the United States, self-identified East Asian Americans often have worse 'metabolic health' (e.g. levels of sugar or certain fat molecules in the blood) at a lower weight than those identifying as White. Ang, Alba, Upadhyay et al. investigated whether this health disparity was linked to variation in the gut microbiome. Samples were collected from 46 lean and obese individuals living in the San Francisco Bay Area who identified as White or East Asian. The analyses showed that while the gut microbiome of White participants changed in association with obesity, the microbiomes of East Asian participants were distinct from their White counterparts even at normal weight, with features mirroring what was seen in White individuals in the context of obesity. Although these differences were connected to people's current address, they were not attributable to dietary differences. Ang, Alba, Upadhyay et al. then transplanted the microbiome of the participants into genetically identical mice with microbe-free guts. The differences between the gut microbiomes of White and East Asian participants persisted in recipient animals. When fed the same diet, the mice also gained different amounts of weight depending on the ethnic identity of the microbial donor. These results show that self-identified ethnicity may be an important variable to consider in microbiome studies, alongside other factors such as geography. Ultimately, this research may help to design better, more personalized treatments for an array of conditions.

Effects of internal dynamics on chemotactic aggregation of bacteria.

The effects of internal adaptation dynamics on the self-organized aggregation of chemotactic bacteria are investigated by Monte Carlo (MC) simulations based on a two-stream kinetic transport equation coupled with a reaction-diffusion equation of the chemoattractant that bacteria produce. A remarkable finding is a nonmonotonic behavior of the peak aggregation density with respect to the adaptation time; more specifically, aggregation is the most enhanced when the adaptation time is comparable to or moderately larger than the mean run time of bacteria. Another curious observation is the formation of a trapezoidal aggregation profile occurring at a very large adaptation time, where the biased motion of individual cells is rather hindered at the plateau regimes due to the boundedness of the tumbling frequency modulation. Asymptotic analysis of the kinetic transport system is also carried out, and a novel asymptotic equation is obtained at the large adaptation-time regime while the Keller-Segel type equations are obtained when the adaptation time is moderate. Numerical comparison of the asymptotic equations with MC results clarifies that trapezoidal aggregation is well described by the novel asymptotic equation, and the nonmonotonic behavior of the peak aggregation density is interpreted as the transient of the asymptotic solutions between different adaptation time regimes.

Assessment of the sanitary quality of ready to eat sesame, a low moisture street food from Burkina Faso.

BACKGROUND: Microbial contamination of edible low moisture food poses a significant public health risk for human. In this study, the microbial quality of sweet dehulled sesame seed croquettes, salted dehulled sesame seed and the raw sesame seed, sold under ambient conditions were examined. The samples were collected in the cities of Burkina Faso. The first type is sweet dehulled sesame seed croquettes (n1 = 25); the second type is salted dehulled sesame seed (n2 = 25) and the third type is raw sesame seed (n3 = 25). Assessment of the microbial quality was based on the total aerobic mesophilic bacteria, the thermotolerant coliforms, the yeasts and moulds, the E. coli, and the Salmonella spp. using ISO methods. RESULTS: The results showed the presence of microorganisms varying from <1.0 to 1.72 × 105 CFU g- 1 for thermotolerant coliforms, from <1.0 to 6,12 × 106 CFU g- 1 for the total mesophilic aerobic flora and from <1.0 to 8.10 × 105 CFU g- 1 for yeasts and moulds. The higher contaminations rates were mostly observed in raw sesame seed samples. No E coli or Salmonella pathogens were detected. Based on international standards of dehydrated food, 50.67% of the ready to eat sesame are satisficing while 17.33% are acceptable and 32% are not satisficing. CONCLUSION: Attention should be emphasized on the processing practices, especially in crowded places where RTE sesames seeds are mostly sold. The high numbers of all microbial groups in these sesame seed samples suggested that the production of RTE sesame seed should be improved by better hygiene. This study highlights also that RTE sesame seed might harbor a wide range of microorganisms when processes are weak of hygiene.

Improved bounds on entropy production in living systems.

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Mechanism and application of Sesbania root-nodulating bacteria: an alternative for chemical fertilizers and sustainable development.

Chemical fertilizers are used in large-scale throughout the globe to satisfy the food and feed requirement of the world. Demanding cropping with the enhanced application of chemical fertilizers, linked with a decline in the recycling of natural or other waste materials, has led to a decrease in the organic carbon levels in soils, impaired soil physical properties and shrinking soil microbial biodiversity. Sustenance and improvement of soil fertility are fundamental for comprehensive food security and ecological sustainability. To feed the large-scale growing population, the role of biofertilizers and their study tends to be an essential aspect globally. In this review, we have emphasized the nitrogen-fixing plants of Sesbania species. It is a plant that is able to accumulate nitrogen-rich biomass and used as a green manure, which help in soil amelioration. Problems of soil infertility due to salinity, alkalinity and waterlogging could be alleviated through the use of biologically fixed nitrogen by Sesbania plants leading to the conversion of futile land into a fertile one. A group of plant growth-promoting rhizobacteria termed as "rhizobia" are able to nodulate a variety of legumes including Sesbania. The host-specific rhizobial strains can be used as potential alternative for nitrogenous fertilizers as they help the host plant in growth and development and enhance their endurance under stressed conditions. The review gives the depth understanding of how the agriculturally important microorganisms can be used for the reduction of broad-scale application of chemical fertilizers with special attention to Sesbania-nodulating rhizobia.

In vivo assessment and characterization of lactic acid bacteria with probiotic profile isolated from human milk powder.

INTRODUCTION: Introduction: breast milk (MH) contains nutrients and bioactive compounds for child development, including probiotic bacteria, which contribute to intestinal maturation. This benefit accompanies the individual until adulthood. There are new methods such as spray drying that give this compound a good conservation without loss of microbiota. Objective: the aim of this study was to analyze the viability of lactic acid bacteria isolated from human milk with probiotic potential after the spray drying process, as well as to evaluate the possible adhesion in the colon of mice of the Balb/C strain after feeding them powdered human milk and a commercial formula milk. Method: we isolated and identified the presence of lactic acid bacteria with possible probiotic potential in powdered human milk using the MALDI-TOF MS technique. Powdered human milk and a commercial formula milk were fed to mice of the Bald/C strain for 14 weeks. Glucose level and weight were measured in the mice. The feces were collected to verify the presence of lactic bacteria. The mice were sacrificed and their intestines were weighed, isolating the lactic acid bacteria both from the intestines and from the feces. The strains isolated from mice fed human milk were evaluated for their probiotic potential, analyzing their ability to inhibit pathogens, resistance to pH, temperature, adhesion, and hydrophobicity. Results: the presence of Lactobacillus fermentum LH01, Lactobacillus rhamnosus LH02, Lactobacullis reuteri LH03, and Lactobacillus plantarum LH05 in powdered human milk was identified. All strains showed a possible probiotic profile due to the ability of bacteria to resist low pH, bile salts, and exposure to gastric enzymes, as well as their hydrophobicity and self-aggregation capacity, and their failure to show hemagglutination or hemolysis activity in a culture medium rich in erythrocytes. We observed that the consumption of powdered human milk prevented weight gain and constipation in mice. Conclusions: after spray drying, strains with possible probiotic potential may be preserved in human milk. The consumption of powdered human milk with probiotic bacteria prevents constipation and weight gain in mice, when compared to those fed a commercial formula milk.

INTRODUCCIÓN: Introducción: la leche materna (HM) contiene los nutrientes y compuestos bioactivos necesarios para el desarrollo infantil, incluidas bacterias probióticas, que contribuyen a la maduración intestinal. Objetivo: el objetivo de este estudio fue analizar la viabilidad de las bacterias acidolácticas aisladas de la leche humana con potencial probiótico, después del proceso de secado, así como evaluar su posible adhesión en el colón de ratones (BAlb/C) alimentados con leche humana en polvo y leche de una fórmula comercial. Método: se aislaron e identificaron mediante la técnica de Maldi-Tof-MS las bacterias acidolácticas con posible potencial probiótico en la leche humana en polvo. Se alimentó con leche humana en polvo y leche de una fórmula comercial a ratones de la cepa Bald/C durante 14 semanas. Se midieron el nivel de glucosa y el peso. Las heces se recolectaron para verificar la presencia de bacterias lácticas. Los ratones se sacrificaron y se pesaron los intestinos, aislando las bacterias lácticas tanto de los intestinos como de las heces. En las cepas aisladas de la leche humana se evaluó el potencial probiótico analizando su capacidad para inhibir patógenos, resistir distintos pH y temperaturas, adherirse y mostrar hidrofobicidad. Resultados: se identificó la presencia de Lactobacillus fermentum LH01, Lactobacillus rhamnosus LH02, Lactobacullis reuteri LH03 y L. plantarum LH05 en la leche humana en polvo. Todas las cepas mostraron resistencia a los pH bajos, a las sales biliares y a la exposición a enzimas gástricas, así como una buena hidrofobicidad y capacidad de autoagregación. Además, no presentaron actividad de hemaglutinación o hemólisis en un medio de cultivo rico en eritrocitos. Observamos que el consumo de leche humana en polvo evita en los ratones el aumento de peso y el estreñimiento. Conclusiones: después del secado por aspersión, las cepas con posible potencial probiótico pueden conservarse en la leche materna. El consumo de leche humana en polvo con bacterias probióticas evita el estreñimiento y el aumento de peso en los ratones, en comparación con los alimentados con leche de una formula comercial.

The stringent response of marine bacteria - assessment of (p)ppGpp accumulation upon stress conditions.

Microorganisms are particularly adapted to alterations in their environment. One of the global regulatory mechanisms involved in these adaptations is the stringent response. The unusual nucleotides, guanosine penta and tetraphosphates, (p)ppGpp act as alarmones of this response, heralding nutrient limitation and stressors. Marine bacteria encounter numerous stresses of sparse nutrient supplies and changes in physicochemical conditions. The aim of this work was to assess whether the stress conditions common in marine environment can induce the stringent response and what is a kinetic of this process. The representative bacterial species, Shewanella baltica, Acinetobacter johnsonii, Vibrio harveyi, and Escherichia coli were subjected to a variety of stressors. We analyzed the kinetics of (p)ppGpp synthesis by labeling in vivo nucleotides and analysis by thin layer chromatography. The (p)ppGpp accumulation followed the elevated temperature and amino acid starvation for all bacteria tested. The carbon and nitrogen limitation resulted in the response limited to V. harveyi and S. baltica. The DNA damaging agents induced the (p)ppGpp production in all strains, while osmotic stress did not result in significant alarmone synthesis. The representative marine bacteria species were shown to induce with varying extent the stringent response upon the onset of stress and limitation conditions. Importantly, the in vivo labeling and subsequent separation of the nucleotides by thin layer chromatography serves as a valid method for the analysis of the stringent response and (p)ppGpp accumulation in environmental bacteria.

Assessment of predatory bacteria and prey interactions using culture-based methods and EMA-qPCR.

Traditional culture-based enumeration methods were compared with the ethidium monoazide quantitative polymerase chain reaction (EMA-qPCR) technique to assess Bdellovibrio-and-like-organisms (BALOs) predator-prey interactions. Gram-negative [Pseudomonas spp. and Klebsiella pneumoniae (K. pneumoniae)] and Gram-positive [Staphylococcus aureus (S. aureus) and Enterococcus faecium (E. faecium)] organisms were employed as prey cells, while a Bdellovibrio bacteriovorus strain (PF13) was used as the predator. The co-culture experiments were also compared in diluted nutrient broth (DNB) and HEPES buffer. In both media, K. pneumoniae (maximum log reduction of 5.13) and Pseudomonas fluorescens (P. fluorescens) (maximum log reduction of 4.21) were sensitive to predation by B. bacteriovorus PF13 as their cell counts and gene copies were reduced during all the co-culture experiments, while the concentration of B. bacteriovorus PF13 increased. The concentration of B. bacteriovorus PF13 also increased in the presence of S. aureus (HEPES buffer) and E. faecium (DNB), indicating that the predator interacted with these Gram-positive prey in order to survive. Moreover, as no predator plaques were produced in the co-culture experiments with P. aeruginosa (DNB and HEPES buffer), S. aureus (DNB and HEPES buffer) and E. faecium (HEPES buffer), EMA-qPCR proved to be beneficial in monitoring the concentration of B. bacteriovorus. In conclusion, the cell counts and/or EMA-qPCR analysis for the HEPES buffer and DNB assays were successfully employed to monitor the predation of P. fluorescens and K. pneumoniae by B. bacteriovorus, while E. faecium was sensitive to predation in DNB and S. aureus was sensitive to predation in HEPES buffer.

Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves.

Previous bioinformatics studies have linked gain or loss of energy reserves with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the theoretical distribution patterns of energy reserves across bacterial species could provide a shortcut route to look into bacterial lifestyle and physiology. So far, five major energy reserves have been identified in bacteria due to their capacity to support bacterial persistence under nutrient deprivation conditions. These include polyphosphate (polyP), glycogen, wax ester (WE), triacylglycerol (TAG), and polyhydroxyalkanoates (PHAs). Although the enzymes related with metabolism of energy reserves are well understood, there is a lack of systematic investigations into the distribution of bacterial energy reserves from an evolutionary point of view. In this study, we sourced 8282 manually reviewed bacterial reference proteomes and combined a set of hidden Markov sequence models (HMMs) to search homologs of key enzymes related with the metabolism of energy reserves. Our results revealed that specific pathways like trehalose-related glycogen metabolism and enzymes such as wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) are mainly restricted within specific types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirms that loss of energy reserves like polyP metabolism absence in Mollicutes is correlated with bacterial genome reduction. Through this analysis, a clearer picture about the metabolism of energy reserves in bacteria is presented, which could serve as a guide for further theoretical and experimental analyses of bacterial energy metabolism.

Biofuel production from straw hydrolysates: current achievements and perspectives.

Straw is an agricultural residue of the production of e.g. cereals, rapeseed or sunflowers. It includes dried stalks, leaves, and empty ears and corncobs, which are separated from the grains during harvest. Straw is a promising lignocellulosic feedstock with a beneficial greenhouse gas balance for the production of biofuels and chemicals. Like all lignocellulosic materials, straw is recalcitrant and requires thermochemical and enzymatic pretreatment to enable access to the three major biopolymers of straw-the polysaccharides cellulose and hemicellulose and the polyaromatic compound lignin. Straw is used for commercial ethanol and biogas production. Considerable research has also been conducted to produce biobutanol, biodiesel and biochemicals from this raw material, but more research is required to establish them on a commercial scale. The major hindrance for launching industrial biofuel and chemicals' production from straw is the high cost necessitated by pretreatment of the material. Improvements of microbial strains, production and extraction technologies, as well as co-production of high-value compounds represent ways of establishing straw as feedstock for the production of biofuels, chemicals and food.

(p)ppGpp: the magic governor of bacterial growth economy.

A fundamental question in microbiology is how bacterial cells manage to coordinate gene expression with cell growth during adapting to various environmental conditions. Although the cellular responses to changing environments have been extensively studied using transcriptomic and proteomic approaches, it remains poorly understood regarding the molecular strategy enabling bacteria to manipulate the global gene expression patterns. The alarmone (p)ppGpp is a key secondary messenger involved in regulating various biochemical and physiological processes of bacterial cells. However, despite of the extensive studies of (p)ppGpp signaling in stringent response during the past 50 years, the connection between (p)ppGpp and exponential growth remains poorly understood. Our recent work demonstrates that (p)ppGpp is strongly involved in regulating cell growth of Escherichia coli through balancing the cellular investment on metabolic proteins and ribosomes, highlighting itself as a magic governor of bacterial global resource allocation. In this mini-review, we briefly summarize some historical perspectives and current progress of the relation between (p)ppGpp and bacterial exponential growth. Two important future directions are also highlighted: the first direction is to elucidate the cellular signal that triggers (p)ppGpp accumulation during poor growth conditions; the second direction is to investigate the relation between (p)ppGpp and exponential growth for bacterial species other than E. coli.

Filamentous phages: masters of a microbial sharing economy.

Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.

Assessment of bacterial viability: a comprehensive review on recent advances and challenges.

Assessing bacterial contamination in environmental samples is critical in determining threats to public health. The classical methods are time-consuming and only recognize species that grow easily on culture media. Viable but non-culturable (VBNC) bacteria are a possible threat that may resuscitate and cause infections. Recent dye-based screening techniques employ nucleic acid dyes such as ethidium monoazide (EMA) and propidium monoazide (PMA), along with many fluorescent dyes, which are an effective alternative for viability assessment. The measurement of cellular metabolism, heat flow and ATP production has also been widely applied in detection approaches. In addition, RNA-based detection methods, including nucleic acid sequence-based amplification (NASBA), have been applied for bacterial pathogen determination. Stable isotope probing using 13C, 15 N and 18O, which are mobilized by microbes, can also be used for effective viability assessment. Future detection tools, such as microarrays, BioNEMS and BioMEMS, which are currently being validated, might offer better microbial viability detection.

Radiative Energy Budgets in a Microbial Mat Under Different Irradiance and Tidal Conditions.

Irradiance and temperature variations during tidal cycles modulate microphytobenthic primary production potentially by changing the radiative energy balance of photosynthetic mats between immersion and emersion and thus sediment daily net metabolism. To test the effect of tidal stages on the radiative energy budget, we used microsensor measurements of oxygen, temperature, and scalar irradiance to estimate the radiative energy budget in a coastal photosynthetic microbial mat during immersion (constant water column of 2 cm) and emersion under increasing irradiance. Total absorbed light energy was higher in immersion than emersion, due to a lower reflectance of the microbial mat, while most (> 97%) of the absorbed light energy was dissipated as heat irrespective of tidal conditions. During immersion, the upward heat flux was higher than the downward one, whereas the opposite occurred during emersion. At highest photon irradiance (800 µmol photon m-2 s-1), the sediment temperature increased ~ 2.5 °C after changing the conditions from immersion to emersion. The radiative energy balance showed that less than 1% of the incident light energy (PAR, 400-700 nm) was conserved by photosynthesis under both tidal conditions. At low to moderate incident irradiances, the light use efficiency was similar during the tidal stages. In contrast, we found an ~ 30% reduction in the light use efficiency during emersion as compared to immersion under the highest irradiance likely due to the rapid warming of the sediment during emersion and increased non-photochemical quenching. These changes in the photosynthetic efficiency and radiative energy budget could affect both primary producers and temperature-dependent bacterial activity and consequently daily net metabolism rates having important ecological consequences.

Antimicrobial assessment of phage therapy using a porcine model of biofilm infection.

Antibiotic resistant bacterial communities persist in many types of wounds, chronic wounds in particular, in the form of biofilms. Biofilm formation is a major cause of severe infections and the main reason for a negative treatment outcome and slow healing progression. Chronic wounds are a silent epidemic essentially affecting people with co-morbid conditions such as diabetes and obesity and elderly persons particularly those with movement limitations. The development of complementary and alternative effective strategies to antibiotics for the treatment of chronic wounds is highly desired. Phage therapy constitutes a very promising approach in the control of topical microbial populations. In this work newly isolated phages were tested for their efficacy to control bacterial species that predominate in chronic wounds. Phage effectiveness was studied on 24-h old biofilms formed in polystyrene microplates and in porcine skin explants using two treatment approaches: individual phage and a cocktail of phages against four main pathogens commonly isolated from chronic wounds. The two models produced variations in the surface colonization ability, assessed by viable bacterial counts and microscopy visualization after using peptide nucleic acid (PNA) or locked nucleic acid probes (LNA) and 2'-O-methyl (2'-OMe) in fluorescence in situ hybridization (FISH), and in the phage-host interactions. Phages alone and combined caused greater reductions in the number of viable cells when biofilms had been formed on porcine skins and with greater variations detected at 4 h and 24 h of sampling. These results suggest that porcine skin models should be preferentially used to assess the use of phages and phage cocktails intended for topical use in order to understand the fate, throughout treatment time, of the population when dealing with biofilm-related infections.

Formation of nanoscale Te0 and its effect on TeO32- reduction in CH4-based membrane biofilm reactor.

Formation and recovery of elemental tellurium (Te0) from wastewaters are required by increasing demands and scarce resources. Membrane biofilm reactor (MBfR) using gaseous electron donor has been reported as a low-cost and benign technique to reduce and recover metal (loids). In this study, we demonstrate the feasibility of nanoscale Te0 formation by tellurite (TeO32-) reduction in a CH4-based MBfR. Biogenic Te0 intensively attached on cell surface, within diameters ranging from 10 nm to 30 nm and the hexagonal nanostructure. Along with the Te0 formation, the TeO32- reduction was inhibited. After flushing, biofilm resumed the TeO32- reduction ability, suggesting that the formed nanoscale Te0 might inhibit the reduction by hindering substrate transfer of TeO32- to microbes. The 16S rRNA gene amplicon sequencing revealed that Thermomonas and Hyphomicrobium were possibly responsible for TeO32- reduction since they increased consecutively along with the experiment operation. The PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis showed that the sulfite reductases were positively correlated with the TeO32- flux, indicating they were potential enzymes involved in reduction process. This study confirms the capability of CH4-based MBfR in tellurium reduction and formation, and provides more techniques for resources recovery and recycles.

Growth of Clostridium perfringens in sous vide cooked ground beef with added grape seed extract.

The growth of Clostridium perfringens from spore inocula was studied in sous vide cooked ground beef with added 0 to 3% grape seed extract (GSE). C. perfringens did not grow at 4 °C with or without GSE present. Lag time (LT) was 95 h in control samples at 15 °C, whereas 1-3% GSE addition significantly (p < .05) extended LT to 244 h or longer. Generation time (GT) in 3% GSE added beef was similar to that of control (19 h, 3% GSE versus 18 h, control) at 15 °C. At 20 °C, GT was 1.5 h in samples without GSE; however, 1-3% GSE addition extended GT about 2-3 folds (p < .05). Lag time at 20 °C was 23 h in control samples, while LT was 40-59 h in samples containing GSE. Interestingly, GSE did not affect LT at 25 °C; however, significantly (p < .05) longer GT was observed in 3% GSE added samples than the other sample groups. Additionally, GSE from 1 to 3% in beef extended the period needed to reach 6 log cfu/g at 15 or 20 °C, while 3% GSE was required at 25 °C. The findings suggest that GSE exhibits concentration and temperature dependent inhibitory effect on growth of C. perfringens in sous vide cooked ground beef. Grape seed extract can be used to extend the shelf-life and ensure the microbiological safety of sous vide cooked meat products.

Label-free bacterial colony detection and viability assessment by continuous-wave terahertz transmission imaging.

Timely and accurate bacterial detection is critical for various health and safety applications, which promotes the continuous development of versatile optical sensors for bacterial investigations. Here, we report a new strategy for bacterial colony sensing using terahertz (THz) imaging with minimal assay procedures. The proposed method utilizes the acute sensitivity of THz wave to the changes in the water content and cellular structures. Single bacterial colonies of 4 bacterial species were directly distinguished using THz imaging by utilizing their differences in THz absorption. In addition, the distribution of mixed bacterial samples has been demonstrated by THz imaging, which demonstrated that the target bacterium could be easily recognized. Furthermore, we investigated the differentiation of bacterial viability, which indicated that bacteria under different living states could be distinguished by THz imaging because of their different hydration levels and cellular structures. Our results suggest that THz imaging has the potential to be used for mixed bacterial sample detection and bacterial viability assessment in a label-free and nondestructive manner.

Identification of spider-mite species and their endosymbionts using multiplex PCR.

Spider mites of the genus Tetranychidae are severe crop pests. In the Mediterranean a few species coexist, but they are difficult to identify based on morphological characters. Additionally, spider mites often harbour several species of endosymbiotic bacteria, which may affect the biology of their hosts. Here, we propose novel, cost-effective, multiplex diagnostic methods allowing a quick identification of spider-mite species as well as of the endosymbionts they carry. First, we developed, and successfully multiplexed in a single PCR, primers to identify Tetranychus urticae, T. evansi and T. ludeni, some of the most common tetranychids found in southwest Europe. Moreover, we demonstrated that this method allows detecting multiple species in a single pool, even at low frequencies (up to 1/100), and can be used on entire mites without DNA extraction. Second, we developed another set of primers to detect spider-mite endosymbionts, namely Wolbachia, Cardinium and Rickettsia in a multiplex PCR, along with a generalist spider-mite primer to control for potential failure of DNA amplification in each PCR. Overall, our method represents a simple, cost-effective and reliable method to identify spider-mite species and their symbionts in natural field populations, as well as to detect contaminations in laboratory rearings. This method may easily be extended to other species.