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In this work, the relationship and kinetics of biodegradation and bio-adsorption of benzo[ a ]pyrene (BaP) by Bacillus and Ascomycota were explored, and the metabolites of BaP under mixed microbial coculture were analyzed and characterized. The results show that BaP was removed through both biosorption and biodegradation. Under mixed microbial coculture, biosorption played a significant role in the early stage and biodegradation was predominant in the later stage. During the removal of BaP, the fungi exhibited remarkable adsorption capabilities for BaP with an adsorption efficiency (AE) of 38.14 %, while bacteria had a best degradation for BaP with a degradation efficiency (DE) of 56.13 %. Under the mixed microbial culture, the removal efficiency (RE) of BaP by the synergistic action of fungi and bacteria reached up to 76.12 % within 15 days. Kinetics analysis illustrated that the degradation and adsorption process of BaP were well fit to the first-order and the pseudo-second-order kinetic models, respectively. The research on the relationship between degradation and adsorption during microbial removal of BaP, as well as the synergistic effects of fungi and bacteria, will provide a theoretical guidance for two or even synthetic microbial communities. [Display omitted] • In the process of the removal of BaP, fungi dominated by adsorption, while mixed bacteria dominated by degradation. • Quasi-second-order kinetics can better describe the adsorption process of BaP by microorganisms. • The quasi-first-order kinetic model can better describe the biodegradation process. [ABSTRACT FROM AUTHOR]

Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation. • Mixed microbial cultures show greater genetic and metabolic capabilities. • Fungal-bacterial consortia exhibit synergistic mechanisms to remove PHs. • Environmental factors impact microbial consortium efficiency. • By using synthetic biology tools, effective artificial communities can be designed. [ABSTRACT FROM AUTHOR]

Ciliate protozoa are key members of the microbial community of the rumen. Their study is important to the health and productivity of cattle, which are their hosts. However, there have been persistent challenges in culturing this microbial group in the laboratory. This review will sum up recent advances along with these persistent challenges. Protozoa have been maintained in three types of cultures (ex vivo , in vitro batch, in vitro continuous). Ex vivo cultures are prepared readily from rumen contents by washing away contaminating cells (e.g., bacteria). They have been useful in making basic observations of metabolism, such as which types of fermentation products protozoa form. However, these cultures can be maintained for only short periods (minutes or hours). In vitro batch and in vitro continuous cultures can be used in longer experiments (weeks or longer). However, it is not currently possible to maintain protozoa in these cultures unless bacteria are also present. We conclude the review with a protocol for preparing ex vivo cultures of protozoa. Our protocol has been standardized and used successfully across animal diets, users, and institutions. We anticipate this review will prepare others to culture rumen ciliate protozoa and reach new insights into this important microbial group. • Ciliate protozoa are key microbes of the rumen of cattle. • Both ex vivo and in vitro techniques have been developed to culture protozoa. • A protocol for ex vivo culturing of protozoa is presented. [ABSTRACT FROM AUTHOR]

We evaluated the effect of open and closed systems used for ovarian tissue vitrification on the microbiological load and preservation of preantral follicles (PAFs) in the red-rumped agoutis. The ovaries from eight females were recovered and fragmented, with four cortexes fragments immediately fixed and evaluated (fresh group). The other fragments were processed for the solid-surface vitrification method (SSV) or an ovarian tissue cryosystem (OTC) using fetal calf serum, ethylene glycol, and sucrose as cryoprotectants, stored for two weeks, and rewarmed. Subsequently, fragments were subjected to a 24-h in vitro culture and assessed for microbiological load, PAF morphology, and DNA integrity. There was no fungal contamination; however, the vitrified samples from two individuals showed bacterial contamination of 79 200 colony forming units per milliliter (CFU)/mL for SSV and 3120 CFU/mL for OTC. From those samples, a total of eight different types of bacterial colonies were isolated and identified as coagulase-negative Staphylococci and Gram-positive bacilli. Regarding PAF morphology, both systems provided adequate preservation, with values higher than 70% normal follicles observed before and after culture. The TUNEL assay revealed that both SSV (52.39%) and OTC (41.67%) could preserve DNA integrity after vitrification and after 24 h of culture. In summary, both open and closed systems were equally efficient in preserving agouti ovarian tissues, especially concerning the preantral follicle morphology and DNA integrity; however, the OTC seems to provide a less adequate environment for bacterial proliferation. [ABSTRACT FROM AUTHOR]

Chlorpyrifos (CPF) is a highly toxic phosphate-rich organic pesticide (OP), identified as an emerging contaminant and used extensively in agricultural production. CPF persistence in the environment and its potential health hazards has become increasingly concerning worldwide in recent years due to exponential rise in food demand. Biodegradation of chlorpyrifos by microbial cultures is a promising approach to reclaiming contaminated soil and aquatic environments. The purpose of this review is to summarize the current understanding of microbiological aspects of xenobiotic chlorpyrifos biodegradation, including microbial diversity, metabolic pathways, and factors that modulate it. In both aerobic and anaerobic environments, CPF is biochemically broken down by a broad spectrum of bacteria and fungi. Hydrolysis, dehalogenation, and oxidation of chlorpyrifos are all enzymatic reactions that lead to its degradation. Biodegradation rate and efficiency are strongly influenced by parametric variables such as co-substrates abundance, pH, temperature, and initial chlorpyrifos concentration. The review provides evidence that microbial biodegradation is a viable method for remediating chlorpyrifos-contaminated sites in a sustainable and safe manner. [ABSTRACT FROM AUTHOR]

Sour liquid noodles are a characteristic traditional food in Luoyang, China. Mung bean sour liquid (MBSL) is fermented from mung beans and used to cook noodles (instead of using water). However, the microbial community, volatile compounds, and physicochemical properties of MBSL are still unclear. Here, a comprehensive study was conducted using a combination of Illumina HiSeq sequencing, gas chromatography‒mass spectrometry detection, and physicochemical analysis methods. Eight phyla and 59 genera of bacteria were identified in MBSL, of which 4 genera were dominant, namely, Lactobacillus , Lactococcus , Leuconostoc , and Lelliottia. Six phyla and 123 genera of fungi were detected, with 11 genera being dominant. The protein content, total acid content, and pH mainly influenced the microbial community. Myroides , Aeromonas , Flavobacterium , and Lactobacillus , etc. May play important roles in balancing MBSL ecosystems. There were 40 volatile compounds in MBSL, with 1-hexanol, eugenol, acetic acid, and hexanoic acid being considered key volatile compounds. Lactobacillus , Algoriella , Lelliottia , and Leuconostoc were significantly correlated with the volatile compounds found in MBSL. The complex correlation between microbial communities, volatile compounds, and physicochemical properties may be elucidated through these findings. Controlling environmental factors and increasing the number of selected microbial cultures may improve the quality of MBSL. [Display omitted] • The microbiota, flavors and physicochemical properties in MBSL were studied. • 59 bacterial genera, 123 fungal genera, and 40 volatiles were detected in MBSL. • Myroides and Lactobacillus were critical for maintain MBSL ecosystem stability. • Microbial community structure was closely related to protein, total acids, and pH. • The contents of hexanol, ethanol, 2-hexenol, and acetic acid were relatively high. [ABSTRACT FROM AUTHOR]

Microorganisms drive the degradation of organic matter thanks to their enzymatic versatility. However, the structure of lignocellulose poses a great challenge for the microbiota inhabiting a compost pile. Our purpose was to increase the biodegradability of vegetable waste in the early stages of the composting process by applying a microbial consortium with lignocelllulolytic capacity. For this, a previous screening was performed among the culturable microbiota from different composting processes to find inoculants with ligninocellulolytic activity. Selected strains were applied as a pure culture and as a microbial consortium. The starting material was composed of tomato plant and pruning remains mixed in a ratio (50:50 v/v), whose humidity was adjusted to around 65%. To determine the ability of both treatments to activate the biodegradation of the mixtures, moisture, organic matter, ash, C/N ratio, 4-day cumulative respirometric index (AT 4) and degradation rates of cellulose, hemicellulose and lignin were evaluated. Subsequently, a real composting process was developed in which the performance of the microbial consortium was compared with the composting process without inoculum (control). According to our tests, three microbial strains (Bacillus safensis , Bacillus licheniformis and Fusarium oxysporum) were selected. The results showed that the application of the bacteria strains at low doses (104 CFU g−1 on the complete residual material of the pile) resulted in higher rates of lignocelullose degradation after 10 days of treatment compared to that observed after application of the fungus in pure culture or untreated controls. The implementation of the strategy described in this work resulted in obtaining compost with better agronomic quality than the uninoculated controls. Therefore, the application of this consortium could be considered as an interesting tool for bioactivation of lignocellulosic waste prior to the composting process. [Display omitted] • Resident lignocellulolytic microbiota is useful to improve the composting process. • A simple protocol for the pretreatment of plant wastes was developed. • Bacillus spp. represent an excellent biotechnological tool in composting processes. • 10 days of pretreatment at low inoculum doses improves the final product quality. [ABSTRACT FROM AUTHOR]

Petrochemical-based synthetic plastics poses a threat to humans, wildlife, marine life and the environment. Given the magnitude of eventual depletion of petrochemical sources and global environmental pollution caused by the manufacturing of synthetic plastics such as polyethylene (PET) and polypropylene (PP), it is essential to develop and adopt biopolymers as an environment friendly and cost-effective alternative to synthetic plastics. Research into bioplastics has been gaining traction as a way to create a more sustainable and eco-friendlier environment with a reduced environmental impact. Biodegradable bioplastics can have the same characteristics as traditional plastics while also offering additional benefits due to their low carbon footprint. Therefore, using organic waste from biological origin for bioplastic production not only reduces our reliance on edible feedstock but can also effectively assist with solid waste management. This review aims at providing an in-depth overview on recent developments in bioplastic-producing microorganisms, production procedures from various organic wastes using either pure or mixed microbial cultures (MMCs), microalgae, and chemical extraction methods. Low production yield and production costs are still the major bottlenecks to their deployment at industrial and commercial scale. However, their production and commercialization pose a significant challenge despite such potential. The major constraints are their production in small quantity, poor mechanical strength, lack of facilities and costly feed for industrial-scale production. This review further explores several methods for producing bioplastics with the aim of encouraging researchers and investors to explore ways to utilize these renewable resources in order to commercialize degradable bioplastics. Challenges, future prospects and Life cycle assessment of bioplastics are also highlighted. Utilizing a variety of bioplastics obtained from renewable and cost-effective sources (e.g., organic waste, agro-industrial waste, or microalgae) and determining the pertinent end-of-life option (e.g., composting or anaerobic digestion) may lead towards the right direction that assures the sustainable production of bioplastics. [Display omitted] [ABSTRACT FROM AUTHOR]

Cryopreservation is an efficient method used to preserve microorganisms for long periods of time, such as up to 30 years, without changes in genetic and physiological characteristics. As cyanobacteria and microalgae are usually maintained as both axenic and xenic cultures, knowledge of co-cultured bacteria and changes in their community structure is important for the successful maintenance of microbial culture collections. In this study, research on the changes in co-cultured bacterial community structure during cyanobacterial cryopreservation were investigated using three different experimental groups by next generation sequencing (NGS): 1) cultured Trichormus variabilis without cryopreservation (control group), 2) cultured T. variabilis after cryopreservation in 10% dimethyl sulfoxide (Me 2 SO) for 14 days (cryo-cell group), and 3) cultured T. variabilis after cryopreservation in 10% Me 2 SO for 14 days within alginate beads (cryo-bead group). The results showed that the abundance of Sphingomonas and Hydrogenophaga (belonging to phylum Proteobacteria) was significantly increased in the cryo-bead group (Sphingomonas, control: 0.25%, cryo-cell: 1.32%, cryo-bead: 41.70%; Hydrogenophaga, control: 5.47%, cryo-cell: 5.24%, cryo-bead: 12.32%). However, the abundance of the phylum Bacteroidetes was significantly decreased in the cryo-bead group compared to that in the other groups (control: 26.29%, cryo-cell: 38.84%, cryo-bead: 11.43%). Bacterial diversity was generally reduced after cryopreservation in the cryo-bead group, where the overgrowth of a few unique bacteria was observed in the co-cultured bacterial community. These results imply that changes in the co-cultured bacterial community during preservation should be considered as an important factor for the development of methods for cyanobacterial cryopreservation. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze the microbiology of buckwheat honey fermentation inoculated with different starter cultures by culturing and PCR-DGGE, taking as a model for comparison a spontaneously fermented batch. The inoculants tested were (i) cider lees (from a cider factory), (ii) sourdough (from a bakery), and (iii) a commercial Saccharomyces cerevisiae strain. The results of the culturing and culture-independent techniques agreed well and detected the same dominant species along the fermentations. Our results suggest that S. cerevisiae strains, which constituted a majority population in all batches including the uninoculated one, carried out the fermentations. The highest microbial diversity was found at the beginning of the fermentation in the uninoculated batch; this contained in addition to S. cerevisiae bacteria (Paracoccus sp., Staphylococcus sp., and Bacillus sp.) and yeast (Candida sp.) species. Candida sp. was also common in batches inoculated with sourdough and cider lees cultures. Lactobacillus species were found throughout the fermentation of the sourdough-inoculated batch. Basic chemical analysis and testing trials demonstrated that the overall sensory acceptance of the four meads were highly similar. Yeast and bacteria isolated in this study could serve as a source of technologically relevant microorganisms for mead production. • The composition and succession of the microbial populations during fermentation of buckwheat honey was assessed. • The eukaryotic microorganisms during mead fermentation were investigated by the culture-independent PCR-DGGE technique. • The sensory analysis by the acceptance test of meads was performed. • Saccharomyces cerevisiae and Candida sp. Are the most competitive species during fermentation. • The strong aroma and flavor of buckwheat honey masks the organoleptic factors produced by lactic acid bacteria. [ABSTRACT FROM AUTHOR]

Pilonidal, buttock, and perianal abscesses are common reasons for surgical consultation in the pediatric emergency department. Treatment typically includes a bedside incision and drainage, often followed by an abscess culture, and a course of oral antibiotics. We aimed to study the impact of culture data on changes in management and clinical outcomes. We hypothesized that management is unaffected by culture data, and therefore, fluid culture from pilonidal, buttock, and perianal abscesses in the pediatric population may represent an unnecessary laboratory test and cost. A single institution's electronic medical record was searched between February 1, 2013 and August 1, 2017, identifying 249 pediatric patients meeting the inclusion criteria: age 0 to 18 y; diagnosis of pilonidal, buttock, or perianal abscess; bedside incision and drainage. Patients were divided into two different comparison groups for data analysis based on the presence or absence of culture and recurrence or no recurrence. Culture results directly altered management in only 5 patient encounters (2.7% of all cultured). When comparing groups by culture or no culture, no statistically significant difference in recurrence rate (P = 0.4) was noted. When comparing groups by recurrence versus no recurrence, we found no statistically significant difference between sex, resident type, vessel loop use, packing use, or antibiotic use (P > 0.05). We conclude that microbiological culture results are of limited utility in the management of pediatric pilonidal, buttock, and perianal abscesses as they do not appear to alter treatment, and omission of culture is not associated with failure of surgical management. [ABSTRACT FROM AUTHOR]

Pancreaticoduodenectomy (PD) is a complex procedure with a morbidity rate of 40%-50%. We evaluated the incidence, associated factors, etiologic characteristics, and outcome of pyogenic liver abscess (PLA), a rare infectious complication of PD. We retrospectively assessed the data of patients who underwent PD (n = 326) between January 2012 and February 2017 at a single institution. Patients who developed PLA after PD were matched (1:3) for age, sex, and pathologic diagnosis with patients without PLA after PD. Patients who developed PLA without abdominal operation history (n = 77) were also reviewed in the same period. Eleven patients (3.4%) developed PLA after PD; diabetes (5/11, 45.5% versus 4/33, 12.1%; P = 0.031) increased the risk of PLA after PD. The preoperative and postoperative fasting blood glucose (FBG) was significantly higher in PLA+ group than PLA− group: preoperative FBG (median: 7.39 versus 4.49; P < 0.01), postoperative FBG (median: 8.98 versus 5.68; P < 0.01). The occurrence of multiple liver abscess was significantly higher in patients with PLA after PD than patients who developed PLA without abdominal operation history (7/11 versus 22/77; P = 0.036). Microbial pus culture was positive in eight patients with PLA after PD (n = 8/11) and in forty-one patients who developed PLA without abdominal operation history (n = 41/77). Klebsiella pneumoniae was the most commonly isolated microorganism in PLA patients with or without a history of PD (5/8, 62.5% versus 34/41, 82.9%; P = 0.333). Patients with diabetes (including impaired fasting plasma glucose) have a higher risk of developing PLA after PD. Multiple liver abscess was the most common type of PLA after PD; K pneumoniae should be covered when empirically treated patients with PLA. [ABSTRACT FROM AUTHOR]

Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria. [Display omitted] • Bacteria from giant pandas and environment have similar trend resistance. • Disinfection decreased the abundance of some pathogens in feces and environment. • Disinfection shapes microbial populations of the giant panda gut and habitat. • Disinfection results in increased antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

• Modeling the energy obtained from substrate metabolism for growth and metabolite degradation. • Detailing the stages of growth through a system of altruistic division of the functions. • Two strategies exist for microbial growth, whether expand quickly or grow slowly. • There exist three types of microbial growth dynamics depending on the environment, with some degree of sensitivity to environmental change. Many researchers have studied the population dynamics of microbe of microbes as a typical example of population dynamics. The Monod equation, which mainly focuses on the growth and stationary phases, is used when plotting a growth curve. However, the growth potential in the late stage of culture has been overlooked. Previous studies considered the direct degradation of products to the limiting substrate. In this study, we considered microbial growth during the stationary phase, which enables us to describe the dynamics precisely. The microbes were divided into two populations: one grew by consuming the limiting substrate and the other degraded the products by metabolism. According to the numerical analysis of our model, microbes may choose one of two strategies: one consumes substrates and expands quickly, and the other grows slowly while cleaning up the environment in which they thrive. Furthermore, we found three types of microbial growth depending on their ability to detect metabolite accumulation. Using experimentally measured data, this model can estimate the dynamics of cell density, the substrates, and the metabolites used. The model's disentangling of growth curves offers novel interpretive possibilities for culture system dynamics. [ABSTRACT FROM AUTHOR]

Fe(II)-mediated autotrophic denitrification in the presence of copper (Cu), nickel (Ni) and zinc (Zn) with four different microbial cultures was investigated in batch bioassays. In the absence of metals, complete nitrate removal and Fe(II) oxidation were achieved with a Thiobacillus -dominated mixed culture and Pseudogulbenkiania sp. 2002 after 7 d. A nitrate removal of 96 and 91% was observed with a pure culture of T. denitrificans and an activated sludge enrichment, respectively, after 10 d of incubation. Cu, Ni and Zn were then supplemented at an initial concentration of 5, 10, 20 and 40 mg Me/L. A decrease of approximately 50% of the soluble metal concentrations occurred in the first 4 d of denitrification, due to metal precipitation, co-precipitation, sorption onto iron (hydr)oxides, and probably sorption onto biomass. A higher sensitivity to metal toxicity was observed for the microbial pure cultures. Pseudogulbenkiania sp. 2002 was the least tolerant among the biomasses tested, resulting in only 6, 8 and 6% nitrate removal for the highest Cu, Ni and Zn concentrations, respectively. In contrast, the highest nitrate removal efficiency and specific rates were achieved with the Thiobacillus -dominated mixed culture, which better tolerated the presence of metals. Averagely, Cu resulted in the highest inhibition of nitrate removal, followed by Zn and Ni. [ABSTRACT FROM AUTHOR]

Triclosan (TCS); a widely used antimicrobial biocide, exists in several pharmaceutical and personal care products. Due to its wide usage, TCS is detected in wastewater at varying concentrations. Biological treatability of TCS and its effect on chemical oxygen demand (COD) removal efficiency were investigated running laboratory-scale pulse-fed sequencing batch reactors with acclimated and non-acclimated cultures. The culture was acclimatized to TCS by gradually increasing its concentration in the synthetic feed wastewater from 100 ng/L to 100 mg/L. There were no effects of TCS on COD removal efficiency up to the TCS concentration of 500 ng/L for both acclimatized and non-acclimatized cases. However, starting from a concentration of 1 mg/L, TCS affected the COD removal efficiency adversely. This effect was more pronounced with non-acclimatized culture. The decrease in the COD removal efficiency reached to 47% and 42% at the TCS concentration of 100 mg/L, under acclimation and non-acclimation conditions respectively. Adsorption of TCS into biomass was evidenced at higher TCS concentrations especially with non-acclimated cultures. 2,4-dichlorophenol and 2,4-dichloroanisole were identified as biodegradation by-products. The occurrence and distribution of these metabolites in the effluent and sludge matrices were found to be highly variable depending, especially, on the culture acclimation conditions. [ABSTRACT FROM AUTHOR]

In order to identify the cause of death of a cattle that suddenly died on a cattle farm in Tongliao City, Inner Mongolia Autonomous Region, we isolated a strain of bacteria from the spleen and identified the pathogen. The study demonstrated that the isolated strain is Bacillus cereus. The isolates were highly pathogenic and contained toxin genes, such as hbl , nhe , and entFM , in addition to the groEL housekeeping gene. The isolated strain has been named TL strain (16S rDNA sequence number: OP028902, whole genome sequence number: CP129005). Isolates were deposited at China General Microbiological Culture Collection Center (CGMCC No.17626). In this study, we also developed a rapid recombinase polymerase amplification-based lateral flow (RPA-LF) for pathogenic Bacillus cereus. The virulence gene (nhe gene) was used as the target sequence to design RPA-LF assay primers and probes. The RPA reaction is fast (results can be observed in about 15 min), the results can be judged by the naked eye, and the specificity of the RPA-LF method is good. The RPA-LF method detects pathogenic Bacillus cereus in food, which reduces the risk of harm to human health. The RPA-LF assay provides a reference for the rapid detection of pathogenic Bacillus cereus. • We isolated pathogenic Bacillus cereus (OP028902) from the spleen of sudden death cattle. • The RPA reaction speed is fast (the results can be observed in about 15 min). • The RPA-LF detection method has strong specificity. [ABSTRACT FROM AUTHOR]

The present study evaluates the biocompatibility of silver and zinc oxide nanoparticles with various effective microorganisms (EM), like beneficial microbial formulations. The respective nanoparticle was synthesised by chemical reduction of metal precursor with reducer via simple route green technology principles. The synthesised nanoparticles were characterised by UV visible spectroscopy, scanning electron microscopy (SEM), and X-ray diffraction (XRD) studies, revealing highly stable, nanoscale particles with marked crystallinity. EM-like beneficial cultures composed of viable cells of Lactobacillus lactis , Streptomyces sp, Candida lipolytica , and Aspergillus oryzae were formulated with rice bran, sugarcane syrup, and groundnut cake. The respective formulation was inoculated into the nanoparticles amalgamated pots raised with green gram seedlings. Biocompatibility was determined by measuring plant growth parameters of a green gram at pre-determined periods associated with enzymatic antioxidants like catalase (CAT), superoxide dismutase (SOD), and glutathione S transferase (GST) levels. Most significantly, the expression level of these enzymatic antioxidants level was also investigated by quantitative real-time polymerase chain reaction (qRT-PCR). The impact of the soil conditioning effect on soil nutrients like nitrogen, phosphorous, potassium, organic carbon, soil enzymes glucosidases, and β-xylosidases activity was also studied. Among the formulation, rice bran-groundnut cake-sugar syrup formulation recorded the best biocompatibility. This formulation showed high growth promotion, soil conditioning effect and no impact on the oxidative stress enzymes genes that revealed the best compatibility of nanoparticles. This study concluded that biocompatible, eco-friendly formulations of microbial inoculants could be used for the desirable agro active properties that show extreme tolerance or biocompatibility to the nanoparticles. This present study also suggests the utilisation of the above said beneficial microbial formulation and metal-based nanoparticles with desirable agro active properties in a synergistic manner due to their high tolerance or compatibility towards the metal or metal oxide nanoparticles. • Mixed microbial beneficial cultures were formulated with biocompatible agro-based ingredients. • Toxic effect of silver and zinc oxide nanoparticles on the respective formulation was evaluated. • Ricebran - sugar syrup - groundnut cake formulation exhibited the best compatibility with the nanoparticles. • The formulation did not affect plant growth promotion associated with the soil conditioning effect. • No sign of oxidative stress markers or expression induction, revealing notable compatibility. [ABSTRACT FROM AUTHOR]

The applicability of a new strain, Weissella confusa M1, as an adjunct culture for gray sufu was investigated for the first time from microbial and flavor perspectives. Results showed that M1 inoculation improved the flavor, color, texture, and taste properties of sufu compared with natural fermentation. M1 increased the contents of 13 free amino acids, especially aspartate and glutamate, and drove the diversity and dynamics of microbial community during fermentation by being involved in the transport and metabolism of amino acids and carbohydrates. Many volatile compounds were produced after M1 inoculation, with n-hexanal and dimethyl trisulfide contributing the most to the flavor of gray sufu. Enterobacter and Weissella were positively correlated with 13 key flavor compounds during fermentation with M1. Enterobacter and Tetragenococcus were associated with the production of various amino acids. These findings prove that M1 is a promising adjunct culture for gray sufu processing. [Display omitted] • Weissella confusa was applied on the fermentation of gray sufu for the first time. • Gray sufu fermented by W. confuse M1 improved the fermentation quality. • The key microbiota were Enterobacter , Tetragenococcus and Weissella at genus level. • The key flavor compounds were n-hexanal and dimethyl trisulfide. • The microbiota was correlated to the flavor-relating metabolites. [ABSTRACT FROM AUTHOR]

The probiotic potential of 5 food grade Lactobacillus strains, of human origin namely Lactobacillus fermentum (S23), Lb. fermentum NCDC77 (S8), Lb. fermentum (S25) and Lb. plantarum (S1), capable of selenium bioaccumulation (in previous studies), was investigated. The cultures, S8 and S23 maintained elevated cell numbers under conditions simulating passage through the human gastrointestinal tract, showing ability to survive in the presence of simulated gastric juice at pH 2. These cultures also survived in the presence of simulated intestinal juice with 1% bile salts. The cultures showed variable and strain dependent cell-surface hydrophobicity and auto-aggregation ability. The cultures were assayed for susceptibility to 20 antibiotics and found susceptible to 14 out of 20 antibiotics while showed variable resistance to remaining 6 antibiotics. S8 and S23 cultures showed superior antibacterial activity in comparison to remaining 3 cultures. These findings suggest that Lb. fermentum NCDC77 (S8) and Lb. fermentum (S23) cultures, endowed with the ability to accumulate high amount of selenium, exhibited high resistance against low pH and bile. Moreover, these cultures possessed adherence and auto-aggregation properties with minimum resistance to antibiotics and hence could be exploited for the development of selenium enriched functional food or nutraceutical as a source of dietary selenium. [ABSTRACT FROM AUTHOR]

Filament formation is a common bacterial defense mechanism and possibly has a broad impact on microbial community dynamics. In order to examine the impact of filament formation on population dynamics, we developed an experimental system with a filamentous bacterium Flectobacillus sp. MWH38 and a ciliate predator Tetrahymena pyriformis . In this system, the effective defense of Flectobacillus resulted in the extinction of Tetrahymena by allowing almost no population growth. The result of a kairomone experiment suggested the existence of chemical signals for filament formation. To examine the mechanism further, we developed a quantitative mechanistic model and optimized the model for the experimental result using the simulated annealing method. We also performed a global parameter sensitivity analysis using an approximated Bayesian computation based on the sequential Monte Carlo method to reveal parameters to which the model behavior is sensitive to. Our model reproduced the population dynamics, as well as the cell size dynamics of Flectobacillus . The model behavior is sensitive to the nutrient uptake of Flectobacillus and the propensity of filament formation. It robustly predicts the extinction of Tetrahymena at the condition used in the experiment and predicts the transition from equilibrium to population cycle at higher nutrient conditions. Contrary to the previous study that disproved the presence of chemical signals for filament formation, our result suggested the importance of chemical signals at low predator density, suggesting the variety in bacterial resistance mechanisms that act at different stages of predator-prey interactions. [ABSTRACT FROM AUTHOR]

A continuous two-phase partitioning bioreactor (C-TPPB), operated with coiled tubing made of the DuPont polymer Hytrel 8206, was tested for the bioremediation of 4-chlorophenol, as a model toxic compound. The tubing was immersed in the aqueous phase, with the contaminated water flowing tube-side, and an adapted microbial culture suspended in the bioreactor itself, with the metabolic demand of the cells creating a concentration gradient to cause the substrate to diffuse into the bioreactor for biodegradation. The system was operated over a range of loadings (tubing influent concentration 750–1500 mg L −1 ), with near-complete substrate removal in all cases. Distribution of the contaminant at the end of the tests (96 h) highlighted biological removal in the range of 87–95%, while the amount retained in the polymer ranged from ∼1 to 8%. Mass transfer of the substrate across the tubing wall was not limiting, and the polymer demonstrated the capacity to buffer the substrate loadings and to adapt to microbial metabolism. The impact of C-TPPB operation on biomass activity was also investigated by a kinetic characterization of the microbial culture, which showed better resistance to substrate inhibition after C-TPPB operation, thereby confirming the beneficial effect of sub-inhibitory controlled conditions, characteristic of TPPB systems. [ABSTRACT FROM AUTHOR]

Waste activated sludge has been frequently used as mixed substrate to produce polyhydroxyalkanoate (PHA). However, insufficient research on microbial metabolism has led to difficulties in regulating PHA accumulation in mixed microbial cultures (MMCs). To explore the variation of functional genes during domestication and the effect of different pH conditions on metabolic pathways during PHA accumulation, MMCs were domesticated by adding acetate and propionate with aerobic dynamic feeding strategy for 60 days. As the domestication progressed, the microbial community diversity declined and PHA-producing bacteria, Brevundimonas , Dechloromonas and Hyphomonas , were enriched. Through bacterial function prediction by PICRUSt the gene rpoE involved in starvation resistance of bacteria was enriched after the domestication. The pH value of 8.5 was the best condition for PHA accumulation in MMCs, under which a maximum PHA content reached 23.50% and hydroxybutyric (HB)/hydroxyvaleric (HV) reached 2.22. Untargeted metabolomics analysis exhibited that pH conditions of 7 and 8.5 could promote the up-regulation of significant differential metabolites, while higher alkaline conditions caused the inhibition of metabolic activity. Functional annotation showed that pH condition of 8.5 significantly affected Pyrimidine metabolism, resulting in an increase in PHA production. Regarding the pathways of PHA biosynthesis, acetoacetate was found to be significant in the metabolism of hydroxybutyric, and the alkaline condition could restrain the conversion from hydroxybutyric (HB) to the acetoacetate to protect PHB accumulation in MMCs compared with neutral condition. Taken together, the present results can advance the fundamental understanding of metabolic function in PHA accumulation under different pH conditions. [Display omitted] • PHA-producing bacteria Proteobacteria is enriched in mixed microbial cultures. • Gene rpoE involved in starvation resistance of bacteria is enriched. • The pH of 7 and 8.5 conditions could up-regulate the differential metabolites. • Alkaline condition restrained the degradation of hydroxybutyric into acetoacetate. • The pH of 8.5 is the best condition for PHA accumulation in mixed microbial cultures. [ABSTRACT FROM AUTHOR]

Ayran is a traditional Turkish milk drink which is fermented and salted. Inadequate production and storage conditions contribute to its variable organoleptic quality and stability during shelf-life. A thorough physico-chemical, nutritional and microbial characterization of artisanal Ayran was carried out in order to standardize its overall quality without altering its original traits. Ayran microbial ecosystem was largely dominated by Streptococcus thermophilus (ST) and Lactobacillus delbrueckii subsp. bulgaricus (LDB). High counts of other lactic acid bacteria species, including Lactobacillus helveticus (LH), Lactobacillus fermentum (LF), and Lactobacillus paracasei (LP), were also found. Selected LDB, LP and LH strains grew well in milk displaying fast acidification and high proteolysis, differently from ST and LF strains that did not cause noticeable changes. A selected autochthonous three-strain culture (TSC), composed of one strain of LDB, LP and ST, was applied for the pilot-scale production of traditional Ayran. The Ayran produced with this TSC resulted in the most extensive shelf-life (one month) and in the best terms of its nutritional and sensory quality nevertheless altering its typical pleasant yogurt and cottage cheese notes. This TSC is at disposal of SMEs who need to standardize the overall quality of this traditional fermented milk, preserving its typical traits. [ABSTRACT FROM AUTHOR]

PHAs are a form of cellular storage polymers with diverse structural and material properties, and their biodegradable and renewable nature makes them a potential green alternative to fossil fuel-based plastics. PHAs are obtained through extraction via various mechanical, physical and chemical processes after their intracellular synthesis. Most studies have until now focused on pure cultures, while information on mixed microbial cultures (MMC) remains limited. In this study, ultrasonic (US) disruption and alkaline digestion by NaOH were applied individually and in combination to obtain PHAs products from an acclimated MMC using phenol as the carbon source. Various parameters were tested, including ultrasonic sound energy density, NaOH concentration, treatment time and temperature, and biomass density. US alone caused limited cell lysis and resulted in high energy consumption and low efficiency. NaOH of 0.05–0.2 M was more efficient in cell disruption, but led to PHAs degradation under elevated temperature and prolonged treatment. Combining US and NaOH significantly improved the overall process efficiency, which could reduce energy consumption by 2/3rds with only minimal PHAs degradation. The most significant factor was identified to be NaOH dosage and treatment time, with US sound energy density playing a minor role. Under the semi-optimized condition (0.2 M NaOH, 1300 W L-1, 10 min), over 70% recovery and 80% purity were achieved from a 3 g L−1 MMC slurry of approximately 50% PHAs fraction. The material and thermal properties of the products were analyzed, and the polymers obtained from US + NaOH treatments showed comparable or higher molecular weight to previously reported results. The products also exhibited good thermal stability and rheological properties, compared to the commercial standard. In conclusion, the combined US and NaOH method has the potential in real application as an efficient process to obtain high quality PHAs from MMC, and cost-effectiveness can be further optimized. [Display omitted] • Ultrasonic (US) and alkaline digestion used to recover PHB from a mixed culture. • US disruption had limited effect of cell lysis and high energy consumption. • NaOH digestion was more efficient but led to PHA degradation under high temperature. • US + NaOH showed synergetic effect, reduced treatment time and energy consumption. • US + NaOH can be cost-effective after optimization, showing potential of scaling-up. [ABSTRACT FROM AUTHOR]

The aim of this study was to study and model the bioleaching of abandoned mine tailings at different pulp densities 1–20% w/v by using an autochthonous mesophilic microbial culture. Because of the importance of the ferrous-iron oxidation as sub-process on the bioleaching of sulphide mineral ores, the ferrous-iron oxidation process by the autochthonous microbial culture was studied at different ferrous-iron concentrations. A mathematical model fitted to the experimental results and the main kinetic and stoichiometric parameters were determined, being the most relevant the maximum ferrous-iron oxidation rate 5.1 (mmol Fe2+/mmol C·h) and the biomass yield, 0.01 mmol C/mmol Fe2+, values very similar to that of mixed cultured dominated by Leptospirillum strains. This autochthonous culture was used in the bioleaching experiment carried out at different pulp densities, obtaining a maximum metal recovery in the tests carried out at 1% w/v, recovering a 90% of Cd, 60% of Zn, 30% of Cu, 25% Fe and 6% of Pb. Finally, the different leaching mechanisms were modelled by using the pyrite as ore model obtaining a bioleaching rate of 0.316 mmol Fe2+/(L·h) for the direct mechanisms and a bioleaching rate for the indirect and cooperative leaching mechanisms of 0.055 Fe2+/(L·h). • Abandoned mine tailings biolixiviation was studied. • The biolixiviation was carried out by using an autochthonous culture. • The optimum bioleaching pulp density was 1% w/v. • 90% of Cd, 60% of Zn, 30% of Cu, 25% Fe and 6% of Pb were recovered. • The direct mechanisms accounted for 85% of the ferrous-iron solubilization. [ABSTRACT FROM AUTHOR]

The microbial population of Traditional Mountain (TM) cheese was investigated and characterized for the selection of cocci suitable for developing new starter cultures. Samples of milk, curd and cheese at different ripening times were enumerated in selective culture media and 640 colonies were isolated from curd and cheese after 24 h of ripening. The Lactic Acid Bacteria (LAB) isolated from M17 were clustered into 231 biotypes by RAPD-PCR analysis and identified as Lactococcus lactis , Streptococcus thermophilus and Enterococcus faecalis . Forty percent of enterococci showed the in vitro ability to inhibit raw milk resident coliforms, but they were excluded as possible starters due to the presence of associated risk factors. All lactococci and streptococci were tested for their technological properties; 4 Lc. lactis subsp. lactis and 2 Sc. thermophilus which were fast acidifiers and did not produce unpleasant flavours were subjected to the freeze-drying stability test. Lc. lactis subsp. lactis biotype 68 and Sc. thermophilus biotype 93 showed the best technological properties and may be appropriate for cheese production. This work gave evidence of the high biodiversity of TM-cheese autochthonous biotypes which could be used as starter cultures for the improvement of TM-cheese technology. [ABSTRACT FROM AUTHOR]

The effectiveness of UV-C light treatments on microbial load and quality of fresh-cut pineapple sticks was studied. At all tested fluencies (200–4800 J/m 2 ), UV-C light did not decrease the initial microbial load of pineapple sticks. Nevertheless, pineapple sticks submitted to 200 J/m 2 UV-C light, packaged in conventional PET/EVOH/PE trays and stored at 6 °C up to 15 days showed slower yeast and lactic acid bacteria growth. In these samples, microbial counts were generally 2 log cycles lower that those observed in the untreated sticks. UV-C light did not promote changes in colour and increased consumer preference. Similar results were also obtained when UV-C light treatment was applied on pineapple sticks previously packaged in highly UV-C light transparent PA/PE pouches to avoid post treatment contamination. [ABSTRACT FROM AUTHOR]

The present study investigates the combined production of biohydrogen and polyhydroxyalkanoates (PHA) from sheep cheese whey through a 3-stage bioprocess, i.e. dark fermentation, selection of PHA storing microorganisms, and PHA accumulation. Batch dark fermentation tests (Stage I) were performed on raw cheese whey under different pH operating conditions, avoiding either the addition of inoculum or substrate pre-treatment to support the economic and technical feasibility of the proposed process. The performance of the fermentative stage was assessed in terms of biohydrogen and soluble metabolites production yields. The dark fermentation effluent was used as organic acid-rich feedstock either for selecting and harvesting PHA storing microorganisms from a mixed microbial culture without the addition of external nutrient sources (Stage II) or for the PHA accumulation by the selected biomass (Stage III). The results of the study support the possibility of achieving combined recovery yields of 5.3 L biohydrogen and 7.6 g PHA per litre of fed sheep cheese whey in the case of optimal dark fermentation pH setting (pH = 6). Such outcomes underline the untapped potential of sheep cheese whey for the recovery of high-added value bioproducts. [Display omitted] • Sheep cheese whey as a promising substrate for a fermentation-based biorefinery. • Dark fermentation performed by indigenous whey microorganisms. • Selection of a PHA storing biomass carried out without an extra nutrient supply. • H 2 biofuel production of 5.3 L per litre of sheep cheese whey. • PHA biopolymer production of 7.6 g per litre of sheep cheese whey. [ABSTRACT FROM AUTHOR]

The predation of Bdellovibrio bacteriovorus on different periodontal pathogens has already been described. However, it is necessary to consider the polymicrobial nature of periodontal disease. The current study explores the predation of Bdellovibrio on oral pathogens organized in multispecies communities. The effect of the predator was evaluated on in vitro six species communities with microbial culturing. Additionally, the effect on ex vivo subgingival plaque and saliva samples from periodontitis patients was assessed. In the latter experiment results were examined with microbial culturing, quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). The latter technique was used to get an overview of the whole mixed microbial population. Results showed that even in more complex models, B. bacteriovorus was still able to predate on Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans . However predation on Prevotella intermedia and Porphyromonas gingivalis could not be validated in multispecies models. The effect of Bdellovibrio was not restricted to the target bacteria. Changes in the overall ecology of the different models were evident. It could be concluded that the efficiency of predation decreased when complexity of the models increased. However, B. bacteriovorus was able to attack two important oral pathogens, F. nucleatum, and A. actinomycetemcomitans, even when present in ex vivo clinical samples. These effects still have to be validated in in vivo models to see the impact of Bdellovibrio on the whole bacterial ecology. [ABSTRACT FROM AUTHOR]

Fermented foods and feeds have been consumed for millennia, and microorganisms isolated from traditional fermentations have been used as probiotics. There is interest in developing new microbial cultures for these uses, but to date safety evaluation procedures have only been discussed in general terms. We propose a comprehensive approach for determining the safety of microbial cultures that lack an established history of safe use for their intended new applications. Three scenarios are considered: (1) substantially increased exposure to a culture that has an established record of safety in a more limited application; (2) a new strain without a history of safe use that was isolated from a food or feed that has a history of safe use; and (3) a new strain isolated from a non-food or non-feed source. Our safety evaluation process is based on scientific procedures and is in the form of a decision tree composed of 13 questions. Our decision tree for determining the safety of microbial cultures for consumption by humans or animals is modeled on previous decision trees that are used worldwide to evaluate the safety of microbial enzymes for use in human food or animal feed. [ABSTRACT FROM AUTHOR]

To detect new potential pathogens in hospital water, we isolated free-living amoebae in water samples taken from three different hospitals in Marseille (France). The samples were inoculated in media containing saline buffer and various bacteria as nutrient sources. The isolated amoebae were identified by gene sequencing. Among the 105 water samples, taken from 19 sites, we isolated 14 amoebae, of which 9 Vermamoeba vermiformis and 5 Acanthamoeba sp. None of the amoebae showed the presence of obligate bacterial endosymbionts. Because V. vermiformis was most commonly isolated, we used an axenic collection strain to isolate amoeba-resistant bacteria from the same sites. The isolated bacterial species included Stenotrophomonas maltophilia and Legionella sp. Legionella taurinensis was isolated for the first time in association with amoebae. A strict intracellular bacterium was isolated, that may represent a new genus among the Chlamydiales. We propose that it be named “ Candidatus Rubidus massiliensis”. Our study shows that the isolation and identification of new pathogens associated with amoebae, which were previously performed using Acanthamoeba sp., should instead use V. vermiformis because this organism is more commonly associated with humans and is an essential complement of Acanthamoeba sp. co-culture to study the ecology of hospital water supplies. [ABSTRACT FROM AUTHOR]

Anaerobic digestion (AD) is widely used for conversion of waste materials into biogas, but inhibition of methane production caused by overloading can be a major problem. The micro-aerobic microbial community MC1 was used to successfully culture methanogens, Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC 101360. The maximum 16S rRNA gene concentrations of Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC101360 were 1.06 × 106 and 1.35 × 103 copies/mL, respectively. The five key bacteria in MC1 were quantified to assess the effect of inoculation on the abundances of the bacteria in the mixed culture. The original MC1 total 16S rRNA gene concentration was 1.93 × 108 copies/mL, and the total 16S rRNA gene concentration had increased to 4.79 × 109 copies/mL on day 9 (p < 0.05). The proportions of the key strains in MC1+MST had changed by day 9. Cells were harvested and used to bioaugment and increase the pH values of the high- and medium-temperature anaerobic systems. After bioaugmentation, thermophilic AD recovered well. The cumulative amounts of gas produced were 44.78% and 28.28% higher in the MC1+MST and MC1 groups, respectively, than the sterilized control. The MC1+MST group gave better results than the chemical addition control group (CaCO 3). There was no clear effect of bioaugmentation in mesophilic AD. When compared with traditional pure culture of methanogens as inoculants, methanogen cultivation in MC1 was simple and there was no need to separate and purify the target strains. This simplified methanogenic bioaugmentation agent was useful to study the mechanism of bioaugmentation for the recovery from low pH inhibition, showing the potential for practical application. [Display omitted] • MC1 provided the necessary conditions for growth of acetoclastic methanogens. • Compared with MC1, the proportions of the key strains changed in MC1+MST. • MC1-grown methanogens accelerated the recovery of the AD process. • By augmented MC1+MST, biogas production increased by 44.78%. • MC1 provided a simple procedure for cultivating bioaugmentation seeds. [ABSTRACT FROM AUTHOR]

Deoxynivalenol (DON) is a mycotoxin mainly produced by Fusarium graminearum and Fusarium culmorum and is commonly found in cereals such as wheat, barley, oats, and their derivatives. Scientists have been working on different strategies for DON detoxification, with biological detoxification being an approach with growing interest. When evaluating the use of microorganisms for mycotoxin detoxification, different phenomena can occur, namely, biotransformation (by microorganism metabolism and by interaction with extracellular cell proteins) and adsorption on cell walls, both of which can be present. In this study, a fast, simple, reliable, and inexpensive method for total DON quantification (dissolved and adsorbed) in bacterial culture assays is presented. This method can be used in screenings designed for searching DON-biodegrading microorganisms without requiring the analysis of the metabolites produced. This method has a good recovery (80.2%), reproducibility (3.2%) and low limit of quantification (0.60 μg/ml) that allows quantification under a wide range of DON concentrations in microbiological culture assays. • Determination of total DON (dissolved + adsorbed) in microbiological cultures. • Adsorbed DON on cell walls is released by ultrasound treatment. • Method is designed for biodegradation assays, without the need to analyse metabolites. • Simple, fast, and reliable method with good reproducibility and recovery. • Quantification of a wide range of DON levels (1–30 μg/ml). [ABSTRACT FROM AUTHOR]

This study aimed at evaluating co-cultures of selected microorganisms for their proteolytic activity and capability to produce fermented milk enriched with ACE-inhibitory (ACEI) peptides. Selected yeasts (Torulaspora delbruekii KL66A, Galactomyces geotrichum KL20B, Pichia kudriavzevii KL84A and Kluyveromyces marxianus KL26A) and lactic acid bacteria strains (Lactobacillus plantarum LAT03, Lb. plantarum KLAT01 and the not virulent Enterococcus faecalis KE06) were screened as single cultures for their capacity of releasing ACEI peptides without producing bitter taste. Three strains cultures (yeast, Lb. plantarum and E. faecalis) were performed to evaluate the combined impact on microbial growth, lactic acid production, citric acid consumption, proteolysis, ACEI activity, and bitter taste after 36 h of fermentation at 28 °C. While G. geotrichum KL20B showed a strong stimulating effect on Lb. plantarum strains and the production of peptides with ACEI activity, the presence of T. delbruekii KL26A in the cultures was deleterious both to ACEI activity and product taste. The most effective combination was P. kudriavzevii KL84A, Lb. plantarum LAT3, E. faecalis KL06, which showed the highest ACEI activity (IC50 = 30.63 ± 1.11 μg ml−1) and gave no bitter taste for 7 days at 6 °C. Our results highlight the importance of choosing the strains combination carefully, to obtain a high yield of ACEI activity without bitter taste. [ABSTRACT FROM AUTHOR]

Abstract: Characterization of the microflora during malting is an essential step towards process management and optimization. Up till now, however, microbial characterization in the malting process has mostly been done using culture-dependent methods, probably leading to biased estimates of microbial diversity. The aim of this study was to characterize the bacterial communities using two culture-independent methods, including Terminal Restriction Fragment Length Polymorphism (T-RFLP) and 454 pyrosequencing, targeting the 16S rRNA gene. Studied samples originated from two harvest years and two malting houses malting the same batch of barley. Besides targeting the entire bacterial community (T-RFLP), emphasis was put on lactic acid bacteria (LAB) (T-RFLP and 454 pyrosequencing). The overall bacterial community richness was limited, but the community structure changed during the process. Zooming in on the LAB community using 454 pyrosequencing revealed a total of 47 species-level operational taxonomic units (OTUs). LAB diversity appeared relatively limited since 88% of the sequences were covered by the same five OTUs (representing members of Weissella, Lactobacillus and Leuconostoc) present in all samples investigated. Fluctuations in the relative abundances of the dominant LAB were observed with the process conditions. In addition, both the year of harvest and malting house influenced the LAB community structure. [Copyright &y& Elsevier]

Abstract: Identification and differentiation of microorganisms has and still is a long arduous task, involving culturing of the organism in question on different growth media. This procedure, which is still commonly applied, is an established method, but takes a lot of time, up to several days or even longer. It has thus been a great achievement when other analytical tools like matrix-assisted laser desorption/ionization (MALDI) mass spectrometry were introduced for faster analysis based on the surface protein pattern. Differentiation and identification of human pathogens as well as plant/animal pathogens is of increasing importance in medical care (e.g. infection, sepsis, and antibiotics resistance), biotechnology, food sciences and detection of biological warfare agents. A distinction between microorganisms on the species and strain level was made by comparing peptide/protein profiles to patterns already stored in databases. These profiles and patterns were obtained from the surface of vegetative forms of microorganisms or even their spores by MALDI MS. Thus, an unknown sample can be compared against a database of known pathogens or microorganisms of interest. To benefit from newly available, metal-based disposable microscope-slide format MALDI targets that promise a clean and even surface at a fraction of the cost from full metal targets or MTP (microtiter plate) format targets, IC/ISMS analysis was performed on these and the data evaluated. Various types of bacteria as well as fungal spores were identified unambiguously on this disposable new type of metal nano-coated targets. The method even allowed differentiation between strains of the same species. The results were compared with those gained from using full metal standard targets and found to be equal or even better in several aspects, making the use of disposable MALDI targets a viable option for use in IC/ISMS, especially e.g. for large sample throughput and highly pathogenic species. [Copyright &y& Elsevier]

Abstract: In this study, the composition of the cultivable microbial populations of 38 nectar honey and honeydew honey samples of different botanical and geographical origin were assessed. After growth in specific media, various colonies with different appearance were isolated and purified before phenotypic (morphological, physiological and biochemical traits) and genotypic [randomly amplified polymorphic DNA (RAPD), repetitive DNA elements-PCR (rep-PCR) and restriction fragment length polymorphism (RFLP)] differentiation. The identification was carried out by 16S rRNA gene sequencing for bacteria and, in addition to RFLP, by sequencing the D1/D2 region of the 26S rRNA gene for yeasts and the 5.8S-ITS rRNA region for filamentous fungi. The results showed the presence of 13 species of bacteria, 5 of yeasts and 17 of filamentous fungi; the species most frequently isolated were Bacillus amyloliquefaciens, Zygosaccharomyces mellis and Aspergillus niger for the three microbial groups, respectively. The highest microbial diversity was found in multifloral honeys. No correlation among the microbial species and the botanical/geographical origin was found, but some strains were highly adapted to these matrices since they were found in several samples of different origin. [Copyright &y& Elsevier]

Abstract: This study aimed to assess bacterial spoilage of half shell Pacific and Sydney rock oysters during storage using microbial culture and 16S rRNA pyrosequencing. Odour and pH of oyster meats were also investigated. Estimation of microbiological counts by microbial culture highlighted growth of psychrotrophic bacteria. During storage, odour scores (a score describing deterioration of fresh odours where a score of 1 is fresh and 4 is completely spoiled) increased from 1.0 to 3.0 for Pacific oysters and from 1.3 to 3.4 for Sydney rock oysters. pH results obtained for both species fluctuated during storage (range 6.28–6.73) with an overall increase at end of storage. Pyrosequencing revealed that the majority of bacteria at Day 0 represented taxa from amongst the Proteobacteria, Tenericutes and Spirochaetes that have not been cultured and systematically described. During storage, Proteobacteria became abundant with Pseudoalteromonas and Vibrio found to be dominant in both oyster species at Day 7. Analysis of the pyrosequencing data showed significant differences in bacterial profiles between oyster species and storage time (both P = 0.001). As oysters spoiled, bacterial profiles between oyster species became more similar indicating a common spoilage profile. Data presented here provides detailed insight into the changing bacterial profile of shucked oysters during storage and has identified two genera, Pseudoalteromonas and Vibrio, as being important in spoilage of shucked oysters. [Copyright &y& Elsevier]

Abstract: Matsoni, a traditional Georgian fermented milk, has variable quality and stability besides a short shelf-life (72–120 h at 6 °C) due to inadequate production and storage conditions. To individuate its typical traits as well as select and exploit autochthonous starter cultures to standardize its overall quality without altering its typicality, we carried out a thorough physico-chemical, sensorial and microbial characterization of traditional Matsoni. A polyphasic approach, including a culture-independent (PCR-DGGE) and two PCR culture-dependent methods, was employed to study the ecology of Matsoni. Overall, the microbial ecosystem of Matsoni resulted largely dominated by Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii subsp. bulgaricus. High loads of other lactic acid bacteria species, including Lb. helveticus, Lb. paracasei and Leuconostoc (Leuc.) lactis were found to occur as well. A selected autochthonous multiple strain culture (AMSC) composed of one Lb. bulgaricus, one Lb. paracasei and one S. thermophilus strain, applied for the pilot-scale production of traditional Matsoni, resulted the best in terms of enhanced shelf-life (one month), sensorial and nutritional quality without altering its overall typical quality. This AMSC is at disposal of SMEs who need to exploit and standardize the overall quality of this traditional fermented milk, preserving its typicality. [Copyright &y& Elsevier]

Abstract: Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose–tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date. [Copyright &y& Elsevier]

Abstract: The Polymyxin Ceftazidime Oxford Medium (PCOM) was developed to recover Listeria monocytogenes from raw or unpasteurized foods. It contains esculin-ferric ammonium citrate as indicator system for Listeria growth, and ceftazidime and polymyxin B as selective agents, which are available in several Latin American countries. Comparison of PCOM, Modified Oxford Medium (MOX) and Tryptic Soy agar with 0.6% yeast extract (TSAYE) indicated that both selective media were equally effective at recovering four individual strains of L. monocytogenes (Scott A, V7, California and broccoli), and a mixture of these strains (LMM) (P > 0.05). The ability of PCOM, MOX, TSAYE and TSAYE supplemented with 4% NaCl to recover heat, acid and freeze-damaged LMM was similar for all media (P > 0.05). The PCOM proved to be effective at isolating colonies of LMM from inoculated raw beef chunks, unpasteurized orange juice, cabbage, and Mexican-style cheese by direct plating and by the US Department of Agriculture's Food Safety and Inspection Service enrichment method. Differentiation of L. monocytogenes colonies was easier on PCOM than on MOX for foods with high levels of background microbiota. Based on the evaluations performed on foods naturally contaminated with L. monocytogenes, PCOM was a more economical alternative than MOX for selective and differential isolation of Listeria from raw or unpasteurized foods. [Copyright &y& Elsevier]

Abstract: Tetrazolium salts (TTZ) such as 2,3,5-triphenyltetrazolium chloride (TTC) are readily reduced by bacterial populations of various genus. The reduced form of these redox indicators is conspicuously colored allowing a quick and easy detection of growth. The studies are mainly confined to Gram negative bacteria because of an important toxic effect of tetrazolium salts on Gram positive bacteria. Indeed, we observed an important impact of different tetrazolium salts on Listeria monocytogenes growth, curiously limited to an increase in the duration of the lag phase. In this study, we demonstrate that increasing the iron concentration in a medium containing TTC leads to a significant decrease of the lag phase. L. monocytogenes growth was kinetically measured and growth parameters were estimated using the Baranyi model. While lag phase diminution was found to be iron concentration dependent, growth rate was not affected. Addition of iron enables growth of some strains totally inhibited by a 0.4 g/l of TTC and for the other a significant reduction of the latency is observed. The nature of the mechanism resulting in a decrease of the observed lag phase remains unclear. Then, the use of iron supplementation may be proposed to overcome the inhibitory effect of TTC on L. monocytogenes. [Copyright &y& Elsevier]

Abstract: The ocular surface is continually exposed to the environment and as a consequence to different types of microbes, but whether there is a normal microbiota of the ocular surface remains unresolved. Using traditional microbial culture techniques has shown that <80% of swabs of the conjunctiva yield cultivable microbes. These usually belong to the bacterial types of the coagulase-negative staphylococci, Propionibacterium sp., with low frequency of isolation of bacteria such as Staphylococcus aureus, Micrococcus sp., Gram-negative bacteria or fungi. Even when these are grown, the numbers of colony forming units (cfu) per swab of the conjunctiva is usually much less than 100 cfu. Swabs of the lid more commonly result in microbial growth, of the same species as from the conjunctiva and slightly higher cfu. Contact lenses have also been cultured, and they yield similar microbial types. Microbes can be isolated from the ocular surface almost immediately after birth. The advent of molecular techniques for microbial identification based on 16S rRNA sequencing has opened up the possibility of determining whether there are non-cultivable microbes that can colonise the ocular surface. Additionally, use of these techniques with cross-sectional and longitudinal studies may help to understand whether the ocular surface harbours its own unique microbiota, or whether the microbiota are only transiently present. [Copyright &y& Elsevier]

Twelve bacteria were isolated from wastewater for the degradation of 17β-estradiol (strain K1, K2, K3, K4, L5, L6, L7, L8, M9, M10, M11 and M12) by enrichment method. Initial screening revealed maximum degradation (78 ± 1.1%, and 86 ± 4.2%) of 17β-estradiol by strains L7, and M10, respectively. The production of manganese peroxidase by bacteria gets involved in the degradation of various contaminants. Almost all strains isolated from the enriched medium produced manganese peroxidase. Based on initial screening on 17β-estradiol degradation and manganese peroxidase production, two bacteria (Flavobacterium longum L7 and Pseudomonas aeruginosa M10) were selected to analyze 17β-estradiol degradation in co-culture system. The co-cultured strains could rapidly remove 17β-estradiol (91.3%) from the culture medium at 10 mg/L 17β-estradiol initial concentration. Moreover, degradation of 17β-estradiol was only 82% and 75% when the strains L7 and M10 were treated individually. Initial 17β-estradiol concentration was 10 mg/L and 0.3% inoculum were optimum and achieved >90% degradation. Alkaline pH was optimum (pH 7.5) and reached 98.4 ± 7.5% degradation in co-culture. Glucose and trehalose improved the growth and degradation of 17β-estradiol. The organic nitrogen sources such as, yeast extract and peptone improved the removal of 17β-estradiol. The selected bacterial strains were resistant against penicillin, erythromycin, oxytetracycline and tetracycline. The present findings demonstrated the application of F. longum L7 and P. aeruginosa M10 co-culture for the removal of steroid hormones in the wastewater. • Steroid estrogen degrading bacterial strains were screened from the wastewater. • 17β-estradiol was degraded by the indigenous bacterial strains. • Co-culture of bacteria improved degradation than individual strains. • Bacterial strains were showing multidrug resistance and high antibiotic tolerance limit. • Low C/N ratio in the culture medium improved degradation efficiency. [ABSTRACT FROM AUTHOR]

The etiology of otitis in dogs and cats is multifactorial and complex, involving bacterial and fungal pathogens. As empiric antimicrobial prescription is a common practice when treating such cases, antimicrobial resistance may represent a complicating factor. The aim of this study was to describe microbiological features and susceptibility profiles of pathogens associated with 142 cases of external otitis, comprising 138 dogs and 4 cats.. The specimens were processed to identify bacterial and fungal etiologies following standard microbiological methods. Antimicrobial susceptibility was determined in vitro against 15 antibiotics and 3 antifungals. Further, Staphylococcus spp. isolates were screened for the detection of β-lactamase enzymes using cefinase paper discs. Pseudomonas spp. and isolates from Enterobacteriaceae family were screened for colistin (Polymyxin E) resistance and for the mcr-1 -mediated colistin resistance gene by PCR. The presence of mixed cultures of Enterobacteriaceae , Pseudomonas spp. and Staphylococcus spp., and co-infections with Malassezia spp., emphasizes the polymicrobial etiology of external otitis in small animals. Emerging rates of multidrug resistance observed in almost 50% of the isolates may alert for a near future of challenging veterinary cases unresponsive to first-line antimicrobials. In addition, these results highlight a potential public health concern of multidrug resistant bacteria, given the proximity of pets and their owners. This study addressed central aspects of external otitis, providing microbiologists and clinicians updated information on the etiology and treatment of challenging cases of multidrug resistant bacteria. It also provides priceless surveillance value in monitoring resistant bacteria in small animals. [Display omitted] • The etiology of small animal external otitis is predominantly polymicrobial. • Co-infections of bacteria and Malassezia spp. were found in 10.2% of the dogs. • Mixed infections of Staphylococcus spp. and Gram-negative bacteria were very common. • Multidrug resistance was observed in almost 50% of the isolates. • Genotypic colistin resistance was detected in 44% of Pseudomonas spp. isolates. [ABSTRACT FROM AUTHOR]

Highlights: [•] Brazil has several culture collections dedicated to preserve fungi. [•] Fungal culture collections can provide a wide range of strains to be exploited for many biotechnological purposes. [•] The use of a polyphasic approach for fungal identification should become part of the culture collection routine. [Copyright &y& Elsevier]

Abstract: Human milk has been traditionally considered sterile; however, recent studies have shown that it represents a continuous supply of commensal, mutualistic and/or potentially probiotic bacteria to the infant gut. Culture-dependent and -independent techniques have revealed the dominance of staphylococci, streptococci, lactic acid bacteria and bifidobacteria in this biological fluid, and their role on the colonization of the infant gut. These bacteria could protect the infant against infections and contribute to the maturation of the immune system, among other functions. Different studies suggest that some bacteria present in the maternal gut could reach the mammary gland during late pregnancy and lactation through a mechanism involving gut monocytes. Thus, modulation of maternal gut microbiota during pregnancy and lactation could have a direct effect on infant health. On the other hand, mammary dysbiosis may lead to mastitis, a condition that represents the first medical cause for undesired weaning. Selected strains isolated from breast milk can be good candidates for use as probiotics. In this review, their potential uses for the treatment of mastitis and to inhibit mother-to-infant transfer of HIV are discussed. [Copyright &y& Elsevier]

Abstract: Shigella spp are exquisitely fastidious Gram negative organisms that frequently get missed in the detection by traditional culture methods. For this reason, this work has adapted a classical PCR for detection of Shigella in food and stool specimens to real-time PCR using the SYBR Green format. This method follows a melting curve analysis to be more rapid and provide both qualitative and quantitative data about the targeted pathogen. A total of 117 stool samples with diarrhea and 102 food samples were analyzed in Public Health Regional Laboratory of Nabeul by traditional culture methods and real-time PCR. To validate the real-time PCR assay, an experiment was conducted with both spiked and naturally contaminated stool samples. All Shigella strains tested were ipaH positive and all non-Shigella strains yielded no amplification products. The melting temperature (T m  = 81.5 ± 0.5 °C) was consistently specific for the amplicon. Correlation coefficients of standard curves constructed using the quantification cycle (C q ) versus copy numbers of Shigella showed good linearity (R 2 = 0.995; slope = 2.952) and the minimum level of detection was 1.5 × 103 CFU/g feces. All food samples analyzed were negative for Shigella by standard culture methods, whereas ipaH was detected in 8.8% culture negative food products. Moreover, the ipaH specific PCR system increased the detection rate over that by culture alone from 1.7% to 11.1% among patients with diarrhea. The data presented here shows that the SYBR Green I was suitable for use in the real-time PCR assay, which provided a specific, sensitive and efficient method for the detection and quantification of Shigella spp in food and stool samples. [Copyright &y& Elsevier]

At public beaches, it is now common to mitigate the impact of water-borne pathogens by posting a swimmer's advisory when the concentration of fecal indicator bacteria (FIB) exceeds an action threshold. Since culturing the bacteria delays public notification when dangerous conditions exist, regression models are sometimes used to predict the FIB concentration based on readily-available environmental measurements. It is hard to know which environmental parameters are relevant to predicting FIB concentration, and the parameters are usually correlated, which can hurt the predictive power of a regression model. Here the method of partial least squares (PLS) is introduced to automate the regression modeling process. Model selection is reduced to the process of setting a tuning parameter to control the decision threshold that separates predicted exceedances of the standard from predicted non-exceedances. The method is validated by application to four Great Lakes beaches during the summer of 2010. Performance of the PLS models compares favorably to that of the existing state-of-the-art regression models at these four sites. [Copyright &y& Elsevier]