Cultures Of Strains Research Articles

Complex profiles of azaspiracid analogues in two culture strains of Azadinium poporum (Amphidomataceae, Dinophyceae) isolated from Japanese coastal waters determined by LC-MS/MS

Lipophilic marine biotoxins azaspiracids (AZAs) are produced by dinoflagellates Azadinium and Amphidoma. Recently, several strains of Azadinium poporum were isolated from Japanese coastal waters. In our present study, AZA analogues in two strains (mdd421 and HM536) of A. poporum were analyzed by several detection techniques on the liquid chromatography-tandem mass spectrometry (LC-MS/MS) and liquid chromatography-quadrupole time of flight mass spectrometry (LC-QTOFMS). The dominant AZA analogue in the Japanese A. poporum strains was AZA2. Other known AZA analogues were AZA11, AZA35, AZA2 methyl ester and AZA2 phosphate ester. Besides these AZAs, thirteen new AZA analogues were discovered in the two strains. A putative AZA analogue (Compound 1) with the smallest molecular weight ever found in nature was also discovered in the two strains. This is the first report describing detailed AZA profiles in Japanese isolates of A. poporum.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

BackgroundCandida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.ResultsHere, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition.ConclusionsThe results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.FVTWG-mFNui5xgWwFcfPTvVideo abstract

Assessment of chemical constitution and aroma properties of kiwi wines obtained from pure and mixed fermentation with Wickerhamomyces anomalus and Saccharomyces cerevisiae.

To improve the aroma of kiwi wine through the utilization of Wickerhamomyces anomalus, kiwi juice was fermented using a selected W. anomalus strain in pure culture and mixed fermentations with Saccharomyces cerevisiae, which was inoculated simultaneously and sequentially. The physicochemical indices, volatile compounds and aroma properties of the kiwi wines were assessed. The study suggested that the ethanol, color indices and organic acids of the wines were closely related to the method of inoculation. Compared with the pure S. cerevisiae fermentation, the mixed fermentations produced more varieties and concentrations of volatiles. The sequential fermentations increased the concentrations of esters and terpenes, improving the flower and sweet fruit notes of the wines. The simultaneous inoculation enhanced the contents of esters and aldehydes, intensifying the flower, sweet and sour fruit of the wines. Partial least-squares regression analysis showed that esters and terpenes contributed greatly to the flower and sweet fruit aroma, whereas aldehydes were the major contributors to the sour note. Based on our results, the mixed fermentations not only enriched the types and concentrations of volatiles, but also had better sensory properties. © 2021 Society of Chemical Industry.

Preparation and Standardization of Nosodes Sourced from Klebsiella Pneumoniae, Salmonella Typhi, Neisseria Gonorrhoeae and Candida Albicans Strains.

Homeopathic nosodes prepared from organisms and pathological tissues have shown biological effects, encouraging more research. There is a need to develop some new nosodes systematically and to re-make others that were developed over a century ago. In our program of work on nosodes, the bacterial strains Klebsiella pneumoniae (BAA 2146), Salmonella typhi and Neisseria gonorrhoeae (ATCC 43069), and the single-celled fungus Candida albicans (24433, 26790, and 60193) have been identified for preparation. The systematic and scientific method of preparation of nosodes includes identification, culture, quantification, characterization, preparation, and standardization. Under laminar flow, a suspension of respective bacterial and fungal cells (20 billion cells/mL) was processed as per the Homoeopathic Pharmacopoeia of India (HPI). Culture tests, sterility tests and molecular testing (polymerase chain reaction) were performed to establish the absence of contamination, live organisms and DNA material. K. pneumoniae, S. typhi (single, bivalent, or polyvalent), N. gonorrhoeae, and C. albicans nosodes (single and polyvalent) were sourced and prepared from different strains of respective cultures. The nosode preparations were processed by serial dilution and potentization, normally following the HPI guidelines. Molecular test results showed the absence of live organisms or DNA material; culture and sterility test results demonstrated the safety profile of the potentized nosodes. K. pneumoniae, S. typhi, N. gonorrhoeae and C. albicans nosodes were successfully prepared. Their therapeutic potential may now be evaluated.

Microbiological status of some street iftar items collected from chalk bazar in Dhaka city, Bangladesh

In Dhaka, the capital of Bangladesh and one of the most densely populated cities of the world, different categories of street foods are widely consumed by all classes of people, especially for iftar during the holy month of Ramadan. The objective of this research was to assess the microbiological quality of street iftar food items collected from a street in Chalk Bazar locality of Dhaka along with the antibiogram profile of the bacterial isolates. A total of 74 samples belong to ten different categories of street food items and 8 different types of street vended juices were collected aseptically. The bacteria were isolated by using different culture media. The antibiotic susceptibility of the bacterial isolates was determined by the disc diffusion method. In case of street food total viable bacteria (on average of 6 log10 CFU/g). On the other hand, an extended number of total viable bacteria were encountered in all juices samples which also on an average of 6 log10 CFU/mL. Fungi, Pseudomonas spp. and Staphylococcus spp. were found in the majority of the samples irrespective of the categories. Few samples were contaminated with Escherichia coli and Klebsiella spp. Most of the cultivated bacterial strains exhibited resistance against commonly used antibiotics, while several isolates were noted to be multi-drug resistant. The present study revealed a huge array of microbial load which indicates a high risk to public health. Presence of antibiotic-resistant bacteria heightened the risk by many folds and urges the need for frequent surveillance.

Microbial colonization and community stability in a marine post-smolt RAS inoculated with a commercial starter culture

The performance of a commercial starter culture was investigated in a new marine post-smolt RAS, analyzing the microbial communities of 100 samples collected monthly over a year from biofilter biofilm carriers, tank wall biofilm, production water and fish skin. Totally 139 operational taxonomic units (OTUs) were defined in the starter culture, of which the classified members of Rhodobacterales, Bacteroidetes, Alteromonadales and Planctomycetes were largely the first colonizers of the biofilter carriers. Early colonizing OTUs that dominated biofilter biofilm carriers (> 5% relative abundance) were stably present over time, but the development went slowly from a few OTUs with very high relative abundance to several dominant ones with lower relative abundance. Operating taxonomic units not associated with the starting culture became prominent on the biofilter biofilm carriers only towards the end of the trial period. These were termed environmental OTUs. Comparing the two OTU quantitives in a ratio, where counts were based on all OTUs in the sample, the starter culture OTUs:environmental OTUs were 1.2 and 0.9 at the first and last sampling time for the biofilter biofilm carriers. Correspondingly, for all defined OTUs in the RAS sampling sites together, the ratio changed from 0.8 to 0.6 during experiment. Independent of origin, omniscient OTUs at a sampling site, did also have the highest relative abundances and were normally shared between biofilter biofilm carriers and the production water. New and lost OTUs between sampling times were on average 44 % of the OTUs defined, and this OTUflow was strongest for low abundant environmental OTUs. The maturation of the biofilter with respect to nitrification took long time, and the Nitrospira strain in the starter culture was not adapted to marine salinities. Still, we report a controlled colonization of the marine RAS by the starter culture.

The Metabolomic-Gut-Clinical Axis of Mankai Plant-Derived Dietary Polyphenols.

Background: Polyphenols are secondary metabolites produced by plants to defend themselves from environmental stressors. We explored the effect of Wolffia globosa ‘Mankai’, a novel cultivated strain of a polyphenol-rich aquatic plant, on the metabolomic-gut clinical axis in vitro, in-vivo and in a clinical trial. Methods: We used mass-spectrometry-based metabolomics methods from three laboratories to detect Mankai phenolic metabolites and examined predicted functional pathways in a Mankai artificial-gut bioreactor. Plasma and urine polyphenols were assessed among the 294 DIRECT-PLUS 18-month trial participants, comparing the effect of a polyphenol-rich green-Mediterranean diet (+1240 mg/polyphenols/day, provided by Mankai, green tea and walnuts) to a walnuts-enriched (+440 mg/polyphenols/day) Mediterranean diet and a healthy controlled diet. Results: Approximately 200 different phenolic compounds were specifically detected in the Mankai plant. The Mankai-supplemented bioreactor artificial gut displayed a significantly higher relative-abundance of 16S-rRNA bacterial gene sequences encoding for enzymes involved in phenolic compound degradation. In humans, several Mankai-related plasma and urine polyphenols were differentially elevated in the green Mediterranean group compared with the other groups (p < 0.05) after six and 18 months of intervention (e.g., urine hydroxy-phenyl-acetic-acid and urolithin-A; plasma Naringenin and 2,5-diOH-benzoic-acid). Specific polyphenols, such as urolithin-A and 4-ethylphenol, were directly involved with clinical weight-related changes. Conclusions: The Mankai new plant is rich in various unique potent polyphenols, potentially affecting the metabolomic-gut-clinical axis.

New Continuous Process for the Production of Lipopeptide Biosurfactants in Foam Overflowing Bioreactor.

In this work, an original culture process in bioreactor named overflowing continuous culture (O-CC) was developed to produce and recover continuously mycosubtilin, a lipopeptide antifungal biosurfactant of major interest. The lipopeptide production was first investigated in shake conical flasks in different culture media [ammonium citrate sucrose (ACS), Difco sporulation medium (DSM), and Landy], followed by a pH condition optimization using 3-(N-morpholino)propanesulfonic acid (MOPS) and 2-(N-morpholino)ethanesulfonic acid (MES) buffered media. A simple theoretical modeling of the biomass evolution combined with an experimental setup was then proposed for O-CC processed in stirred tank reactor at laboratory scale. Seven O-CC experiments were done in modified Landy medium at the optimized pH 6.5 by applying dilution rates comprised between 0.05 and 0.1 h–1. The O-CC allowed the continuous recovery of the mycosubtilin contained in the foam overflowing out of the reactor, achieving a remarkable in situ product removal superior to 99%. The biomass concentration in the overflowing foam was found to be twofold lower than the biomass concentration in the reactor, relating advantageously this process to a continuous one with biomass feedback. To evaluate its performances regarding the type of lipopeptide produced, the O-CC process was tested with strain BBG116, a mycosubtilin constitutive overproducing strain that also produces surfactin, and strain BBG125, its derivative strain obtained by deleting surfactin synthetase operon. At a dilution rate of 0.1 h–1, specific productivity of 1.18 mg of mycosubtilin⋅g–1(DW)⋅h–1 was reached. Compared with other previously described bioprocesses using almost similar culture conditions and strains, the O-CC one allowed an increase of the mycosubtilin production rate by 2.06-fold.

Isolation and Characterization of Beneficial Bacteria from Food Process Wastes.

Significant quantities of food waste are accumulated globally on an annual basis, with approximately one-third of the food produced (equivalent to 1.3 billion tons of food) being wasted each year. A potential food waste recycling application is its utilization as a soil conditioner or fertilizer, whereby it increases the soil organic content and microbial biomass. This study evaluated the effectiveness of food waste as a microbial resource by analyzing the microbial community composition and isolating plant growth-promoting bacteria (PGPB) in food waste obtained from various sources. High-throughput sequencing identified 393 bacterial operational taxonomic units in the food process waste (FPW) samples. Moreover, the results showed that Firmicutes was abundant in the waste samples, followed by Bacteroidetes and Proteobacteria. A total of 92 bacteria were isolated from FPW. Moreover, the cultivable strains isolated from FPW belonged to the genus Bacillus, followed by Streptomyces and Proteus. Six isolated bacteria exhibited beneficial traits, including indole acetic acid production, antifungal resistance and extracellular lysis. FPW is a valuable microbial resource for isolation of PGPB, and its use as a fertilizer may enable a reduction in chemical fertilizer usage, thereby mitigating the corresponding adverse environmental impacts on sustainable crop development.

Perturbed Microbiota/Immune Homeostasis in Multiple Sclerosis.

ObjectiveBased on animal models and human studies, there is now strong suspicion that host/microbiota mutualism in the context of gut microbial dysbiosis could influence immunity and multiple sclerosis (MS) evolution. Our goal was to seek evidence of deregulated microbiota-induced systemic immune responses in patients with MS.MethodsWe investigated gut and systemic commensal-specific antibody responses in healthy controls (n = 32), patients with relapsing-remitting MS (n = 30), and individuals with clinically isolated syndromes (CISs) (n = 15). Gut microbiota composition and diversity were compared between controls and patients by analysis of 16S ribosomal ribonucleic acid (rRNA) sequencing. Autologous microbiota and cultivable bacterial strains were used in bacterial flow cytometry assays to quantify autologous serum IgG and secretory IgA responses to microbiota. IgG-bound bacteria were sorted by flow cytometry and identified using 16S rRNA sequencing.ResultsWe show that commensal-specific gut IgA responses are drastically reduced in patients with severe MS, disease severity being correlated with the IgA-coated fecal microbiota fraction (r = −0.647, p < 0.0001). At the same time, IgA-unbound bacteria elicit qualitatively broad and quantitatively increased serum IgG responses in patients with MS and CIS compared with controls (4.1% and 2.5% vs 1.9%, respectively, p < 0.001).ConclusionsGut and systemic microbiota/immune homeostasis are perturbed in MS. Our results argue that defective IgA responses in MS are linked to a breakdown of systemic tolerance to gut microbiota leading to an enhanced triggering of systemic IgG immunity against gut commensals occurring early in MS.

Endopolyploidy Variation in Wild Barley Seeds across Environmental Gradients in Israel.

Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissues and embryo) and in the triploid endosperm. We found that wild barley accessions collected at harsher xeric environmental conditions produce higher proportion of endoreduplicated nuclei in endosperm tissues. Also, a comparison of wild and cultivated barley strains revealed a higher endopolyploidy level in the endosperm of wild barley, that is accompanied by temporal changes in the timing of the major developmental phases. In summary, we present a new direction of research focusing on connecting spatiotemporal patterns of endoreduplication in barley seeds and possibly buffering for stress conditions.

Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis.

SummaryBackgroundWhile patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature.ObjectivesTo address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health‐ and AD‐associated strains of Roseomonas mucosa and Staphylococcus spp.MethodsUse of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre‐biotic potential. A proof‐of‐concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing.ResultsNumerous chemicals possessed antibiotic properties, including many not marketed as anti‐microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health‐associated isolates over disease‐associated strains in bacterial culture and enhanced microbe‐specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof‐of‐concept human studies.ConclusionsOur results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.

Geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response

Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth.

A basic scheme of soybean transformation for glyphosate tolerance using Agrobacterium tumefaciens through an approximation of patents: a review

Concern has been expressed on the control of agricultural biotechnology through patents that may adversely affect the development of competing crops. Soybean is one of the most important crops around the world (~287 million t per year), above potatoes (45 million t per year), tomatoes (23 million t per year), or wheat (116 million t per year), with prices for American producers ranging between USD 278.8 and USD 650.3 t-1. Soybean belongs to the Fabaceae family and has been genetically modified (GM) to improve its tolerance to herbicides, including glyphosate, its resistance to insect pests, and the quality of soy oil. Glyphosate-tolerant soybean has received a gene coding for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). There are a number of variables that contribute to the development of a GM soybean event. Such variables include tissue culture, selection methods, cloning vectors, and Agrobacterium strains that affect transformation efficiency and can be associated with patents. Chlorine gas disinfection is the most appropriate technique for plant material. Production of explants with shoots and molecular and phenotypic features (e.g., antibiotic susceptibility) of bacterial strain must be assessed. A long-term glyphosate selection arrangement is the most suitable and a consistent approach for the selection of events of GM soybean with tolerance to glyphosate. Freedom-to-operate evaluation must be carried out to find the specific elements neccesary for GM plant development that do not infringe the rights of third parties. These rights come into effect from the patent application date for a definite geographical region involving construct design and its synthesis, transformation vector, bacterial strain, methods, or reporter gene. In this review, the protocols relating to experiments for the development of GM soybean using an epsps gene are included, and considerations relating to intellectual property rights are involved. The major elements associated with each stage of the development of patents are described including the following: the soybean genotype, seed disinfection, genetic construct design and its synthesis, tissue culture protocols, selection strategy without gene reporter, and Agrobacterium strain. This review is a guide for carrying out technical procedures when the desired product is the off-patent GM soybean with tolerance to glyphosate.

The Diversity of Root-Associated Endophytic Fungi from Four Epiphytic Orchids in China

Root-associated endophytic fungi (RAF) are found asymptomatically in almost all plant groups. However, little is known about the compositions and potential functions of RAF communities associated with most Orchidaceae species. In this study, the diversity of RAF was examined in four wild epiphytic orchids, Acampe rigida, Doritis pulcherrima, Renanthera coccinea, and Robiquetia succisa, that occur in southern China. A culture-independent method involving Illumina amplicon sequencing, and an in vitro culture method, were used to identify culturable fungi. The RAF community diversity differed among the orchid roots, and some fungal taxa were clearly concentrated in a certain orchid species, with more OTUs being detected. By investigating mycorrhizal associations, the results showed that 28 (about 0.8%) of the 3527 operational taxonomic units (OTUs) could be assigned as OMF, while the OTUs of non-mycorrhizal fungal were about 99.2%. Among the OMFs, Ceratobasidiaceae OTUs were the most abundant with different richness, followed by Thelephoraceae. In addition, five Ceratobasidium sp. strains were isolated from D. pulcherrima, R. succisa, and R. coccinea roots with high separation rates. These culturable Ceratobasidium strains will provide materials for host orchid conservation and for studying the mechanisms underlying mycorrhizal symbiosis.

Enhanced diversity and rock-weathering potential of bacterial communities inhabiting potash trachyte surface beneath mosses and lichens — A case study in Nanjing, China

Mosses and lichens have been shown to play an important role in enhancing global chemical weathering of the surface rock. However, there are no studies concerning the effects of mosses and lichens on the microbial communities inhabiting rock surfaces. In this study, culture-dependent and culture-independent analyses were employed to compare the diversity, composition, and rock-weathering activity of bacterial communities inhabiting potash trachyte surfaces covered by mosses (MR) and lichens (LR) with those inhabiting surrounding bare rock surfaces (BR). Analyses of 16S rRNA gene Miseq sequencing revealed that the order of alpha (α) diversity indices, in terms of the number of unique operational taxonomic units (OTUs) and Faith's index of phylogenetic diversity, was MR > LR > BR. Moreover, α-diveristy indices were positively correlated with the content of available phosphorus (AP) in rock samples (r = 0.87–0.92), and this explained 70% of the variation in bacterial community structure. The culture-dependent analyses revealed that 100% of the culturable bacterial strains could enhance potash trachyte weathering, and the order of rock-weathering acitivity of bacterial strains was MR > LR > BR. Acidolysis was found to be the major mechanism involved in the bacteria-mediated weathering of potash trachyte. Moreover, bacterial strians related to the genera Dyella and Ralstonia showed the highest rock-weatheirng activity, and both Dyella and Ralstonia were enriched in MR. The results of this study enhance our understanding of the roles of bacteria facilitated by mosses and lichens in rock weathering, element cycling, and soil formation, and provide new insights into the interaction between non-vascular plants and the bacteria on rock surfaces.

Putative Novel Atypical BTV Serotype '36' Identified in Small Ruminants in Switzerland.

We identified a putative novel atypical BTV serotype ‘36’ in Swiss goat flocks. In the initial flock clinical signs consisting of multifocal purulent dermatitis, facial oedema and fever were observed. Following BTV detection by RT-qPCR, serotyping identified BTV-25 and also a putative novel BTV serotype in several of the affected goats. We successfully propagated the so-called “BTV-36-CH2019” strain in cell culture, developed a specific RT-qPCR targeting Segment 2, and generated the full genome by high-throughput sequencing. Furthermore, we experimentally infected goats with BTV-36-CH2019. Regularly, EDTA blood, serum and diverse swab samples were collected. Throughout the experiment, neither fever nor clinical disease was observed in any of the inoculated goats. Four goats developed BTV viremia, whereas one inoculated goat and the two contact animals remained negative. No viral RNA was detected in the swab samples collected from nose, mouth, eye, and rectum, and thus the experimental infection of goats using this novel BTV serotype delivered no indications for any clinical symptoms or vector-free virus transmission pathways. The subclinical infection of the four goats is in accordance with the reports for other atypical BTVs. However, the clinical signs of the initial goat flock did most likely not result from infection with the novel BTV-36-CH0219.

Performance of QMAC-dRASTTM (Direct Rapid Antimicrobial Susceptibility Testing) - a Newcomer in Phenotypic Automatic AST

Objective: QMAC-dRASTTM is a phenotypic automatized Antibiotic Susceptibility Testing (AST) system based on microfluidic chip technology enabling observation of changes in a single bacterial cell under antibiotic treatment conditions. The 96 wells plate with dried antibiotics comprises 19 and 17 antibiotics for the Gram-Negatives (GNs) and Gram-Positives (GPs), respectively. Categorical (Sensitive, Intermediate or Resistant) results were compared to results obtained by our laboratory standard susceptibility testing procedure and given as Categorical Agreement (CA). Methods: In a 3-month period (2019/2020), blood cultures detected positive were included. Excluded were known off-panel strains of QMAC-dRASTTM, such as Gram-positive bacilli, Streptococcus and Candida species. Percentages of CA (CA, %) between QMAC-dRASTTM and routine testing methods used in the laboratory (EUCAST disc diffusion and/or etest/Broth Micro Dilution MIC), were calculated. Results: 255 positive blood cultures from as many patients were examined. Of the positive blood culture strains, 144 were GNs, and 111 were GPs. An overall combined CA,% of 96.3 (2410 of 2502 determinations) was obtained, and discrepancies were noted in 92 of 2502 test results (3.7%). The percentage of very major errors (VMEs) was 0.7% for GNs and 2.2% for GPs. For 87% of blood culture specimens examined, susceptibility reports were available within 6-7 hours. Conclusion: The high CA,% for as well GNs as GPs are promising. The presented time to report data obtained by QMAC-dRASTTM in this study being of 3-8 hours for blood culture specimens examined strongly support a further possible improvement in the workflow for handling blood stream infections.

In-vitro compatibility assay of indigenous Trichoderma and Pseudomonas species and their antagonistic activities against black root rot disease (Fusarium solani) of faba bean (Vicia faba L.)

BackgroundFaba bean (Vicia faba L.) cultivation is highly challenged by faba bean black root rot disease (Fusarium solani) in high lands of Ethiopia. To ensure sustainable production of faba beans, searching for eco-friendly disease management options is necessary to curb the progress of the disease timely. The indigenous biocontrol agents that suit local environments may effectively strive with in-situ microorganisms and suppress local pathogen strains. This study aimed to screen antagonistic indigenous compatible Trichoderma and Pseudomonas strains against Fusarium solani. In the pathogenicity test, soil-filled pots were arranged in complete random block design and sown with health faba bean seeds. The effect of some fungicides was evaluated against Fusarium by food poisoning methods to compare with the biocontrol agents. The antagonistic efficacy of biocontrol agents and their compatibility was investigated on Potato dextrose agar medium.ResultsFusarium solani AAUF51 strain caused an intense root rotting in faba bean plant. The effect of Mancozeb 80% WP at 300 ppm was comparable with Trichoderma and Pseudomonas strains against Fusarium. The mycelial growth of test the pathogen was significantly (P ≤ 0.05) reduced to 86.67 and 85.19% by Trichoderma harzianum AAUW1 and Trichoderma viridae AAUC22 strains in dual culture, respectively. The volatile metabolites of Pseudomonas aeruginosa AAUS31 (77.78%) found the most efficient in reducing mycelial growth of Fusarium followed by Pseudomonas fluorescens AAUPF62 (71.11%) strains. The cell-free culture filtrates of Pseudomonas fluorescens AAUPF62 and Pseudomonas aeruginosa AAUS31 were more efficient than the Trichoderma strain in reducing the growth of Fusarium isolates. There was no zone of inhibition recorded between Trichoderma harzianum AAUW1, Trichoderma viridae AAUC22, Pseudomonas aeruginosa AAUS31, and Pseudomonas fluorescens AAUPF62 strains, hence they were mutually compatible.ConclusionsThe compatible Trichoderma and Pseudomonas strains showed antagonistic potentiality that could be explored for faba bean protection against black root rot disease and might have a future dual application as biocontrol agents.

A fattening factor to quantify the accumulation ability of microorganisms under N-starvation

Many microorganisms can accumulate biomass in the form of lipids and polysaccharides, which can be used for biofuels, bioplastics, food and feed. Some innovative bioprocesses exploit the competitive advantage provided by such accumulation ability, mainly under N-starvation, to select high-accumulating strains against biological contaminants, by using uncoupled nutrient feeding. However, there is no general and easily comparable parameter available to compare biomass accumulation ability among different microbial strains, which could measure the competitive advantage. Here, a parameter termed “fattening factor” (ηx) is described to quantify such strain-specific biomass accumulation ability in bacteria, yeasts and microalgae. This parameter measures how many fold a microbial population can increase its biomass just as the result of accumulation. It is derived from considerations about the main metabolic aspects of cells’ response to N-starvation, which induces variations in cell cycle, biomass production and biochemical composition. The fattening factor described here should be easily estimatable in N-starvation for every culturable microbial strain, by measuring the amount of accumulated biomass.