Conventional Laboratory Media Research Articles

CodY and pdhA Expression Is Induced in Staphylococcus epidermidis Biofilm and Planktonic Populations With Higher Proportions of Viable but Non-Culturable Cells.

Staphylococcus epidermidis biofilm cells can enter a physiological state known as viable but non-culturable (VBNC), where, despite being alive, they do not grow in conventional laboratory media. As such, the presence of VBNC cells impacts the diagnosis of S. epidermidis biofilm-associated infections. Previous transcriptomics analysis of S. epidermidis strain 9142 biofilms with higher proportions of VBNC cells suggested that the genes pdhA, codY and mazEF could be involved in the induction of the VBNC state. However, it was previously demonstrated that VBNC induction is strain-dependent. To properly assess the role of these genes in VBNC induction, the construction of mutant strains is necessary. Thus, herein, we assessed if VBNC cells could be induced in strain 1457, a strain amenable to genetic manipulation, and if the previously identified genes were involved in the modulation of the VBNC state in this strain. Furthermore, we evaluated the formation of VBNC cells on planktonic cultures. Our results showed that despite being commonly associated with biofilms, the proportion of VBNC cells can be modulated in both biofilm and planktonic cultures and that the expression of codY and pdhA was upregulated under VBNC inducing conditions in both phenotypes. Overall, our study revealed that the formation of VBNC cells in S. epidermidis is independent of the mode of growth and that the genes codY and pdhA seem to be relevant for the regulation of this physiological condition.

Evaluation of a New Culture-Based AtbFinder Test-System Employing a Novel Nutrient Medium for the Selection of Optimal Antibiotics for Critically Ill Patients with Polymicrobial Infections within 4 h.

Here, we describe the validation of a new phenotypic culture-based AtbFinder method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. AtbFinder, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. The method uses a novel TGV medium that allows more rapid bacterial growth of Gram-positive and Gram-negative monoisolates compared with that achieved with conventional laboratory media, demonstrating overall sensitivity, specificity, PPV, NPV values of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, after 4 h. For polymicrobial infections, AtbFinder utilized a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing of a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media, and enabled, within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, the AtbFinder system may be a valuable tool in improving antibiotic selection, and enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.

MICROBIAL INDUCED SLOPE SURFACE STABILIZATION USING INDUSTRIAL-GRADE CHEMICALS: A PRELIMINARY LABORATORY STUDY

One of the promising soil improvement techniques that have recently gained increased attention in Geotechnical and Civil Engineering is microbial induced carbonate precipitation (MICP). The MICP is mediated by ureolytic bacteria through a chain of biochemical reactions which lead to the formation of calcium carbonate cement in soil matrix and persuades the substantial bonds between the soil particles. The study presented herein focuses on surficial stabilization of slope soil (Hokkaido, Japan) by mediating industrial-grade chemicals through two different scales of preliminary laboratory investigations: small-scale columns and bench-scale slopes. Locally isolated Psychrobacillus sp. was cultivated in both industrial-grade media (beer yeast) and laboratory-grade media (NH4-YE: tris-buffer, ammonium sulfate and yeast extract), and the urease activities were compared. The results showed that the cultivation of bacteria in beer yeast resulted in higher urease activity (0.9 U/mL) compared to that in conventional laboratory media (0.4 U/mL). Also, UCS of the specimen treated using industrial-grade chemicals (urea fertilizer, beer yeast and snow melting reagent) was about two times higher than the specimen treated using conventional laboratory-grade chemicals (urea, CaCl2 and nutrient broth). The benchtop-scale test revealed that the highest surface strength (UCS of 1.02 MPa) was achieved while treating the soil by 0.5 M cementation solution at 30oC. Sets of colorimeter measurements were undertaken on treated slope models to compare precipitation profile at different locations. These findings suggest that industrial-grade chemicals can contribute as potential candidates in MICP applications from the perspective of cost reduction.

Biodiversity of the human oral mycobiome in health and disease.

The organisms that colonize the human body over a lifetime are diverse, extensive and gargantuan. A fair proportion of the microbiota that constitutes this human microbiome live within our oral cavities mostly as harmonious associates causing only sporadic disease. An important core constituent of the microbiome is the mycobiome, representing various fungal genera. Up until recently, only a few species of fungi, mainly Candida species, were thought to constitute the human oral mycobiome. The reasons for this are manifold, although the uncultivable nature of many fungi in conventional laboratory media, and their complex genetic composition seem to be the major factors which eluded their detection over the years. Nevertheless, recent advances in computing and high-throughput sequencing such as next-generation sequencing (NGS) platforms have provided us a panoramic view of a totally new world of fungi that are human oral cohabitués. Their diversity is perplexing, and functionality yet to be deciphered. Here, we provide a glimpse of what is currently known of the oral mycobiome, in health and disease, with some future perspectives.

Clinically Relevant Growth Conditions Alter Acinetobacter baumannii Antibiotic Susceptibility and Promote Identification of Novel Antibacterial Agents.

Biological processes that govern bacterial proliferation and survival in the host-environment(s) are likely to be vastly different from those that are required for viability in nutrient-rich laboratory media. Consequently, growth-based antimicrobial screens performed in conditions modeling aspects of bacterial disease states have the potential to identify new classes of antimicrobials that would be missed by screens performed in conventional laboratory media. Accordingly, we performed screens of the Selleck library of 853 FDA approved drugs for agents that exhibit antimicrobial activity toward the Gram-negative bacterial pathogen Acinetobacter baumannii during growth in human serum, lung surfactant, and/or the organism in the biofilm state and compared those results to that of conventional laboratory medium. Results revealed that a total of 90 compounds representing 73 antibiotics and 17 agents that were developed for alternative therapeutic indications displayed antimicrobial properties toward the test strain in at least one screening condition. Of the active library antibiotics only four agents, rifampin, rifaximin, ciprofloxacin and tetracycline, exhibited antimicrobial activity toward the organism during all screening conditions, whereas the remainder were inactive in ≥ 1 condition; 56 antibiotics were inactive during serum growth, 25 and 38 were inactive toward lung surfactant grown and biofilm-associated cells, respectively, suggesting that subsets of antibiotics may outperform others in differing infection settings. Moreover, 9 antibiotics that are predominantly used for the treatment Gram-positive pathogens and 10 non-antibiotics lacked detectable antimicrobial activity toward A. baumannii grown in conventional medium but were active during ≥ 1 alternative growth condition(s). Such agents may represent promising anti-Acinetobacter agents that would have likely been overlooked by antimicrobial whole cell screening assays performed in traditional laboratory screening media.

Description of 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis', two intranuclear bacteria of freshwater amoebae.

Two novel bacteria of the phylum Proteobacteria were isolated during searches for amoeba-resistant micro-organisms in natural and constructed water systems. Strain HT99 was isolated from amoebae found in the biofilm of an outdoor hot tub in Cookeville, Tennessee, USA, and strain CC99 was isolated from amoebae in the biofilm of a cooling tower in the same city. Both bacteria were Gram-stain-negative cocci to coccobacilli, unculturable on conventional laboratory media, and were found to be intranuclear when maintained in Acanthamoeba polyphaga. The genomes of both isolates were completely sequenced. The genome of CC99 was found to be 3.0 Mbp with a 37.9 mol% DNA G+C content, while the genome of HT99 was 3.6 Mbp with a 39.5 mol% DNA G+C content. The 16S rRNA gene sequences of the two isolates were 94 % similar to each other. Phylogenetic comparisons of the 16S rRNA, mip and rpoB genes, the DNA G+C content and the fatty acid composition demonstrated that both bacteria are members of the order Legionellales, and are most closely related to Coxiella burnetii. The phenotypic and genetic evidence supports the proposal of novel taxa to accommodate these strains; however, because strains HT99 and CC99 cannot be cultured outside of the amoeba host, the respective names 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis' are proposed.

Generation of superoxide anions by a glycation reaction in conventional laboratory media

We reported that generation of superoxide anion (O(2)(-)) was detected from conventional laboratory media. The generated O(2)(-) is non-enzymatic converted to hydroxyl radicals, which cause damage to lipids, proteins, and nucleic acids. However, the O(2)(-) generating mechanism from culture media is unclear. We considered that the O(2)(-) generation was implicated in a glycation reaction between reducing sugar and proteins, which is the early stage of Maillard reaction. It has been suggested that the glycated proteins, such as Schiff base and Amadori compounds, undergo a spontaneous autoxidation reaction, catalyzed by transition metal ions, involving the O(2)(-) generation. Therefore, we investigated the effect of Chelex 100 on the O(2)(-) generation from brain-heart-infusion (BHI) medium, which is a nutritional culture medium for bacteria. However, the O(2)(-) generation from the BHI medium treated with Chelex 100 was significantly increased in comparison to it treated without Chelex 100. The quantity of O(2)(-) generation from BHI medium was significantly increased by addition of glucose, and in alkaline environment as well as a glycation reaction model system that autoclaved a mixture solution of glucose and tryptophan. In addition, the O(2)(-) generation from BHI medium was significantly inhibited by pyridoxamine that is a Maillard reaction inhibitor. Therefore, it was suggested that the O(2)(-) generation from BHI medium is closely related to the glycation reaction of amide compounds such as proteins containing in the medium without the transition metals.

Generation of reactive oxygen species from conventional laboratory media

We previously reported that superoxide anion was generated from glucose-peptone-meat extract medium. We found that superoxide anion was generated from other conventional laboratory media, Nutrient Broth, Tryptic Soy Broth, and Mueller Hinton Broth as well as glucose-peptone-meat extract medium. The glucose-peptone-meat extract medium consisting of 1% glucose, 0.5% peptone, 0.5% meat extract, and 0.3% NaCl showed the highest superoxide anion generation among the media tested. The meat extract and peptone, which are natural nutrient sources in the medium, showed an increase in absorbance intensity by WST-1 formazan products upon reaction with superoxide anion. The specific type of reactive oxygen species was measured by SOD-inhibitable reduction of cytochrome c and WST-1 (for superoxide anion), Fluoro H(2)O(2) kit (for hydrogen peroxide), hydroxyphenyl fluorescein (for hydroxyl radical), and Singlet Oxygen Sensor Green (for singlet oxygen). The generation of hydroxyl radical was also evaluated by ESR-spin trapping method. We detected superoxide anion, hydrogen peroxide, and hydroxyl radical but not singlet oxygen. These results suggest that the superoxide anion spontaneously generated from glucose-peptone-meat extract medium is finally converted to hydroxyl radical.

Optimization of Low-Cost Culture Media for the Production of Biomass and Bacteriocin by a Urogenital Lactobacillus salivarius Strain.

The aim of this work was to formulate a culture medium of lower cost than conventional laboratory media, in order to simultaneously obtain high amounts of both biomass and bacteriocin of vaginal Lactobacillus salivarius CRL 1328. The growth assays under different culture conditions were performed by using a 2(8-2) central composite experimental design, with a central point and sixteen additional points. The factors taken into consideration were glucose, lactose, yeast extract, tryptone, ammonium citrate, sodium acetate, MgSO4 and MnSO4. The simultaneous presence of a carbon source (mainly glucose), a nitrogen source (mainly yeast extract) and salts (mainly MnSO4, MgSO4 and sodium acetate) allowed the highest cell biomass and bacteriocin levels to be reached in the experimental design. Through the application of the desirability function, several optimal medium compositions to achieve efficient production of biomass and bacteriocin were predicted. The optimized growth media allow a cost reduction of around 25 to 40% compared with conventional broths. The results obtained represent an advance in the search of the most suitable strategies for the production of bioactive compounds for pharmaceutical products to prevent or treat female urogenital infections.

Efficacy of microcin J25 in biomatrices and in a mouse model of Salmonella infection

To study the possible therapeutic utility of microcin J25 (MccJ25), a peptide RNA polymerase inhibitor. We subjected the antibiotic to two types of assays. First, with an ex vivo assay, we evaluated the stability and efficacy of MccJ25 in complex fluid biomatrices such as human whole blood, plasma and serum, compared with that in conventional laboratory media. Antimicrobial efficacy of MccJ25 was assessed by quantitative culture 2 h after inoculation of the biomatrices with a Salmonella Newport target organism and compared with that of MccJ25-free controls. Second, the antibiotic was tested in a mouse model of Salmonella infection. The latter was induced by intraperitoneal inoculation of 10(6) cfu of Salmonella Newport and the treatment with MccJ25 was initiated at 2 h post-infection. MccJ25 retained full activity after 24 h of incubation in whole blood, plasma or serum. In addition, it did not show any haemolytic activity. In whole blood, homologous plasma and serum, introduction of MccJ25 was associated with a significant reduction in cfu versus the respective peptide-free controls. The counts of viable bacteria in the spleen and liver of mice treated with MccJ25 at a total dosage of 3 mg/mouse during either 24 h (0.5 mg/mouse every 4 h) or 6 days (0.5 mg/mouse every 24 h) significantly decreased by two or three orders of magnitude (P <or= 0.05) compared with those in control mice. Collectively, these findings indicate that the biological activity of MccJ25 is not affected in complex biological matrices. The potent in vitro activity of MccJ25 against Salmonella translates into good in vivo efficacy in a mouse infection model.