Influence of amino acids on low-density Escherichia coli responses to nutrient downshifts

The High Impact of Staphylococcus aureus Biofilm Culture Medium on In Vitro Outcomes of Antimicrobial Activity of Wound Antiseptics and Antibiotic

The staphylococcal biofilm-based infections of wounds still pose a significant therapeutical challenge. Treated improperly, they increase the risk of limb amputation or even death of the patient. The present algorithms of infected wound treatment include, among others, the application of antiseptic substances. In vitro wound biofilm models are applied in order to scrutinize their activity. In the present work, using a spectrum of techniques, we showed how the change of a single variable (medium composition) in the standard in vitro model translates not only to shift in staphylococcal biofilm features but also to the change of efficacy of clinically applied wound antimicrobials such as octenidine, polyhexamethylene biguanide, chlorhexidine, hypochlorite solutions, and locally applied gentamycin. The data presented in this study may be of a pivotal nature, taking into consideration the fact that results of in vitro analyses are frequently used to propagate application of specific antimicrobials in hospitals and ambulatory care units.

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Burkholderia cenocepacia is among the important pathogens isolated from cystic fibrosis (CF) patients. It has attracted considerable attention because of its capacity to evade host immune defenses during chronic infection. Advances in systems biology methodologies have led to the emergence of methods that integrate experimental transcriptomics data and genome-scale metabolic models (GEMs). Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. We observed substantial differences in pathway response to different growth conditions and alternative pathway susceptibility to extracellular nutrient availability. For instance, we found that blockage of the reactions was vital through the lipid biosynthesis pathways in the exponential phase and the absence of microenvironmental lysine and tryptophan are essential for survival. During biofilm development, bacteria mostly had conserved lipid metabolism but altered pathway activities associated with several amino acids and pentose phosphate pathways. Furthermore, conversion of serine to pyruvate and 2,5-dioxopentanoate synthesis are also identified as potential targets for metabolic remodeling during biofilm development. Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases.

Changes in Gut Microbial Community of Pig Feces in Response to Different Dietary Animal Protein Media

Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.

Transcriptomic Behavior of Salmonella enterica Newport in Response to Oxidative Sanitizers

ABSTRACT

Agricultural water is a known source of contamination to fresh produce and can contain foodborne pathogens including Salmonella enterica, pathogenic Escherichia coli, Listeria monocytogenes, and Campylobacter jejuni. To mitigate such risks, antimicrobial agents such as hypochlorites and peroxyacetic acid (PAA) can be applied to in-line irrigation systems as well as to water used in postharvest washing. Although these compounds are effective and widely used, some pathogenic bacteria adapt to survive exposure. RNA sequencing was used to analyze the Salmonella Newport transcriptome after exposure to sodium hypochlorite (NaOCl) and PAA in a simulated agricultural water system. Overall cellular adaptive response was determined quantitatively as a function of overall gene expression of the >4,000 genes in the Salmonella Newport genome. Differentially expressed genes ranged from 11 due to 10-ppm NaOCl treatment, 316 due to 20-ppm NaOCl treatment, 1,719 due to 10-ppm PAA treatment, and 2,010 due to 20-ppm PAA treatment compared with that of the controls (water only). Differentially expressed transcripts included cellular functions such as biosynthesis, degradation, energy generation, and nonmetabolically linked functions. Oxidative exposure upregulated genes associated with key virulence, attachment, and gene transfer. Amino acid biosynthesis was upregulated due to NaOCl exposure but primarily downregulated when Salmonella Newport was exposed to PAA. Slight upregulation occurred in nucleoside and nucleotide biosynthesis, a known DNA repair mechanism seen during exposure to sanitizers. Our results indicate that Salmonella Newport reacts differently when exposed to NaOCl versus PAA, despite oxidative activity being the primary modes of antimicrobial action of both compounds.

HIGHLIGHTS

Effect of plants and their root exudate on bacterial activities during rhizobacterium-plant remediation of phenol from water

We investigated remediation of phenol from water using microbe-plant partnerships. Co-introduction of maize seedlings, Pseudomonas fluorescens rifampicin-resistant P13 and P. stutzeri P7 carrying self-transmissible TOL-like plasmids reduced phenol content in water at lower phenol concentrations (25, 50, and 75 mg/L), similar to individual introduction of the bacteria. Co-introduction of plants and bacteria significantly reduced phenol content in water at higher phenol concentrations (100, 125, and 150 mg/L) compared to using individual introduction of the bacteria. Moreover, TOL-like plasmids were transferred from P7 to P13. Addition of plants promoted the growth of both strains, leading to increased plasmid transfer. At higher phenol concentrations, addition of plants resulted in increases of catechol 2, 3-dioxygenase (C23O) activity and reduction in level of reactive oxygen species (ROS) of bacteria in the degradation experiments. Increased plasmid transfer and C23O activity and reduction in ROS level might be the major reasons why plants promote bacterial degradation of phenol at higher phenol concentrations. Furthermore, root exudate of maize seedlings and artificial root exudate (ARE) constructed using major components of the root exudate had the same effects on bacterial activities. Unlike the ARE, deletion of glucose, arabinose, or fructose or all the monosaccharides from ARE resulted in no increase in numbers of both strains and in plasmid transfer. At the higher phenol concentrations, deletion of glutamic acid, aspartic acid, alanine, or glycine or all the amino acids did not stimulate bacterial C23O activity. Deletion of fumaric, oxaloacetic or citric acids still reduced bacterial ROS level as ARE did, but, deletion of all the organic acids or DIMBOA, a hydroxamic acid, did not reduce bacterial ROS level as ARE did. The data showed that each monosaccharide might be important for sufficient numbers of plant-associated bacteria and increased plasmid transfer while each amino acid might be important for maintaining bacterial C23O activity and that DIMBOA might be responsible for the decrease in ROS levels. These results are the basis for efficient remediation of phenol from water by microbe-plant partnerships and further studies on the mechanism of rhizobacterium-plant interaction.

Influence of Laboratory Culture Media on in vitro Growth, Adhesion, and Biofilm Formation of Pseudomonas aeruginosa and Staphylococcus aureus

OBJECTIVE

Pseudomonas aeruginosa and Staphylococcus aureus dual-species biofilm infections are notoriously difficult to manage. This study aimed at investigating the influence of four different culture media on the planktonic growth, adhesion, and biofilm formation of P. aeruginosa and S. aureus.

MATERIALS AND METHODS

We monitored four different culture media including Nutrient Broth, Brain Heart Infusion (BHI) broth, Luria-Bertani broth, and RPMI 1640 medium on the planktonic growth, adhesion, and biofilm formation of P. aeruginosa (ATCC 27853) and S. aureus (ATCC 25923) using MTT assay and scanning electron microscopy (SEM).

RESULTS

The most robust growth of the mono- and dual-species cultures was noted in BHI broth. On the contrary, RPMI 1640 medium promoted maximal initial adhesion of both the mono- and dual-species, but BHI broth fostered the maximal biofilm growth. SEM images showed profuse extracellular polysaccharide production in biofilms, particularly in coculture, in BHI medium.

CONCLUSION

Our data demonstrate that BHI broth, relative to the other tested media, is the most conducive for in vitro evaluation of biofilm and planktonic growth kinetics of these two pathogens, both in mono- and coculture.

Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin

High levels of antibiotic tolerance are a hallmark of bacterial biofilms. In contrast to well-characterized inherited antibiotic resistance, molecular mechanisms leading to reversible and transient antibiotic tolerance displayed by biofilm bacteria are still poorly understood. The physiological heterogeneity of biofilms influences the formation of transient specialized subpopulations that may be more tolerant to antibiotics. In this study, we used random transposon mutagenesis to identify biofilm-specific tolerant mutants normally exhibited by subpopulations located in specialized niches of heterogeneous biofilms. Using Escherichia coli as a model organism, we demonstrated, through identification of amino acid auxotroph mutants, that starved biofilms exhibited significantly greater tolerance towards fluoroquinolone ofloxacin than their planktonic counterparts. We demonstrated that the biofilm-associated tolerance to ofloxacin was fully dependent on a functional SOS response upon starvation to both amino acids and carbon source and partially dependent on the stringent response upon leucine starvation. However, the biofilm-specific ofloxacin increased tolerance did not involve any of the SOS-induced toxin–antitoxin systems previously associated with formation of highly tolerant persisters. We further demonstrated that ofloxacin tolerance was induced as a function of biofilm age, which was dependent on the SOS response. Our results therefore show that the SOS stress response induced in heterogeneous and nutrient-deprived biofilm microenvironments is a molecular mechanism leading to biofilm-specific high tolerance to the fluoroquinolone ofloxacin.

Biofilm surface-attached communities have the capacity to tolerate high concentrations of antibiotics, and bacterial biofilms formed on indwelling medical devices are difficult to eradicate and often lead to the onset of chronic or systemic infections. The physiological heterogeneity of multicellular biofilms has been associated with development of subpopulations highly tolerant to multiple antibiotics. Here we demonstrate that, upon starvation for specific essential growth nutrients, biofilm bacteria become highly tolerant to fluoroquinolone ofloxacin. The SOS response plays a critical role in this phenomenon, while the stringent response plays only a minor role. Taken together, these results support the hypothesis that bacteria localized within nutrient-limited niches of the biofilm structure may temporarily enter a physiological state enabling them to tolerate bactericidal concentrations of antibiotics.

Induction of cadBA in an Escherichia coli lysine auxotroph transformed with a cad-gfp transcriptional fusion

CadBA functions as a part of overall Escherichia coli response to low extracellular pH. A gfpmut3 structural gene transcriptionally fused to the cadBA promoter (Pcad) was used as a reporter to monitor changes in intracellular lysine as a potential factor influencing cadBA induction. Different patterns of cadBA induction were observed in two E. coli strains with different lysine biosynthetic capabilities. In E. coli ZK126 (pJBA25-Pcad), a lysine prototroph, maximum levels of induction were detected 3 h after the transfer of bacterial cells under inducing conditions (pH 5.8; 3.4 microM extracellular lysine). The induction subsequently decreased until hour 7 after which no further change in expression was observed. However, in the lysine depleted strain E. coli ATCC 23812 (pJBA25-Pcad) which is an auxotroph for lysine, no decrease in cadBA expression was observed over time under the same induction conditions. Although no time dependent statistical differences in intracellular lysine were observed, bacterial cells depleted for no longer than 4 h (1.38 +/- 0.25 micromol lysine/g cell dry weight) exhibited more rapid induction of cadBA (after 3 h) and a lower maximum level of induction compared to cells with relatively lower intracellular lysine (approximately 1.08 micromol/g cell dry weight). For the latter, the detectable level of induction was delayed for 1 h but the maximum level of induction response was higher.

Defined spatial structure stabilizes a synthetic multispecies bacterial community

This paper shows that for microbial communities, "fences make good neighbors." Communities of soil microorganisms perform critical functions: controlling climate, enhancing crop production, and remediation of environmental contamination. Microbial communities in the oral cavity and the gut are of high biomedical interest. Understanding and harnessing the function of these communities is difficult: artificial microbial communities in the laboratory become unstable because of "winner-takes-all" competition among species. We constructed a community of three different species of wild-type soil bacteria with syntrophic interactions using a microfluidic device to control spatial structure and chemical communication. We found that defined microscale spatial structure is both necessary and sufficient for the stable coexistence of interacting bacterial species in the synthetic community. A mathematical model describes how spatial structure can balance the competition and positive interactions within the community, even when the rates of production and consumption of nutrients by species are mismatched, by exploiting nonlinearities of these processes. These findings provide experimental and modeling evidence for a class of communities that require microscale spatial structure for stability, and these results predict that controlling spatial structure may enable harnessing the function of natural and synthetic multispecies communities in the laboratory.