Targeted metagenomics of active microbial populations with stable-isotope probing

The ability to explore microbial diversity and function has been enhanced by novel experimental and computational tools. The incorporation of stable isotopes into microbial biomass enables the recovery of labeled nucleic acids from active microorganisms, despite their initial abundance and culturability. Combining stable-isotope probing (SIP) with metagenomics provides access to genomes from microorganisms involved in metabolic processes of interest. Studies using metagenomic analysis on DNA obtained from DNA-SIP incubations can be ideal for the recovery of novel enzymes for biotechnology applications, including biodegradation, biotransformation, and biosynthesis. This chapter introduces metagenomic and DNA-SIP methodologies, highlights biotechnology-focused studies that combine these approaches, and provides perspectives on future uses of these methods as analysis tools for applied and environmental microbiology

Activity of a novel protonophore against methicillin-resistant Staphylococcus aureus

Aim: Compound 1-(4-chlorophenyl)-4,4,4-trifluoro-3-hydroxy-2-buten-1-one (compound 1) was identified as a hit against methicillin-resistant Staphylococcus aureus (MRSA) strain MW2. Methods & results: The MIC of compound 1 against MRSA was 4 μg/ml. The compound showed enhanced activity at acidic pH by lowering bacterial intracellular pH and exhibited no lysis of human red blood cells at up to 64 μg/ml and its IC50 against HepG2 cells was 32 μg/ml. The compound reduced 1-log10 colony forming units of intracellular MRSA in macrophages and prolonged the survival of MRSA-infected Caenorhabditis elegans (p = 0.0015) and Galleria mellonella (p = 0.0002). Conclusion: Compound 1 is a protonophore with potent in vitro and in vivo activity against MRSA and no toxicity in mammalian cells up to 8 μg/ml that warrants further investigation as a novel antibacterial

Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile

The emergence of multidrug-resistant bacterial strains has heightened the need for new antimicrobial agents based on novel chemical scaffolds that are able to circumvent current modes of resistance. We recently developed a whole-animal drug-screening methodology in pursuit of this goal and now report the discovery of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile (PSPC) as a novel antibacterial effective against resistant nosocomial pathogens. The minimum inhibitory concentrations (MIC) of PSPC against Staphylococcus aureus and Enterococcus faecium were 4 μg/mL and 8 μg/mL, respectively, whereas the MICs were higher against the Gram-negative bacteria Klebsiella pneumoniae (64 μg/mL), Acinetobacter baumannii (32 μg/mL), Pseudomonas aeruginosa (\u3e64 μg/mL), and Enterobacter spp. (\u3e64 μg/mL). However, co-treatment of PSPC with the efflux pump inhibitor phenylalanine arginyl β-naphthylamide (PAβN) or with sub-inhibitory concentrations of the lipopeptide antibiotic polymyxin B reduced the MICs of PSPC against the Gram-negative strains by \u3e4-fold. A sulfide analog of PSPC (PSPC-1S) showed no antibacterial activity, whereas the sulfoxide analog (PSPC-6S) showed identical activity as PSPC across all strains, confirming structure-dependent activity for PSPC and suggesting a target-based mechanism of action. PSPC displayed dose dependent toxicity to both Caenorhabditis elegans and HEK-293 mammalian cells, culminating with a survival rate of 16% (100 μg/mL) and 8.5% (64 μg/mL), respectively, at the maximum tested concentration. However, PSPC did not result in hemolysis of erythrocytes, even at a concentration of 64 μg/mL. Together these results support PSPC as a new chemotype suitable for further development of new antibiotics against Gram-positive and Gram-negative bacteria

Insect-Derived Cecropins Display Activity against Acinetobacter baumannii in a Whole-Animal High-Throughput Caenorhabditis elegans Model

The rise of multidrug-resistant Acinetobacter baumannii and a concomitant decrease in antibiotic treatment options warrants a search for new classes of antibacterial agents. We have found that A. baumannii is pathogenic and lethal to the model host organism Caenorhabditis elegans and have exploited this phenomenon to develop an automated, high-throughput, high-content screening assay in liquid culture that can be used to identify novel antibiotics effective against A. baumannii. The screening assay involves coincubating C. elegans with A. baumannii in 384-well plates containing potential antibacterial compounds. At the end of the incubation period, worms are stained with a dye that stains only dead animals, and images are acquired using automated microscopy and then analyzed using an automated image analysis program. This robust assay yields a Z′ factor consistently greater than 0.7. In a pilot experiment to test the efficacy of the assay, we screened a small custom library of synthetic antimicrobial peptides (AMPs) that were synthesized using publicly available sequence data and/or transcriptomic data from immune-challenged insects. We identified cecropin A and 14 other cecropin or cecropin-like peptides that were able to enhance C. elegans survival in the presence of A. baumannii. Interestingly, one particular hit, BR003-cecropin A, a cationic peptide synthesized by the mosquito Aedes aegypti, showed antibiotic activity against a panel of Gram-negative bacteria and exhibited a low MIC (5 μg/ml) against A. baumannii. BR003-cecropin A causes membrane permeability in A. baumannii, which could be the underlying mechanism of its lethality

Studies on the Mechanism of Electron Bifurcation Catalyzed by Electron Transferring Flavoprotein (Etf) and Butyryl-CoA Dehydrogenase (Bcd) of Acidaminococcus fermentans

Electron bifurcation is a fundamental strategy of energy coupling originally discovered in the Q-cycle of many organisms. Recently a flavin-based electron bifurcation has been detected in anaerobes, first in clostridia and later in acetogens and methanogens. It enables anaerobic bacteria and archaea to reduce the low-potential [4Fe-4S] clusters of ferredoxin, which increases the efficiency of the substrate level and electron transport phosphorylations. Here we characterize the bifurcating electron transferring flavoprotein (EtfAf) and butyryl-CoA dehydrogenase (BcdAf) of Acidaminococcus fermentans, which couple the exergonic reduction of crotonyl-CoA to butyryl-CoA to the endergonic reduction of ferredoxin both with NADH. EtfAf contains one FAD (α-FAD) in subunit α and a second FAD (β-FAD) in subunit β. The distance between the two isoalloxazine rings is 18 Å. The EtfAf-NAD+ complex structure revealed β-FAD as acceptor of the hydride of NADH. The formed β-FADH- is considered as the bifurcating electron donor. As a result of a domain movement, α-FAD is able to approach β-FADH- by about 4 Å and to take up one electron yielding a stable anionic semiquinone, α-FAD-, which donates this electron further to Dh-FAD of BcdAf after a second domain movement. The remaining nonstabilized neutral semiquinone, β-FADHˑ, immediately reduces ferredoxin. Repetition of this process affords a second reduced ferredoxin and Dh-FADH- that converts crotonyl-CoA to butyryl-CoA

Catalytic reduction of anionic and cationic toxic dyes and evaluation of antimicrobial activity using green synthesized palladium nanoparticles employing Carica papaya aqueous leaf extract

The present study offers a flexible method for the ecologically friendly synthesis of palladium nanoparticles and their assessment as a catalyst and antibacterial agent. Using an aqueous leaf extract of Carica papaya as a capping and reducing agent with Total Organic Carbon (TOC) measured at 959 mg/L, palladium nanoparticles (PdNPs) were biochemically created. This is undoubtedly a modest green synthesis method, and the structural characteristics of the nanoparticles were investigated utilizing the techniques of UV, FTIR, powder XRD, SEM, and HR-TEM. According to FTIR studies, the polyphenols in Carica papaya leaf extract may be what causes Pd2+ to be converted into PdNPs. The face-centered cubic geometry of the PdNPs was extremely crystalline, as shown by the X-ray diffraction., and SEM images confirmed their spherical shape. The particle size of the synthesized PdNPs was found to be 20 nm as determined by HR-TEM. In the reduction of anionic Congo red (CR) and cationic Methylene blue (MB) dyes, green-produced PdNPs showed substantial catalytic activity. The PdNPs may have a catalytic impact as seen by the decrease in absorption band intensity with passing time, which results in 92 % degradation of Congo red, an anionic dye, and 95 % degradation of Methylene Blue, a cationic dye. Significant antibacterial action was also shown by the synthetic green PdNPs against bacterial and fungi strains