Reference Bacteria Research Articles

Meat Native Lactic Acid Bacteria Capable to Inhibit Salmonella sp. and Escherichia coli.

In this study, lactic acid bacteria (LAB) strains were isolated from ground beef, and it was analyzed if they have any effect on the growth of two reference bacteria (Salmonella sp. and Escherichia coli). It was found that five isolates showed an inhibitory effect in both reference bacteria by spot at the lawn assay. These bacteria were selected to perform growth kinetics in co-culture to determine if they modify the growth parameters of the reference bacteria. Subsequently, LAB cultures and three treatments (crude extract, thermally treated and thermally treated with neutral pH) of cells free supernatants (CFS) were screened by the agar well diffusion assay. In co-culture, selected LAB altered the growth rate and reduce the maximum population of both reference bacteria. While, LAB cultures and CFS also showed antimicrobial activity, and there was no significant difference among CFS treatments. LAB isolated from ground beef showed an antimicrobial effect against the reference bacteria that could be used for meat biopreservation purposes.

Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment.

Chloromethane (CH3Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (εCl) associated with the major abiotic and biotic CH3Cl sinks in the environment, namely, CH3Cl degradation by hydroxyl (·OH) and chlorine (·Cl) radicals in the troposphere and by reference bacteria Methylorubrum extorquens CM4 and Leisingera methylohalidivorans MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CH3Cl with ·OH and ·Cl radicals, whereas a large chlorine isotope fractionation (εCl) of -10.9 ± 0.7‰ (n = 3) and -9.4 ± 0.9 (n = 3) was found for CH3Cl degradation by M. extorquens CM4 and L. methylohalidivorans MB2, respectively. The large difference in chlorine isotope fractionation observed between tropospheric and bacterial degradation of CH3Cl provides an effective isotopic tool to characterize and distinguish between major abiotic and biotic processes contributing to the CH3Cl sink in the environment. Our findings demonstrate the potential of emerging triple-element isotopic approaches including chlorine to carbon and hydrogen analysis for the assessment of global cycling of organochlorines.

Identification and functional characterization of the astacidin family of proline-rich host defence peptides (PcAst) from the red swamp crayfish (Procambarus clarkii, Girard 1852)

This study reports the identification of four novel proline-rich antimicrobial peptides (PR-AMP) from the transcriptome of the red swamp crayfish Procambarus clarkii. The newly identified putative peptides (PcAst-1b, -1c, −2 and −3), which are related with the previously identified hemocyte-specific PR-AMP astacidin-1, are encoded by the multi-genic astacidin gene family. The screening of available and proprietary transcriptomes allowed to define the taxonomical range of distribution of this gene family to Astacoidea and Parastacoidea. The antimicrobial properties of three synthetic PcAst peptides (PcAst-1a, -1b/c and −2), were characterized against reference bacteria or multidrug resistant clinical isolates, and their cytotoxicity was evaluated towards human transformed cell lines. The antimicrobial activity ranged from potent and broad-spectrum, in low-salt medium, to poor, whereas it was generally low in full nutrient broth. No significant toxic effects were observed on cultured human cells. RNA-seq data from 12 different tissues indicated a strong specificity for haemocytes under naïve physiological condition, with moderate expression (5-fold lower) in gills. Quantitative real time PCR revealed a rapid (within 2 h) and significant up-regulation of PcAst-1a (Astacidin 1) and PcAst-2 expression in response to LPS injection. Due to the variation in antimicrobial potency and inducibility, the roles of the other astacidins (PcAst-1b, -1c and −3) need to be further investigated to determine their significance to the immune responses of the red swamp crayfish.

Enzymatic, antimicrobial, and leishmanicidal bioactivity of gram-negative bacteria strains from the midgut of Lutzomyia evansi, an insect vector of leishmaniasis in Colombia

Knowledge regarding new compounds, peptides, and/or secondary metabolites secreted by bacteria isolated from the intestine of phebotominae has the potential to control insect vectors and pathogens (viruses, bacteria, and parasites) transmitted by them. In this respect, twelve Gram-negative bacteria isolated from the intestine of Lutzomyia evansi were selected and screened for their enzymatic, antimicrobial, and leishmanicidal activity. E. cancerogenus, E. aerogenes, P. otitidis, E. cloacae, L. soli, and P. ananatis exhibited enzymatic activity. 83.3% of the isolates displayed lipolytic and nitrate reductase activity and 58.3% of the isolates displayed protease activity. Hemolytic activity (17%) was identified only in E. hormaechei, and P. ananatis. E. cancerogenus, A. calcoaceticus, and P. otitidis showed cellulolytic activity. A. gyllenbergii, P. aeruginosa, and E. hormaechei showed amylolytic activity. In general, the totality of methanolic extracts exhibited antimicrobial activity, where E. hormaechei, A. calcoaceticus, and E. cancerogenus presented the highest activity against the evaluated reference bacteria strains. Cell-free supernatants (CFSS) of the Gram-negative bacteria showed higher growth inhibitory activity against the reference Gram-positive bacteria. The CFS of A. gyllenbergii was the most active antimicrobial in this study, against S. aureus (AAODs = 95.12%) and E. faecalis (AAODs = 86.90%). The inhibition percentages of CFS against Gram-positive bacteria showed statistically significant differences (repeated measure ANOVA df= 2; F= 6.095; P= 0.007832). The E. hormaechei methanolic extract showed leishmanicidal activity (CE-50 μg/ml = 47.7 + 3.8) against metacyclic promastigotes of Leishmania braziliensis (UA301). Based on this finding, we discuss the possible implications of these bacteria in digestion and physiological processes in the Lu. evansi intestine. P. ananatis, E. cloacae, E. hormaechei, and P. otitidis were considered the most promising bacteria in this study and they could potentially be used for biological control.

Caracterización química y actividad antibacteriana del aceite esencial de Mangifera indica L. de tres regiones de Venezuela

Los aceites esenciales (AE) de las hojas de Mangifera indica L. recolectadas en los estados Mérida (M), Barinas (B) y Portuguesa (P), Venezuela, fueron obtenidos por el método de hidrodestilación, utilizando la trampa de Clevenger, obteniéndose 0,1 mL (0,0025%), 1,4 mL (0,035%) y 1,0 mL (0,025%), respectivamente. Los AE se caracterizaron por el método de cromatografía de gases acoplado a espectrometría de masas (CG/EM), se identificaron 30 compuestos en la muestra recolectada en M, 24 en B y 14 en P, siendo los mayoritarios en M: β-selineno (22,56%), α-gurjuneno (14,66%), β-cariofileno (10,40%), en B: β-cariofileno (36,32%), α-humuleno (22,71%), α-gurjuneno (21,43%) y en P: β-cariofileno (36,07%), α-gurjuneno (22,55%) y α-humuleno (21,24%). Debido al rendimiento, solo se determinó la actividad antibacteriana en los AE de B y P, por el método de difusión en agar con discos, frente a bacterias de referencia internacional (Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 23357 y Pseudomonas aureginosa ATCC 27853). Ambos AE inhibieron el desarrollo de S. aureus y E. faecalis con una concentración inhibitoria mínima de 200 µL/mL y 300 µL/mL, respectivamente. Este es el primer estudio comparativo y actividad antibacteriana del aceite esencial obtenido de las hojas de M. indica L. de tres regiones de Venezuela.

Electrons selective uptake of a metal-reducing bacterium Shewanella oneidensis MR-1 from ferrocyanide

The extracellular electron transfer of Shewanella oneidensis MR-1 (MR-1) has been extensively studied due to the importance of the biosensors and energy applications of bioelectrochemical systems. However, the oxidation of metal compounds by MR-1, which represents the inward extracellular electron transfer from extracellular electron donors into the microbe, is barely understood. In this study, MR-1 immobilized on an electrode electrocatalyzes the oxidation of [Fe(CN)6]4- to [Fe(CN)6]3- efficiently and selectively. The selectivity depends on midpoint potential and overall charge(s) of redox molecules. Among 12 investigated redox molecules, the negatively charged molecules with high midpoint potentials, i.e., [Ru(CN)6]4- and [Fe(CN)6]4-, show strong electrocatalysis. Neither reference bacteria (Escherichia coli K-12 nor Streptococcus mutans) electrocatalyze the oxidation of [Fe(CN)6]4-. The electrocatalysis decays when MR-1 is covered with palladium nanoparticles presumptively involved with cytochromes c. However, cytochromes c MtrC and OmcA on MR-1 do not play an essential role in this process. The results support a model that [Fe(CN)6]4- donor electrons to MR-1 by interacting with undiscovered active sites and the electrons are subsequently transferred to the electrode through the mediating effect of [Fe(CN)6]4-/3-. The selective electron uptake by MR-1 provides valuable and fundamental insights of the applications of bioelectrochemical systems and the detection of specific redox molecules.

Antibacterial, Antibiofilm, Antiquorum Sensing, Antimotility, and Antioxidant Activities of Green Fabricated Ag, Cu, TiO2, ZnO, and Fe3O4 NPs via Protoparmeliopsis muralis Lichen Aqueous Extract against Multi-Drug-Resistant Bacteria.

Consideration of lichen organisms as the ecofriendly source of metal nanoparticles (MNPs) and metal oxide NPs (MONPs) synthesis is seldom. In this study, Ag and Cu MNPs as well as TiO2, ZnO, and Fe3O4 MONPs were green synthesized by Protoparmeliopsis muralis lichen aqueous extract. First, physicochemical characterization by UV-vis spectroscopy, XRD, FT-IR, FESEM, and TEM techniques demonstrated the presence possibility of secondary metabolites around formed MNPs/MONPs with different diameters and shapes (spherical, triangular, polyhedral, and cubic). The antibacterial, antibiofilm, antiquorum sensing, and antioxidant abilities of these MNPs/MONPs against multi drug resistant (MDR) bacterium (Staphylococcus aureus ATCC 43300) and reference bacteria (Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853) were then evaluated by in vitro tests. Results of disc diffusion and MIC/MBC assays of Ag NPs as an effective antibacterial agent illustrated a higher sensitivity of the P. aeruginosa pathogen than E. coli and S. aureus. In next steps, a significant reduction was observed in the biofilm formation of each bacterium and pyocyanin synthesis by P. aeruginosa under Ag NPs. This investigation presents novel clean production of five MNPs/MONPs with prominent advantages of being ecofriendly and cost-effective and having antipathogen properties.

Optimization of manganese bioleaching activity and molecular characterization of indigenous heterotrophic bacteria isolated from the sulfuric area

Abstract. Prasidya DA, Wilopo W, Warmada IW, Retnaningrum E. 2019. Optimization of manganese bioleaching activity and molecular characterization of indigenous heterotrophic bacteria isolated from the sulfuric area. Biodiversitas 20: 1904-1909. The present research evaluated the manganese bioleaching potency of a heterotrophic bacteria KB3B1. This bacterial strain has been isolated from sulfuric area located at Ungaran, Middle of Java, Indonesia using modified 9K medium by adding of several organic nutrients. The manganese bioleaching activities of the strain was analysed by applying of varying glycine concentrations (0, 5, 10, 15 mg mL-1) with pyrolusite pulp densities of 0.02 g cm-3 on a rotary shaker at 180 rpm for 18 days incubation. Several parameters, including the growth of bacteria, pH values, the concentration of soluble manganese and cyanide, were investigated at the interval of 3 days. Molecular characteristics of the strain were further analyzed based on 16S rDNA gene sequences. After 15 days, the maximum yield of manganese 16.6% was achieved under the addition of 10 mg mL-1 glycine. This maximum extract obtained was followed by the maximum bacterial growth, pH, and cyanide product of the strain. Phylogenetic analysis showed that the strain was closely related with Bacillus niacini EP89. Besides, the average frequencies of guanine and cytosine (G+C) of the strain was in same range as that of the reference bacteria in the GenBank and Bergey's Manual Systematics of Bacteria.

NodC-based evaluation of the occurrence of bacteria in nodules of Pisum sativum isolated on YEM agar

Summary The bacterial nodulation (nod) genes are essential in the formation process of root nodules. This study was aimed to verify the occurrence of nodule-associated bacteria in two pea varieties (“Tarchalska” and “Klif ”) inoculated with Rhizobium inoculants – Nitragine™ and a noncommercial one produced by the Polish Institute of Soil Science and Plant Cultivation (IUNG). The number of colonies isolated on yeast extract mannitol (YEM) agar from the nodules of “Klif ” inoculated with IUNG inoculants was significantly higher than the number of colonies isolated from other variants. Species identification was based on sequencing of 16S rDNA, which revealed that despite careful sterilization of nodules, sequences of other bacterial species were detected. Among them, one sequence belonged to Rhizobium leguminosarum (isolated from IUNG inoculant). To assess the presence of nodulation-capable Rhizobium, amplification of the nodC gene was performed, which revealed that of 29 samples, 19 were positive. The remaining isolates, including reference strain and bacteria isolated from Nitragine™, lacked this gene. The results show that pea nodules harbor a very diverse community of bacteria. The lack of nodC gene in some strains isolated from plants inoculated with Nitragine™ and with IUNG inoculant proves that even if R. leguminosarum are abundant, they may not be efficient in nodulation.

Zanthoxylum zanthoxyloides and Zanthoxylum leprieurii: a micromorphological, phytochemical and antibacterial evaluation

Introduction: The biosynthesis of a large diversity of secondary metabolites, that includes terpenic compounds, alkaloids, flavonoids and phenolics, is one of the most relevant adaptive mechanism presented by plants in order to survive on harsh environment. The objective of this work was to carry out preliminary studies on micromorphology, phytochemical profile and antibacterial activity of two Rutaceae species, native to Guinea-Bissau, Zanthoxylum zanthoxyloides and Z. leprieurii. Both species are currently used as medicine and their antimicrobial properties, among others, are reported in the regions of their geographical distribution. Materials and methods: Plant material was collected in Guinea-Bissau during 2016–2017. Plant identification was confirmed and vouchers deposited at LISC. Leaves were subject to the usual procedures for light and scanning electron microscopy studies [1]. For anatomical studies the plant material was processed with the paraffin micro technique [2]. Extracts were obtained by a sequential extraction of the dry plant powder with n-hexane, CH2Cl2, EtOAc, MeOH and water, filtered, concentrated and stored at −20ºC. Evaluation of the semi quantitative phytochemical profile was carried out thought TLC on silica gel, developed with appropriated solvents. Spots were revealed with proper revelators, according to Wagner and Bladt [3]. The extracts were tested against six Gram-positive bacteria: Staphylococcus aureus (ATCC 6538, 43866, CIP 106706) S. epidermidis (ATCC 12228) and Enterococcus hirae (CIP 5855) and two Gram-negative Pseudomonas aeruginosa (ATCC 9027) and Escherichia coli (ATCC 8739). The minimum inhibitory concentrations (MIC) were determined by the serial broth microdilution method. The MIC values were considered negative when >100 μg/mL. Results: The micromorphological characteristics of both species leaves were carried out and similar outcomes were found: i) polyhedral epidermal cells on the upper and lower leaf surfaces; ii) hypostomatic leaves; iii) internal secretory structures with a lipid nature. The most significant differences were the leaves thickness, thinner in Z. leprieurii and the large internal secretory structures and idioblasts with druse type calcium oxalate crystals, in the parenchyma cells of this same species. The extracts of leaves and roots, with increasing polarities, were prepared and their antibacterial activity against the reference bacteria were evaluated. The extracts with the highest activity were the most apolar Z. leprieurii leaves extracts, which were able to inhibit the growth of E. hirae and all the Staphylococcus strains assayed, including the resistant ones, with MIC between 15–60 µg/mL Discussion and conclusions: These are preliminary results that allow species differentiation and point to the validation of their use in traditional medicine and emphasize the worthwhile of additional studies.

Novel functionalized β-nitrostyrenes: Promising candidates for new antibacterial drugs

The process of searching for new antibacterial agents is more and more challenging due to the increasing drug resistance which has become a major concern in the field of infection management. Our study presents a synthesis and characterization by IR, UV, 1H NMR and 13C NMR spectra of a homogenous series of 1-EWG functionalized 2-aryl-1-nitroethenes which could prove good candidates for the replacement of traditional antibacterial drugs In vitro screening against a panel of the reference strains of bacteria and fungi and their cytotoxicity towards cultured human HepG2 and HaCaT cells was performed. Antimicrobial results indicated that four of the synthesized compounds exhibited a significant antimicrobial activity against all tested reference bacteria and fungi belonging to yeasts with a specific and strong activity towards B. subtilis ATCC 6633. Two of these compounds had no detectable cytotoxicity towards the cultured human cell lines, making them promising candidates for new antibacterial drugs.

Genetic Relatedness among Escherichia coli Isolated from Clinical Samples

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to determine genotypic diversity among clinical strains of E. coli. Test isolates were identified by biochemical, culture-based and molecular tests. Partial sequence of 16s rDNA was determined by Polymerase Chain Reaction using universal primers. The sequences were used as input in Basic Local Alignment Search Tool (BLAST) to reconfirm the identity of the isolates. Sequences were edited in Chromas and aligned in Bioedit. Afterwards, sequences were fed into Mega 5 and a dendogram was constructed. We used three sequences deposited in GenBank for comparison with our test sequences. It was found that two of our sequences showed similarity to the reference sequences. One of the isolates was similar to a Uropathogenic and a commensal E. coli. The other isolate showed similarity to a UPEC strain. It is possible that both of these isolates were commensal bacteria that led to opportunistic infection in the patients. The rest of the nine strains were different from the reference sequences. These isolates may be opportunistic pathogens that have undergone mutation events leading to sufficiently different rDNA sequences from the reference bacteria. Or they may also be pathogenic strains that caused infection in patients. This study indicated that clinical isolates of E. coli show variation in terms of their rDNA sequences. In order to study their phylogeny, other supporting tools such as investigation for phylogenetic markers, RAPD, ARDRA, ERIC-PCR, ribotyping, etc. may be used to study variation among isolates to a more significant extent.
 Bangladesh J Microbiol, Volume 34 Number 2 December 2017, pp 97-101

Diagnosis of Bacterial Pathogens in the Urine of Urinary-Tract-Infection Patients Using Surface-Enhanced Raman Spectroscopy.

(1) Background: surface-enhanced Raman spectroscopy (SERS) is a novel method for bacteria identification. However, reported applications of SERS in clinical diagnosis are limited. In this study, we used cylindrical SERS chips to detect urine pathogens in urinary tract infection (UTI) patients. (2) Methods: Urine samples were retrieved from 108 UTI patients. A 10 mL urine sample was sent to conventional bacterial culture as a reference. Another 10 mL urine sample was loaded on a SERS chip for bacteria identification and antibiotic susceptibility. We concentrated the urine specimen if the intensity of the Raman spectrum required enhancement. The resulting Raman spectrum was analyzed by a recognition software to compare with spectrum-form reference bacteria and was further confirmed by principal component analysis (PCA). (3) Results: There were 97 samples with single bacteria species identified by conventional urine culture and, among them, 93 can be successfully identified by using SERS without sample concentration. There were four samples that needed concentration for bacteria identification. Antibiotic susceptibility can also be found by SERS. There were seven mixed flora infections found by conventional culture, which can only be identified by the PCA method. (4) Conclusions: SERS can be used in the diagnosis of urinary tract infection with the aid of the recognition software and PCA.

Inhibitory Effect of Quercus ilex Wood Ash on the Growth of Pathogenic Microorganisms

This study was conducted to determine the antimicrobial (antibacterial and antifungal) activity of green oak (Quercus ilex) wood ash from Beni Snous region (Tlemcen, Algeria). For the evaluation of antimicrobial potency, we tested the effect of different ash concentrations on reference bacteria (Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterobacter cloacae, and Proteus mirabilis) and reference yeasts (Candida albicans ATCC 10231 and Candida albicans 444IP). The antibacterial activity test results show that Gram-positive bacteria have a higher sensitivity than Gram-negative bacteria. Concerning the antifungal activity, inhibition of yeast growth was found even at low ash concentrations (5%). The results of this preliminary investigation thus revealed that wood ash from green oak exerts a remarkable antimicrobial activity.

Synthesis, Spectroscopic Characterization, and In Vitro Antibacterial Evaluation of Novel Functionalized Sulfamidocarbonyloxyphosphonates.

Several new sulfamidocarbonyloxyphosphonates were prepared in two steps, namely carbamoylation and sulfamoylation, by using chlorosulfonyl isocyanate (CSI), α-hydroxyphosphonates, and various amino derivatives and related (primary or secondary amines, β-amino esters, and oxazolidin-2-ones). All structures were confirmed by 1H, 13C, and 31P NMR spectroscopy, IR spectroscopy, and mass spectroscopy, as well as elemental analysis. Eight compounds were evaluated for their in vitro antibacterial activity against four reference bacteria including Gram-positive Staphylococcus aureus (ATCC 25923), and Gram-negative Escherichia coli (ATCC 25922), Klebsiella pneumonia (ATCC 700603), Pseudomonas aeruginosa (ATCC 27853), in addition to three clinical strains of each studied bacterial species. Compounds 1a–7a and 1b showed significant antibacterial activity compared to sulfamethoxazole/trimethoprim, the reference drug used in this study.

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans

The aim of the study was to investigate the metabolism of non-digestible oligo- and polysaccharides by fecal microbiota, using isothermal microcalorimetry. The five tested substrates were raffinose, melibiose, a mixture of oligo- and polysaccharides produced from raffinose by levansucrase, levan synthesized from raffinose, and levan from timothy grass. Two inocula were comprised of pooled fecal samples from overweight or normal-weight children, from healthy adult volunteers and a pure culture of Bacteroides thetaiotaomicron as a reference bacterium for colon microbiota. The growth was analyzed based on the heat evolution curves, and the production of organic acids and gases. Taxonomic profiles of the microbiota were assessed by 16S rDNA sequencing.Raffinose and melibiose promoted the growth of bifidobacteria in all fecal pools. Several pool-specific substrate-related responses to raffinose and melibiose were revealed. Lactate-producing bacteria (Streptococcus and Enterococcus) became enriched in the pool of overweight children resulting in lactic acid as the major fermentation product on short saccharides. Acetic and butyric acids were prevalent at fermentation in the normal-weight pool coinciding with the enrichment of Catenibacterium. In the adult pool, the specific promotion of Bacteroides and Lachnospiraceae by levans was disclosed. In the fecal pool of normal-weight children, levans stimulated the growth of Senegalimassilia and Lachnoclostridium and this particular pool also showed the highest maximum heat production rate at levan fermentation. Levans and raffinose-derived oligosaccharides, but not raffinose and melibiose were completely fermented by a pure culture of Bacteroides thetaiotaomicron.The main conclusion from the study is that fecal microbiota of normal and overweight children have different compositions and they respond in specific manners to non-digestible oligo- and polysaccharides: raffinose, melibiose, raffinose-derived oligosaccharides and levans. The potential of the tested saccharides to support a healthy balance of colon microbiota requires further studies.

N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization

Methylobacterium strains can use one-carbon compounds, such as methanol, for methylotrophic growth. In addition to methanol, a few strains also utilize dichloromethane, a major industrial chlorinated solvent pollutant. With a fully assembled and annotated genome, M. extorquens DM4 is the reference bacterium for aerobic dichloromethane degradation. The doublet N-terminal oriented proteomics (dN-TOP) strategy was applied to further improve its genome annotation and a differential proteomics approach was performed to compare M. extorquens DM4 grown either with methanol or dichloromethane as the sole source of carbon and energy. These approaches led to experimental confirmation of 259 hypothetical proteins, correction of 78 erroneous predicted start codons, discovery of 39 new proteins and annotation of 66 signal peptides, including essential enzymes involved in methylotrophic growth. SignificanceDichloromethane (methylene chloride, CH2Cl2, DCM) is one of the most widely used industrial halogenated solvents and a potential carcinogen. Microbial rehabilitation of worldwide-contaminated sites involves DCM breakdown by bacteria that are able to grow using this pollutant as their sole carbon and energy source. The most-studied methylotrophic DCM degrader is Methylobacterium extorquens strain DM4. Proteomic studies of the Methylobacterium genus have been performed previously, but genome-wide investigation of N-termini of expressed proteins has not yet been performed. Differential quantitative proteomic analysis also opens new research perspectives to better monitor and understand bacterial growth with DCM.

Antibiotic resistance characteristic and genes analysis of a marine water sourced Klebsiella pneumoniae

Objective: Both antibiotic resistant bacteria (ARBs) and antibiotic resistant genes (ARGs) are considered as one of the most dangerous environmental pollutants in the 21st century by the WHO. This study aims to understand the ARGs of Klebsiella pneumoniae (K. pneumoniae) with multiple drug resistance bacterium from the marine water collected from a beach at Sanya Bay, and to explore the antibiotic resistance mechanism of the K. pneumoniae, providing a basis for exploring the transfer of drug resistance genes of beach, and preventing and controlling the health risk of entertainment population. Methods: The sample of marine water were collected and screened by Mcconkey plate. The drug sensitive test was detected by Merieux VITEK2, The DNA was extracted and one strain of 16srDNA was sequenced and identified as K. pneumoniae. Whole-genome resequencing was performed using Illumina HiseqXten platform, and the obtained sequences were compared with NCBI blasting. The reference bacterium were multi-resistant K. pneumoniae HS11286. Plasmids were extracted and the resistant genes were identified. Results: The ARGs encoding protein was 117/4801 (identity > 40%) and the carrying rate was 2.436 9%. The identity of following ARGs of OKPB, sul1, rpoB, ef-tu, phoP, sul2, AAC(6’)-ib-cr, QnrB, floR, aadA16 were more than 99%. The strain showed resistance to ampicillin, ticacillin/clavulanic acid and chloramphenicol, and was intermediate to ampicillin/sulbactam, compound sulfamethoxazole, ciprofloxacin, minocycline. Preliminary positioning showed that Qnrs, sul1, tetA, cat, QacE were carried on plasmid. Conclusion: The multiple drug resistant bacteria strain has a variety of different resistant phenotypes, some ARGs can be easily spread by plasmid. It probably will bring exposure risk to people for entertainment. Sensibility of some antibiotics were on the brink of resistance, It is necessary to tracking corresponding antibiotics pollution and strengthening monitoring of ARBs and mobile resistant elements of bacteria.

Volatile Oils of Nepeta tenuifolia (Jing Jie) as an Alternative Medicine against Multidrug-Resistant Pathogenic Microbes.

Essential oils from the dried spikes of Nepeta tenuifolia (Benth) are obtained by steam distillation. Pulegone was identified as the main component in the spikes of N. tenuifolia through analysis, with greater than 85% purity obtained in this study. The essential oils are extremely active against all Gram-positive and some Gram-negative reference bacteria, particularly Salmonella enterica, Citrobacter freundii, and Escherichia coli. The minimum inhibitory concentration was found to be between 0.08 and 0.78% (against S. enterica), 0.39 and 0.78% (against C. freundii), and 0.097 and 0.39% (against E. coli), whereas the minimum bactericidal concentration varied in range from 0.097% to 1.04%. In general, the essential oils show a strong inhibitory action against all tested reference strains and clinical isolates. However, the antibacterial activity of EOs against both Pseudomonas aeruginosa reference strains and clinical isolates was relatively lower than other Gram-negative pathogens. The essential oils of N. tenuifolia also displayed bactericidal activities (MBC/MIC < 4) in this study. These findings reflect the bactericidal activity of the essential oils against a wide range of multidrug-resistant clinical pathogens in an in vitro study. In addition, we propose the fragmentation pathways of pulegone and its derivatives by LC-ESI-MS/MS in this study.

FusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.

Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.