Oropharyngeal microbiome of an HIV-positive patient.

Studies on understanding the human microbiome continue to grow rapidly; nonetheless, reports on alterations in the microbiome post HIV infection are limited. Human microbiome is an aggregate of bacteria, fungi, viruses and archaea that have co-evolved with humans. These microbes have important roles in immune modulation, vitamin synthesis, metabolism etc. The human pharyngeal microbiome, which resides in the junction between digestive and respiratory tracts, might have a key role in the prevention of respiratory tract infections, akin to the actions of the intestinal microbiome against enteric infections. The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. HIV infection is associated with alterations in the respiratory microbiome. The aim of this study was to use next-generation sequencing to determine the composition of the oropharyngeal microbiome in a HIV-positive individual. The bacterial composition was determined by illumina sequencing using MiSeq of partial 16S rRNA genes (V3-V4). A total of 3, 57,926 reads were analyzed. Overall, the genera Proteus, Enterococcus, Bacteroides, Prevotella and Clostridium were most prevalent bacterial populations in the oropharynx of an HIV positive patient.

Blowing epithelial cell bubbles with GumB: ShlA-family pore-forming toxins induce blebbing and rapid cellular death in corneal epithelial cells.

Medical devices, such as contact lenses, bring bacteria in direct contact with human cells. Consequences of these host-pathogen interactions include the alteration of mammalian cell surface architecture and induction of cellular death that renders tissues more susceptible to infection. Gram-negative bacteria known to induce cellular blebbing by mammalian cells, Pseudomonas and Vibrio species, do so through a type III secretion system-dependent mechanism. This study demonstrates that a subset of bacteria from the Enterobacteriaceae bacterial family induce cellular death and membrane blebs in a variety of cell types via a type V secretion-system dependent mechanism. Here, we report that ShlA-family cytolysins from Proteus mirabilis and Serratia marcescens were required to induce membrane blebbling and cell death. Blebbing and cellular death were blocked by an antioxidant and RIP-1 and MLKL inhibitors, implicating necroptosis in the observed phenotypes. Additional genetic studies determined that an IgaA family stress-response protein, GumB, was necessary to induce blebs. Data supported a model where GumB and shlBA are in a regulatory circuit through the Rcs stress response phosphorelay system required for bleb formation and pathogenesis in an invertebrate model of infection and proliferation in a phagocytic cell line. This study introduces GumB as a regulator of S. marcescens host-pathogen interactions and demonstrates a common type V secretion system-dependent mechanism by which bacteria elicit surface morphological changes on mammalian cells. This type V secretion-system mechanism likely contributes bacterial damage to the corneal epithelial layer, and enables access to deeper parts of the tissue that are more susceptible to infection.

Analysis of CRISPR/Cas system of Proteus and the factors affected the functional mechanism.

BACKGROUND: The Proteus is one of the most common human and animal pathogens. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR/Cas) are inheritable genetic elements found in a variety of archaea and bacteria in the evolution, providing immune function against foreign invasion. OBJECTIVES: To analyze the characteristics and functions of the CRISPR/Cas system in Proteus genomes, as well as the internal and external factors affecting the system. METHODS: CRISPR loci were identified and divided into groups based on the repeat sequence in 96 Proteus strains by identification. Compared the RNA secondary structure and minimum free energy of CRISPR loci through bioinformatics, the evolution of cas genes, and the effects of related elements were also discussed. RESULTS: 85 CRISPR loci were identified and divided into six groups based on the sequence of repeats, and the more stable the secondary structure of RNA, the smaller the minimum free energy, the fewer base mutations in the repeat, the more stable the CRISPR and the more complete the evolution of the system. In addition, Cas1 gene can be a symbol to distinguish species to some extent. Of all the influencing factors, CRISPR/Cas had the greatest impact on plasmids. CONCLUSIONS: This study examined the diversity of CRISPR/Cas system in Proteus and found statistically significant positive/negative correlations between variety factors (the RNA stability, free energy, etc.) and the CRISPR locus, which played a vital role in regulating the CRISPR/Cas system.

Determination of epidemiology and antimicrobial susceptibility of extended spectrum beta lactamase producing uropathogens.

OBJECTIVE: To find the most suitable antibiotic against urinary tract infection caused by Extended Spectrum Beta Lactamase producing uropathogens, and the epidemiology of Extended Spectrum Beta Lactamase producers. METHODS: The cross-sectional study was conducted at Pir Mehr Ali Shah University of Arid Agriculture, Rawalpindi, Pakistan, from July 2014 to July 2015, and comprised urine samples of patients suffering from urinary tract infection which were cultured on Cysteine Lactose Electrolyte Deficient agar medium. Analysis was done on Muller- Hintonagar plates and optical density was set as 0.1 at 530nm. Antimicrobial sensitivity was tested using Kirby-Bauer disc diffusion method. Further confirmation was done through gram staining and biochemical tests. Extended Spectrum Beta Lactamase production was confirmed through phenotypic methods, including phenotypic confirmatory disc diffusion test, double disc synergy test and Epsilometer test. RESULTS: Of the 150 samples, 98(65%) showed growth of a total of 114 pathogenic isolates. Escherichia coli was the commonest organism in 94(82%) samples. Piperacillin Tazocin was the most suitable antimicrobial drug in 88(90%) cases. Overall, 23(20%) isolates were producers of Extended Spectrum Beta Lactamase. CONCLUSION: Piperacillin Tazocin was found to be the drug of choice for patient suffering from urinary tract infection.

Indigo- and indirubin-producing strains of Proteus and Psychrobacter are associated with purple rind defect in a surface-ripened cheese.

The rinds of surface-ripened cheeses have expected aesthetic properties, including distinct colors, that contribute to overall quality and consumer acceptance. Atypical rind pigments are frequently reported in small-scale cheese production, but the causes of these color defects are largely unknown. We provide a potential microbial explanation for a striking purple rind defect in a surface-ripened cheese. A cheese producer in the United States reported to us several batches of a raw-milk washed-rind cheese with a distinctly purple rind. We isolated a Proteus species from samples with purple rind defect, but not from samples with typical rind pigments, suggesting that this strain of Proteus could be causing the defect. When provided tryptophan, a precursor in the indigo and indirubin biosynthesis pathway, the isolated strain of Proteus secreted purple-red pigments. A Psychrobacter species isolated from both purple and normal rinds also secreted purple-red pigments. Using thin-layer chromatography and liquid chromatography-mass spectrometry, we confirmed that these bacteria produced indigo and indirubin from tryptophan just as closely related bacteria make these compounds in purple urine bag syndrome in medical settings. Experimental cheese communities with or without Proteus and Psychrobacter confirmed that these Proteobacteria cause purple pigmentation of cheese rinds. Reports of purple rinds in two other cheeses from Europe and the observation of pigment production by Proteus and Psychrobacter strains isolated from other cheese rinds suggest that purple rind defect has the potential to be widespread in surface-ripened cheeses.

Impact of pH regulation on multicopper oxidase production and swarming motility in the bacterium Proteus hauseri ZMd44.

Proteus hauseri ZMd44, a biodecolorizing bacterium, has been known to produce electricity and multicopper oxidase (Mco-laccase) under copper induction. However, optimization and regulation of production have not been explored. This study is the first attempt to evaluate several parameters on biomass and Mco-laccase production of P. hauseri ZMd44. Through orthogonal experiments with Taguchi's L9, it was found that P. hauseri ZMd44 was sensitive to pH value. The cells grew relatively quickly at pH 7, thus the biomass and Mco-laccase production reached 1.66 g/L and 1043.6 U/L, respectively. Higher pH values also influenced the swarming motility, which is an important characteristic of P. hauseri ZMd44 that affects urinary tract infection. The swarming circle and the diameter of the swarm, represented by the motility velocity, were found to be more controlled after 24 h of growth at pH 6. The swarming ability of P. hauseri was completely inhibited by the addition of 3 mM copper or zinc ions. Therefore, the Mco-laccase and swarming motility could be controlled by regulating pH and ion content.

Kinetic study of Reactive Black 5 degradation by Fe2+/S2O82- process via interactive model-based response surface methodology.

This study aimed to kinetically discover optimal conditions on characteristics of Reactive Black 5 decolorization/degradation via ferrous (Fe2+)-activated potassium persulfate (PS). Monod-like kinetics and interactive model-based response surface methodology (RSM) were applied to fitting and predict optimize treatment. Biodegradability of the intermediates was also tested by shaking culture with two species (Proteus hauseri ZMd44 and Shewanella sp. WLP72). Results showed that the optimal degradation efficiency was predicted (through RSM) as pH 3.72, (PS) = 0.39 mM, and (Fe2+) = 0.29 mM. The transformation products (dl-4-hydroxymandelic acid, benzoic acid, benzene, formic acid, oxalic acid and acetic acid) were less toxic than the original dye solution. According to those results, clean-up of dye pollutants by the Fe2+/S2O82- process is feasible as a pre-processing for the biodegradation, and the predicted optimal conditions are meaningful for further industry utilization.

Novel approach for the ammonium removal by simultaneous heterotrophic nitrification and denitrification using a novel bacterial species co-culture.

Agricultural activities lead excessive emission of ammonia nitrogen in the environment and can profoundly interfere the equilibrium of the natural ecosystems leading to their contamination. Actually, the biological purification of wastewaters is the most adopted technique thanks to its several advantages such as high performance and low energy consumption. For this reason, two novel strains of Alcaligenes sp. S84S3 and Proteus sp. S19 genus were isolated from an activated sludge and applied in the treatment of ammonium and nitrite in aqueous solution. Under the optimum operating conditions of temperature (30 °C), pH (7), carbon substrate (2 g/L of glucose) and duration of incubation time (69 h), the strain Alcaligenes sp. S84S3 could oxidize 65% of the ammonium as high as 272.72 mg-NH4(+)/L. Moreover, during 48 h, the nitrate reduction rate performed by the strain Proteus S19 was about 99 % without production of nitrite intermediate (negligible concentration). Moreover, the coculture of the strains Alcaligenes sp. S84S3 and Proteus sp. S19 could eliminate 65.83% of the ammonium ions without production of toxic forms of nitrogen oxides during a short time of incubation (118 h) at the same operational conditions with providing the aeration in the first treatment phase. The coculture of our isolated strains is assumed to have a good potential for nitrification and denitrification reactions applied in the treatment of wastewater containing ammonium, nitrite and nitrate. As a result, we can consider that the mixed culture is a practical method in the treatment of high-strength ammonium wastewater with reducing of sludge production.

Significance and Roles of Proteus spp. Bacteria in Natural Environments.

Proteus spp. bacteria were first described in 1885 by Gustav Hauser, who had revealed their feature of intensive swarming growth. Currently, the genus is divided into Proteus mirabilis, Proteus vulgaris, Proteus penneri, Proteus hauseri, and three unnamed genomospecies 4, 5, and 6 and consists of 80 O-antigenic serogroups. The bacteria are known to be human opportunistic pathogens, isolated from urine, wounds, and other clinical sources. It is postulated that intestines are a reservoir of these proteolytic organisms. Many wild and domestic animals may be hosts of Proteus spp. bacteria, which are commonly known to play a role of parasites or commensals. However, interesting examples of their symbiotic relationships with higher organisms have also been described. Proteus spp. bacteria present in soil or water habitats are often regarded as indicators of fecal pollution, posing a threat of poisoning when the contaminated water or seafood is consumed. The health risk may also be connected with drug-resistant strains sourcing from intestines. Positive aspects of the bacteria presence in water and soil are connected with exceptional features displayed by autochthonic Proteus spp. strains detected in these environments. These rods acquire various metabolic abilities allowing their adaptation to different environmental conditions, such as high concentrations of heavy metals or toxic substances, which may be exploited as sources of energy and nutrition by the bacteria. The Proteus spp. abilities to tolerate or utilize polluting compounds as well as promote plant growth provide a possibility of employing these microorganisms in bioremediation and environmental protection.

Insights into copper effect on Proteus hauseri through proteomic and metabolic analyses.

This is the first-attempt to use liquid chromatography coupled with tandem mass (LC-MS-MS) in deciphering the effects of copper ion on Proteus hauseri. Total 941 proteins in copper-addition (+Cu) group and 898 proteins in non-copper-addition (-Cu) group were found, which containing 221 and 178 differential proteins in +Cu and -Cu group, respectively. Differential proteins in both groups were defined into 14 groups by their functional classification which transport/membrane function proteins were the major different part between the two groups, which took 19.5% and 7.7%, respectively. The result of BioCyc and KEGG analyses on metabolic pathway indicated that copper could interrupted the pathway of chemotaxis CheY and inhibited the swarming of P. hauseri, which provided a potential in controlling the pathogenicity of this strain.

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium.

In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.

Simultaneous nitrification and denitrification by novel heterotrophs in remediation of fish processing effluent.

Three isolates viz. Lysinibacillus sp. HT13, Alcaligenes sp. HT15 and Proteus sp. HT37 isolated from fish processing effluent and having a C/N ratio of 2, removed 218, 169, and 400 µg cell(-1) day(-1) NH4(+)-N, respectively without subsequent build up of nitrite or nitrate. Ability of the selected isolates in removing NH4(+)-N, NO2(-)-N, and NO3(-)-N was checked in the presence of four commonly reported and tested effluent carbon sources viz. pyruvate, glycerol, methanol, and acetate. Further, when supplemented to fish processing wastewater containing 234 ppm total Kjeldahl's nitrogen, Lysinibacillus sp. HT13, Alcaligenes sp. HT15, and Proteus sp. HT37 could remediate 95.74, 86.17, and 76.6% nitrogen, respectively in 48 h. This is the first report of a Lysinibacillus sp. carrying out aerobically the process of simultaneous nitrification and denitrification. The results demonstrate the potential of the isolates for use in treatment of fish processing effluents and demonstrating the efficient removal of ammonia.

Role of plant growth promoting rhizobacteria in modulating the efficiency of poultry litter composting with rock phosphate and its effect on growth and yield of wheat.

The present study was aimed to evaluate the role of Plant Growth Promoting Rhizobacteria (PGPR) in P solubilisation from rock phosphate through composting with poultry litter, and further to study the effects of prepared enriched composts on growth, yield, and phosphorus uptake of wheat crop. Various phosphorus-enriched composts were prepared from rock phosphate and poultry litter (1:10) with and without inoculation of plant growth promoting rhizobacterias (Pseudomonas sp. and Proteus sp.). Results showed that the rock-phosphate-added poultry litter had higher total phosphorus, available (Mehlic-3 extracted) phosphorus, microbial biomass (carbon and phosphorus), and lower total organic carbon, total nitrogen, and carbon/nitrogen ratio over poultry litter alone. Inoculation of Pseudomonas sp. with rock phosphate-added poultry litter showed maximum increase in available phosphorus (41% of total phosphorus) followed by Proteus sp. inoculation (30% of total phosphorus) over uninoculated treatment (23% of total phosphorus) on the 120th day of composting. Microbial biomass (carbon and phosphorus) increased up to Day 45 and tended to decrease till the 120th day of composting, irrespective of the treatments. However, in pot experiments, wheat seeds receiving inoculation with plant growth promoting rhizobacterias, subsequently treated with rock phosphate-enriched compost proved highly stimulatory to plant height, phosphorus uptake, grain yield, and seed phosphorus content over uninoculated untreated control. The plant growth promoting rhizobacterias inoculation can be a sustainable source releasing phosphorus from low grade rock phosphate through composting and application of rock phosphate-enriched compost can be an alternative to chemical fertilisers for better crop production.

Copper response of Proteus hauseri based on proteomic and genetic expression and cell morphology analyses.

The copper response of Proteus hauseri ZMd44 was determined using one-dimensional (1D) gel electrophoresis coupled with MALDI-TOF-TOF mass spectrometry for a similarity analysis of proteins isolated from P. hauseri ZMd44 cultured in CuSO4-bearing LB medium. Candidate proteins identified as a copper-transporting P-type ATPase (CTPP), phosphoenolpyruvate carboxykinase (PEPCK), flagellin (Fla), and outer membrane proteins (Omps) were the major copper-associated proteins in P. hauseri. In a comparative analysis of subcellular (i.e., periplasmic, intracellular, and inner membranes) and cellular debris, proteomics analysis revealed a distinct differential expression of proteins in P. hauseri with and without copper ion exposure. These findings were consistent with the transcription level dynamics determined using quantitative real-time PCR. Based on a genetic cluster analysis of copper-associated proteins from P. hauseri, Fla and one of the Omps showed greater diversity in their protein sequences compared to those of other Proteus species. Transmission electron microscopy (TEM) and the observed growth on LB agar plates showed that the swarming motility of cells was significantly suppressed and inhibited upon Cu(II) exposure. Thus, copper stress could have important therapeutic significance due to the loss of swarming motility capacity in P. hauseri, which causes urinary tract infections.

2-methylbutanal, a volatile biomarker, for non-invasive surveillance of Proteus.

Pathogen detection needs a paradigm shift from time-consuming conventional microbiological and biochemical tests to much simpler identification methods with higher sensitivity and specificity. In this regard, a simple detection method for frequently isolated nosocomial uropathogen, Proteus spp., was developed using the characteristic volatile 2-methylbutanal released in Luria Bertani broth. The instant reaction of the compound with 5-dimethylaminonaphthalene-1-sulfonylhydrazine (DNSH) has been adapted to develop a sensitive fluorescence assay named "ProteAl" (Prote, "Proteus" & Al, "Aldehyde"). The assay was performed by direct addition of the fluorescence reagent to the culture after 7 h of growth. The distinct green fluorescence by Proteus (other organisms show orange fluorescence) served as the simplest and quicker identification test available for Proteus. In the laboratory, it exhibited 100% specificity and 100% sensitivity during testing of 95 strains including standard and known clinical isolates representing frequently encountered uropathogens.

Decolorization of textile azo dye and Congo red by an isolated strain of the dissimilatory manganese-reducing bacterium Shewanella xiamenensis BC01.

Shewanella xiamenensis BC01 (SXM) was isolated from sediment collected off Xiamen, China and was identified based on the phylogenetic tree of 16S rRNA sequences and the gyrB gene. This strain showed high activity in the decolorization of textile azo dyes, especially methyl orange, reactive red 198, and recalcitrant dye Congo red, decolorizing at rates of 96.2, 93.0, and 87.5%, respectively. SXM had the best performance for the specific decolorization rate (SDR) of azo dyes compared to Proteus hauseri ZMd44 and Aeromonas hydrophila NIU01 strains and had an SDR similar to Shewanella oneidensis MR-1 in Congo red decolorization. Luria-Bertani medium was the optimal culture medium for SXM, as it reached a density of 4.69 g-DCW L(-1) at 16 h. A mediator (manganese) significantly enhanced the biodegradation and flocculation of Congo red. Further analysis with UV-VIS, Fourier Transform Infrared spectroscopy, and Gas chromatography-mass spectrometry demonstrated that Congo red was cleaved at the azo bond, producing 4,4'-diamino-1,1'-biphenyl and 1,2'-diamino naphthalene 4-sulfonic acid. Finally, SEM results revealed that nanowires exist between the bacteria, indicating that SXM degradation of the azo dyes was coupled with electron transfer through the nanowires. The purpose of this work is to explore the utilization of a novel, dissimilatory manganese-reducing bacterium in the treatment of wastewater containing azo dyes.

Comparative evaluations on bio-treatment of hexavalent chromate by resting cells of Pseudochrobactrum sp. and Proteus sp. in wastewater.

Two marine bacterial strains, B5 and H24, were isolated from long-term Cr(VI) contaminated seawater and identified as Pseudochrobactrum and Proteus, respectively, based on 16S rRNA gene sequence analyses. Both strains were examined for their tolerance to Cr(VI) and other metal salts and their abilities to reduce Cr(VI) to trivalent chromium [Cr(III)]. Growing cells of Pseudochrobactrum sp. B5 and Proteus sp. H24 could tolerate Cr(VI) at a concentration of 2000 and 1500 mg/l and completely reduce 1000 mg/l Cr(VI) in LB medium within 96 and 144 h, respectively. Resting cells of the two strains were able to reduce 200mg/l Cr(VI) in Tris-HCl buffer within 16 and 24h, respectively. Furthermore, resting cells of both strains were able to reduce Cr(VI) in industrial wastewaters three times consecutively. Overall, this study provides evidence of the potential for application of chromate-reducing bacteria to direct Cr(VI) decontamination of industrial effluents.

Deciphering mediating characteristics of decolorized intermediates for reductive decolorization and bioelectricity generation.

As decolorized intermediates could play a role of electron-shuttling mediator to enhance the performance of dye decolorization and bioelectricity generation, this study selected model compounds with auxochromes (e.g., benzene-1,2-diol, 1,2-diaminobenzene) to explore how chemical structure(s) affected color removal and power producing capabilities in microbial fuel cells (MFCs). According to cyclic voltammetry, respiratory testing and MFC data, promising electron-shuttling capabilities of aforementioned compounds were revealed using Proteus hauseri ZMd44, Aeromonas sp. C78, Acinetobacter johnsonii NIUx72 bearing MFCs. These findings clearly indicated that chemical structure(s) of decolorized mediators directly affected characteristics of simultaneous reductive decolorization and bioelectricity generation in MFCs, suggesting feasible operation strategy of MFCs for industrial applications.

Deciphering simultaneous bioelectricity generation and dye decolorization using Proteus hauseri.

This first-attempt study disclosed how and why electron-shuttling mediators were capable to stimulate bioelectricity-generating capabilities of dye-bearing microbial fuel cells (MFCs) using Proteus hauseri. Due to significant biotoxicity of 4-aminophenol (4AP) and the absence of electron-mediating potential of 3AP, only 2AP among all isomers could work as an exogenous mediator to stimulate bioelectricity generation of P. hauseri. Dye toxicity to cells on anodic biofilm in MFCs apparently affected the performance of simultaneous bioelectricity production and color removal (SBP&CR) in MFCs. Plus, dose-response analysis upon toxicity potency of reactive blue 160 revealed that cells on anodic biofilm in MFCs had a higher tolerance to reactive blue 160 than suspended cells. Apparently, augmentation of electron mediator(s) with low toxicity was a feasible means to facilitate bioelectricity-generating capability of SBP&CR.

Understanding interactive characteristics of bioelectricity generation and reductive decolorization using Proteus hauseri.

This first-attempt study quantitatively explored interactive characteristics of bioelectricity generation and dye decolorization in air-cathode single-chamber microbial fuel cells (MFCs) using indigenous Proteus hauseri ZMd44. After approx. 15 cycles (30 days) acclimatization in dye-bearing cultures, P. hauseri could express its stable capability of simultaneous bioelectricity generation and color removal (SBP&CR) in MFCs. Evidently, appropriate acclimation strategy for formation of the electrochemically active anodic biofilm played a crucial role to enhance the performance of SBP&CR in MFCs. Gradually increased supplementations of C.I. reactive blue 160 resulted in progressively decreased decay rate of bioelectricity generation. That is, a dye decolorized in a faster rate would result in a lower capability for bioelectricity generation and vice versa. In addition, a reduced dye with less toxicity potency (e.g., 2-aminophenol) might work as a redox mediator of electron transport to anodic biofilm for bioelectricity generation in MFCs.