Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Case report and mini-review: Sarcina ventriculi in the stomach of an 80-year-old female

Sarcina ventriculi, also known as Zymosarcina ventriculi and, incorrectly, as Clostridium ventriculi, is rarely encountered in clinical settings. A patient with a complicated gastrointestinal (GI) history, who was acutely presenting with small-bowel obstruction, was found to be colonized by S. ventriculi. The distinctive morphology of this species, with large Gram-variable cocci (up to 3 µm) arranged in two-by-two cuboid clusters reaching up to 20 µm, was key in identifying this bacterium in a stomach biopsy specimen. Sarcina ventriculi appears to be ubiquitously found in nature, and related bacterial species can cause GI-related disease in various animals. Clinical manifestations in humans are broad and often related to other underlying comorbidities. Isolation of S. ventriculi in the laboratory requires anaerobic culture on select media but its absence from standard MALDI-TOF databases complicates identification. Susceptibility data do not exist, so empiric treatment is the only option for this rare pathogen.

Optimization of production conditions of Mahyaveh, a traditional Iranian fish sauce, with low microbial load

BACKGROUND AND OBJECTIVES

Mahyaveh is a traditional Iranian fish sauce produced by fermentation and hydrolysis. The main production of Mahyaveh has been traditionally and scientific research and industrial measures has not been done on it with the aim to achieve a production with less microbial load. Therefore, the aim of this research was to study the type of fish, salt concentration and fermentation time on the bacterial population of Iranian fish sauce (Mahyaveh).

MATERIALS AND METHODS

For this purpose, the effects of fish type (tuna, anchovy and sardine), salt concentration (15%, 25% and 35%) and fermentation time (30, 75 and 120 days) on the total microbial count, Micrococcus, Enterobacteriaceae and Bacillus were investigated. 15 treatments were designed according to the Box-Behnken Response Surface Methodology.

RESULTS

Simultaneous optimization to achieve the minimum total microbial count, Micrococcus, Enterobacteriaceae and Bacillus in the Mahyaveh sauce was obtained with 99.49% desirability at the time of 103.63 days of fermentation with the third type of fish (Sardine) and at a salt concentration of 29.38%.

CONCLUSION

By optimizing the conditions of producing Mahyaveh sauce, fish sauce can be produced with the least amount of microbial load with more health safety.

Cytotoxic potential of Nephthea sp.-derived actinomycetes supported by metabolomics analysis

Soft corals and associated microorganisms are known to produce leads for anticancer drugs. Keeping this in mind, Nephthea sp.; a Red Sea soft coral was investigated for the first time using the OSMAC approach. Two isolates, Streptomyces sp. UR63 and Micrococcus sp. UR67 were identified. Their extracts revealed the presence of alkaloids, macrolides, quinones, fatty acids and terpenoids. Further comparison through a set of multivariate data analyses revealed their unique chemical profiles. The extracts displayed inhibitory potencies against HepG-2, Caco-2 and MCF-7 tumor cell lines with IC₅₀ values ranging from 11.4 to 38.7 μg/mL when compared with the positive control, doxorubicin. The study not only highlights the cytotoxic potential of soft coral-associated actinomycetes but also shows the advantage of using the OSMAC approach in this regard.

Cliona varians-Derived Actinomycetes as Bioresources of Photoprotection-Related Bioactive End-Products

Sunscreen and sunblock are crucial skincare products to prevent photoaging and photocarcinogenesis through the addition of chemical filters to absorb or block ultraviolet (UV) radiation. However, several sunscreen and sunblock ingredients, mostly UV filters, have been associated with human and environmental safety concerns. Therefore, the exploration and discovery of promising novel sources of efficient and safer compounds with photoprotection-related activities are currently required. Marine invertebrates, particularly their associated microbiota, are promising providers of specialized metabolites with valuable biotechnological applications. Nevertheless, despite Actinobacteria members being a well-known source of bioactive metabolites, their photoprotective potential has been poorly explored so far. Hence, a set of methanolic extracts obtained from Cliona varians-derived actinomycetes was screened regarding their antioxidant and UV-absorbing capacities (i.e., photoprotection-related activities). The active extract-producing strains were identified and classified within genera Streptomyces, Micrococcus, Gordonia, and Promicromonospora. This is the first report of the isolation of these microorganisms from C. varians (an ecologically important Caribbean coral reef-boring sponge). The in vitro cytotoxicity on dermal fibroblasts of oxybenzone and the selected active extracts revealed that oxybenzone exerted a cytotoxic effect, whereas no cytotoxic effect of test extracts was observed. Accordingly, the most active (SPFi > 5, radical scavenging > 50%) and nontoxic (cell viability > 75%) extracts were obtained from Streptomyces strains. Finally, LC-MS-based characterization suggested a broad chemical space within the test strains and agreed with the reported streptomycetes' chemodiversity. The respective metabolite profiling exposed a strain-specific metabolite occurrence, leading to the recognition of potential hits. These findings suggest that marine Streptomyces produce photoprotectants ought to be further explored in skincare applications.

Airborne bacteria in show caves from Southern Spain

This work presents a study on the airborne bacteria recorded in three Andalusian show caves, subjected to different managements. The main differences within the caves were the absence of lighting and phototrophic biofilms in Cueva de Ardales, the periodic maintenance and low occurrence of phototrophic biofilms in Gruta de las Maravillas, and the abundance of phototrophic biofilms in speleothems and walls in Cueva del Tesoro. These factors conditioned the diversity of bacteria in the caves and therefore there are large differences among the CFU m-3, determined using a suction impact collector, equipment widely used in aerobiological studies. The study of the bacterial diversity, inside and outside the caves, indicates that the air is mostly populated by bacteria thriving in the subterranean environment. In addition, the diversity seems to be related with the presence of abundant phototrophic biofilms, but not with the number of visitors received by each cave.

Biogenic Selenium Nanoparticles: A Fine Characterization to Unveil Their Thermodynamic Stability

Among the plethora of available metal(loid) nanomaterials (NMs), those containing selenium are interesting from an applicative perspective, due to their high biocompatibility. Microorganisms capable of coping with toxic Se-oxyanions generate mostly Se nanoparticles (SeNPs), representing an ideal and green alternative over the chemogenic synthesis to obtain thermodynamically stable NMs. However, their structural characterization, in terms of biomolecules and interactions stabilizing the biogenic colloidal solution, is still a black hole that impairs the exploitation of biogenic SeNP full potential. Here, spherical and thermodynamically stable SeNPs were produced by a metal(loid) tolerant Micrococcus sp. Structural characterization obtained by Scanning Electron Microscopy (SEM) revealed that these SeNPs were surrounded by an organic material that contributed the most to their electrosteric stabilization, as indicated by Zeta (ζ) potential measurements. Proteins were strongly adsorbed on the SeNP surface, while lipids, polysaccharides, and nucleic acids more loosely interacted with SeNMs as highlighted by Fourier Transform Infrared Spectroscopy (FTIR) and overall supported by multivariate statistical analysis. Nevertheless, all these contributors were fundamental to maintain SeNPs stable, as, upon washing, the NM-containing extract showed the arising of aggregated SeNPs alongside Se nanorods (SeNRs). Besides, Density Functional Theory (DFT) calculation unveiled how thiol-containing molecules appeared to play a role in SeO₃²⁻ bioreduction, stress oxidative response, and SeNP stabilization.

Group therapy on in utero colonization: seeking common truths and a way forward

The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief that a broad understanding of human development, health, physiology, and disease requires understanding of the microbiome along with the genome and epigenome. We are learning daily of the interdependent relationships between microbiome/microbiota and immune responses, mood, cancer progression, response to therapies, aging, obesity, antibiotic usage, and overusage and much more. The next frontier in microbiome field is understanding when does this influence begin? Does the human microbiome initiate at the time of birth or are developing human fetuses already primed with microbes and their products in utero. In this commentary, we reflect on evidence gathered thus far on this question and identify the unknown common truths. We present a way forward to continue understanding our microbial colleagues and our interwoven fates.

Anthocyanins in Blueberries Grown in Hot Climate Exert Strong Antioxidant Activity and May Be Effective against Urinary Tract Bacteria

Anthocyanins are extensively studied for their health-related properties, including antibacterial activity against urinary tract infections (UTI). Among common fruits, blueberries, with their remarkable antioxidant capacity, are one of the richest sources. Anthocyanin-rich extracts were obtained from four varieties: Snowchaser, Star, Stella Blue and Cristina Blue, grown in the hot climate of Southern Spain. Their total anthocyanins contents (TAC) were determined spectrophotometrically, and the anthocyanin profile by ultra high performance liquid chromatography—tandem mass spectrometer (UHPLC-MS/MS). Their antioxidant activity was assessed by oxygen radical absorbance capacity (ORAC) assay, while antibacterial activity against strains isolated from UTI patients was assessed in vitro, helping to select the varieties with the highest bioactive potential. Star showed the highest TAC and antioxidant activity (1663 ± 159 mg of cyanidin-3-O-glucoside (cy-3-O-glu) equivalents/100 g fresh weight (FW), 6345 ± 601 μmol Trolox equivalents (TE)/100 g FW, respectively), followed by Cristina Blue, Stella Blue and Snowchaser. As far as we know, this is the first time that cyanidin-3-rutinoside has been identified in blueberries. The extracts inhibited all the tested strains, MICs ranging from 0.4 mg/mL (for Stella Blue extract against UTI P. aeruginosa) to 9.5 mg/mL (for all extracts against UTI K. pneumoniae ssp. pneumoniae). This is the first study that assessed in vitro the antibacterial activity of blueberries against Klebsiella pneumoniae, Providencia stuartii and Micrococcus spp. strains isolated from UTI.

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

A pair of geometrically isomeric unsaturated keto fatty acids, (6E,8Z)- and (6E,8E)-5-oxo-6,8-tetradecadienoic acids (1 and 2), were isolated from the culture broth of an actinomycete of the genus Micrococcus, which was associated with a stony coral, Catalaphyllia sp. Their chemical structures were elucidated by spectroscopic analysis including NMR and MS, with special assistance of spin system simulation studies for the assignment of an E geometry at C8 in 2. As metabolites of microbes, compounds 1 and 2 are unprecedented in terms of bearing a 2,4-dienone system. Both 1 and 2 showed antibacterial activity against the plant pathogen Rhizobium radiobacter and the fish pathogen Tenacibaculum maritimum, with a contrasting preference that 1 is more effective to the former strain while 2 is so to the latter. In addition, compounds 1 and 2 displayed agonistic activity against peroxisome proliferator-activated receptors (PPARs) with an isoform specificity towards PPARα and PPARγ.

Deciphering operation of tryptophan-independent pathway in high indole-3-acetic acid (IAA) producing Micrococcus aloeverae DCB-20

Genus Micrococcus is considered a high IAA producer. However, interestingly, there is no report on the tryptophan- independent pathway operation in this genus. Consequently, the present study was undertaken to evaluate high IAA production by Micrococcus aloeverae DCB-20 and generate reasonable evidence for the occurrence of the tryptophan-independent pathway. Strain DCB-20 produced a high quantity of 880.51 µM or 154.3 µg/mL IAA in LB broth supplemented with L-tryptophan. The tryptophan-independent pathway operation was supported by IAA production in Tris-minimal broth (TM broth) medium supplemented with acid hydrolyzed casein hydrolysate (casein acid hydolysate), which lacks tryptophan. The HPLC analysis showed the absence of tryptophan either from exogenous or endogenous sources in TM broth in the presence of casein acid hydrolysate inoculated with M. aloeverae DCB-20. The absence of tryptophan was further confirmed by the appearance of non-pigmented colonies of Chromobacterium violaceum strain TRFM-24 on Tris-minimal agar (TM agar) containing acid-hydrolyzed casein. This is probably the first report on IAA biosynthesis by M. aloeverae DCB-20 employing tryptophan-independent pathway. This simple technique can also be adapted to detect operation of the tryptophan-independent pathway in other bacteria.

Growth-promoting bacteria and arbuscular mycorrhizal fungi differentially benefit tomato and corn depending upon the supplied form of phosphorus

The ability of plants to take up phosphorus (P) from soil depends on root morphology and root exudates release and can be modulated by beneficial soil microbes. These microbes can solubilize P, affect root elongation and branching, and lead to a higher uptake of P and other nutrients. However, coordination of these mechanisms is unclear, especially the mechanism for changing the available form of P. We aimed to dissect the effects of two different beneficial microbial taxa (plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF)) on root morphological traits, plant nutrient content, and growth in tomato and corn fertilized with either Gafsa rock phosphate (RP) or triple superphosphate (TSP), which have contrasting solubility levels. Tomato and corn were grown in pots and inoculated with one of three PGPB species or a mix of two AMF species or were not inoculated. Root traits, botanical fractions, and the contents of various mineral nutrients were measured. TSP stimulated tomato biomass accumulation compared to RP but did not stimulate corn biomass accumulation. PGPB improved the growth of both plant species under RP, with limited differences among the strains, whereas AMF only improved tomato growth under TSP. These differences between microbial systems were explained by a bacterial effect on the total root length but not on the mean root diameter and by the ability of AMF to improve the mineral nutrient content. The effects of PGPB were less dependent on the plant species and on P form than the effects of AMF.These results have implications for the improvement of the early plant growth through the management of beneficial microbes.

Native valve infective endocarditis due to Micrococcus luteus in a non-Hodgkin's lymphoma patient

Micrococcus species are typically considered contaminants from skin and mucous membranes. However, especially in severely immunocompromised patients, a blood culture with Micrococcus could be the cause of a significant infection. We report a 65-year-old female with non-Hodgkin's lymphoma who developed native valve infective endocarditis due to Micrococcus luteus. There is no defined therapeutic regimen for infective endocarditis due to Micrococcus luteus; however, our patient was successfully treated for six weeks with vancomycin and rifampin. To our knowledge, there is only one other case report of native valve endocarditis due to Micrococcus luteus.

Micrococcus aloeverae - A Rare Cause of Peritoneal Dialysis-Related Peritonitis Confirmed by 16S rRNA Gene Sequencing

The number of patients receiving peritoneal dialysis has increased worldwide. Herein, we report the first case to our knowledge of continuous ambulatory peritoneal dialysis (CAPD) peritonitis caused by Micrococcus aloeverae, which was initially reported to be caused by Micrococcus luteus in the dialysate culture report but later identified by 16S ribosomal ribonucleic acid (rRNA) gene sequencing as M. aloeverae. A 59-year-old woman visited the emergency room due to abdominal pain. She was hospitalized with CAPD peritonitis. The patient initially responded to empirical antibiotic treatment comprising intraperitoneal cefazolin (15 mg/kg/day) and ceftazidime (1 g/day); however, the leukocyte count of dialysate effluent increased again. M. luteus was isolated four times from peritoneal dialysate cultures. We treated the patient with intraperitoneal administration of vancomycin (2 g loading, followed by 1 g every 7 days) but needed to switch from CAPD to temporary hemodialysis. We analyzed the 16S rRNA sequence to confirm the exact causative organism, and the results revealed that the organism was M. aloeverae. Because M. aloeverae and M. luteus have sequence similarity, 16S rRNA sequencing is a useful method to distingush them.

SELfies and CELLfies: Whole Genome Sequencing and Annotation of Five Antibiotic Resistant Bacteria Isolated from the Surfaces of Smartphones, An Inquiry Based Laboratory Exercise in a Genomics Undergraduate Course at the Rochester Institute of Technology

Are touchscreen devices a public health risk for the transmission of pathogenic bacteria, especially those that are resistant to antibiotics? To investigate this, we embarked on a project aimed at isolating and identifying bacteria that are resistant to antibiotics from the screens of smartphones. Touchscreen devices have become ubiquitous in society, and it is important to evaluate the potential risks they pose towards public health, especially as it pertains to the harboring and transmission of pathogenic bacteria that are resistant to antibiotics. Sixteen bacteria were initially isolated of which five were unique (four Staphylococcus species and one Micrococcus species). The genomes of the five unique isolates were subsequently sequenced and annotated. The genomes were analyzed using in silico tools to predict the synthesis of antibiotics and secondary metabolites using the antibiotics and Secondary Metabolite Analysis SHell (antiSMASH) tool in addition to the presence of gene clusters that denote resistance to antibiotics using the Resistance Gene Identifier (RGI) tool. In vivo analysis was also done to assess resistance/susceptibility to four antibiotics that are commonly used in a research laboratory setting. The data presented in this manuscript is the result of a semester-long inquiry based laboratory exercise in the genomics course (BIOL340) in the Thomas H. Gosnell School of Life Sciences/College of Science at the Rochester Institute of Technology.

Variances in cellular sedimentation behavior as an effective enrichment method of hydrocarbon-overproducing Micrococcus luteus strains

BACKGROUND

Aliphatic hydrocarbons of microbial origin are highly interesting candidate biofuels because these molecules are identical or very similar to the main components of petroleum-based gasoline and diesel fuels. The high-GC Gram-positive bacterium Micrococcus luteus is capable of naturally synthesizing long-chain, iso- and anteiso-branched alkenes which are formed via the head-to-head condensation of fatty acid thioesters by a dedicated enzyme system. The present study describes the relation we observed between olefin production and cell buoyancy in Micrococcus luteus and the use of this phenotype to simply and efficiently separate cells from a mixture based on their hydrocarbon content.

METHODS

We generated M. luteus mutants producing different amounts of olefins and used them in mixing and sedimentation experiments, olefin content analysis by GC-MS and in equilibrium centrifugation in Percoll gradients.

RESULTS

We found well-detectable differences in the buoyant densities of the examined strains, which correlated with the amounts of hydrocarbons produced by the cells. We also demonstrate how our observations can be used to simply and efficiently fractionate cells based on their hydrocarbon content.

CONCLUSIONS

In summary, we show that cultures of M. luteus cells sediment at distinct rates depending on the amounts of alkenes produced. Our results indicate that buoyant cell density is the primary cause for the observed differences in sedimentation behaviour. The simple separation strategy described here can be a valuable tool in various mutagenesis and enrichment protocols, aimed at generating and isolating strains with increased olefin productivity.

Umbilical Sepsis Caused by Multidrug Resistant Strain of Kocuria kristinae in a New Born: A Case Report

Kocuria species were placed previously under the genus Micrococcus, are skin and oropharynx commensals in mammals, including man. A rare bacteria, Kocuria kristinae isolated from a new born with umbilical sepsis. Identification and antibiotic susceptibility was done by Vitek 2 compact system (Biomerieux). The isolate was sensitive to higher antibiotics like vancomycin, teicoplanin and linezolid. As this new pathogen resembles coagulase negative staphylococcus, it should not be misidentified.

Microbiological burden in air culture at various units of a tertiary care government hospital in Nepal

BACKGROUND

The environmental matrices (water, air, and surfaces) play a vital role as reservoirs of Legionella spp. and Pseudomonas aeruginosa (Pseudomonas spp.). Hence, hospital environment control procedures are effective measures for reducing nosocomial infections.

AIMS

This study was carried out to explore the profiles of microorganisms in air culture at various wards/units of a tertiary care hospital in Nepal.

METHODS

A descriptive cross-sectional study was carried out at various wards/units of a tertiary care hospital in Nepal between January and September 2015 to explore the microbiological burden in inanimate objects. Each week one ward or unit was selected for the study. Bed, tap, the entire room, trolley, computer, phone, rack handles, table, chair, door, stethoscope, oxygen mask, gown, cupboard handles, and wash basins were selected for air culture testing. Ten different wards/units and 77 locations/pieces of equipment were selected for air culture by employing a simple random sampling technique. Information about the organisms was entered into the Statistical Package for the Social Sciences (SPSS) Version 22 (IBM: Armonk, NY) and descriptive analyses were carried out.

RESULTS

Staphylococcus aureus (S. aureus), Micrococcus, coagulase negative staphylococcus (CONS), Bacillus, Pseudomonas aeruginosa, yeast, and Acinetobacter were the most commonly detected organisms. In the postoperative ward, S. aureus was the most frequently detected microorganism. Micrococcus was detected in four out of 10 locations. In the x-ray unit, S. aureus was detected in three out of four locations.

CONCLUSION

S. aureus, Micrococcus, CONS, Bacillus, Pseudomonas, yeast, and Acinetobacter were the most common organisms detected.

Oral Microflora: A Comparative Study in HIV and Normal Patients

The study was designed to compare the oral microbiota in normal and HIV-infected individuals. The study tries to establish a significant shift in oral microflora in HIV-infected patients. Antibiotic sensitivity testing was performed to establish any rise in resistance against the antibiotics. It was a two and half year prospective study conducted in a tertiary care centre. The study group consisted of eighty subjects divided into two groups of control and HIV. The age range for this group was 9-75 years. The mean age in this group was 39.7 years. The male:female ratio was 2.75:1. Tuberculosis was the most common opportunistic infection in patients with HIV infection. The most common commensal micro organism isolated was the Viridans streptococci in 60% followed by Streptococcus pneumoniae in 23.33%. HIV Group: The most common commensal micro organism isolated was the Viridans streptococci in 42%; this was followed by the Micrococci spp. in 22% cases. S. pneumoniae was isolated in 6% of cases. The colony count for Viridans streptococci showed a heavy growth in 55.56% of cases in controls whereas the same in HIV group was 62.5%. Micrococcus spp. was isolated from 11 subjects in HIV group while it was not isolated from the controls. 50% subjects in the HIV group showed a heavy growth of Klebsiella spp. whereas controls showed only moderate and scanty growth. In patients with CD4+ T cell count less than 50 cells/μl we found a heavy colonization of the oral cavity with Micrococcus spp., Acinetobacter and Klebsiella spp. Viridans streptococcus was not isolated in any of the patients with CD4+ T cell count less than 50 cells/μl. As CD4+ T cells counts improved to 51-100 cells/μl Viridans streptococcus colonies returned and 37.5% patients showed a heavy growth. Micrococcus spp. colonies were isolated till the CD4+ T cells improved up to 300 cells/μl. At counts > 300 cells/μl the oral microbiota became comparable to that of the controls. Many of the opportunistic infections in HIV are caused by commensal bacteria which are otherwise harmless in a normal individual. Our study is unique in that such a study of the oral commensals in HIV patients has never been reported. We found an increased colonization of the oral cavity by Micrococcus spp. which is a normal commensal of the skin.

DBS 2

Soil and sediment samples obtained from Orange MR dye contaminated habitat were screened for heterotrophic bacterial population. The heterotrophic bacterial density of dye-contaminated soil was 2.14 × 10(6) CFU/g. The generic composition of heterotrophic bacterial population was primarily composed of 10% of Proteus sp., 15% Aeromonas sp., 20% Bacillus sp., 25% Pseudomonas sp. and 30% Micrococcus sp. The bacterial strain that decolorized the azo dye Orange MR up to 900 ppm was identified as Micrococcus sp. The optimum inoculum load, pH and temperature were found to be 5%, 6 and 35°C, respectively. The rate of decolorization was assessed using spectrophotometer at 530 nm and the percentage of decolorization was ascertained. The autochthonous bacterial isolate was able to utilize the dye as both nitrogen and carbon source.