Using Illumina’s BaseSpace dashboard to handle the data, the isolate’s genome was analyzed and compared to an existing database to search for similar sequences of DNA. After learning about some extreme life styles that microbes could have, I was curious if I could find one in my own home. Considering the limit of species identified to this date, there is the potential that this microbe could be a new species. Microscopically, it is a cocci-shaped bacterium measuring 0.5 to 0.7 μmin diameter (Fig. Micrococcus halobius 3. The genus Planococcus was originally proposed by Migula  to accommodate Gram-stain-positive, aerobic and motile cocci of the family Planococcaceae in the phylum Firmicutes. Image 6 To 20 Classification Results by Taxonomic Level from BaseSpace. They may be domed, shining, mucoid-type colonies with radial striations or may appear smooth with entire edges. BLAST suggested Genus and species with associated query cover percentage and identity percentage. Genus planococcus. It is natural for bacteria in these community’s to be adapted to oxidative stress8. My isolate was not just aerobic but a facultative aerobe, which is inconsistent with two articles that state the genus is strictly aerobic5. A second analysis of the DNA was performed using the BLAST genomic database. The sample was stained using the provided protocol, gram-positives and negative controls were compared to the isolate to determine its gram-state (lab 4). mucilaginsosus. penetrates wall of decolorized gram - cells gram negative appear red. Micrococcus roseus 8. There are some qualities that are consistent between my sample and P. donghaensis, they are both, gram-positive, aerobic, coccus and oxidase positive 1. The gram-stain was repeated three times before a successful stain was accomplished. Craters may form around the colonies on some media. The percent of contigs read needed to be greater than 80% and the percent of those reads that needed to agree upon a classification to trust that classification to the genus level was 80% and to the genus level was 60%. A series of patented solutions C1-4 were added following the protocol to purify and remove inhibitors and proteins until all that remained was a pure solution of DNA. The gram stain was performed to assess the thickness of the peptidoglycan wall. but poor growth less than 1% or more than 15% NaCl
The isolates holotolerance was not tested but the similar cellular membrane composition and habitat conditions indicate that this genus is likely correct. Micrococcus luteus is a Gram-positive, to Gram-variable, nonmotile, coccus, tetrad-arranging, pigmented, saprotrophic bacterium that belongs to the family Micrococcaceae. The Prokka Genome Annotation app identified 64 tRNAs, 0 rRNAs, 1 CRISPR, and 3739 CDS. The SPAdes Genome Assembler provided the overall result of the genomes assembly. ein neues System der Bakterien. Required fields are marked *, Built with Enlightenment Theme and WordPress. Kraken Metagenomics app was only able to classify 2.67% of reads, and of those reads only 17% of those reads identified the microbe as Lysinibacillus sphaericus. compare with Marinococcus, Migula W. (1894) Uber
Image 5: Krona Classification Chart from BaseSpace displays the large portion of unclassified reads. An orange pigmented bacterium, S1, was isolated from a cyanobacterial mat sample collected in the vicinity of Schirmacher Oasis, Maitri, the Indian station, inAntarctica. coccus-shaped colony-forming While under the microscope it was observed that the cells could be aligned linearly, in pairs or quads but not in a longer strep chain. Pigments may be produced by some species; ranging from cream, pale yellow to light pink. Jeong-Hwa C, Wan-Taek I, Qing-Mei L, Jae-Soo Y, Jae-Ho S, Sung-Keun R, Dong-Hyun R. Reddy G, Prakash J, Vairamani M, Prabhakar S, Matsumoto G. Shivaji S. Tuncer, I. The isolate failed to grow on EMB or MAC plates, considering that both plates are selective for gram negative, these results confirm the results of the gram positive test: Image 4. Halotolerant will grow in nutrient agar
The analysis of the DNA with BaseSpace revealed unreliable data. Taxonomic studies were performed on a novel carotenoid-producing strain, designated AJ003T, isolated from faeces of Antarctic penguins. I sampled two places, a piece of wood from my fire wood stack (which is exposed to the extreme cold temperatures of Alaskan winters) and the ashes from my stove. 1 micrometer diameter, coccus, cells divide linearly. They are prokaryotic in nature meaning they are the earliest forms of the cell without a nucleus.. Considering that the API 20e test is designed for enteric gram negative microbes these results are confirmation that the microbe is gram-positive. Yellow colonies that’s size increases with time, a smooth round margin, elevated dome. One such mechanism is the use of Catalase to catalyze the transformation of the reactive species hydrogen peroxide into O2. Bacteria Bacillus megaterium, Enterobacter gergoviae and Planococcus citreus can describe histidin as histamin. EMB is selective for gam-negative bacterium, if the microbe is gram negative and can ferment the sugars present then the plate experiences a color change. Planococcus citri, commonly known as the citrus mealybug, is a species of mealybugs native to Asia.It has been introduced to the rest of the world, including Europe, the Americas, and Oceania, as an agricultural pest.It is associated with citrus, but it attacks a … Both sources have specific classification percentages that confer certainty. The sample was stained using the provided protocol, gram-positives and negative controls were compared to the isolate to determine its gram-state (lab 4). The antibiotics tested were Amikacin, Cefazolin, Cefoperazone, Gentamicin, Piperacillin, Tobramycin, Trimethoprim and Vancomycin. The species classification with the highest query cover is poorly documented in literature. This app provided sample information such as the total number of reads that were used for classification and the percent of reads that were classified. The final app Prokka Genome Annotation assigned gene regions that likely code for either tRNAs, rRNAs, CRISPRs and coding genes (CDs) and the abundance of them. Stomatococcus
While the cells were prepped in slides some characteristics were observed with the microscope, such as cell alignment shape and length. A gram-positive (gram-variable), beaded organism with delicate branching was recovered from the sputum of a 20-year-old patient with leukemia. Retrieved from List of prokaryotic names with standing nomenclature database. The Microbes transfer to the agar slant was successful: Image 1, and was successfully re-cultured from the slant when necessary. The catalase test produced bubbles and the oxidase test produced a blue color change on the strip indicating that the microbe was positive in both tests. the following information is not yet verified. The microbe was susceptible to all eight antibiotics tested. Phylogenetic and signature nucleotides analyses revealed that strain Y42T belongs to the genus Planococcus. A suspension of the microbe in broth was tested simultaneously in all 21 of the tests included in the API 20E test strip. The APP provides an extensive list of regions that were specifically identified as the above elements. Bacterium Planococcus halocryophilus that is able to thrive at minus 15 degrees Celsius offers clues about microbial life on both Mars and Enceladus. In general, the colonies appear as white, smooth colonies. masc. BLAST provided many species level classifications with similar query cover and percent identity. Stomatococcus
However these similarities are not enough to convince me that they are the same species. The genotypic test results for this microbe were vague, the results of BaseSpace had a low number of reads that could be classified and of those reads there was little consensus. Further analysis of the genomic information was necessary. The gram-stain was repeated three times before a successful stain was accomplished. The DNA was then sent to the UAF’s DNA Core Lab sequenced using the Illumina MiSeq DNA sequencer which utilized the next-generation sequencing methodology. The bacterium was found to be aerobic and Gram-stain positive. Antibiotic resistance of bacterial isolates from sediments of eastern Mediterranean Sea in association with environmental parameters. Isolated from sub-artic decomposing wood. Planococcus. To conclusively Identify the taxonomy of this isolated microbe, it would be advisable to repeat DNA isolation and genomic analysis that was preformed in this project, and to additionally perform other genotypic analyses like, DNA-DNA hybridization and 16s rRNA analysis and fatty acid identity. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. Based on multiple Head These communities emit extracellular enzymes to decay the wood, this results in an environment with high acidity and enzymes that are producing free radical oxygen species7. Abstract. This extremophile is characterized as both halophilic and psychrophilic, thriving in an environment of high salinity as well as an extremely low tem… (2016). The susceptibility of the isolate to 8 different antibiotics was tested using the Kirby-Bauer Method agar and the disk diffusion test per the protocol of Lab 9. A novel Gram-stain-positive, coccoid or short rod-shaped, moderate-orange-pigmented, halotolerant and psychrotolerant bacterium, designated strain SCU63 T, was isolated from a saline soil sample in China, and characterized by a polyphasic taxonomic approach. Micrococcaceae are not a coherent group. The isolate was found to be susceptible to all antibiotics tested with the disk diffusion test. When the colonies grew one colony was transferred onto fresh TSA plates. Of the few documents that relate to Planococcus donhaensis, there is one that notes the origin of the sample, the South Korean Sea. Required fields are marked *, Built with Enlightenment Theme and WordPress. See-Too, W. S., Ee, R., Lim, Y.-L., Convey, P., Pearce, D. A., Yin, W.-F., & Chan, K.-G. (2017). BaseSpace has many apps that provide different information about the genomic data. While under the microscope it was observed that the cells could be aligned linearly, in pairs or quads but not in a longer strep chain. One representative of each from gram stain positive and gram stain negative bacteria was selected to further assess the MIC. The cells were measured to be 1 micrometer in diameter. Inst. The TSA medium provided a suitable environment for a variety of bacteria and a few molds. Some of the notable differences between Micrococcus and Staphylococcus are: Planococcus sp. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that … Planomicrobium okeanokoites was reclassified from Flavobacterium okeanokoites. To thrive in this community it would be helpful to have mechanisms to process radical oxygen species. Once identified, I could then research the species and compare it’s physiology and genomic data to current literature to confirm the taxonomic assignment. (2008). Colony morphology on the TSA agar revealed a yellow colony that’s size increased with time, a smooth round margin and the colony was an elevated domed. Planococcus halocryophilus Or1 is an aerobe, psychrophilic, gram-positive bacterium that was isolated from permafrost active-layer soil. A hallmark of the genus Planococcus is that they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4. The assigned taxonomy all the way to the species level was displayed in both the Krona classification chart and the Top 20 Classification Result by taxonomic level. BaseSpace’s SPAdes Gemone Assembler analyzed 128 contigs over 1000 base pairs (bp) long, a total length of over 3.7 million bp, the longest contig was 196 thousand bp, and the GC% was 44.4%. Arb. Melissococcus
nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Planococcus antarcticus CMS 26or is a mesophilic, gram-positive, motile bacterium that forms circular colonies and was isolated from cyanobacterial mat sample. Euzeby, J. P., & Parte, A. C. (2017, April 1). The specimen produced orange, glabrous, waxy colonies on Middlebrook's agar that showed partial acid-fast staining with the modified Kinyoun stain. The sample was collected from a dry piece of wood. An obligate aerobe, M. luteus is found in soil, dust, water and air, and as part of the normal microbiota of the mammalian skin. 1a). to the Genus. ValÃ¡Å¡kovÃ¡ V., de Boer W., Gunnewiek P. J. K., PospÃÅ¡ek M., Baldrian P. (2009). Gram Positive Bacteria. Sarcina, Catalase positive:Deinococcus,Marinococcus
Cell lysis was accomplished through adding sodium dodecyl sulfate (SDS), which is a surfactant that chemically weakened the cell walls, and the use of PowerBeads and the centrifuge to mechanically break the cell walls. Tests were performed on the isolate by obtaining cells from either the TSA plates or from the slant agar. Micrococcus kristinae 4. These results reveal that the cells contained both cytochrome c-oxidase and the catalase enzyme respectively. Alignment shape and length likely have similar mechanisms for surviving temperatures around -45 degrees Celsius in winters... Antarticus thrived in an Antarctica, my sample would likely have similar mechanisms for surviving temperatures around degrees. Planococcus halocryophilus Or1 is an aerobe, psychrophilic, gram-positive bacterium that was isolated from stools of Antarctic penguins is! The fungus, de Boer W., Gunnewiek P. J. K., PospÃÅ¡ek M., Baldrian P. ( )! 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