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Granulicatella adiacens

Lilian Sool-Esol MicrobeWiki Prof. Angela Hahn 16 December, 2013

                   Granulicatella adiacens

In 1961, Frenkel and Hirsch were the first to describe the Granulicatella bacteria genus as a nutritionally variant streptococcus (NVS) (Christensen et al., 2001). The Granulicatella genus is known to be a normal flora of the upper respiratory, gastrointestinal and urogenital tracts of humans. Normal flora is a microorganism that normally resides at a given site and under normal circumstances does not cause disease. Granulicatella adiacens whose genus name was formerly known as Abiotrophia because the bacteria genus is believed to be nutritionally deficient and even when samples are strained in the laboratory, a supplemented media with rich agar is used to culture samples of these bacteria. The word “Abiotrophia” means life nutrition deficiency (Bizzarro et al., 2011). Granulicatella adiacens, a species of this genus is found in the oral cavity, intestine and genitourinary tract of humans (Vandana et al., 2010). Infections in these areas lead to endovascular, central nervous system, ocular, oral bone and joint and urogenital tracts infections. It is also associated with diseases like endocarditis, bacteremia and septic arthritis (Bizzarro et al., 2011). The G. adiacens has a normal commensal relationship with most the human mucosal surfaces which allows it to affect those areas of the human body and although it has the possibilities of infecting all these areas, it rarely causes diseases (Gardenier et al., 2011).

G. adiacens bacteria are gram positive with streptococcus morphology. Sometimes it appears as cocci, coccobacilli or rod shaped cells. The cellular morphology depends on growth conditions. Their sizes range from 0.4 to 0.6 microns. G+C content of G. adiacens bacteria DNA is around 36.6 – 37.4 mol%. This bacteria is also known to be monophyletic. It is a facultative anaerobe which can survive in both aerobic and anaerobic environments with a temperature of about thirty seven (37) degrees Celsius (Collins MD et al., 2000). A Granulicatella genus bacterium is a fastidious microorganism; meaning, it has a complex nutritional requirement and can only grow in a specific diet of nutrients. Most fastidious microorganisms require blood or hemoglobin, amino acids and some vitamins to grow. These types of microorganisms are known to cause infections in humans and other organisms that have blood or hemoglobin. This makes its identification difficult because a unique culture media is required for the growth of isolates of G. adiacens. The type of media used to culture these fastidious bacteria in the laboratory is known as BD Chocolate Agar. The chocolate agar is supplemented with hemoglobin (blood) and yeast concentrate. There are two common types of chocolate agars used; the BD Chocolate Agar (GC II Agar with IsoVitalex) and the BD Chocolate Agar (Blood Agar No. 2 Base). The GC II Agar with IsoVitalex base nutrients contains blood; casein; selected meat peptones as a source of nitrogen; phosphates, which helps to regulate pH; and corn starch which helps to neutralize toxic fatty acids that may be present in the agar. The Blood Agar base is sometimes used as a substitute. The Blood base agar contains blood, liver digest, Proteose peptone and yeast extract which serves as a source of nitrogen and other vitamins for the growth of the microbe that needs to be cultured. However, Granulicatella adiacens is plated on the BD Chocolate Agar (GC II Agar with IsoVitalex) to reveal growth of nutritionally variant streptococci. Most laboratories use either horse or sheep blood as a source of hemoglobin. A way of identifying these bacteria is that when plated on a BD Chocolate Agar (Blood Agar No. 2 Base), it shows a very slow growth compare to BD Chocolate Agar (GC II Agar with IsoVitalex) (Perkins et al., 2003 & “Instructions for Use – Ready-To-Use Plated Media." 2011).

Scientists find this bacteria genus difficult to identify because it also appears as a gram negative bacteria sometimes and it has a range of form of shapes in which it appears which makes it uneasy to diagnose patience suffering with infections or diseases from this microbe. On normal circumstance, clinical diseases caused by G. adiacens are identified based on their phenotypic character by 16S rRNA gene sequencing. (Collins MD et al., 2000).

Taxonomy: Bacteria, Firmicutes, Bacilli, Lacotabacillales, Carnobacteriaceae, Granulicatella, Granulicatella adiacens. BIOS: Taxonomy (http://www.gbif.org/species/119570537)

Below are links to pictures of G. adiacens culture growth of isolated colonies after two days of streaking each plate. We notice that there is a slower growth on the Blood base Agar. (Please Click on the links to view pictures)

Sample of G. adiacens growth in BD Chocolate Agar (GC II Agar with IsoVitalex) (http://hampc168.blog.163.com/blog/static/1697976200701910515808/)

BD Chocolate Agar (Blood Agar No. 2 Base) showing slow rate of G. adiacens growth (http://hampc168.blog.163.com/blog/static/1697976200701910515808/)

A case of an infected endocarditis (http://upload.wikimedia.org/wikipedia/commons/7/73/Haemophilus_parainfluenzae_Endocarditis_PHIL_851_lores.jpg)





References:

Christensen JJ, Facklam RR. 2001. Granulicatella and Abiotrophia species from Human Clinical Specimens. J. Clin. Microbiol. 39(10): 3520-3523 http://jcm.asm.org/content/39/10/3520.full

Bizzarro MJ, Callan DA, Farrel PA, Dembry L-M, Gallagher PG. 2011. Granulicatella Adiacens and Early-Onset Sepsis in Neonate. Emrg Infect Dis 17(10): 1971-1973 http://jmm.sgmjournals.org/content/61/Pt_6/755.full

Vandana KE, Mukhopadhyay C, Rau NR, Ajith V, Rajath P. 2010. Native Valve Endocarditis and Femoral Emolism due to Granulicatella Adiacens: A Rare Case Report. Braz J Infect Dis 14(6) http://dx.doi.org/10.1590/S1413-86702010000600015

Perkins A, Osorio S, Serrano O, Del Ray MC, Sarria C, Domingo D, Lopez-Brea M. 2003. A Case of Endocarditis due to Granulicatella adiacens. Clinical Microbiology and Infection 9(6): 576-577 http://onlinelibrary.wiley.com/doi/10.1046/j.1469-0691.2003.00646.x/full

Gardenier JC , Hranjec T, Sawyer RG, Bonatti H. 2011. Granulicatella Adiacens Bacteremia in an Elderly Trauma Patient. Surg Infect (Larchmt) 12(3): 251-3 http://www.ncbi.nlm.nih.gov/pubmed/21524203

Collins MD, Lawson PA. 2000. The Genus Abiotrophia (Kawamura et al.) is not Monophyletic: Proposal of Granulicatella gen. nov., Granulicatella adiacens comb. nov., Granulicatella Elegans comb. nov. and Granulicatella Balaenopterae comb. nov. International Journal of Systematic and Evolutionary Microbiology. 50:365-369 http://ijs.sgmjournals.org/content/50/1/365.full.pdf

Collins MD, Lawson PA. 2000: Granulicatella adiacens (Bouvet et al., 1989) BIOS:Baceteriology Insight Orienting System in the Catalogue of Life in The Catalogue of Life Partnership: Catalogue of Life. http://www.gbif.org/species/119570537

“Instructions for Use – Ready-To-Use Plated Media." Bd.com. Becton Dickinson, Sept. 2011. Web. 12 Dec. 2013. http://www.bd.com/resource.aspx?IDX=8994

Oenococcus kitaharae

Samantha Hosch

December 16,2013

Microbiology

Dr. Hahn


Lineage

• Kingdom- Bacteria

• Division- firmicutes

• Class- Bacilli

• Family- Lactobacillus

• Genius- Oenococcus

• Species- Kitaharae


No picture available

Basic

Oenococcus kitaharae is a bacteria microbe that is gram positive. It can make acid from maltose. It also helps with D-glucose fermentation. Oenococcus kitaharae is made up 42 percent guanine cytosine bonds according too Lactobacillus florum sp. nov., a fructophilic species isolated from flowers by Endo, Futagawa-Endo, Sakamoto, Kitahara, and Dicks.

It does not have the mutSL gene, which fixes some mutations and is believed by scenticsts to have not had this gene for a long time. According to the article Role of Hypermutability in the evolution of the genus Oenococcus kitaharae has a rate of 1/13 protein mutation and that most of it its mutations are random ones without any real meaning.

Oenococcus kitaharae can be grown in the lab and cultured but it does take it own time to do so, for to five days longer than most similar bacteria.

O. kitaharae can not break down anything made of organic acids but is lactic acid loving bacteria microbe. This explains why it was in shochu residue and not wine.


History

Oenococcus kitaharae was discovered in 2006. It is currently the second member of only a two-member genus. Its genus partner is Oenococcus onei, which has been renamed.


Information

The Oenococcus genus is known for their ability to be involved with fermentation for this reason and the fact that it is present in wine the genus is studied often. However onei and kitaharae have different living environments but can have crossovers, this has been shown through PCR reactions from wine samples.
Some sources show that O. kitaharae can cause fermentation in some of O. onei environments well other show that it does just want it needs to stay a live.
No matter what there is no disagreement on the fact the fact that they can be found together. 

Oenococcus kitaharae is much able to survive in difficult environment. Apparently, It has more DNA in the Oenococcus kitaharae. The extra pieces of DNA resemble that of a virus according an article titled Comparative Genomics of Oenococcus kitaharae. It is found in Japan in several things including flowers.


Sources

Borneman, A. R., McCarthy, J. M., Chambers, P. J., & Bartowsky, E. J. (2012). Functional divergence in the genus oenococcus as predicted by genome sequencing of the newly- described species, oenococcus kitaharae. PLoS One, 7(1), e29626. doi: 10.137

Endo, A., Futagawa-Endo, Y., Sakamoto, M., Kitahara, M., & Dicks, D. M. T. (2010). Lactobacillus florum sp. nov., a fructophilic species isolated from flowers. International Journal of Systematic and Evolutionary Microbiology, 60, 2478–2482. doi: 10.1099/ijs.0.019067-0

Endo, A., & Okada, S. (2006). Oenococcus kitaharae sp. nov., a non-acidophilic and non- malolactic-fermenting oenococcus isolated from a composting distilled shochu residue. International Journal of Systematic and Evolutionary Microbiology, (56), 2345-2348. doi: 10.1099/ijs.0.64288-0 Gonzalez-Arenzana, L., Lopez, R., Santamaría, P., & Lopez-Alfaro, I. (2013). Dynamics of lactic acid bacteria populations in rioja wines by pcr-dgge comparison with culture-dependent methods . Appl Microbial Biotechnol, (97), 6931-6941. doi: 10.1007/s00253-013-4974-y Marcobal, A. M., Sela , D. A., Wolf, Y. I., Makarova, K. S., & Mills, D. A. (2008). Role of hypermutability in the evolution of the genus oenococcus. Journal Of Bacteriology, 190(2), 564-570. doi: 10.1128/JB.01457-07

Michlmayr, H., Schümann, C., Wurbs, P., arreira Braz da Silva, N. M., Rogl, V., Kulbe, K. D., & del Hierro, A. M. (2010). A β-glucosidase from oenococcus oeni atcc baa-1163 with potential for aroma release in wine: Cloning and expression in e. coli. World J Microbiol Biotechnol, 26(7), 1281-1289. doi: 10.1007/s11274-009-0299-5

Pseudomonas fluorescens

Pseudomonas fluorescens Microbe Wiki

Classification Kingdom: Bacteria Phylum: Proteobacteria Class: Gammaproteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: P. fluorescens

Habitat Information: The soil organism was collected in the front yard of an Austin, TX home on January 26, 2018. Soil was a little moist Picked up on a day that had 83% humidity Zero rainfall Calm wind 51℉ air temperature.

Pseudomonas fluorescens is mainly found in plants, soil, and water surfaces.

Description and Significance: Pseudomonas fluorescens are gram-negative bacilli shaped bacteria. It grows best in temperatures that are 25-30℃. Certain strains of Pseudomonas fluorescens have been found to help stop plant disease by protecting the root and seed from fungal infection[REF]. Other strains contribute to plant growth. Due to P. fluorescens having different flagella it has different strains which cause it to be in different environments including the bloodstream. [REF]

Cell Structure, Metabolism, and Life Cycle: Cell Structure

P. fluorescens are small-to-medium sized Gram-negative, rod-shaped bacilli. They are often found with multiple flagella in a lophotrichous arrangement. These many flagella, along with its ability to generate a biofilm, make P. fluorescens a great colonizer on various different surfaces and in different hosts and able to easily adapt to its environment[REF]. One particularly prominent role of this biofilm is to serve as a protective agents to plants against parasitic fungi. Less is known about how P. fluorescens’ structure allows it to bind to mammalian cells, however it has been known to adhere to red blood cells in humans, which is one reason it is believed that, when found as a pathogenic agent in humans (which is very rare), it is almost always in the bloodstream. This organism follows a similar life cycle pattern found with other biofilm generating species, as discussed in “Life Cycle” [REF].

Metabolism P. fluorescens is well-known for having an extensive variety of metabolic capabilities, which allows it to live in so many different environments such as on the surfaces of plants, in soil, in the rhizosphere, and even in the bloodstream of humans and other animals[REF].

P. fluorescens is a obligate aerobe, however, it has a unique ability to use nitrate (NO3) instead of atmospheric oxygen (O2) as its final electron acceptor in the Electron Transport Chain [REF]

A unique metabolic feature of P. fluorescens is that it secretes a fluorescent pigment, pyoverdine, which imparts fluorescent properties to the organism under UV light, which is what led to its name. Pyoverdine is a high-affinity iron-chelating molecule that is essential for the organism’s acquisition of iron from the environment and used for bacterial growth. [REF] See more in “Physiology” for biochemical tests conducted in class.

Life Cycle P. fluorescens follows a typical “biofilm” life cycle in that generally proceeds as follows: Attachment: planktonic cells adhere to a surface and become sessile Growth: cells exude exoenzymes and proteins to create a protective biofilm in which to flourish and grow. Detachment: individual cells or clusters of cells will detach from the biofilm in order to move and colonize new surfaces/hosts

Genome Structure P. fluorescens’ genome is composed of a single, circular chromosome with a median length of 6,300,000 base pairs. Guanine and Cytosine make up 60.3% of the nucleotides found in its DNA (its G/C ratio). [REF]



Physiology and Pathogenesis: Physiology

Gelatin Hydrolysis: Negative DNA Hydrolysis: Negative Lipid Hydrolysis: Positive Phenol Red Broth: No fermentation Starch Hydrolysis: Negative Casein Hydrolysis: Positive Methyl Red: Negative Voges-Proskauer: Negative Citrate: Positive SIM: Negative Nitrate Reduction: Positive Urea Hydrolysis: Negative Triple Sugar Iron: No fermentation, does not reduce sulfur Decarboxylation: Arginine is positive, lysine and ornithine are negative Phenylalanine: Negative Oxidase: Positive EMB Agar: Positive HE Agar: Negative Catalase: Positive Blood Agar: Positive Mannitol Salts Agar: Negative PEA Agar: Negative

Bile Esculin: Negative 6.5% Salt Tolerance: Negative Kirby-Bauer Antimicrobial Susceptibility Test for disinfectants: Kirby-Bauer Antimicrobial Susceptibility Tests for antibiotics: sensitive to several antibiotics [REF]

Pathophysiology Although P. fluorescens itself is largely considered non-pathogenic, it contains a number of metabolic abilities to allow it to thrive in mammalian hosts, including, but not limited to: Production of bioactive secondary metabolites P. fluorescens produces a long list of secondary metabolites that allow it to successfully compete with other, similar organisms, such as phenazine, hydrogen cyanide, 2,4-diacetylphloroglucinol (DAPG), rhizoxin, and pyoluteorin. [REF] Production of biofilms As aforementioned, one of the key structural components of P. fluorescens is its ability to produce biofilms. Type III secretions Type III secretion systems (T3SSs) are molecular, needle-like complexes that inject cellular products into the cells of its host/surface, known as effectors. The most common T3SS in P. fluorescens is the Hrp1 family[REF]. These “hypersensitive response” secretion systems trigger a hypersensitive response in resistant plants, but leads to infection in vulnerable plants. Less is known about T3SSs involved in this organism’s infections in mammals, but different strains have been found to adhere to human Red Blood Cells, as well as human glial cells in culture. [REF]

References Ramette A, Moënne-Loccoz Y, Défago G, Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiol Ecol. 2003 May 1; 44(1):35-43. Gibaud M, Martin-Dupont P, Dominguez M, Laurentjoye P, Chassaing B, Leng B. Pseudomonas fluorescens septicemia following transfusion of contaminated blood. Presse Med. 1984 Nov 24; 13(42):2583-4. Scales BS, Dickson RP, LiPuma JJ, Huffnagle GB. 2014. Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. Clin Microbiol Rev 27:927–948. doi:10.1128/CMR.00044-14. Hernández-Salmerón JE, et al. Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270. Stand Genomic Sci 2016 Ghiglione JF, Gourbiere F, Potier P, Philippot L, Lensi R. Role of respiratory nitrate reductase in ability of Pseudomonas fluorescens YT101 to colonize the rhizosphere of maize. Appl Environ Microbiol. 2000;66(9):4012–4016. Doi: 10.1128/AEM.66.9.4012-4016.2000 Hohnadel D, Meyer JM. Specificity of pyoverdine-mediated iron uptake among fluorescent Pseudomonas strains. J Bacteriol. 1988 Oct; 170(10):4865-73. Baum MM, Kainović A, O'Keeffe T, Pandita R, McDonald K, Wu S, Webster P. Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil. BMC Microbiol. 2009 May 21; 9():103 Adebusuyi AA, Foght JM. An alternative physiological role for the EmhABC efflux pump in Pseudomonas fluorescens cLP6a. BMC Microbiol. 2011;11:252. doi: 10.1186/1471-2180-11-252. [Online.] Preston GM, Bertrand N, Rainey PB. Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Mol Microbiol. 2001 Sep; 41(5):999-1014. Chapalain A, Rossignol G, Lesouhaitier O, Merieau A, Gruffaz C, Guerillon J, Meyer JM, Orange N, Feuilloley MG. Comparative study of 7 fluorescent pseudomonad clinical isolates.Can J Microbiol. 2008 Jan; 54(1):19-27.