What usual first step in the identification of a bacterial species is like a litmus test in that the results are identified by colors (blue/purple for positive and pink/red for negative)?
"argue that the Archaea and Eukaryotes evolved from gram-positive bacteria. The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. The ""Gram stain"", developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the ""gram-positive"" cell wall stain purple, while the thin ""gram-negative"" cell wall appears pink. By combining morphology and Gram-staining,"
"as Giemsa stain or crystal violet allows a microscopist to describe its size, shape, internal and external components and its associations with other cells. The response of bacteria to different staining procedures is used in the taxonomic classification of microbes as well. Two methods, the Gram stain and the acid-fast stain, are the standard approaches used to classify bacteria and to diagnosis of disease. The Gram stain identifies the bacterial groups Firmicutes and Actinobacteria, both of which contain many significant human pathogens. The acid-fast staining procedure identifies the Actinobacterial genera ""Mycobacterium"" and ""Nocardia"". Biochemical tests used in the identification of"
"or enzyme-based tests. A Gram stain is first performed to guide the way, which should show typical Gram-positive bacteria, cocci, in clusters. Second, the isolate is cultured on mannitol salt agar, which is a selective medium with 7–9% NaCl that allows ""S. aureus"" to grow, producing yellow-colored colonies as a result of mannitol fermentation and subsequent drop in the medium's pH. Furthermore, for differentiation on the species level, catalase (positive for all ""Staphylococcus"" species), coagulase (fibrin clot formation, positive for ""S. aureus""), DNAse (zone of clearance on DNase agar), lipase (a yellow color and rancid odor smell), and phosphatase (a"
"most bacteria can be classified as belonging to one of four groups (gram-positive cocci, gram-positive bacilli, gram-negative cocci and gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or ""Nocardia"", which show acid-fastness on Ziehl–Neelsen or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum"
"staining has been suggested to be as effective a diagnostic tool as PCR in one primary research report regarding gonococcal urethritis. Gram stains are performed on body fluid or biopsy when infection is suspected. Gram stains yield results much more quickly than culturing, and is especially important when infection would make an important difference in the patient's treatment and prognosis; examples are cerebrospinal fluid for meningitis and synovial fluid for septic arthritis. Gram-positive bacteria have a thick mesh-like cell wall made of peptidoglycan (50–90% of cell envelope), and as a result are stained purple by crystal violet, whereas gram-negative bacteria"
"hemin synthesis indicates that the organism is likely ""Haemophilus"". The aminopeptidase test analyzes bacteria for the production of the enzyme L-alanine-aminopeptidase, an enzyme found in many gram-negative bacteria. Adding L-Alanine-4-nitroanilide hydrochloride to a bacterial culture works as an indicator, changing to a yellow color in the presence of L-alanine-aminopeptidase. An analytical profile index is a fast identification system based on biochemical incubation tests. Usually, this test is used to quickly diagnose clinically relevant bacteria by allowing physicians to run about 20 tests at one time. Antibiotic disks are used to test the ability for an antibiotic to inhibit growth of"
"the specific target protein. This reduces background in the final product of the western blot, leading to clearer results, and eliminates false positives. During the detection process the membrane is ""probed"" for the protein of interest with a modified antibody which is linked to a reporter enzyme; when exposed to an appropriate substrate, this enzyme drives a colorimetric reaction and produces a color. For a variety of reasons, this traditionally takes place in a two-step process, although there are now one-step detection methods available for certain applications. The primary antibodies are generated when a host species or immune cell culture"
"broth, through the sides of the tube. The development of stable red color in the surface of the medium indicates sufficient acid production to lower the pH to 4.4 and constitute a positive test. Since other organism may produce lesser quantities of acid from the test substrate, an intermediate orange color between yellow and red may develop. This does not indicate positive test. Positive and negative controls should be run after preparation of each lot of medium. Positive control: ""Escherichia coli"" Negative control: ""Klebsiella"" It is used to determine the ability of some organisms to produce a neutral end product,"
"days. Positive : Growth on the medium even without colour change will be considered as positive. A colour change in the medium would be observed if the test organism produces acid or alkali during its growth. The usual colour change observed is from green (neutral) to blue (alkaline). Negative : No growth observed. Citrate test The citrate test detects the ability of an organism to use citrate as the sole source of carbon and energy. Bacteria are inoculated on a medium containing sodium citrate and a pH indicator such as bromothymol blue. The medium also contains inorganic ammonium salts, which"
"Gram stain Gram stain or Gram staining, also called Gram's method, is a method of staining used to distinguish and classify bacterial species into two large groups (gram-positive and gram-negative). The name comes from the Danish bacteriologist Hans Christian Gram, who developed the technique. Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in the cell wall of Gram-positive bacteria. Gram-negative cells also contain peptidoglycan, but a very small layer of it that is dissolved when the alcohol is added. This is why the cell loses its initial color"
"its peptidoglycan. The decolorization step is critical and must be timed correctly; the crystal violet stain is removed from both gram-positive and negative cells if the decolorizing agent is left on too long (a matter of seconds). After decolorization, the gram-positive cell remains purple and the gram-negative cell loses its purple color. Counterstain, which is usually positively charged safranin or basic fuchsine, is applied last to give decolorized gram-negative bacteria a pink or red color. Gram-positive bacteria generally have a single membrane (""monoderm"") surrounded by a thick peptidoglycan. This rule is followed by two phyla: ""Firmicutes"" (except for the classes"
"tests on bacteria, results of an indole test are indicated by a change in color following a reaction with an added reagent. Pure bacterial culture must be grown in sterile tryptophan or peptone broth for 24–48 hours before performing the test. Following incubation, five drops of Kovac's reagent (isoamyl alcohol, para-Dimethylaminobenzaldehyde, concentrated hydrochloric acid) are added to the culture broth. A positive result is shown by the presence of a red or red-violet color in the surface alcohol layer of the broth. A negative result appears yellow. A variable result can also occur, showing an orange color as a result."
"a suspected bacterial infection despite lack of a specific bacterial diagnosis. Definitive diagnosis of the species of bacteria often occurs through culture of blood, sputum, or urine, and can be delayed by 24 to 72 hours. Antibiotics are generally given ""after"" the culture specimen has been taken from the patient in order to preserve the bacteria in the specimen and ensure accurate diagnosis. Alternatively, some species may be identified through a urine or stool test. Clinicians often use a step-wise approach to determining appropriate empiric therapy. First, the potential diagnoses are established (for example, lobar pneumonia) and any predisposing risk"
"growing (Auramine-rhodamine stain for mycobacteria) or difficult to grow (such as Legionella pneumophila species) and where the test result would alter standard management and empirical therapy. Biochemical testing of bacteria involves a set of agars in vials to separate motile from non-motile bacteria. In 1970 a miniaturized version was developed, called the analytical profile index. Successful identification via e.g. genome sequencing and genomics depends on pure cultures. While the most rapid method to identify bacteria is by sequencing their 16S rRNA gene, which has been PCR-amplified beforehand, this does method not require isolation. Since most bacteria cannot be grown with"
"culture the bacteria. This can help in the diagnosis. Once a culture is established, there are two possible ways to get an antibiogram: Once the MIC is calculated, it can be compared to known values for a given bacterium and antibiotic: e.g. a MIC > 0,06 µg/ml may be interpreted as a penicillin-resistant ""Streptococcus pneumoniae"". Such information may be useful to the clinician, who can change the empirical treatment, to a more custom-tailored treatment that is directed only at the causative bacterium. Often clinical specimens are sent to the clinical laboratory for culture and sensitivity (C&S), which is culture and"
"cannot identify bacteria to the species level, and for most medical conditions, it should not be used as the sole method of bacterial identification. In clinical microbiology laboratories, it is used in combination with other traditional and molecular techniques to identify bacteria. Some organisms are gram-variable (meaning they may stain either negative or positive); some are not stained with either dye used in the Gram technique and are not seen. In a modern environmental or molecular microbiology lab, most identification is done using genetic sequences and other molecular techniques, which are far more specific and informative than differential staining. Gram"
"turns pink when it reacts with alkaline byproducts generated by the bacteria when it grows. Alternatively, oxidation-fermentation polymyxin-bacitracin-lactose (OFPBL) agar can be used. OFPBL contains polymyxin (which kills most Gram-negative bacteria, including ""Pseudomonas aeruginosa"") and bacitracin (which kills most Gram-positive bacteria and ""Neisseria"" species). It also contains lactose, and organisms such as BCC that do not ferment lactose turn the pH indicator yellow, which helps to distinguish it from other organisms that may grow on OFPBL agar, such as ""Candida"" species, ""Pseudomonas fluorescens"", and ""Stenotrophomonas"" species. Treatment typically includes multiple antibiotics and may include ceftazidime, doxycycline, piperacillin, meropenem, chloramphenicol, and"
"color change to red can occur without it. Procedure: First, add the alpha-naphthol; then, add the potassium hydroxide. A reversal in the order of the reagents being added may result in a weak-positive or false-negative reaction. VP is one of the four tests of the IMViC series, which tests for evidence of an enteric bacterium. The other three tests include: the indole test [I], the methyl red test [M], and the citrate test [C]. VP positive organisms include ""Enterobacter"", ""Klebsiella"", ""Serratia marcescens"", ""Hafnia alvei"", ""Vibrio cholera"" biotype eltor"", and ""Vibrio alginolyticus"". VP negative organisms include ""Citrobacter"" sp., ""Shigella"", ""Yersinia"", ""Edwardsiella"","
"publication he remarked, ""I have therefore published the method, although I am aware that as yet it is very defective and imperfect; but it is hoped that also in the hands of other investigators it will turn out to be useful."" A Gram stain is made using a primary stain of crystal violet and a counterstain of safranin. Bacteria that turn purple when stained are called 'Gram-positive', while those that turn red when counterstained are called 'Gram-negative'. Gram's initial work concerned the study of red blood cells in men. He was among the first to recognise that macrocytes were characteristic"
"(yellow, orange, red, brown, and black), ""Fusarium"" sp., ""Rhodotorula"" sp., and ""Scopulariopsis brevicaulis"". Protist species used include ""Euglena gracilis"" (photosynthetic, green) and ""Physarum polycephalum"" (yellow-green). A technique called ""bacteriography"" involves selectively killing certain areas of a bacterial culture with radiation, in order to produce artistic patterns. After incubation, the culture is sealed with acrylic. Alexander Fleming, the man most commonly credited with the discovery of penicillin, was known for creating germ paintings. The biochemist Roger Tsien won the 2008 Nobel prize for chemistry for his contributions to knowledge of green fluorescent protein (GFP). A researcher in his laboratory, Nathan Shaner,"
"body fluids, or tissues, but serological methods may be the only tests available in many settings. Positive blood culture yield ranges between 40% and 70% and is less commonly positive for ""B. abortus"" than ""B. melitensis"" or ""B. suis"". Identification of specific antibodies against bacterial lipopolysaccharide and other antigens can be detected by the standard agglutination test (SAT), rose Bengal, 2-mercaptoethanol (2-ME), antihuman globulin (Coombs’) and indirect enzymelinked immunosorbent assay (ELISA). SAT is the most commonly used serology in endemic areas. An agglutination titre greater than 1:160 is considered significant in nonendemic areas and greater than 1:320 in endemic areas."
"shock. However, this test is not considered reliable in adults. This is known as the CRT or blanch test. The fingernail bed is briefly depressed to turn the nail-bed white. When the pressure is released, the normal pink colour should be restored within a second or two. Delayed return to pink color can be an indicator of certain shock states such as hypovolemia. Nail growth record can show the history of recent health and physiological imbalances, and has been used as a diagnostic tool since ancient times. Deep, horizontally transverse grooves known as ""Beau's lines"" may form across the nails"
"bacteria, that classify bacteria into gram-positive bacteria and gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species. Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C gram-positive bacteria, respectively) have the"
"and not the ones used for venipuncture, the vials are sent to the clinical pathology microbiology department. Here the bottles are entered into a blood culture machine, which incubates the specimens at body temperature. The blood culture instrument reports positive blood cultures (cultures with bacteria present, thus indicating the patient is ""bacteremic""). Most cultures are monitored for five days, after which negative vials are removed. If a vial is positive, a microbiologist will perform a Gram stain on the blood for a rapid, general identification of the bacteria, which the microbiologist will report to the attending physician of the bacteremic"
"ways. Firstly, the Phytoplankton Colour Index (PCI) is determined for each sample. The colour of the silk is evaluated against a standard colour chart and given a 'green-ness' value based on the visual discoloration of the CPR silk produced by green chlorophyll pigments; the PCI is a semi-quantitative estimate of phytoplankton biomass. In this way the PCI takes into account the chloroplasts of broken cells and small phytoplankton which cannot be counted during the microscopic analysis stage. After determination of the PCI, microscopic analysis is undertaken for each sample, and individual phytoplankton and zooplankton taxa are identified and counted. Nearly"
"mushrooms: Developed by Julius Schäffer to help with the identification of ""Agaricus"" species. A positive reaction of Schaeffer's test, which uses the reaction of aniline and nitric acid on the surface of the mushroom, is indicated by an orange to red color; it is characteristic of species in the section ""Flavescentes"". The compounds responsible for the reaction were named schaefferal A and B to honor Schäffer. Two intersecting lines are drawn on the surface of the cap, the first with aniline or aniline water, the second with an aqueous solution of 65% nitric acid. The test is considered positive when"
"the types of organisms causing it). Such color hints are best detected when the sputum is viewed on a very white background such as white paper, a white pot, or a white sink surface. The more intense the yellow color, the more likely it is a bacterial infection (bronchitis, bronchopneumonia, or pneumonia). The best sputum samples contain very little saliva, as saliva contaminates the sample with oral bacteria. This is especially true for samples for lab testing in cytology or microbiology. Specimen adequacy is assessed by the laboratory technologists by examining a Gram stain or cytology stain of the sputum."
"staining is a mild technique that may not destroy the microorganisms, and is therefore unsuitable for studying pathogens. Gram staining is used to determine gram status to classify bacteria broadly. It is based on the composition of their cell wall. Gram staining uses crystal violet to stain cell walls, iodine as a mordant, and a fuchsin or safranin counterstain to mark all bacteria. Gram status is important in medicine; the presence or absence of a cell wall changes the bacterium's susceptibility to some antibiotics. Gram-positive bacteria stain dark blue or violet. Their cell wall is typically rich with peptidoglycan and"
"for protein expression is built. Expression vectors are introduced in E.coli and after the growth of these bacteria the supernatant is tested for biochemical activity on different substrates. To identify to which microorganisms belong the enzymes which have been identified, and check if metagenome assembly was right, a separation of different species of bacteria from the sample can be done by flow cytometry. The use of specific antibodies labelled with fluorochromes makes possible to separate the different cell types of the sample which belong to different phylogenetic groups. This technique is called Fluorescence Activated Cell Sorting (FACS). Once the different"
"pink color) tests are all done. For staphylococcal food poisoning, phage typing can be performed to determine whether the staphylococci recovered from the food were the source of infection. Recent activities and food that a patient has recently eaten will be inquired about by a physician, and a physical examination is conducted to review any symptoms. With more severe symptoms, blood tests and stool culture may be in order. Diagnostic microbiology laboratories and reference laboratories are key for identifying outbreaks and new strains of ""S. aureus"". Recent genetic advances have enabled reliable and rapid techniques for the identification and characterization"
"microscope for detection of fungal elements. ""T. rubrum"" cannot be distinguished from other dermatophytes in this direct examination. It can distinguished ""in vitro"" from other dermatophytes by means of characteristic micromorphology in culture, usually consisting of small, tear-drop-shaped microconidia, as well as its usual blood-red colony reverse pigmentation on most growth media. In addition, the Bromocresol purple (BCP) milk solid glucose agar test can be used to distinguish it. Different ""Trichophyton"" species release different amounts of ammonium ion, altering the pH of this medium. In this test, medium supporting ""T. rubrum"" remains sky blue, indicating neutral pH, until 7 to"
"exposed to a basic compound, the hydrogen ions react with the added base. The conjugate base, formed from the litmus acid, has a blue color, so the wet red litmus paper turns blue in alkaline solution. Litmus Litmus is a water-soluble mixture of different dyes extracted from lichens. It is often absorbed onto filter paper to produce one of the oldest forms of pH indicator, used to test materials for acidity. Litmus was used for the first time about 1300 AD by Spanish physician Arnaldus de Villa Nova. From the 16th century on, the blue dye was extracted from some"
"is usually performed using culture, biochemical and sometimes optical methods. When indicator organisms levels exceed pre-set triggers, specific analysis for pathogens may then be undertaken and these can be quickly detected (where suspected) using specific culture methods or molecular biology. The most reliable methods are direct plate count method and membrane filtration method. mEndo Agar is used in the membrane filtration while VRBA Agar is used in the direct plate count method. VRBA stands for violet red bile agar. A media that contains bile salts which promotes the growth of gram negative and has inhibitory characteristic to gram positive although"