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A flowchart. A square plate with a grid of circles is labeled grow microorganisms on MALDI-plate. Then irradiate sample. Then use mass spectrometer to measure gaseous ions released. Then compare mass spectrum of sample to reference spectra; two small graphs are shown here. Then identify specied.
MALDI-TOF methods are now routinely used for diagnostic procedures in clinical microbiology laboratories. This technology is able to rapidly identify some microorganisms that cannot be readily identified by more traditional methods. (credit “MALDI plate photo”: modification of work by Chen Q, Liu T, Chen G; credit “graphs”: modification of work by Bailes J, Vidal L, Ivanov DA, Soloviev M)

Microbes can also be identified by measuring their unique lipid profiles. As we have learned, fatty acids of lipids can vary in chain length, presence or absence of double bonds, and number of double bonds, hydroxyl groups, branches, and rings. To identify a microbe by its lipid composition, the fatty acids present in their membranes are analyzed. A common biochemical analysis used for this purpose is a technique used in clinical, public health, and food laboratories. It relies on detecting unique differences in fatty acids and is called fatty acid methyl ester (FAME) analysis . In a FAME analysis , fatty acids are extracted from the membranes of microorganisms, chemically altered to form volatile methyl esters, and analyzed by gas chromatography (GC) . The resulting GC chromatogram is compared with reference chromatograms in a database containing data for thousands of bacterial isolates to identify the unknown microorganism ( [link] ).

A flowchart. A bacterial culture is grown (image is of an agar plate). Then fatty acids are extracted and converted to methyl esters (image is of a test tube). Then gas chromatography analyzes methyl ester fingerprints (image is of a chromatography machine). Then bacteria are identified (image is of a graph). The X axis of the graph is column retention time. The Y axis is of detector signal. The line has various peaks.
Fatty acid methyl ester (FAME) analysis in bacterial identification results in a chromatogram unique to each bacterium. Each peak in the gas chromatogram corresponds to a particular fatty acid methyl ester and its height is proportional to the amount present in the cell. (credit “culture”: modification of work by the Centers for Disease Control and Prevention; credit “graph”: modification of work by Zhang P. and Liu P.)

A related method for microorganism identification is called phospholipid-derived fatty acids (PLFA) analysis . Membranes are mostly composed of phospholipids, which can be saponified (hydrolyzed with alkali) to release the fatty acids. The resulting fatty acid mixture is then subjected to FAME analysis, and the measured lipid profiles can be compared with those of known microorganisms to identify the unknown microorganism.

Bacterial identification can also be based on the proteins produced under specific growth conditions within the human body. These types of identification procedures are called proteomic analysis . To perform proteomic analysis, proteins from the pathogen are first separated by high-pressure liquid chromatography (HPLC) , and the collected fractions are then digested to yield smaller peptide fragments. These peptides are identified by mass spectrometry and compared with those of known microorganisms to identify the unknown microorganism in the original specimen.

Microorganisms can also be identified by the carbohydrates attached to proteins (glycoproteins) in the plasma membrane or cell wall. Antibodies and other carbohydrate-binding proteins can attach to specific carbohydrates on cell surfaces, causing the cells to clump together. Serological tests (e.g., the Lancefield groups tests, which are used for identification of Streptococcus species) are performed to detect the unique carbohydrates located on the surface of the cell.


Penny stopped using her new sunscreen and applied the corticosteroid cream to her rash as directed. However, after several days, her rash had not improved and actually seemed to be getting worse. She made a follow-up appointment with her doctor, who observed a bumpy red rash and pus-filled blisters around hair follicles ( [link] ). The rash was especially concentrated in areas that would have been covered by a swimsuit. After some questioning, Penny told the physician that she had recently attended a pool party and spent some time in a hot tub. In light of this new information, the doctor suspected a case of hot tub rash , an infection frequently caused by the bacterium Pseudomonas aeruginosa , an opportunistic pathogen that can thrive in hot tubs and swimming pools, especially when the water is not sufficiently chlorinated. P. aeruginosa is the same bacterium that is associated with infections in the lungs of patients with cystic fibrosis .

The doctor collected a specimen from Penny’s rash to be sent to the clinical microbiology lab. Confirmatory tests were carried out to distinguish P. aeruginosa from enteric pathogens that can also be present in pool and hot-tub water. The test included the production of the blue-green pigment pyocyanin on cetrimide agar and growth at 42 °C. Cetrimide is a selective agent that inhibits the growth of other species of microbial flora and also enhances the production of P. aeruginosa pigments pyocyanin and fluorescein, which are a characteristic blue-green and yellow-green, respectively.

Tests confirmed the presence of P. aeruginosa in Penny’s skin sample, but the doctor decided not to prescribe an antibiotic. Even though P. aeruginosa is a bacterium, Pseudomonas species are generally resistant to many antibiotics. Luckily, skin infections like Penny’s are usually self-limiting; the rash typically lasts about 2 weeks and resolves on its own, with or without medical treatment. The doctor advised Penny to wait it out and keep using the corticosteroid cream. The cream will not kill the P. aeruginosa on Penny’s skin, but it should calm her rash and minimize the itching by suppressing her body’s inflammatory response to the bacteria.

Skin with red raised bumps.
Exposure to Pseudomonas aeruginosa in the water of a pool or hot tub can sometimes cause a skin infection that manifests as “hot tub rash.” (credit: modification of work by “Lsupellmel”/Wikimedia Commons)

Go back to the previous Clinical Focus box.

Key concepts and summary

  • Accurate identification of bacteria is essential in a clinical laboratory for diagnostic and management of epidemics, pandemics, and food poisoning caused by bacterial outbreaks.
  • The phenotypic identification of microorganisms involves using observable traits, including profiles of structural components such as lipids, biosynthetic products such as sugars or amino acids, or storage compounds such as poly-β-hydroxybutyrate.
  • An unknown microbe may be identified from the unique mass spectrum produced when it is analyzed by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) .
  • Microbes can be identified by determining their lipid compositions, using fatty acid methyl esters ( FAME ) or phospholipid-derived fatty acids ( PLFA ) analysis .
  • Proteomic analysis , the study of all accumulated proteins of an organism; can also be used for bacterial identification.
  • Glycoproteins in the plasma membrane or cell wall structures can bind to lectins or antibodies and can be used for identification.

Fill in the blank

A FAME analysis involves the conversion of _______ to more volatile _____ for analysis using ____________.

fatty acids, methyl esters, gas chromatography

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MALDI-TOF relies on obtaining a unique mass spectrum for the bacteria tested and then checking the acquired mass spectrum against the spectrum databases registered in the analysis software to identify the microorganism.


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Lancefield group tests can identify microbes using antibodies that specifically bind cell-surface proteins.


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Short answer

Compare MALDI-TOF, FAME, and PLFA, and explain how each technique would be used to identify pathogens.

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Questions & Answers

i wante to study medicine in university so how i should prepare my self
Lissa Reply
microorganism functions
NUHU Reply
how does the helicobacteri pylori affect the stomach walls?
Erick Reply
when the stomach is been affected with helicobacteria what are the preventive measure to be considered to ensure specific outcome?
what is microbiology
vijay Reply
microbiology is the scientific study of microorganisms .microorganisms are those organisms that are too small to see with the naked eye ex-bacteria fungi
a branch of biological science concerned with organisms that can not be observed with a naked eye
what are the types of granulocytes and explain
polymorpho nuclear leukocyte, known as granulocyte are divide into three,1-polymorpho eosinophil 2-polymorpho basophil 3-polymorpho neutrophil
microbiology is scientific study of microorganism which can nt be seen by naked eye,for example bacteria,viruses, protozoa ad fungi.
microbiology is the scientific study of microorganisms
I want to know more about sample collection on the field
Ama Reply
blood collection and urinarysis
In the periodic table the number on the upper left hand side is what
Aurelia Reply
am not talking about the elements
Is it the atomic number or the mass number
differences between acid fast and non acid fast bacilli
acid fast have cell wall that holds to carbol fuschin stain while non acid fast doesn't have. it readily releases out the primary stain the carbol fuschin.
where do I post a question that isn't related to that topic
hi everyone
for sure, this question is not related to the topic.
can someone explain the process of glycolysis and the electron transport chain? I'm so freakin lost. it loses carbons, gains hydroxyls, gains, loses Hydrogens....ugh it's like a foreign language to me! or direct me to a youTube video or something that will make this seem easier to concept?
it's a loaded question, sorry!
why is DNA a genetic material
Mcbeth Reply
DNA is genetic material because it contains chromosome contains the traits which includes characters and behavioral characteristics
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Muhammed Reply
good hygiene
way of preventing disease causing germs
maintenance of sterilization
describe the components of the epidemiology triangle
Muhammed Reply
where from you
i am Indian
Hello friend
How are you people doing
أ‌) Host factor ب) pathogen ج) environment
hey hi
The epidemiologic triangle is made up of three parts: agent, host and environment
please can a microbiologist will work at hospital
what are the fluids used in biochemistry Lab used to diagnose diseases
Jb Reply
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fadumo Reply
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history of microbiology
Balqees Reply
Penicillin is caused by what microorganism
Penicillin is caused by what microorganism
penicillium notatum
M sorry I mean penicillin is caused by what Fungi
penicillium fungi
when I finish with my bsc in microbiology where wil I work
Why can we see ourselves in a mirror?
mention 5 characteristics of prokaryotic cell and also 5 characteristics of euryotic cell
Grace Reply
PROKARYOTES _ does not have nucleus _does not have membrane bound organels like eukaryotes -does not have endoplasmic reticulum _does not have a mitchochondrion _it have plasmid instead of chromosome EUKARYOTE S _have true nucleus _have all membrane bound organels _have mitochondria have
continuation _have endoplasmic reticulum _have chromosomes does not have plasmid
antigenisity define
explanation of spores
nahida Reply
Practice MCQ 5

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Source:  OpenStax, Microbiology. OpenStax CNX. Nov 01, 2016 Download for free at http://cnx.org/content/col12087/1.4
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