Michael Surette

Article / Updated 09-27-2022

The way that DNA encodes the instructions for proteins is through a set of four molecules called bases, each of which represents a letter of the genetic code (A = adenine, C = cytosine, G = guanine, and T = thymine). The bases are made of carbon and nitrogen rings and are bound to a sugar and a phosphate to form a nucleotide The nucleotides are connected together to form a long chain with the bases pointing out. Because the nitrogenous bases can interact with each other — A binding with T and C binding with G — two such chains placed opposite to each other form the ladderlike structure of DNA, with paired bases making the rungs of the ladder. Nucleotide bases will always pair in the same way, so each strand of DNA has the same sequence when read in the opposite direction to one another. The fact that each of the two DNA strands has the same sequence is called complementarity; it’s essential to making sure that all cells get the same instructions during DNA replication and cell division. Covalent bonds attach the subunits of the backbone together, whereas hydrogen bonds hold the paired bases together. Because these hydrogen bonds are much weaker than the rest of the bonds, the bases can be pulled apart, allowing things like DNA replication or RNA synthesis to occur. The genomes of bacteria and archaea are, for the most part, arranged as a single circular chromosome and some extra-chromosomal genetic material, called plasmids. The chromosome contains all the essential genes required for life, whereas plasmids contain useful but not strictly essential genes. Eukaryotic genomes are usually contained in multiple linear chromosomes, although they can also have plasmids. In both cases, the types of genes in the genome include Biosynthesis and metabolism genes Ribosomal RNA genes and transfer RNA genes DNA replication and repair genes A bacterial genome is twisted up on itself to compactly fit inside a bacterial cell. The DNA for the genome of a eukaryote is wound around proteins called histones that help compact it without the DNA strand getting tangled. Archaea have a single circular chromosomelike bacteria that is wound with histones like eukaryotes. The genomes of viruses are much shorter and made up of RNA, double-stranded DNA, or single-stranded DNA.

Cheat Sheet / Updated 02-18-2022

When you're studying microbiology, you need to know the key differences between the three domains of life, how scientists name and classify organisms, and how scientists identify microorganisms.

Article / Updated 11-25-2019

Prokaryotic cells come in many different shapes and sizes that you can see under a microscope. A description of the shape of a cell is called the cell morphology. The most common cell morphologies are cocci (spherical) and bacilli (rods). Coccibacillus are a mix of both, while vibrio are shaped like a comma, spirilla are shaped like a helix (a spiral, sort of like a stretched-out Slinky), and spirochetes are twisted like a screw. The illustration shows these common cell morphologies. Although prokaryotes are unicellular organisms, their cells can be arranged in a few different ways, like chains or clusters, depending on how the cells divide: Cocci bacteria that divide along a single plane form small chains of two cells called diplococci or long chains of multiple cells called streptococci. Cocci bacteria can also divide along multiple planes to form tetrads (two planes), cubelike sarcinae (three planes), or grapelike clusters called staphylococci (multiple planes). Similarly to the cocci, rod-shaped bacteria can divide to form double-celled diplobacilli or longer chains called streptobacilli. The shape of a cell is encoded in its genes. Although it's known how cell shape is controlled, the reason behind the many different shapes remains a mystery. You may notice that some of the morphologies are also the names of bacteria — for example, Streptococcus pneumoniae, Staphylococcus aureus, Bacillus anthracis, and Vibrio cholerae. That’s because morphologies are sometimes characteristic of bacterial genera. Morphology is a descriptive characteristic — it doesn’t give you enough information to know exactly what type of bacteria you’re looking at or its function.

Article / Updated 03-26-2016

There are three domains of life: Bacteria (also known as Eubacteria), Archaea, and Eukarya. The Bacteria and Archaea are made up entirely of microorganisms; the Eukarya contains plants, animals, and microorganisms such as fungi and protists. The Bacteria and Archaea have been grouped together and called Prokaryotes because of their lack of a nucleus, but the Archaea are more closely related to the Eukaryotes than to the Bacteria. Here are other major differences between the three domains. Bacteria Archaea Eukaryotes Cell type Prokaryotic Prokaryotic Eukaryotic Cell wall Made of peptidoglycan Does not contain peptidoglycan In plants and fungi, composed of polysaccharides Sensitivity to antibiotics Yes No No First amino acid during protein synthesis Formylmethionine Methionine Methionine DNA Mostly circular chromosome and plasmids Circular chromosome and plasmids Linear chromosome, rarely plasmids Histones No Yes Yes Organelles No No Yes Ribosomes 70S 70S 80S

Article / Updated 03-26-2016

A fecal transplant, also known as fecal biotherapy (FBT) or fecal microbiota transplant (FMT), is the administration of fecal matter from a healthy donor to a recipient. The donor may or may not be related to the recipient. In some cases, fecal matter can be transferred via a naso-gastric tube, but fewer side effects are observed when fecal transplants are administered via an enema. The idea of using feces from a healthy person to treat the sick is not new — it dates back to ancient Chinese healers — but the treatment has recently become popular again as people learn more about the role of gastrointestinal microbes in health and disease. Fecal transplants are commonly used to treat a reoccurring gastrointestinal infection known as a Clostridium difficile infection. For chronic C. diff infections, fecal transplant is lifesaving and successful 95 percent of the time. Researchers are examining the therapeutic potential of fecal transplants to treat chronic gastrointestinal diseases (rather than infections), such as ulcerative colitis and Crohn's disease. So, why does fecal transplant work? The answer to this question, surprisingly, is unknown. In terms of C. diff infections, researchers think that the good bacteria from the healthy donor's stool kick out the bad bacteria, in effect stopping the infection, and recolonize the gut themselves. Currently, fecal transplant is approved only for patients with C. diff and should not be completed without approval or supervision of a doctor. There is a do-it-yourself fecal transplant movement for people with other gastrointestinal disorders, but the risks can be significant. Numerous pathogenic microbes are passed through the feces, so transmission of disease from the donor to the recipient is a major concern. Monitoring by a doctor can not only ensure the safety of the procedure but also measure whether the therapy is working.

Article / Updated 03-26-2016

The flu is characterized by a fever, aches, sore throat, and nausea. Seasonal flu epidemics are caused by the influenza viruses A and B. There are several subtypes of influenza A that also circulate every year. The natural source of influenza A is wild birds, but they can infect a host of other animals, including pigs and humans. The viruses are able to mutate very quickly, shuffling proteins around to avoid the immune system of their host. Two or even three different viruses can recombine with one another in a single host and give rise to new, often more infectious, strains. Every year, scientists predict the strains most likely to be present in the human population based on the subtypes seen the previous year, and this prediction is used to design an appropriate flu vaccine. Most influenza A strains affect very young or very old people, because their immune systems are not able to mount a strong enough immune response. The term stomach flu is usually used to refer to the condition characterized by the sudden onset of vomiting and diarrhea. It's actually a misnomer — the term flu is related to the influenza virus, which is not at all a cause of this condition. It's more appropriately called gastroenteritis, stomach bug, or winter vomiting disease. Several different microbes can cause this condition, including Viruses like rotavirus and norovirus, which infect children and adults, respectively: These viruses are infectious, pass from person to person, and can still be passed on days after a person's symptoms have stopped. Bacteria such as Campylobacter, E. coli, Salmonella, and Shigella: These bacteria usually come from another source, such as undercooked contaminated meat, but they can be spread between people if the people come in contact with the stool or vomit of a sick person. Gastroenteritis from bacteria or viruses usually lasts 24 to 48 hours and is accompanied by a mild fever, painful bloating, and aches and pains. Dehydration can be a dangerous side effect, so it's important that sick people drink clear fluids and are monitored for worsening of symptoms. Traveler's diarrhea is a type of gastroenteritis that occurs in people as they travel, specifically to the developing countries of Latin America, Africa, the Middle East, and Asia. It's most often caused by enterotoxigenic Escherichia coli (ETEC for short), but it can also be caused by any of the organisms that cause general gastroenteritis. Exposure is from water or food contaminated with fecal matter, and the symptoms are identical to those for gastroenteritis. Preventive treatments are available. Antibiotics, although effective are not recommended because they're a major cause of antibiotic resistance and have side effects on the body. Pepto-Bismol is effective, but it doesn't work for viruses and can't be used for more than a week or two. Finally, an over-the-counter cholera vaccine, also aimed at ETEC, is available that has an effectiveness of between 25 percent and 50 percent. In the end, you may be better off simply paying attention to the foods and beverages you consume to avoid undercooked meats, unpeeled fruit, and tap water.

Article / Updated 03-26-2016

Microorganisms can't be seen with the naked eye, so they're identified in several indirect ways: Microscopy to identify cell shape or appearance of spores. Cells are often stained to enhance cellular features, and the properties of the cell wall are used in the classification of microorganisms. Appearance of colonies on laboratory media is a widely used method of distinguishing between different microbes, mainly bacteria. Rich media allows the growth of a broad range of bacteria. Selective media allow the growth of only a narrow range of bacteria. Differential media contain dyes that react with the chemical processes of certain types of bacteria, allowing their identification. Characteristics of bacterial colony growth are described in terms of shape, appearance, and color. The differences in DNA sequence can be used to identify organisms. Marker genes include, but are not limited to, ribosomal RNA (16S in bacteria and archaea and 18S in eukaryotes except fungi where the internal transcribed spacer [ITS] region of the gene is used) and cpn60 (chaperonin-60) genes. Biochemical tests can be used to identify the type of metabolism a microorganism uses based on the products it makes from defined substrates. Bergey's Manual of Systematic Bacteriology is used to identify bacteria based on microscopy, ability to grow on specific media, appearance of colonies, and biochemical tests of metabolism.

Article / Updated 03-26-2016

To keep the many organisms on earth straight, in the 18th century the Swedish botanist Carl Linnaeus developed a simple nomenclature system to classify and name all organisms including bacteria. This system ranks all organisms using the following headings, shown with the example of the bacterium E. coli. Domain: Bacteria Phylum: Proteobacteria Class: Gammaproteobacteria Order: Enterobacteriales (Order names always end in –iales.) Family: Enterobacteriaceae (Family names always end in –aceae.) Genus: Escherichia Species: coli Organisms are uniquely identified by the genus and species names, which are always either italicized or underlined, the genus is often shortened to the first letter (for example, E. coli).

Article / Updated 03-26-2016

Since the beginning of their widespread use in 1943, antibiotics have saved countless lives and changed the way medicine is practiced. Before their discovery, people suffered or died from infectious diseases that today are a mere annoyance, like sexually transmitted diseases and post-operative infections. Today antibiotics are essential in treating life-threatening bacterial infections, like pneumonia and sepsis, and are used preventively in a number of medical procedures (like surgery) and treatments (like cystic fibrosis). But when you have a sore throat, cough, or cold, your doctor may opt not to prescribe antibiotics. Here are ten reasons why: Antibiotics do not treat viral infections. Most common ailments (such as the common cold and influenza) are due to viral infections rather than bacterial infections. Antibiotics are designed to treat illnesses caused by bacteria. They don't treat viral infections. Your immune system can usually handle things on its own. Upon being infected with a virus that your body has never seen before, your immune system fights the offending pathogen (disease-causing agent). The first time your body encounters a virus, it takes some time to mount this immune response. But when the virus is eradicated, the body "remembers" the composition of the viral antigen (the part of the virus that stimulates an immune response). So, the next time your body encounters the same virus, your body will be able to mount an immune response much more quickly and effectively in order to stop the virus in its tracks. High doses of antibiotics can cause suppression of your immune system. Antibiotics given in high doses can alter the regular response of your immune system. Initially, when the body recognizes an infection, it elicits an inflammatory response. This response is invaluable to the body's ability to fight infection. Some antibiotics, like erythromycin, have anti-inflammatory properties, so although your symptoms seem to get better initially, ultimately it will take longer for you to get better. Overuse (and misuse) of antibiotics can lead to antibiotic resistance. Antibiotics that are given for an infection that is not caused by bacteria or antibiotics that aren't specific for the bacterial pathogen can contribute to the development of antibiotic-resistant bacteria in that individual. In any population of bacteria, there is always a small number of mutants. Although the mutations are random, at any given time there's a small chance that one is resistant to an antibiotic. Every time you expose the bacteria in your body to antibiotics, the susceptible bacteria are killed but any antibiotic-resistant mutants are spared. These bacteria are then capable of reproducing a new population of bacteria with the mutation that allows them to evade antibiotic therapy. This process of creating a situation where some members of a population survive and others die is called selection, and it results in certain traits, like antibiotic resistance, becoming more abundant than they would in the normal course of events. Placing the bacteria in the body under the selection pressure of antibiotics, by using them too often, doesn't select only for antibiotic-resistant members of the pathogenic population but from all species of bacteria in the body. And when any of these become problematic, they're much more difficult to treat. When an individual uses more antibiotics, that leads to more antibiotic exposure by bacteria, creating an even greater selective pressure on bacteria and ultimately leading to more resistant strains overall. Overuse of antibiotics causes the emergence of superbugs. Drug-resistant microorganisms have a large impact on human health. The U.S. Centers for Disease Control (CDC) estimates that over two million people are infected by drug-resistant microorganisms, including bacteria and fungi, in the United States each year, with 23,000 people dying as a direct result and many more dying as an indirect result. Superbugs are bacteria that have the ability to evade multiple different antibiotics. As their name suggests, superbugs, or multidrug-resistant bacteria, are very difficult to eradicate. Some, like Clostridium difficile and drug-resistant Neisseria gonorrhoeae, are not widespread, but there is no other treatment for them, making them a big potential threat for the future. Others like, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE), are seen more often and can still be managed by a small number of drugs. Currently, there are not many promising new antibiotics being developed. Traditionally, these were thought of as hospital-acquired infections, but as inappropriate antibiotic use continues, these infections are now being seen in the community at large. Antibiotics are far more useful when we use the right ones. Some antibiotics, called broad-spectrum drugs, are general and target a wide range of microbes, whereas others are specific for a smaller group of microbes. Likewise, different bacteria are vulnerable to some antibiotics and unaffected by others. So, it makes sense to treat a bacterial infection with the drug that will be most effective against the pathogen in question. To determine the cause of an infection, it's important to collect a sample from the sick person and send it to be identified by the medical lab. Without a culture of the infection, your doctor can't know which organism is causing the symptoms. In the past, doctors used broad-spectrum antibiotics to treat infections, and the majority of people got better. Recently, it has been discovered that this practice has lead to the development of superbugs, as well as contributed to the increasing number of cases of antibiotic-related infections (such as C. diff) and antibiotic-resistant bugs (such as MRSA). Antibiotics can leave you susceptible to opportunistic infections. The use of antibiotics can kill the good bacteria that live in your body. All the surfaces of your body are teeming with bacteria, called the microbiota, that have been there since you were born and protect you from invading pathogens every day. For example, the intestine and, in women, vaginal microbiota contain a balance of good and potentially bad microorganisms. The use of antibiotics can cause the good bacteria to be wiped out, leaving an environment that favors the potentially harmful microorganisms. Antibiotics have nasty side effects. Though the common side effects of antibiotics are mostly just a nuisance, some side effects can be quite dangerous. Diarrhea, nausea, and vomiting are common and are likely due to an inflammatory response in your stomach and intestinal lining. It can be difficult to distinguish these side effects from the more dangerous diarrhea caused by C. diff. Overgrowth of Candida albicans can occur in both the mouth and the vagina. Perhaps the most serious of side effects is allergic reactions. These reactions can range from hypersensitivity reactions (hives, itching, and redness) to a more severe anaphylactic reaction (throat and tongue swelling) that can lead to death. Antibiotics can interact with other prescription and over-the-counter medications. Antibiotics can interact with other medications you're taking and cause potentially serious consequences. Some antibiotics can interact with nonsteroidal anti-inflammatory drugs (NSAIDs) to cause damage to your kidneys, while others can interact with antacids and cause decreased absorption of nutrients from your intestine. Some antibiotics can make birth control pills ineffective. Still others can interfere with anticoagulation medications and cause a substantial increase in the amount of time it takes blood to clot, which can lead to excessive bleeding if you suffer an injury. Hypoglycemia, bone marrow suppression, and drug-related toxicity can also occur with the use of antibiotics combined with some other medications. Your doctor will take into consideration the other medications you're taking before prescribing an antibiotic. Antibiotic use in pregnancy may have effects on the child. There is evidence to suggest that when women use antibiotics inappropriately during pregnancy, their offspring have an increased risk of developing allergies. If you're pregnant, your doctor will keep the health of your baby in mind before prescribing antibiotics.

Article / Updated 03-26-2016

At birth, an infant's immune system is extremely tolerant of everything, which is why infants are more vulnerable to infection. Slowly over the first couple years of life, the immune system matures. This process is complex, and it involves learning about which microorganisms are acceptable and can be ignored and which are harmful and should be killed. The microbes in and on the body help to train the immature immune system in a process that is not yet completely understood but ends with proper responses by the mature immune system. Many different illnesses — including type 1 diabetes, celiac disease, asthma, Crohn's disease, and ulcerative colitis — are thought to have complex causes stemming partially from a genetic predisposition and partially from an environmental stimulus. A loss of some beneficial microbes from the human microbiota (the community of microorganisms that live in and on us) could also be contributing to the development of these conditions in increasing numbers of people. What's causing these microbes to disappear? Possibly overuse of antibiotics, as well as the widespread use of antibiotics given to livestock that end up in our systems. The increased use of caesarean section instead of vaginal delivery may also interfere with inoculation of an infant with the mother's microbes. What's the impact of this loss of a healthy microbiota? Consider the case of one bacteria in particular, Helicobacter pylori. Over 30 years ago, H. pylori was found in one out of every four adults, colonizing the lining of the stomach. It was causing people to become very ill with gastritis and peptic ulcers that could turn into stomach cancer. H. pylori was degrading the mucosa of the stomach and allowing gastric juices to destroy the lining even more. The treatment for these conditions was to get rid of an H. pylori infection with antibiotics, a strategy that effectively reduced its presence in most developed countries. In the years since, high rates of ulcers and H. pylori have decreased, but rates of esophageal cancer have increased. This has led H. pylori expert Dr. Martin Blaser to look into the link between the loss of this bacteria that was not causing harm in most people and esophageal reflux and cancer. It's unclear how loss of a pathogenic microbe can contribute to another human disease, but it appears that over the long course of our co-evolution with this bacterium, we may have come to need each other. What does this mean for you? As we learn about microorganisms, we find they may be causing disease in some people, but this does not necessarily mean they're harmful in all people. By eliminating harmless bacteria, we're shifting the community of microorganisms in ways that we don't yet fully understand. Understanding how microorganisms work together in their communities, especially when associated with humans, is still a very young science with a lot of progress yet to be made before we know all the downstream consequences of many treatments against microbes.