# All Things Microbiology > Small things make a big difference! ## Posts - [The deadliest epidemic sweeping the United States](https://textbookconsortia.com/the-deadliest-epidemic-sweeping-the-united-states/): Whooping cough cases are out of control in the United States – as of December 20th, there were 27,871 cases and 13 deaths. In 2024, there were 41,922 cases. This is a massive increase in incidence from the period 1970 to 90 where cases averaged about 2,600 per year. There has been a significant increase since 2003, with cases averaging between 10,000 to 20,000. Pertussis is a nasty disease characterized by a severe, violent cough, where people cough so much they run out of breath and then, in between coughs, inhale strongly, making a whooping sound, hence giving the disease… - [Influenza Activity is Increasing in the US](https://textbookconsortia.com/influenza-activity-is-increasing-in-the-us/): It’s shaping up to be an active influenza season this year. At the end of the year, infections are accelerating, and we just hit a 6% infection rate, which crashed through the national baseline of 3% infection. Quite a few people’s Christmas plans were interrupted by the flu. I know of one recent instance where a nurse went into work, even though they were not feeling well, infecting their coworkers! If you are not feeling well and have sick leave, stay home!* The most common strains circulating right now are Influenza A (H3N2). While having the flu is never fun,… - [A loss of anaerobes in the gut may have a role in IBD](https://textbookconsortia.com/a-loss-of-anaerobes-in-the-gut-may-have-a-role-in-ibd/): A newly published study in the journal Gastroenterology by Peter Rimmer, Fan Zhang, and colleagues digs into the observation that there is a shift in the microbiome in newly diagnosed patients with irritable bowel disease. The two most common IBD types are Crohn’s disease and ulcerative colitis, with the global prevalence exceeing 0.3%. That’s nearly 2.5 million people! The underlying causes of IBD are not clear, but there seems to be an interplay between several contributors: barrier dysfunction, genetic predisposition, environmental factors, and the gut microbiome. Alterations in the gut bacteria in IBD patients have been widely reported. This leads… - [Measles is here](https://textbookconsortia.com/measles-is-here/): On November 22nd, I wrote a post about the alarmingly low vaccination rate against measles in certain parts of this country. This is incredibly dangerous, and our infectious disease present has arrived early. The Washington Post reports on South Carolina public health officials who warn that an outbreak of measles is accelerating. So far, 111 measles cases have been reported, with 105 of them being in unvaccinated individuals. (There is a small chance you can get measles even if you are vaccinated. One dose of the measles vaccine is 93% effective, while two doses are 97% effective at stopping the… - [Finding the incidence of a disease](https://textbookconsortia.com/finding-the-incidence-of-a-disease/): Are you curious about the levels of illness in your city, state, or the whole country? There are now public web pages that publish tracking data on measles, SARS-CoV-2, RSV, influenza, norovirus, and more. As two examples, wastewater scan is a collection of wastewater treatment plants that test for a variety of illnesses in the water. It can be an early warning sign that illness is rising in the community. Wastewater is a great medium to test because pathogens eventually end up in it, and it is a completely non-invasive way to monitor an area without violating anyone’s privacy. I… - [The gut microbiome produces metabolites that might have a role in obesity and diabetes](https://textbookconsortia.com/the-gut-microbiome-produces-metabolites-that-might-have-a-role-in-obesity-and-diabetes/): Insulin resistance is a major problem in the US and is a hallmark of type 2 diabetes. Over 34 million Americans are living with type 2 diabetes. Type 2 diabetes causes a myriad of health problems including increases in heart disease, high blood pressure, poor circulation, eye problems, and foot and nerve damage. Beyond the health issues for the individual, type 2 diabetes leads to an economic cost of 412 billion dollars. In other words this is a huge deal! In the last few years, researchers have identified the gut microbiome as playing an important role in diabetes outcomes, modifying… - [ChatGPT is not the end of essays in education](https://textbookconsortia.com/chatgpt-is-not-the-end-of-essays-in-education/): The takeover of AI is upon us! AI can now take all our jobs, is the click-bait premise you hear from the news. While I cannot predict the future, I am dubious that AI will eliminate all our jobs. Some of them? Sure. Another assertion of the doomsayers is that the prowess of ChatGPT has made the college essay a thing of the past. I do not think the college essay is dead. Writing is one of the best ways for students to recall and formulate their ideas as they are trying to learn. So what will I do as… - [There have got to be better uses of genetics and probiotics](https://textbookconsortia.com/could-there-maybe-be-better-uses-of-genetics-and-probiotics/): Professor Meng Dong and his laboratory have created a probiotic that can metabolize alcohol quickly and maybe prevent some of the adverse effects of alcohol consumption. The scientists cloned a highly active human alcohol dehydrogenase gene (ADH1B) into Lactococcus lactis. ADH1B is responsible for detoxifying ethyl alcohol (it is a poison after all). The engineered bacterium was fed to mice along with alcohol. The researchers found that mice became less impaired and had less alcohol-related damage. So I have two questions.  One, how do you tell if a mouse is drunk? The answer is you place them on their backs.… - [Clues are beginning to emerge on asymtomatic SARS-CoV-2 infection](https://textbookconsortia.com/clues-are-beginning-to-emerge-on-asymtomatic-sars-cov-2-infection/): COVID-19.  I suspect that was when I was exposed to the virus.  I was in the SARS-CoV-2 monitoring program and was being tested weekly for signs of the virus. Sure enough, I got a notice from the program that I was COVID-positive.  I dutifully went into isolation, nervously waiting for symptoms to appear. They never did. Neither my wife nor daughter, who were living with me, contracted the virus or showed symptoms.* Scientists suspected that some people just didn’t get that sick from the virus, and they hypothesized that these individuals may have a genetic background that makes them more… - [Converting Electrons into ATP](https://textbookconsortia.com/converting-electrons-into-atp/): The cell can create high-energy electrons from all sorts of sources and convert them into ATP. It needs to do this to grow. This animation shows how the membrane is involved in this process. - [Enzymes are biological catalysts](https://textbookconsortia.com/enzymes-are-biological-catalysts/): Here is an example figure from the textbook demonstrating how enzymes affect reactions. This animation helps the learner understand the physical chemistry of biological reactions. Number of Acetyl CoA: 0 Timer: Reset Animation Carbon Dioxide: CFeSP w/ Methyl: Coenzyme A (CoA): - [America may get Measles for Xmas](https://textbookconsortia.com/america-may-get-measles-for-xmas/): Measles is a highly contagious virus. How infectious is it? It has a reproduction number of 12 – 18, although recent studies show that this can be quite variable. So what does the reproduction number mean? That is the number of susceptible individuals someone with measles infects. In other words, if a child is sick with measles, they will, on average, infect 12 to 18 naive individuals with the virus. That is wildly higher than many other viruses. The seasonal influenza virus has a reproduction number of 1.2 to 1.4. Measles spreads like crazy. If a child enters a daycare… - [7 - 2 Bacterial immune systems provide the tools to change genetics](https://textbookconsortia.com/7-2-bacterial-immune-systems-provide-the-tools-to-change-genetics/): The first discovery has to do with bacteriophage, viruses that infect bacteria. Yep you heard that right, there are viruses that prey on bacteria. In fact any time we have looked for viruses of an organism, we have been able to find them. Most of the nucleic acid in the world is tied up in viruses. Whilst doing experiments in their laboratory Salvador Luria and Mary Human and Giuseppe Bertani and Jean Weigle observed that bacteriophage would grow well on one E. coli strain, but poorly on another. If you picked some phage that had somehow been able to grow… - [15 - 4 There are some threats that we do face that have nothing to do with microbes.](https://textbookconsortia.com/15-4-there-are-some-threats-that-we-do-face-that-have-nothing-to-do-with-microbes/): There has been an erosion of trust in authorities. Given how often governments, corporations, and other people with influence have lied to us, this is understandable. Many people have used instances of broken public trust to proceed to ignore all experts on everything. Only a third of Americans now trust their government to do what is right. This blanket rejection is dangerous. Several individuals who are part of the flat earth society are trying to build rockets to prove that the earth is flat by showing it has no curvature. (You can only view this 10.5 kilometers above the Earth’s… - [15 - 3 Small things matter](https://textbookconsortia.com/15-3-small-things-matter/): DNA Sequence shows that we share a common ancestry with all life forms One of the most profound inventions of the latter half of the 20th century was the discovery of the hereditary molecule DNA and development of technology to sequence it. We could now copy down the letters and words of the book of life. There has been an explosion of sequencing data in the last four decades going from just a few sequences of genes in a few organisms to trillions of base pairs in thousands of organisms. The consequences of this avalanche of information is profound. All… - [15 - 2 Appreciate the role that chance plays in all things](https://textbookconsortia.com/15-2-appreciate-the-role-that-chance-plays-in-all-things/): Thonis Philipsoon (who wrote under the pen name Antony van Leeuwenhoek) was a tradesman of Delft, Holland. The major quality he shared with most scientists was an endless curiousity about the world. He had no other qualifications (a university education, an independent fortune, or the ability to speak any languages besides his native Dutch) that would make him a likely natrual philosopher. (In his time scientists called themselves natural philosophers.) Around 1668 he came across a copy of Robert Hooke’s book Micrographia which desscribed his observations using a compound microscope. Due to the technical limitations of the 17th century, compond… - [15 - 1 Why science, especially microbiology, matters](https://textbookconsortia.com/15-1-why-science-especially-microbiology-matters/): You made it. You are now at the end of this book and since it is the end, I have a few things I want to emphasize. These thoughts will be given from least to most important, but since I am mentioning them, they are all important! Ready? Let’s begin Bacteria are your buddies Bacteria, and all microorganisms do far more good for you than bad. For centuries humans have taken advantage of the action of bacteria on food to preserve it. Bread, wine, beer, cheese, Kimchi, sauerkraut, kombucha are just a few examples of fermented foods that humans enjoy.… - [14 - 8 A call to action: what you can do to fight infectious disease](https://textbookconsortia.com/14-8-a-call-to-action-what-you-can-do-to-fight-this-epidemic/): I hope this chapter has helped you learn more about SARS-CoV-2 and the disease it causes. Even in the best of circumstances, COVID-19 was going to be a long, hard fight. All the frightening news stories left many feeling powerless against this disease. But that was not the case. There is a lot you can do to help in an epidemic. Much of this advice is no longer needed in some parts of the world, but I leave it here as a reminder. And maybe for the next pandemic, which I hope is many years in our future. One thing… - [14 - 7 Conspiracy Theories About COVID-19](https://textbookconsortia.com/14-7-conspiracy-theories-about-covid-19/): The advent of the internet, web browsers, and cheap content servers has made it possible for anyone to publish their ideas. In many ways, this is a beautiful thing, but it has a darker side. Someone with little expertise can present inaccurate, misleading, and dangerous ideas in compelling ways that may sway some individuals. This blind leading the blind can have tragic consequences. It’s gotten so bad that I wrote a whole chapter about the problem and how you can combat it. The COVID-19 pandemic is no exception and is fertile ground for numerous conspiracies. In this section, I will… - [14 - 6 Vaccine development. How does it work?](https://textbookconsortia.com/14-6-vaccine-development-how-does-it-work/): The spread of COVID-19 could be shut down with the development of safe and effective vaccines that create sterilizing immunity. The goal of any vaccine is to create an immune response in the host that mimics a natural infection close enough to raise a protective immune response. Vaccines expose the host to enough of the pathogen to create this immune response without causing disease or any other life-threatening reactions. The good news was that we had studied coronaviruses for years, which points out why basic research on seemingly “esoteric” topics is essential. Ground floor research increases our foundational knowledge and… - [14 - 5 Treatments for SARS-CoV-2](https://textbookconsortia.com/14-5-treatments-for-sars-cov-2/): A historical perspective on the hysteria There was an understandable keen interest in potential treatments because of the increased risk of death from COVID-19 compared to other infectious diseases. The public and news media looked to scientists to find remedies, and any drug that showed promise gave rise to intense publicity. Finding and testing effective treatments is a complicated and time-consuming business. Many journalists and the public at large do not have the necessary training to judge the validity of studies published in the literature or the background to evaluate appropriate controls, randomization, and all the other subtle nuances that… - [14 - 4 Stopping COVID-19](https://textbookconsortia.com/14-4-stopping-covid-19/): So we clearly dropped the ball on this infection. Our constitution is a primary difference between the United States and governments that have been more successful in dealing with the pandemic. In the United States, due to its constitutional structure, the primary responsibility for public health rests with the states. In the ordinary course of daily life, this is not a problem, but in extraordinary times, such as a global pandemic, decisive national action is necessary. States and the federal government can activate emergency powers to expand their ability to protect the life and health of citizens. Unfortunately, the divided… - [14 - 3 Various responses to COVID-19](https://textbookconsortia.com/14-3-various-responses-to-covid-19/): How to stop the spread of COVID-19 A virus spreads in society because those ill with the virus make contact with others who are susceptible. If the virus transmits to more than one other person for each person it infects, it will cause an epidemic. This ratio is called the reproduction number and is denoted as R naught (R0) by epidemiologists. Each infectious disease has a base-line R0 that indicates how well it naturally spreads in a population, but it is possible to alter this number by changing behavior. For example, it appears COVID-19 has a maximum incubation period of… - [14 - 2 Origins, spread, and risk of COVID-19](https://textbookconsortia.com/14-2-origins-spread-and-risk-of-covid-19/): There is significant controversy about the source of the COVID-19 outbreak. Currently, the earliest known existence of a virus resembling SARS-CoV-2 came from samples harvested from Dead Pangolins brought to the Guangdong Wildlife Rescue Center of China on October 24th, 2019. The government of China monitors wildlife to sound the alarm if a potential pandemic strain is detected. Patients ill with viral pneumonia of no known cause began to appear in December in Wuhan, China. The first case was diagnosed on December 1st in China and had no apparent link to the market. There were another 41 cases, with 28… - [14 - 1 SARS-CoV-2, the virus that causes COVID-19](https://textbookconsortia.com/14-1-sars-cov-2-the-virus-that-causes-covid-19/): What is a virus? Before we can talk about COVID-19, you need to understand some background about the virus, SARS-CoV-2 (COVID-19 is the name of the disease, SARS-CoV-2 is the name of the virus). And before you can do that, you need to understand the definition of a virus. A virus is not a living thing. It is more like a machine. It has an outer shell, and within that shell is a small set of recipes that describes how to make a set of enzymes. This recipe book uses the same language that living things of this planet use:… - [13 - 3 The CDC Response to H1N1](https://textbookconsortia.com/13-3-the-cdc-response-to-h1n1/): Later analysis of the H1N1 virus indicated it was a new combination of North American swine, Eurasian swine, birds, and humans viruses. The emergence of H1N1 was alarming because this type of viral reassortment would result in an influenza virus to which humans would have little immunity. What this meant was that more people would get sick and their illness would be more severe. How severe was the most critical question. On April 21st, just six days after the first case was detected, the CDC started work to develop a vaccine against this emerging virus, eventually resulting in the creation… - [13 - 2 Why do we have these organizations?](https://textbookconsortia.com/13-2-why-do-we-have-these-organizations/): The Story of John Snow Epidemiology, the monitoring of disease and taking actions to mitigate it, really begins with John Snow. No, not that Jon Snow from Game of Thrones. Besides, he should be Jon Stark. The John Snow I am talking about is a British Physician from the 19th century. This John Snow more than likely affects your life far more than a GoT character. John Snow was concerned with controlling cholera, which had reached epidemic levels in the Golden Square of London. He noticed a substantial increase in cholera patients in his practice in 1854 and began carefully… - [13 - 1 The threat of influenza](https://textbookconsortia.com/13-1-the-threat-of-influenza/): You may have heard about the influenza pandemic of 1918. It was a killer virus. In the fall of 1918, a virulent strain of flu began to spread. Within a year it would sicken 500 million people worldwide (one-third of the world’s population) and kill 20 to 50 million people. (Exact estimates are had to come by because of a lack of accurate record keeping). Since the time, governments have been ever watchful for the rise of another influenza pandemic. The H1N1 pandemic virus emerges From 2005 until 2009 there had been about a dozen sporadic reports of influenza occurring… - [12 - 3 Antimicrobials](https://textbookconsortia.com/12-3-antimicrobials/): Antimicrobials are another powerful weapon against infectious disease. I begin this section with two stories, one about Alexander Fleming, and a second about Bob. Alexander flemings story By 1885, it was becoming clear that the causative agents of many illnesses were microorganisms. As scientists manipulated these microbes in the lab, they found that certain dyes and other compounds were able to inhibit their growth. This observation inspired Paul Ehrlich to propose that chemicals may exist that kill the microbe, but not the patient, thus curing the illness. One of the diseases Ehrlich hoped to cure was syphilis, which had reached… - [12 - 2 Vaccination](https://textbookconsortia.com/12-2-vaccination/): Smallpox had been around for millennia. It struck fear into every community where it appeared as 40% of children, and 25% of adults infected with the disease would die. Even if you survived, there was a fair chance you would be blinded or debilitated for life. It was also one of the first diseases to which physicians found an effective treatment. As far back as the 11th century in India and China, it was realized that liquid from the pustules of a smallpox victim, when scratched on the skin of a healthy patient, would most often cause a mild disease.… - [12 - 1 Fighting Disease is more than pills and shots](https://textbookconsortia.com/12-1-fighting-disease-is-more-than-pills-and-shots/): When you think of fighting disease, you mostly think of the doctor administering drugs that treat the infection or giving your children vaccines that build up their immunity so that they don’t get the targeted infection. However fighting disease also includes a whole host of other things. Health departments and your local, state, and federal governments play a huge role in keeping you healthy. In this chapter, we will spend a little time in each of these areas. Quarantine Early in human civilization, it was realized that an ill person could sometimes pass on their illness to others. One of… - [11 - 5 Three examples of the immune system in action](https://textbookconsortia.com/11-5-three-examples-of-the-immune-system-in-action/): You now have a complete picture of the immune system. To tie it all together, I finish the chapter by presenting three little stories of the whole immune system in action. How each infection occurs is unique, and this is, of course, an imagination of potential events. No harm came to any immune during the telling of these stories. Bacterial infection Here we will use the example of Streptococcus pyogenes, the causative agent of strep throat, a disease familiar to almost everyone. Figure 11.6 summarizes the process of infection with S. pyogenes and the body’s immune response. For our example,… - [11 - 4 Your immune system can make mistakes](https://textbookconsortia.com/11-4-your-immune-system-can-make-mistakes/): Sometimes the immune system fails and I don’t mean by not defending against threats, but the opposite. The immune system identifies something benign as a threat and marshals a chronic, damaging immune response. The two cases we will describe here are allergies and autoimmune diseases. Allergic reactions are immune reactions to non-threatening antigens, called allergens. Even worse, most of these allergens are chronically or periodically present in the environment leading to sustained immune responses. Many people are all too familiar with allergic reactions to pollen, cat dander, dog hair, dust, and more. Often these reactions are a nuisance, but sometimes… - [11 - 3 Adaptive immunity](https://textbookconsortia.com/11-3-adaptive-immunity/): The adaptive immune system is that part of the immune system that becomes stronger when exposed to an antigen. It involves a whole set of cells, but once activated it carries out many of its actions in conjunction with the cells of innate immunity. Features of the immune system The adaptive immune system has certain features that make it a distinct and potent method of fighting infections. The first is specificity. While the innate immune system can recognize general patterns that many pathogens share, for example, the presence of peptidoglycan, the adaptive immune response binds to and reacts with precise… - [11 - 2 Innate immunity](https://textbookconsortia.com/11-2-innate-immunity/): Innate immunity consists of the general mechanisms in a healthy animal that prevent colonization by microorganisms and antagonize or kill those that do enter the host. Innate immunity is always present, and the strength of its reaction does not increase upon repeated exposure to an antigen or microorganism. Anatomical structures Your body is put together in ways that prevent infection (Figure 11.3). You constantly secrete tears in your eyes and saliva in your mouth. These fluids are not just water, but also contain numerous antimicrobial compounds that help to repel would-be colonizers. A nasty protein (at least it’s nasty if… - [11 - 1 General Concepts](https://textbookconsortia.com/11-1-general-concepts/): How do I survive in a world teeming with microbes? You are an excellent growth medium. The viruses, bacteria, fungi, and protozoa that surround you would love to use all the nutrients that you represent. Since you are outnumbered in the world by the billions of critters living on you, how is it possible that you can fend off all the nasty pathogens that are out there and not just survive, but thrive? Much of the credit goes to your immune system, and in this chapter, we will give you an introductory primer into how it works. Before we begin,… - [10 - 6 Malaria](https://textbookconsortia.com/10-6-malaria/): If you are in the United States, you may have never thought about Malaria or know anyone who has contracted the disease. It is at best, a remote problem in other countries. However, Malaria is a massive problem worldwide. Transmission of the protozoan occurs in tropical and subtropical regions with over 3.4 billion people at risk for malaria infection. The World Health Organization estimates that there were 212 million cases of Malaria in 2015. Malaria is a protozoal disease, caused by five species of Plasmodium, that is carried by mosquitoes. The liberal use of DDT worldwide significantly reduced the incidence… - [10 - 5 Tuberculosis and the human immunodeficiency virus (HIV)](https://textbookconsortia.com/10-5-tuberculosis-and-the-human-immunodeficiency-virus-hiv/): Up until 120 years ago, tuberculosis was the primary cause of death in humans. It was called the white plague in Europe infecting close to 100% of the population, with nearly 25% of adult deaths being caused by it. Tuberculosis was formerly the leading cause of death in the United States before the advent of antimicrobial therapy against the causative bacterium. While the developed countries have mostly conquered TB, it is still a problem in the developing world. Over one-third of the worldwide population is infected with tuberculosis. It is the 3rd leading cause of death from infectious disease worldwide… - [10 - 4 Diarrheal diseases](https://textbookconsortia.com/10-4-diarrheal-diseases/): Diarrheal diseases cause 1.5 million deaths annually, with many occurring in developing countries with poor sanitation and a lack of potable drinking water. The rapid fluid loss because of diarrhea, combined with the common occurrence of malnourishment in impoverished areas, leads to death. Many of these deaths are preventable with better water sanitation and education on how to care for ill patients. These illnesses are of most significant concern in the very young and the elderly. A number of different bacteria and viruses cause diarrheal disease. In this section, we will concentrate on two important causes of these illnesses, Vibrio… - [10 - 3 Today’s most important pathogens](https://textbookconsortia.com/10-3-todays-most-important-pathogens/): First and foremost I want to point out that the leading cause of death in industrialized countries is not infectious disease. The tremendous progress that has been made in vaccines, antibiotics, and sanitation has removed infectious disease as a major killer in these countries. The 20th century was nothing short of miraculous in the progress we made in fighting infections. This advance can be attributed to the hard work done by scientists to understand the nature of infectious diseases and find treatments for them. For the undeveloped world, however, infectious disease still kills millions of people every year. Infectious disease… - [10 - 2 The black death changes the world](https://textbookconsortia.com/10-2-the-black-death-changes-the-world/): Arabella had found the perfect spot. It was still in the bounds that they had agreed to for hide and seek, but it was behind a barrel in a very dark part of the alley. No one would find her here! She squeezed herself behind the barrel and crouched down. But almost instantly let out a shriek, there was a dead rat beside her behind the barrel. Her older brother, who was it, immediately ran over and yelled “Found ya, silly girl! You can’t be screaming during the game if you want to win.” Her older brother Bryce, a large… - [10 - 1 What causes infectious disease?](https://textbookconsortia.com/10-1-what-causes-infectious-disease/): Humans, just like any other animal, are susceptible to infectious disease. However, the cause of these diseases was a mystery. Illness was thought to be a punishment from the gods or due to an imbalance of the humors. It was not until the late 19th century that we understood the true nature of infectious disease. The pioneering work of Louis Pasteur and Robert Koch helped to develop the germ theory of infectious disease — The replication of a microorganism in the body causes illness and removal of that microbe, either through the action of the immune system or medical treatment,… - [9 - 6 Changes in the microbiome change you](https://textbookconsortia.com/9-6-changes-in-the-microbiome-change-you/): In any case, a “healthy” microbiome contributes significantly to the overall health of the individual. So, how do you keep your microbiome healthy? The frustrating answer is scientists don’t know yet. There are however all sorts of folks who will tell you that they have the answer! Just consume whatever powder or potion that they are selling, and you will lose weight, your sex life will be better, your digestion will improve, your skin will clear, and you will be able to fly. One of my favorites is the canard of Candida overgrowth. I briefly touch on this in Chapter… - [9 - 5 You are covered in microorganisms, and that’s a good thing: The human microbiome](https://textbookconsortia.com/9-5-you-are-covered-in-microorganisms-and-thats-a-good-thing-the-human-microbiome/): And now we come to the host-microbe interaction that you have probably heard a lot about over the last few years, the human microbiome. We have known for decades that humans harbor an extensive collection of microorganisms on the outside of their bodies. (By the way, your intestinal tract is outside your body. If you stop and think for a minute, it is a tube that runs through your body, but those microbes that inhabit it are still living outside of you.) Microbiologists and health professionals also knew that many of the bacteria that inhabit the body were not doing… - [9 - 4 Bacteria can count](https://textbookconsortia.com/9-4-bacteria-can-count/): Another fun example of a mutualistic interaction is the symbiosis between the Hawaiian squid, Euprymna scolopes, and the bioluminescent bacteria Aliivibrio fischeri as shown in Figure 9.4. The bacteria propagate inside the squid’s body in a centrally located light-emitting organ that contains a culture exclusively made up of A. fischeri. The microbe enjoys a stable habitat and grows on the nutrients provided by the squid, reaching populations as high as 10 billion bacteria per ml. In return, the light produced by the microbe helps the squid hide from predators. This attempt at camouflage appears paradoxical since light would seem to… - [9 - 3 Insects would die without their bacterial partners](https://textbookconsortia.com/9-3-insects-would-die-without-their-bacterial-partners/): Insects are everywhere! They are one of the most prolific groups of animals being able to inhabit nearly every environment. I will posit that one of the reasons for their success is the close partnerships they have formed with microorganisms. Of course, I would say this, since I am a microbiologist. Of all eukaryotes, insects are the most tolerant of invasion by microbial partners. These relationships are essential to the success of the insect, and a majority of insects will form a symbiosis with one or several different microbial symbionts. All attempts to culture these microbes have met with failure,… - [9 - 2 Plant/fungi relationships](https://textbookconsortia.com/9-2-plant-fungi-relationships/): If you look at a plant, what you see is the portion that is above ground. What you don’t see is the half that is below the ground, and this is crucial in the plant’s interactions with microbial species. The area of soil where a plant grows is called the rhizosphere. There are many relationships between plants and the microbes that surround them, too many to cover here. We will spend time talking about two significant mutualistic relationships, plants – mycorrhizal fungi and legumes – nodulating bacteria. Mycorrhizal fungi (Figure 9.1) associate with plant roots to help them absorb nutrients.… - [9 - 1 Would we be better off without microbes?](https://textbookconsortia.com/9-1-would-we-be-better-off-without-microbes/): In the macro world, it is evident that living things all intertwine in a web, dependent upon one another for survival. The fox needs rabbits and mice to eat to survive, but the rabbits and mice need the fox to keep their populations under control. If the foxes are killed or move away, rodent populations then grow out of control, diminishing their food supply and leading to mass starvation. What may not be as obvious is that these rules apply to the microbial world as well. Microorganisms will often be dependent upon one another and will share resources. Something that… - [8 - 6 Microbes and Food: Friends and Foes](https://textbookconsortia.com/8-6-microbes-and-food-friends-and-foes/): Why is there a section on food microbiology in a chapter on the environment? Well, food is part of the environment too, we just happen to eat it. It’s worth talking about because the microbes present can have profound effects on food, either spoiling it, preserving it, or making us sick. All of these have significant impacts on our nutrition and health. Besides, I wanted to talk about it in this book and right now is as good a place as any. What the heck is that nasty stuff in the back of the fridge (food spoilage) We waste about… - [8 - 5 Microbes of the water](https://textbookconsortia.com/8-5-microbes-of-the-water/): Water covers 75% of the Earth’s surface, and that is a good thing since water is central to biological life. These waters are full of fish, plants, cephalopods, and all sorts of other creatures. By this time you will not be shocked to learn that there are billions of tiny microorganisms too. Many are unique to these habitats. Each environment needs a primary producer. These are the organisms that take inorganic carbon (often in the form of carbon dioxide or methane) and convert it into organic biochemicals that many other species can use. The primary producers are the essential foundation… - [8 - 4 Microbes of the Land](https://textbookconsortia.com/8-4-microbes-of-the-land/): Why do old abandoned mines leech sulfuric acid streams? One of the first environments that were explored using molecular microbial ecology was acid mines. Why here? First, there was funding to fix a problem. When a company abandons a mine after its useful life, they are sometimes left open. Water will often flow through the shafts and tunnels of these mines, making contact with ore. Water that exits the mine turns highly corrosive, having the same pH as a concentrated solution of sulfuric acid. Acidity is a high concentration of very reactive protons (see chapter 3 for more information on… - [8 - 3 Where do all the dead things go?](https://textbookconsortia.com/8-3-where-do-all-the-dead-things-go/): The goal of all catabolism is to create the substrates and energy needed to survive, grow, and move about (if the organism does that). The energy generated comes in two currencies, ATP and high-energy electrons. These two types of energy power movement and help to build the structures of the cell. Degradation is one type of catabolism that breaks apart organic molecules and extracts energy from them in the process. Degradation follows a similar pattern in all environments as shown in Figure 8.5. The first step of this process is to break down the large polymers that make up most… - [8 - 2 Learning to look the right way](https://textbookconsortia.com/8-2-learning-to-look-the-right-way/): Why should you read the rest of this chapter? Well first, you are an info geek. Why else would you buy this book and have read this far in the chapter? Beyond that, the microorganisms that live in any environment often have the most significant impact on the flow of organic material through them. Knowing what microbes are there, and what they are doing, goes a long way toward understanding that environment and predicting what perturbations such as pollution, invasive species, and climate change will have on an ecosystem. These can change how much life an environment can support and… - [8 - 1 The history of environmental microbiology](https://textbookconsortia.com/8-1-the-history-of-environmental-microbiology/): For years the existence of microorganisms was suspected, but could not be proven, since bacteria were too small to be seen with the naked eye. It took the microscope to expose their tiny world, and that instrument has been linked to microbiology ever since. In 1664, Robert Hooke devised a compound microscope and used it to observe fleas, sponges, bird feathers, plants, and molds, among other items. He published the work in Micrographia, which became a popular and widely read book at the time. Several years later Anton van Leeuwenhoek, a fabric merchant and amateur scientist (or “natural philosopher” as… - [7 - 7 The development of CRISPR shows the promise and danger of genetic technologies](https://textbookconsortia.com/7-7-the-development-of-crispr-shows-the-promise-and-danger-of-genetic-technologies/): CRISPR can successfully target specific pieces of DNA and when combined with other techniques insert desired modifications into the target. Unlike other methods of genetic engineering, CRISPR methods have high efficiency and there is no need for a selection step and thus no need for a selectable marker. For example, CRISPR can be used to cut out disease-causing genes and replace them with a healthy copy. In a landmark experiment reported in the journal Nature, Shoukhrat Mitalipov, from Oregon Health & Science University, along with scientists from the Salk institute, China, and South Korea, report the fixing of a genetic… - [7 - 6 How genetic engineering impacts your life](https://textbookconsortia.com/7-6-how-genetic-engineering-impacts-your-life/): Overexpressing needed proteins Do you know someone who has diabetes? Do they use insulin to control their diabetes? You have genetic engineering and the scientists at Genentech to thank. Genentech started in the 1970s as an outgrowth of the groundbreaking work in cloning DNA. The company was a manifestation of the realization that we could now clone out gene products and overexpress any protein of interest. However, the reality of implementing what we imagine can often be daunting. One of Genentech’s first successes was a proof of concept experiment where they synthesized the human hormone somatostatin (a peptide made of… - [7 - 5 The polymerase chain reaction (PCR)](https://textbookconsortia.com/7-5-the-polymerase-chain-reaction-pcr/): In 1969 Thomas D. Brock reported the isolation of Thermus aquaticus, a new species of bacterium that was living in a hot spring in Yellowstone National Park. T. aquaticus was notable in its ability to grow at temperatures of 70°C, much higher than typical microbes known at that time. Investigation of this bacterium surprised most scientists because scientists thought that growth at such high temperatures was impossible. While work in this area was of great interest to understand protein structure and function at high temperature, it was the work of a quirky scientist at Cetus corporation that vaulted it into… - [7 - 4 The second bacterial immune system - CRISPR](https://textbookconsortia.com/7-4-the-second-bacterial-immune-system-crispr/): DNA sequencing became accessible to many research labs in the 1980s and scientists began to sequence all sorts of DNA. In 1987, researchers in Japan reported the sequencing of the alkaline phosphatase gene of E. coli. The paper by Ishino et al. main focus was to sequence the gene and describe its expression. In a final paragraph, they described an unusual region that contained five homologous sequences of 29 bp with spacers of 32 bp. It was not clear to the researchers what the significance of this sequence was, but they reported the observation. In the next 13 years as… - [7 - 3 DNA Sequencing](https://textbookconsortia.com/7-3-dna-sequencing/): Having large quantities of DNA of the area you are interested in is quite handy, but one of the first things you want to know is the location of the genes. While you could use restriction enzymes to create maps of the DNA, this does not indicate gene position. It was also possible to map gene location, by doing genetic exchange experiments between two strains. This genetic mapping would give you a pretty accurate estimate of gene location, but it was a challenging, laborious process to build the strains you wanted and then cross them. It would be so much… - [7 - 1 Is genetic manipulation of living things by humans a new thing?](https://textbookconsortia.com/7-1-is-genetic-manipulation-of-living-things-by-humans-a-new-thing/): Ever since humans let go of their hunter-gatherer ways, settled down and began an agricultural society, we have manipulated the animals and plants we grow for food. First, we selected the plants and animals that had desirable properties. The biggest pig or best milk producing cow was bred to produce more of the same. The wheat or corn plant that gave the most kernels was chosen as planting seed for the next year. Farmers also realized that if they mated their most productive bull with their most productive cow, the offspring resulting would be of higher quality. They carried this… - [6 - 4 All the ways microbial enzymes touch your life](https://textbookconsortia.com/6-4-all-the-ways-microbial-enzymes-touch-your-life/): We have gone in-depth on two processes where microbes can benefit your life. Now let me list some of the different ways microbes and their enzymes impact your life. Fermentations. We talked about beer, but microbes are also involved in making a vast number of foods that you enjoy. Wine, pickles, yogurt, kombucha, soy sauce, cheese, sausages, vinegar, hams, chocolate, coffee, kimchi, sauerkraut, and olives are just a few examples of fermented foods. Other foods. Enzymes are often used to process food products. Starch is digested by amylases to provide syrups to the soft drink industry. Fruit drinks can be… - [6 - 3 Fueling our Economy](https://textbookconsortia.com/6-3-fueling-our-economy/): Our modern economy needs energy. Since the beginning of the industrial age, this has been provided by burning things. First coal, then oil, and now natural gas. Over the last 200 years, we have extracted and burned billions of tons of coal, oil, and gas to power our economy. Right now we are dependent upon them. The problem is, pumping tons of carbon dioxide into the atmosphere increases the greenhouse effect and leads to climate change. Climate change? Isn’t that some sort of hoax cooked up by scientists and hippies to tear down American capitalism? Well, let’s take a diversion… - [6 - 2 Enzymes in Cheese and Yogurt](https://textbookconsortia.com/6-2-enzymes-in-cheese-and-yogurt/): Besides alcoholic fermentation, there is a second fermentation essential to the manufacture of a significant amount of the food we eat. It is carried out by the lactic acid bacteria (LAB) who, unsurprisingly, perform a lactic acid fermentation and make lactic acid as an end product. There is an enormous variety of fermented foods that depend on the action of LAB to create their distinctive flavors, including cheese, yogurt, sauerkraut, kimchi, and kombucha. Before we dive into the details of the fermentative pathway, let’s take a look at the production of yogurt, cheese, and kombucha. Yogurt Yogurt is a milk… - [6 - 1 Enzymes and Beer](https://textbookconsortia.com/6-1-enzymes-and-beer/): Why did humans move from a hunter-gatherer society to an agricultural society? The transition of early humans from hunter-gatherer to farmer was momentous. It was a crucial point in the history of the world because it brought large groups of people together and from this civilization was born. The question is, why? There have been many different theories proposed, but one I find the most entertaining is beer! Yep, civilization started so that we could make beer. As put forth by Brian Hayden, an archeologist at Simon Fraser University, in Canada, growing crops such as wheat, barley, and rice is… - [5 - 5 Using the central dogma to blow your mind](https://textbookconsortia.com/5-5-using-the-central-dogma-to-blow-your-mind/): This chapter has walked you through the essential tasks that every cell must complete, DNA replication, transcription, and translation. Your head may be hurting trying to understand it all, and that is a good thing. You’re expanding your knowledge. But now I am going to up the ante by pointing out some extraordinary issues the cell faces. The bacterial chromosome is thin, but very long – in E. coli, the chromosome is about 1.5 mm long. The cell has to manage this large tangle of DNA inside a bacterium that is no more than 0.01 mm. It’s like trying to… - [5 - 4 Translation](https://textbookconsortia.com/5-4-translation/): The players in making proteins The creation of a copy of a gene in the form of mRNA doesn’t get you much closer to making a protein. It’s still nucleic acid. The process of converting a nucleic acid to a protein happens at a little protein factory inside cells called the ribosome. Ribosomes are the defining characteristic of living things on this planet. The functionality of the ribosome was likely one of the first capabilities to appear when life began. It takes the instructions present in our nucleic acid and translates them into proteins that carry out the functionality of… - [5 - 3 Transcription](https://textbookconsortia.com/5-3-transcription/): Creating the message from the DNA The enzyme RNA polymerase is the one that reads these signals in the DNA and forms the short recipes, or messages. Each recipe in the messenger RNA (mRNA), describes how to make one protein. In prokaryotes, there can be multiple recipes on one message whereas in eukaryotes, you have one recipe per message. Where RNA polymerase binds in the DNA is dictated by a set of proteins that interacts with the enzyme, Figure 5.4. In bacteria, proteins called sigma factors bind to the RNA polymerase and guide it to promoters that the sigma factors… - [5 - 2 DNA sequence directs its replication, transcription, and translation](https://textbookconsortia.com/5-2-dna-sequence-directs-its-replication-transcription-and-translation/): Quick, here is a small section of DNA sequence (Figure 5.2). It is from one of the smallest known genomes and comes from an intracellular parasite, a Mycoplasma species. Tell me what it encodes! Impossible you say? Of course it is. DNA to the untrained eye is just a long string of As, Ts, Gs, and Cs. It seems to make no sense at all. Just like when looking at a foreign language you cannot read. However, once you understand the punctuation marks, can translate its words, and know the grammar, it all makes sense. One of the golden ages… - [5 - 1 The thoughts of Francis Crick](https://textbookconsortia.com/5-1-the-thoughts-of-francis-crick/): Francis Crick is known as one of the discoverers of the structure of DNA along with James Watson, Maurice Wilkins, and Rosalind Franklin, but in my opinion, one of his equally significant contributions to biology was describing the essential functions of the cell, which he off-hand called the central dogma (Figure 5.1). When he gave this lecture in 1957, humbly entitled, Protein Synthesis, he outlined the process of how information in DNA can manifest itself as a living organism through the synthesis of proteins. Crick had numerous ideas in this lecture. He correctly predicted that DNA was the hereditary material… - [4 - 6 Tracing back to LUCA](https://textbookconsortia.com/4-6-tracing-back-to-luca/): All life on Earth is related. That may seem obvious, but it is more profound than you think. We appear to have all come from the same, far-distant ancestor. What’s the evidence for this? First, we are all made of the same four basic monomers, sugars, amino acids, lipids, and nucleic acids. Second, these monomers form just a few classes of polymers: proteins, polysaccharides, and nucleic acids. I would think that if we had different originations, we would have different, unique components, but we don’t. Third, at the cellular level, every living thing looks remarkably similar, containing a DNA compartment,… - [4 - 5 A self-replicative genome](https://textbookconsortia.com/4-5-a-self-replicative-genome/): The next big step is the creation of ways to remember these catalytic reactions. Instead of always needing the formed molecules to be present for copying, the cell remembers the recipe for making the enzyme. In the early stages of these networks “enzymes” were the cofactor and a small peptide or nucleotide chain that helped speed up the reaction. Thus we need a way of remembering these short chains. But before we can remember these small chains, we need to be able to polymerize RNA since the end result is to have nucleic acid as the hereditary material. Here is… - [4 - 4 Building up complexity](https://textbookconsortia.com/4-4-building-up-complexity/): RNA world hypothesis From the primordial soup, we have nucleobases. To get to RNA, we have to make nucleotides, which are the nucleobase with ribose (a sugar) and a phosphate added. Ribose was undoubtedly present, formed by the Formose reaction, as was phosphate. These three compounds could come together and produce reactive nucleotides. Once you have these activated nucleotides, experiments show that activated nucleotide molecules will polymerize and form RNA chains dozens of nucleotides long. These would be random sequences of bases, but at some point, the assembly of a short nucleotide that had a catalytic ability to direct its… - [4 - 3 Building from the Bottom](https://textbookconsortia.com/4-3-building-from-the-bottom/): Can this primordial soup make macromolecules? We have our soup; how do we make it live? First, let’s take a step back. We need enzymatic reactions to make macromolecules, and to make it self-sustaining, it would be ideal if these macromolecules could catalyze their own reactions. Two biological macromolecules can catalyze reactions, enzymes (made of amino acids) and RNA (made of nucleotides). The trick now is tracing the path from the primordial soup to the formation of self-perpetuating macromolecules. The primordial soup, even with the best estimates, would be pretty dilute. Dilute solutions are a problem because higher concentrations are… - [4 - 2 Life’s ingredients](https://textbookconsortia.com/4-2-lifes-ingredients/): What is life? If you want to think about the origin of life (we will call it by the cool acronym, OOL), you first have to define life. The presence of life may seem obvious to you but think a little deeper. How do you identify a living thing versus an inanimate object? Your friend bumps his head. How do you tell if he is all right? Is he breathing? Does his heartbeat? That would work for your friend, but it doesn’t work for plants or anything that does not contain a heart and lungs. Does it make copies of… - [4 - 1 Open hearts and open minds](https://textbookconsortia.com/4-1-open-hearts-and-open-minds/): If you take a walk in any wild area (or even a park) and carefully look at what is around you, you should be overwhelmed by the vast collection of living things. The Earth is teeming with life. From where did it all come? Humankind has been pondering this question for millennia, and many creation myths have sprung (Norse, Greek, Egyptian, Christian, Hindu, Muslim, etc.) Many of these entertaining stories contain songs of creation and fantastic creatures. Still, they don’t get into the details of how physical, inorganic chemicals ended up creating self-replicating, living things. What does science have to… - [3 - 7 Strange aliens among us](https://textbookconsortia.com/3-7-strange-aliens-among-us/): Before I end this chapter, I want to point out one more amazing group of microorganisms. If you want to find alien life forms, you don’t need to watch Sigourney Weaver blast away in Aliens or Bill Pullman lead the world’s fighter pilots in Independence Day. The earth is covered in aliens, and I don’t mean lizard people that are controlling our government. They live all around you: in the soil; in Salt Lake, Utah; in deep-sea ocean vents at 100°C (212°F); and in the sulfur springs of Yellowstone National Park. They are tough, some being able to withstand a… - [3 - 6 Structure in the context of multicellular organisms](https://textbookconsortia.com/3-6-structure-in-the-context-of-multicellular-organisms/): Tree Plants form a second classification of macroscopic organisms. A distinguishing characteristic of plants versus animals is their stationary nature. Because of this, there is more focus on withstanding the environment in place. Plants create sturdy, strong polymers to help them and because of this, they can grow to tremendous heights. This book is not a plant anatomy book, so I am only going to talk about two unique polymers that plants create. Cellulose, as mentioned previously, is a large polymer of glucose, Figure 3.15. These polymers are arranged in parallel to make microfibrils that are held together by hydrogen… - [3 - 5 Structure in the context of fungi](https://textbookconsortia.com/3-5-structure-in-the-context-of-fungi/): Around 2.7 billion years ago, two bacteria types got together and formed the first eukaryotic cell. I will have more to say about that later in the chapter. Eukaryotic organisms share much of the same fundamental structures to bacteria, which makes sense since they evolved from them. But they have differences. In our examples here, S. cerevisiae we will point out a few of these differences. Figure 3.13 shows typical cells of the yeast. We choose S. cerevisiae because you depend upon it to make your bread, brew your beer, and ferment your wine. First, eukaryotic cells tend to be… - [3 - 4 Structure in the context of bacteria](https://textbookconsortia.com/3-4-structure-in-the-context-of-bacteria/): Escherichia coli If we are going to have a few examples of microorganisms, we have to start with Escherichia coli or E. coli (Figure 3.9). This microbe is the most studied and best understood species in all of biology. Since its description by Theodor Escherich in 1885, it was known to be an inhabitant of the large intestine of humans. Most strains of E. coli have a mutualistic relationship with humans, while a few strains cause diarrheal disease or urinary tract infections. Early in the 20th century, it became a useful tool for understanding biological processes because it has simple… - [3 - 3 Molecules, monomers, and polymers](https://textbookconsortia.com/3-3-molecules-monomers-and-polymers/): What is a carbohydrate? If you have paid attention to nutrition even a little bit, you have heard of carbohydrates. In the common vernacular they are explained as fuel for our bodies, and that is one of the roles they have. Carbohydrates are organic molecules that have a ratio of carbon to oxygen to hydrogen of 1:1:2 and can be expressed as C(H2O). I bet you can see where the name comes from, a carbon hydrated with water. Carbohydrates can serve as sources of carbon for building other things and can be metabolized to release energy. Carbohydrates can also serve… - [3 - 1 Why knowing what we are made of matters](https://textbookconsortia.com/3-1-why-knowing-what-we-are-made-of-matters/): This chapter is going to delve into the details of what makes up all biological systems, including you, your cat (or dog), the lawn outside your home or apartment, the tree in the park, the pond, and the fish in the lake. We will look at the basic chemistry of life and then how these combine to make living things. I can hear you now, “Oh, no! Are you serious? You want me to learn chemistry! What good did any of that ever do me? I hate chemistry!” It seems I need to start this chapter with a sales pitch.… - [3 - 2 The simplest Legos - atoms](https://textbookconsortia.com/3-2-the-simplest-legos-atoms/): What makes up everything? Learning about chemical structures and how they are put together to make organisms (including you) is worth knowing in and of itself. This information also unlocks a deeper appreciation of life, and I bet you will be surprised at the underlying simplicity and elegance of biological systems. This foundation in structure will make the rest of the biology we talk about make sense — If you know the structure of something, it becomes much easier to understand how it functions. So let’s begin at with the sub-atomic particles that make up matter, they are not the… - [2 - 9 Instructions for buying Why Microbes Matter](https://textbookconsortia.com/2-9-instructions-for-buying-why-microbes-matter/): If you enjoyed this chapter, consider buying access to the rest of Why Microbes Matter. We designed Why Microbes Matter as an online resource, unlike most textbooks on the market that create online resources as an afterthought to sell you their overpriced hard copy. Thus, the pricing model is different. You are paying for a subscription to gain access to the material. Buying the book is easy, and it’s only $15! It’s easy to purchase a subscription. You know you want to! - [2 - 8 Some examples of ideas and the evidence for and against them](https://textbookconsortia.com/2-8-some-examples-of-ideas-and-the-evidence-for-and-against-them/): So, now you know that being awash in information is a double-edged sword. I have shown you the types of information at your fingertips, what’s most reliable and why, and I have given you a blueprint for how to manage it all and find the truth. We end this chapter by looking at a few examples that show you how to use these methods. Vaccines and autism We began this chapter by showing the harm that has been caused by a small proportion of the population losing their trust in the MMR vaccine. Where did this mistrust originate? Autism Spectrum… - [2 - 7 Things to look for](https://textbookconsortia.com/2-7-things-to-look-for/): Practice looking for the shams and flimflams. Always be on the lookout for things that don’t seem right. Remember, an argument is only valid if all its premises are true. If you find one untrue premise, then the argument falls apart. I once bought a book that claimed to have a sure-fire cure for acid reflux. It presented all sorts of background information on the illness, which was correct, and then changes to diet and behavior that seemed like they might help. It then started talking about how having Candida overgrowth can aggravate acid reflux and how you can determine… - [2 - 6 A Recipe for Truth and Understanding Part 2](https://textbookconsortia.com/2-6-a-recipe-for-truth-and-understanding-part-2/): Graphics can lie to you If you want to persuade people, display the data in a chart! Charts are great for taking complex, hard to understand data sets, and creating a visual representation of the data that is easier to interpret. However, honesty is crucial when converting numbers into a chart. The hucksters of the world have found all sorts of magic tricks to lie with graphs. This section will point out some of the more egregious methods. If you want to persuade your audience that something significant has happened, but your data won’t cooperate, what is the charlatan to… - [2 - 5 A Recipe for Truth and Understanding](https://textbookconsortia.com/2-5-a-recipe-for-truth-and-understanding/): Our goal in this section is to help you find the information you can trust. Here you will learn habits that can help you to become and remain an informed citizen. Briefly, you should: read widely, verify references, be aware of data manipulation, know the difference between causation and correlation, identify the shams and flimflams, trust peer-review, consider the source, and be skeptical. One significant pitfall of the wealth of information available online is that it is easy to fall into like-minded groups that agree with your worldview. You wrap yourself in a cocoon of self-assurance with friends that reinforce… - [2 - 4 The Four Levels of Information](https://textbookconsortia.com/2-4-the-four-levels-of-information/): If you are going to test arguments, you need information from experts to measure the truthfulness of statements that you hear or read. Where can you get reliable information? One of the magical things about the world we live in today is that much of human knowledge that has been generated from antiquity until the present day is online and available using a smartphone or computer in a matter of seconds. Stop and think about that! That is wonderous. Humans today would be considered wizards and sorcerers by those living a hundred years ago. This information comes in many forms,… - [2 - 3 Who Can You Trust](https://textbookconsortia.com/2-3-who-can-you-trust/): I am going to give you the punchline first. Initially, you should trust no one. Those who want your trust have to earn it. How then does a source earn your trust? By the use of solid, fair arguments and verifiable facts. So, what is a good, fair argument? To answer that question, we are going to delve a little into logic and argument analysis. Don’t close the book! Trust me. I will try to make it entertaining. Here is a logical argument: That seems logical enough, and I think most people would agree with it. But before we verify… - [2 - 2 The Age of Misinformation](https://textbookconsortia.com/2-2-the-age-of-misinformation/): We live in amazing times. I have been around long enough to know the world before there was a global network connecting us all. Before the internet, people got their information from newspapers, radio, television, and books written by experts. If you wanted to dig deeply into a topic, it meant a trip to your local library and searching manually through something called the card catalog. In every library, there was a room full of cabinets with tiny little drawers, each of them packed with 3 x 5 index cards with subjects and locations written on them. You dug through… - [2 - 1 Misinformation matters](https://textbookconsortia.com/2-1-misinformation-matters/): Science is a way to teach how something gets to be known, to what extent things are known (for nothing is known absolutely), how to handle doubt and uncertainty, what the rules of evidence are, how to think about things so that judgments can be made, how to distinguish truth from fraud and from show. -– Robert Feynman While the story I am about to tell is fictional, this fact is still true; a young, immunocompromised woman recently died from measles. This death was the first confirmed case of mortality from measles in over a decade. She had so much… - [1 - 2 How to Read This Book](https://textbookconsortia.com/1-2-how-to-read-this-book/): How should you read this book? Easy! Look at each page, scan the letters from left to the right, and, when done, turn the page. Simple! Oh, you know how to do that, you wanted tips on where you should start. At the beginning. Still not good enough? Sheesh! Honestly, you can read it any way you like. Most of the chapters do not need you to understand previous concepts. However, I do think it would be wise to at least skim chapters 1 to 6, especially if you need a brush up on biology, or you were not paying… - [1 - 3 Summary of Chapters](https://textbookconsortia.com/1-3-summary-of-chapters/): In this section, I summarize the content of the book. It will give you a hint as to what each chapter is about and whether each is worth your time. Chapter 1 – Introduction Do I need to explain what is here? You are reading it. Chapter 2 – Staying in the Real World Before we begin talking about the science of microbiology, I spend some time teaching you to think like a scientist. These are the most important lessons this book can teach you. Not only will you better appreciate the information in the rest of the book, but… - [1 - 1 Why I Wrote this Book](https://textbookconsortia.com/1-1-why-i-wrote-this-book/): The discovery of microbes occurred over 300 years ago, and we began to understand their essential roles in health and the environment in the 19th century. Throughout the 20th century, we began to understand the nature of many diseases that were caused by microbes, and then how to combat them. Ironically, the key to defeating many bacterial infections came from other microbes in the form of antibiotics. Vaccines lead to the defeat of many other diseases. In the second half of the 20th-century, experiments in bacteria were crucial to unlocking the secrets of life, and this work led to the… - [15 - 7 Phagocytes kills invaders](https://textbookconsortia.com/15-7-phagocytes-kills-invaders/): Learning Objectives Phagocytes Engulf and Kill Foreign Cells An important result of inflammation is the recruitment of phagocytes. These cells function to engulf and attack particles in the host that have been signaled for removal by various mechanisms. In this section we describe the synthesis and properties of phagocytes. Phagocytes originate in the bone marrow from stem cells that first differentiate into myeloid precursor cells. These are a set of intermediate cells that can take a number of paths. Under the influence of various cytokines, the myeloid precursor cells then differentiate into different kinds of phagocytic cells such as polymorphonuclear… - [30 - 4 Molecular techniques](https://textbookconsortia.com/30-4-molecular-techniques/): Many modern techniques for detecting the presence of microorganisms and determining the sequence of their DNA depend on molecular biology techniques that first began to appear in the middle of the 1970’s. In this section we give a somewhat detailed explanation of common methodologies that were used in part to generate much of the information we have talked about throughout this textbook. Of course the techniques talked about here are not comprehensive, but they do cover some of the more common (and oft mentioned) procedures of microbial molecular biology in use today. Gel electrophoresis It is often very useful to… - [30 - 3 Visualizing microbes](https://textbookconsortia.com/30-3-visualizing-microbes/): Another important facet of microbiology is the observation of microbes and due to their small size, microscopes are necessary. Besides being able to visualize cell morphology and specialized structures, microscopes can even be used to identify bacteria in mixed samples when combined with certain fluorescent probes. These instruments are thus becoming indispensable tools in microbial ecology as well as their traditional use for observation and in identification. Staining microbes Before observing microorganisms, they must be placed on a suitable physical support so that they can be observed under a microscope. For light microscopes this simply entails placing a bit of… - [30 - 2 Counting microorganisms](https://textbookconsortia.com/30-2-counting-microorganisms/): There are many different reasons one might need to known the population of microorganisms in a given sample. For example, determining the rate at which a microbe is killed by UV light requires analysis of the number of viable cells before, and at various times during, UV exposure. In other experiments, it is important to know that you have the right density or growth stage to use, such as required for transforming a plasmid constructed in vitro into an E. coli strain. Assessment of bacterial populations in applied industries is also important. Many food-processing plants measure the level and type… - [30 - 1 Culturing Bacteria](https://textbookconsortia.com/30-1-culturing-bacteria/): To study microorganisms and their metabolism, it is almost always desirable to bring them into the laboratory and grow them under controlled conditions. This is largely because it is necessary to have pure cultures (that is growth of only one unique type of microorganism) to be confident about assigning a characteristic or behavior to that single species. Therefore, it is necessary to create conditions where an individual microbe can grow free from other living organisms. How do scientists create suitable nutrient conditions so that microorganisms will grow? Then, once you get a group of microbes growing from a certain environment,… - [29 - 7 Summary](https://textbookconsortia.com/29-7-summary/): The archaea were recognized about a century after the culture of microorganisms began. Understandably our knowledge of them is less than that of bacteria, but is rapidly increasing. One immediate impact of investigations into their physiological characteristics was the realization that they were a unique form of life, as distinct from bacteria as they are from eukaryotes. This has lead to a revolution in classification and the creation of the three domains of life. In this chapter we have examined the various branches of archaea. Molecular phylogenetic analysis reveals that they cluster as deep branches, some of which diverged very… ## Pages - [About the Author](https://textbookconsortia.com/about-the-author/): Welcome to my website/textbook/blog. I am Timothy Paustian, a Distinguished Teaching Professor at the University of Wisconsin-Madison. I teach Advanced Laboratory Techniques in Microbiology, Prokaryotic Microbiology Lecture and Lab, and The Microbial World (a course for non-majors). I enjoy teaching and have been honored to work with students for over 34 years. My research interest is in microbiology education, where I led the development of the Microbiology Concept Inventory and am currently working on an updated version with a collection of gifted faculty from around the country. I also have an interest in the impact of artificial intelligence on higher… - [Thank you for subscribing to Why Microbes Matter](https://textbookconsortia.com/thank-you-for-subscribing-to-why-microbes-matter/): The book has many features to offer. Make sure you make the most of them! To find the sections you want to read, go to the table of contents. If you are looking for specific information, you can search for it. Each page contains features that list a glossary of words. If you don’t know what something means and it is underlined, hover over it for a definition. If you have any questions, the authors are always ready to response. Just contact us - [Why Microbes Matter - Table of Contents](https://textbookconsortia.com/why-microbes-matter-table-of-contents/): Why Microbes Matter is an introduction to the world of microbiology and provides the information you need to learn about microbiology at a fair price. This page lists all the chapters of the book with links to each section. If a chapter you want to read is not accessible, you probably need to buy a subscription. If you have already purchased a subscription, you may be logged out. Log back in. - [Textbooks for All](https://textbookconsortia.com/): Tired of paying high prices for your textbook? Feeling guilty for asking your students to shell out hundreds of dollars to get a decent reference to supplement your course? Well, so was I! (I am Dr. Timothy Paustian by the way.) I have taught microbiology for over 30 years, and in that time, I have seen textbook prices skyrocket at rates much higher than the rate of inflation. 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There are also many animations throughout the book that will help you learn. Here is one from chapter 8 that shows you an animation of a respiratory chain. The authors are always… - [Through the Microscope - Table of Contents](https://textbookconsortia.com/through-the-microscope-table-of-contents/): Through the Microscope is a textbook written for students to provide them with the information they need to learn about microbiology at a fair price. This page lists all the chapters of the book with links to each section. If a chapter you want to read is not accessible, you probably need to buy a subscription. If you already purchased a subscription, you may be logged out. Log back in. - [Privacy Policy](https://textbookconsortia.com/privacy-policy/): Who we are Suggested text: Our website address is: https://textbookconsortia.com. 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