An Invisible World Test

An Invisible World

FIGURE 1.1

INTRODUCTION

From _________ thermal hot springs to deep beneath the _________ ice, _________ can be found almost everywhere on earth in great _________. Microorganisms (or microbes, as they are also called) are small organisms. Most are so small that they cannot be seen without a microscope.

Most _________ are _________ to _________ and, in fact, many are _________. They play fundamental _________ in _________ everywhere on earth, _________ the _________ of many food _________. People use them to make _________, medicines, and even _________. Without _________, there would be no bread, _________, or _________. Our _________ are _________ with _________, and our skin alone is home to _________ of _________ Some of them we can’t live without; _________ cause _________ that can make us sick or even _________ us.

Although much more is known today about _________ life than ever before, the _________ majority of this _________ world _________ unexplored. _________ continue to identify new ways that microbes _________ and _________ humans.

1.1 What Our Ancestors Knew

CLINICAL _________

Part _________

Cora, a 41-year-old _________ and mother of two, has recently been _________ severe _________, a high fever, and a _________ neck. Her husband, who has _________ Cora to see a doctor, _________ that _________ also _________ confused at times and unusually _________. Based on these _________, the doctor suspects that Cora may have _________, a _________ life-threatening _________ of the tissue that surrounds the brain and spinal _________.

Meningitis has several _________ causes. It can be brought on by _________, fungi, _________, or even a _________ to _________ or _________ to heavy metals. Although people with viral _________ usually _________ on their own, _________ and _________ meningitis are quite serious and _________ treatment.

Cora’s doctor orders a lumbar _________ (spinal _________) to take three _________ of _________ fluid (_________) from around the _________ cord (Figure 1.2). The samples will be sent to _________ in three different _________ for _________: clinical _________, microbiology, and hematology. The samples will first be visually _________ to _________ whether the CSF is abnormally _________ or _________; then the CSF will be _________ under a microscope to see if it _________ a _________ number of red and white blood cells and to check for any abnormal _________ types. In the _________ lab, the specimen will be _________ to _________ any _________ in a sediment; this sediment will be _________ on a slide and stained with a _________ stain. _________ staining is a _________ used to differentiate between two different types of bacteria (_________ and _________).

About _________ of _________ with _________ meningitis will show _________ in their CSF with a _________ stain.2 _________ Gram _________ did not show any bacteria, but her doctor decides to prescribe her antibiotics just in case. Part of the _________ sample will be _________ in special dishes to see if bacteria or fungi will grow. It takes some time for most _________ to _________ in _________ quantities to be _________ and _________.

• What types of microorganisms would be _________ by _________ treatment?

FIGURE 1.2

Jump to the next Clinical _________ box.

Most people today, even those who know very little about microbiology, are familiar with the _________ of _________, or "_________," and their role in human _________. Schoolchildren learn about _________, viruses, and other _________, and many even _________ specimens under a _________. But a few hundred years ago, before the invention of the _________, the _________ of many types of microbes was impossible to prove. By definition, _________, or _________, are very small _________; many _________ of _________ are too small to see without a _________, although some parasites and fungi are visible to the _________ eye.

Humans have been living with—and _________ for much longer than they have been able to see them. _________ evidence _________ that _________ have had some _________ of _________ life since prehistoric _________ and have used that knowledge to develop _________ as well as prevent and _________ disease. In this section, we will explore some of the historical _________ of _________ as well as the early _________ of _________ as a science.

Fermented _________ and _________

People across the world have _________ fermented _________ and _________ like _________, wine, bread, yogurt, _________, and _________ vegetables for all of recorded history. Discoveries from several _________ sites _________ that even prehistoric people took _________ of _________ to _________ and _________ the _________ of food. Archaeologists _________ pottery _________ from a Neolithic village in _________ found that people were making a fermented _________ from _________, honey, and fruit as early as 7000 _________

Production of these _________ and _________ requires _________ fermentation, a process that uses _________, mold, or yeast to convert _________ (carbohydrates) to alcohol, _________, and _________ acids (Figure 1.3). While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had _________ or old grape _________ that had fermented—they later learned to harness the power of fermentation to make _________ like bread, cheese, and wine.

FIGURE 1.3

The _________ and Evidence of Early Treatments###

Prehistoric _________ had a very _________ understanding of the _________ of disease, and various cultures _________ different _________ and _________. While many believed that illness was punishment for angering the gods or was _________ the result of _________, archaeological evidence suggests that prehistoric people attempted to treat _________ and _________. One example of this is _________ the _________, a _________ mummy found frozen in the ice of the Ötzal _________ on the Austrian-Italian _________ in _________. Because _________ was so well _________ by the ice, _________ discovered that he was infected with the _________ of the parasite _________ trichiura, which may have caused him to have abdominal _________ and _________. Researchers also found evidence of _________ burgdorferi, a bacterium that causes _________ disease.4 Some researchers think Ötzi may have been trying to treat his infections with the _________ fruit of the _________ betulinus _________, which was discovered _________ to his belongings.5 This fungus has both _________ and _________ properties. _________ was also covered in tattoos that were made by _________ incisions into his skin, filling them with _________, and then burning the herbs.6 There is _________ that this may have been another attempt to treat his health _________.

Early _________ of Disease, Contagion, and Containment###

Several ancient civilizations appear to have had some understanding that disease could be _________ by _________ they could not see. This is especially _________ in _________ attempts to contain the spread of disease. For example, the Bible _________ to the practice of quarantining people with _________ and other diseases, _________ that people understood that diseases could be _________. Ironically, while leprosy is communicable, it is also a disease that _________ slowly. This means that people were likely _________ after they had already spread the disease to others.

Clean water and _________ are among the most important _________ of healthy societies. The earliest _________ of _________ sanitation _________ are from the ancient Indus Valley Civilization _________ of _________ and _________, located in current-day _________. Constructed in 2500 _________ (about _________ years ago), the _________ had _________ networks of wells, _________, and _________ systems that stored fresh water and carried waste away. About two thousand years later, people in the ancient Greek _________ attributed disease to bad air, _________, which they called "_________ odors." They developed _________ practices that built on this idea. In _________, they built aqueducts, which brought fresh water into the city, and a giant _________, the _________ Maxima, which carried waste away and into the river _________ (Figure 1.4). Some _________ believe that this _________ helped protect the _________ from _________ of _________ Illnesses.

Even before the _________ of the microscope, some doctors, _________, and _________ made great strides in understanding the invisible _________ we now know as microbes—that can cause _________, disease, and death.

FIGURE 1.4

The _________ physician _________ (460–370 _________) is _________ the "father of _________ medicine" (Figure 1.5). _________ many of his _________ and _________, he _________ the idea that disease was _________ by _________ forces. Instead, he _________ that _________ had natural causes from within _________ or their environments. _________ and his heirs are believed to have _________ the _________ Corpus, a collection of texts that make up some of the _________ surviving _________ books.7 _________ is also often _________ as the author of the _________ Oath, _________ by new physicians to pledge their dedication to diagnosing and treating _________ without _________ harm.

While _________ is _________ the father of _________ medicine, the Greek _________ and _________ Thucydides (_________ BC) is considered the father of scientific history because he advocated for evidence-based _________ of _________ reasoning (Figure 1.5). Among his most important _________ are his observations _________ the _________ plague that killed _________ of the population of Athens between 430 and 410 _________. Having _________ the _________ himself, _________ made the important _________ that _________ did not get _________ with the disease, even when _________ care of actively _________ people.8 This observation _________ an early understanding of the _________ of _________.

Marcus _________ Varro (_________ BC) was a _________ Roman _________ who was one of the first people to propose the concept that things we cannot see (what we now _________ microorganisms) can cause disease (Figure 1.5). In _________ Rusticae (On Farming), _________ in _________ BC, he said that "precautions must also be taken in neighborhood _________ . ._________ . because certain minute creatures _________ minuta] grow there which cannot be seen by the eye, which _________ in the air and enter the body through the mouth and nose and there cause serious diseases."9

Centuries later, Islamic _________, mainly in Persia, built on the knowledge from Hippocrates as well as from _________ and _________ medicine. _________ among them was _________ Bakr _________, usually _________ to as al-Razi or by his Latinized _________, Rhazes. He developed a range of experimental _________ to test various _________ of medicine. For example, to _________ a _________ for a hospital, _________ hung _________ meat around the city, and located the _________ in the place where the meat took the longest to rot. He also was the first to _________ measles and smallbox, and undertook _________ to _________ which available treatments were most _________ for each. While _________ did not have the technology to understand the role of microbes, his efforts to identify the causes of illnesses, rather than _________ focusing on the _________, were _________ influential.

Islamic _________ created one of the most important medical _________ in history, the _________ of Medicine (Arabic: _________- Qānūn _________ al-Ṭibb). _________ in _________ by _________ and _________ Ibn _________ (often _________ to as Avicenna), the encyclopedia _________ detailed _________ of the parts of the body, a _________ account of over _________ medicinal _________, and _________ of several illnesses _________ by body part or health event. In the work, _________ Sina _________ mechanisms of contagion, _________ that _________ could be infected by foreign _________, and that illness could be _________ by breath. He is also _________ with _________ the practice of _________ people who are _________, laying the foundation for historical and contemporary _________ methods. The Canon was translated into many _________, and was a _________ resource for teaching medicine around the world, through the _________ and beyond.

FIGURE 1.5

The _________ of _________

While the ancients may have _________ the _________ of _________ "minute _________," it _________ until the invention of the _________ that their existence was definitively _________. While it is _________ who exactly invented the microscope, a Dutch _________ merchant _________ Antonie _________ Leeuwenhoek (_________) was the first to develop a lens _________ enough to view _________. In _________, using a simple but powerful _________, Leeuwenhoek was able to observe _________ organisms, which he _________ as "_________" or "_________ little _________," swimming in a drop of rain water. From his _________ of these little _________, we now know he was _________ at _________ and _________. (We will explore _________ contributions to microscopy further in How We See the _________ World.)

Nearly _________ years after van _________ got his first _________ of _________, the "_________ Age of Microbiology" _________ a _________ of new discoveries between 1857 and 1914. Two famous _________, Louis _________ and _________ Koch, were especially _________ in _________ our _________ of the unseen world of _________ (Figure 1.6). Pasteur, a French _________, showed that individual _________ strains had unique _________ and _________ that _________ is _________ by _________. He also invented _________, a process used to kill _________ responsible for spoilage, and developed _________ for the treatment of diseases, _________ rabies, in animals and humans. _________, a _________ physician, was the first to _________ the _________ between a single, _________ microbe and a _________ human disease. For example, he _________ the _________ that cause anthrax (_________ anthracis), _________ (Vibrio _________), and _________ (Mycobacterium _________ We will discuss these famous _________, and _________, in later chapters.

FIGURE 1.6

As _________ has _________, it has allowed the broader _________ of _________ to grow and _________ in _________ unimagined _________. Much of what we know about human _________ comes from our _________ of _________, and many of the tools we use today to study cells and their _________ derive from work with microbes.

MICRO _________

Microbiology _________

Because individual microbes are generally too small to be seen with the naked eye, the science of _________ is _________ on _________ that can artificially _________ the _________ of our natural _________ of _________. Early _________ like _________ and _________ had _________ tools at their _________ than are found in modern _________, making their discoveries and innovations that much more impressive. Later chapters of this _________ will _________ many _________ of _________ in _________, but for now, here is a brief _________ of some of the fundamental _________ of the microbiology _________

• _________ produce _________ images of microorganisms, human cells and tissues, and many other types of specimens too small to be _________ with the naked eye.

• _________ and _________ are _________ to add color to microbes so they can be better observed under a _________. Some _________ can be used on living _________, whereas _________ require that the _________ be _________ with _________ or heat before _________. Some _________ only work on certain types of microbes because of _________ in their cellular _________ composition.

• _________ media are used to grow _________ in a lab _________. Some _________ are _________; others are more solid or _________. A _________ medium _________ nutrients, _________ water, various salts, a source of carbon (like glucose), and a _________ of _________ and _________ acids (like yeast _________) so _________ can grow and _________. Ingredients in a _________ medium can be _________ to grow unique _________ of _________.

• A Petri _________ is a flat-lidded _________ that is typically _________ centimeters (_________) in _________ and _________ cm high. Petri _________ made out of either plastic or glass are used to hold _________ media (Figure 1.7).

• Test tubes are cylindrical _________ or glass tubes with rounded _________ and open tops. They can be used to grow _________ in _________, or _________ or solid growth _________.

• A Bunsen _________ is a metal _________ that _________ a _________ that can be _________ to _________ pieces of equipment. A rubber tube carries gas (fuel) to the _________. In many labs, _________ burners are being _________ out in favor of infrared _________, which _________ a similar purpose without the _________ risks of an open flame.

• An inoculation _________ is a handheld _________ that _________ in a small wire loop (Figure 1.7). The loop can be _________ to _________ microorganisms on agar in a _________ dish or to _________ them from one test tube to another. Before each use, the _________ loop must be _________ so _________ do not become _________.

FIGURE 1.7

1.2 A Systematic Approach

Once _________ became _________ to _________ with the help of microscopes, _________ began to realize their enormous _________. Microorganisms _________ in all sorts of ways, _________ their size, their _________, and their rates of reproduction. To study this incredibly _________ new _________ of _________, researchers _________ a way to _________ organize them.

The Science of _________

Taxonomy is the _________, description, _________, and _________ of living organisms. _________ is the practice of organizing _________ into different groups _________ on their shared _________. The most famous early taxonomist was a _________ botanist, _________, and _________ named _________ Linnaeus (_________). In _________, Linnaeus _________ Systema _________, an _________ booklet in which he proposed the Linnaean _________, a system of _________ and _________ organisms _________ a standard format so scientists could discuss _________ using _________ terminology. He continued to revise and add to the book, which grew into _________ volumes (Figure 1.8).

FIGURE 1.8

In his taxonomy, _________ divided the natural world into three kingdoms: animal, plant, and mineral (the mineral _________ was later abandoned). Within the animal and _________ kingdoms, he grouped _________ using a hierarchy of increasingly _________ levels and sublevels _________ on their similarities. The names of the _________ in _________ original _________ were _________, class, order, family, _________ (plural: _________), and _________. Species was, and _________ to be, the most specific and basic _________ unit.

Evolving _________ of Life (Phylogenies)

With _________ in _________, other _________ gradually made refinements to the _________ system and eventually _________ new _________ for _________ organisms. In the _________, there was a _________ interest in developing _________ that took into account the _________ relationships, or phylogenies, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a _________ tree (or tree of life). In these _________, groups of organisms are arranged by how _________ related they are thought to be. In early phylogenetic _________, the _________ of _________ was _________ by their visible _________, such as the _________ or _________ of hair or the number of limbs. Now, the _________ is more complicated. Today, phylogenic _________ include _________, biochemical, and embryological _________, as will be _________ later in this chapter

Linnaeus’s tree of life contained just two main branches for all living things: the animal and plant _________. In _________, Ernst _________, a _________ biologist, _________, and _________, proposed another kingdom, _________, for _________ organisms (Figure 1.9). He later _________ a _________ kingdom, _________, for _________ organisms whose cells _________ nuclei, like bacteria.

FIGURE 1.9

Nearly _________ years later, in _________, American _________ Robert _________ (1920–1980) _________ adding another kingdom—Fungi—in his tree of life. _________ tree also contained a level of categorization above the _________ level—the _________ or _________ level—to _________ between _________ that have membrane-bound _________ in their cells (_________) and those that do not (_________). Empire _________ contained just the _________ Monera. The Empire _________ contained the other four kingdoms: _________, Protista, _________, and _________. Whittaker’s _________ tree was considered the standard _________ for many years.

Figure 1.10 shows how the tree of life has _________ over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to _________ where they would fit into a tree of Life.

FIGURE 1.10

CLINICAL _________

Part _________

Antibiotic _________ are _________ designed to kill or inhibit the growth of bacteria. But after a couple of days on antibiotics, _________ shows no signs of improvement. Also, her _________ cultures came back from the _________ negative. Since bacteria or fungi were not _________ from _________ CSF _________, her doctor rules out bacterial and fungal _________. Viral _________ is still a _________.

However, _________ now _________ some _________ new _________. She is starting to have _________ walking. Her muscle _________ has spread from her neck to the rest of her body, and her _________ sometimes _________ involuntarily. In addition, _________ cognitive _________ are _________. At this point, _________ doctor _________ very _________ and _________ more _________ on the CSF _________.

• What types of microorganisms could be _________ Cora’s _________

The _________ of _________ in Modern Taxonomy###

Haeckel’s and Whittaker’s _________ presented _________ about the phylogeny of different _________ based on readily _________ characteristics. But the _________ of _________ genetics in the late 20th century revealed other ways to organize _________ trees. _________ methods _________ for a standardized way to compare all living organisms without relying on observable _________ that can often be subjective. Modern taxonomy _________ heavily on comparing the nucleic _________ (deoxyribonucleic _________ [DNA] or ribonucleic _________ [RNA]) or proteins from different _________. The more similar the nucleic _________ and _________ are between two _________, the more closely _________ they are considered to be

In the 1970s, American microbiologist _________ Woese _________ what _________ to be a "living record" of the _________ of _________. He and his _________ George _________ created a genetics-based tree of life based on similarities and differences they observed in the _________ sequences _________ for small subunit _________ RNA (_________) of different organisms. In the process, they _________ that a certain type of _________, called _________ (now _________ simply as archaea), were significantly different from other bacteria and eukaryotes in terms of their small subunit _________ gene _________. To _________ this difference, they _________ a tree with three Domains above the level of _________: Archaea, _________, and _________ (Figure 1.11). Analysis of small _________ rRNA _________ sequences _________ archaea, _________, and _________ all _________ from a common _________ cell type. The tree is _________ to show a _________ evolutionary _________ between _________ and _________ than they have to Bacteria.

FIGURE 1.11

Scientists continue to use analysis of RNA, _________, and _________ to _________ how _________ are _________. One _________, and _________, discovery is that of horizontal _________ transfer—when a gene of one _________ is _________ into another organism’s _________. Horizontal _________ transfer is especially common in _________ and can make it difficult to determine how organisms are evolutionarily _________. Consequently, some scientists now think in terms of "webs of life" rather than "_________ of life."

Naming _________

In _________ his _________, Linnaeus _________ a system of _________ nomenclature, a two-word _________ system for identifying _________ by _________ and _________ epithet. For example, modern humans are in the genus _________ and have the _________ epithet _________ sapiens, so their _________ name in binomial _________ is _________ sapiens. In binomial _________, the _________ part of the _________ is always capitalized; it is _________ by the specific _________ name, which is not capitalized. Both names are italicized. When referring to the _________ of _________, the _________ nomenclature would be _________ sapiens.

Taxonomic _________ in the 18th through 20th _________ were _________ derived from Latin, since that was the common language _________ by _________ when _________ systems were first _________. Today, _________ discovered _________ can be given _________ derived from Latin, _________, or English. Sometimes these names _________ some _________ trait of the _________; in other cases, _________ are _________ after the scientists who discovered them. The _________ Haloquadratum _________ is an example of both of these _________ schemes. The genus, _________, describes the microorganism’s _________ habitat (_________ is _________ from the Greek _________ for "salt") as well as the arrangement of its square cells, which are _________ in square clusters of four _________ (quadratum is Latin for "foursquare"). The species, _________, is _________ after _________ Edward _________, the _________ who _________ Haloquadratum _________ in _________. While it might seem easier to give an organism a common _________ name—like a red-headed _________ can imagine how that could become problematic. What happens when another _________ of _________ with red head _________ is _________ The _________ nomenclature _________ use _________ this _________ problem by assigning each organism a single, _________ two-word _________ that is recognized by scientists all over the world

In this text, we will _________ abbreviate an organism’s _________ and _________ after its first _________. The _________ form is simply the first _________ of the genus, _________ by a period and the full name of the _________. For example, the _________ Escherichia _________ is _________ to _________. coli in its _________ form. You will _________ this same convention in other _________ texts as well.

Bergey’s _________

Whether in a tree or a web, _________ can be difficult to identify and classify. Without easily _________ macroscopic _________ like _________, feet, or fur, _________ must _________, grow, and devise _________ to study their _________ properties to differentiate and classify _________. Despite these hurdles, a group of microbiologists _________ and _________ a set of _________ for _________ and _________ microorganisms. First published in 1923 and since _________ many _________, Bergey’s _________ of _________ Bacteriology and Bergey’s _________ of _________ Bacteriology are the standard references for identifying and classifying different prokaryotes. (_________ D of this _________ is _________ based on Bergey’s _________; it _________ how the organisms that appear in this _________ are _________.) Because so many _________ look _________, methods _________ on _________ characteristics must be _________ to _________ them. For example, _________ tests can be _________ to _________ chemicals _________ to certain species. _________, serological _________ can be used to identify _________ antibodies that will _________ against the proteins found in certain species. _________, DNA and rRNA _________ can be used both for _________ a particular bacterial _________ and for classifying _________ discovered _________.

MICRO _________

Same _________, Different _________

Within one species of microorganism, there can be several _________ called _________. While different strains may be _________ identical _________, they can have very different _________. The _________ Escherichia _________ is _________ for _________ food _________ and _________ diarrhea. However, there are actually many different _________ of _________. coli, and they _________ in their ability to cause disease.

One _________ (disease-causing) _________. coli _________ that you may have heard of is _________. coli _________. In _________, infection from E. _________ O157:H7 can cause _________ cramps and diarrhea. _________ usually _________ from _________ water or food, _________ raw _________ and _________ meat. In the _________, there were several large outbreaks of E. _________ O157:H7 thought to have originated in undercooked _________.

While _________. coli _________ and some other _________ have _________ E. _________ a bad name, most E. _________ strains do not cause disease. In fact, some can be helpful. Different strains of E. _________ found _________ in our gut help us _________ our food, provide us with some needed _________, and fight against _________ microbes.

1.3 Types of Microorganisms

Most _________ are _________ and small enough that they _________ artificial _________ to be seen. However, there are some _________ microbes that are _________ to the naked eye, and some multicellular _________ that are microscopic. An object must measure about 100 _________ (μm) to be _________ without a microscope, but most _________ are many times _________ than that. For some perspective, consider that a typical animal cell _________ roughly _________ μm across but is still _________. Bacterial _________ are _________ about _________ μm, and viruses can be _________ times _________ than _________ (Figure 1.12). See Table 1.1 for units of length _________ in _________.

FIGURE 1.12

TABLE 1.1- Units of Length Commonly Used in Microbiology

Microorganisms _________ from each other not only in size, but also in structure, _________, metabolism, and many other characteristics. While we _________ think of microorganisms as being _________, there are also many multicellular _________ that are too small to be seen without a _________. Some _________, such as viruses, are even _________ (not _________ of _________).

Microorganisms are found in each of the three domains of life: _________, Bacteria, and Eukarya. _________ within the domains _________ and _________ are all prokaryotes (their cells _________ a _________), whereas _________ in the domain _________ are _________ (their _________ have a nucleus). Some microorganisms, such as _________, do not fall within any of the three domains of life. In this section, we will briefly _________ each of the _________ groups of microbes. Later chapters will go into greater _________ about the diverse _________ within each group.

Prokaryotic _________

Bacteria are found in nearly every habitat on earth, _________ within and on _________. Most _________ are _________ or _________, but some are _________, causing disease in _________ and other animals. _________ are _________ because their genetic material (DNA) is not _________ within a true _________. Most _________ have _________ walls that contain _________.

Bacteria are often _________ in _________ of their general shape. Common _________ include _________ (coccus), _________ (bacillus), or curved (_________, spirochete, or vibrio). Figure 1.13 _________ examples of these _________.

FIGURE 1.13

They have a wide range of metabolic _________ and can grow in a variety of _________, using different combinations of nutrients. Some bacteria are photosynthetic, such as _________ cyanobacteria and anoxygenic green sulfur and green _________ bacteria; these bacteria use energy _________ from _________, and _________ carbon _________ for _________. Other _________ of _________ are _________, obtaining their energy from organic or inorganic _________ in their environment

Archaea are also _________ prokaryotic _________. Archaea and bacteria have different _________ histories, as well as significant _________ in _________, metabolic _________, and the composition of their _________ walls and membranes. _________ most _________, archaeal _________ walls do not contain peptidoglycan, but their _________ walls are often _________ of a similar _________ called _________. Like _________, archaea are found in nearly every habitat on earth, even extreme _________ that are very cold, very hot, very basic, or very acidic (Figure 1.14). Some archaea live in the human body, but none have been shown to be human pathogens.

FIGURE 1.14

Eukaryotic _________

The _________ Eukarya _________ all _________, including _________- or _________ eukaryotes such as _________, fungi, plants, and animals. The major defining _________ of _________ is that their _________ contain a nucleus.

Protists###

Protists are an _________ grouping of eukaryotes that are not plants, animals, or _________. Some _________ are _________ and _________ are _________; all _________ are _________ of _________.

Algae (_________: alga) are mostly made up of protists that can be either _________ or _________ and _________ widely in size, _________, and _________ (Figure 1.15). Algal _________ are _________ by _________ walls made of _________, a type of _________. Algae are photosynthetic _________ that _________ energy from the sun and _________ oxygen and carbohydrates into their environment. Cyanobacteria, a type of bacteria, is also _________ an _________, but these organisms are bacterial _________ and therefore have a peptidoglycan-based _________ wall, _________ the _________ cell wall of the algal _________. Because other organisms can use the waste _________ of all algae for energy, _________ are important parts of many _________. Many _________ products contain ingredients _________ from _________, such as carrageenan or alginic _________, which are found in some _________ of ice cream, _________ dressing, _________, lipstick, and toothpaste. A derivative of algae also plays a prominent _________ in the microbiology _________. Agar, a gel _________ from _________, can be mixed with various _________ and _________ to grow microorganisms in a _________ dish. _________ are also being _________ as a possible _________ for _________.

FIGURE 1.15

FIGURE 1.16

Protozoa (_________: protozoan) are protists that make up the _________ of many food _________ by _________ nutrients for other _________. Protozoa are very _________. Some _________ move with help from hair-like _________ called _________ or _________ structures called flagella. _________ extend part of their cell _________ and _________ to _________ themselves forward. These _________ extensions are called _________ ("false feet"). Some _________ are _________; others feed on _________ material. Some are _________, whereas _________ are _________, only able to _________ by _________ nutrients from a _________ organism. Most protozoa are harmless, but some are pathogens that can cause disease in animals or humans (Figure 1.16).

Fungi###

Fungi (_________: fungus) are also _________. Some _________ fungi, such as _________, resemble plants, but they are actually quite different. Fungi are not _________, and their cell _________ are usually made out of _________ rather than cellulose.

Unicellular _________ included within the study of _________. There are more than 1000 _________ species. _________ are found in many different _________, from the deep sea to the human _________. Some _________ have _________ uses, such as _________ bread to rise and beverages to ferment; but yeasts can also cause food to spoil. Some even cause diseases, such as _________ yeast _________ and _________ thrush (Figure 1.17).

FIGURE 1.17

Other _________ of interest to _________ are _________ organisms called molds. _________ are made up of long _________ that form visible _________ (Figure 1.18). Molds are found in many different environments, from soil to rotting food to _________ bathroom _________. Molds play a _________ role in the _________ of dead plants and animals. Some molds can cause _________, and _________ produce _________ metabolites called mycotoxins. _________ have been used to make _________, including _________, which is one of the most commonly _________ antibiotics, and cyclosporine, _________ to prevent organ _________ following a transplant.

FIGURE 1.18

Helminths###

Multicellular _________ worms called helminths are not _________ microorganisms, as most are large enough to see without a microscope. However, these _________ fall within the field of _________ because _________ caused by helminths _________ microscopic _________ and _________. One example of a helminth is the _________ worm, or Dracunculus _________, which _________ dizziness, _________, diarrhea, and painful _________ on the legs and feet when the _________ works its way out of the skin (Figure 1.19). _________ typically _________ after a person _________ water _________ water _________ infected by guinea-worm _________. In the mid-1980s, there were an estimated _________ million _________ of _________ disease, but the disease has been largely _________. In _________, there were only _________ cases _________, thanks to the _________ efforts of the World Health _________ (WHO) and other _________ committed to improvements in drinking water sanitation.11 _________

FIGURE 1.19

Viruses###

Viruses are acellular _________, which _________ they are not _________ of _________. Essentially, a virus _________ of _________ and _________ material—either _________ or _________, but never both—that are inert outside of a host _________. However, by incorporating themselves into a host _________, viruses are able to co-opt the host’s _________ mechanisms to multiply and infect other hosts.

Viruses can infect all types of cells, from human _________ to the cells of other _________. In _________, viruses are responsible for numerous _________, from the common cold to _________ Ebola (Figure 1.20). However, many _________ do not cause disease.

FIGURE 1.20

Microbiology as a Field of _________

Microbiology is a _________ term that encompasses the study of all different types of microorganisms. But in practice, microbiologists _________ to _________ in one of several subfields. For example, _________ is the study of bacteria; _________ is the study of fungi; _________ is the study of protozoa; _________ is the study of helminths and other _________; and _________ is the study of viruses (Figure 1.21). _________, the study of the immune system, is often included in the study of _________ because _________ interactions are central to our _________ of _________ disease _________. Microbiologists can also _________ in certain areas of microbiology, such as _________ microbiology, _________ microbiology, _________ microbiology, or food _________.

In this textbook, we are _________ concerned with clinical _________ of _________, but since the various subfields of microbiology are highly _________, we will often discuss applications that are not strictly _________.

FIGURE 1.21

EYE ON ETHICS###

Bioethics in Microbiology###

In the 1940s, the U.S. government was _________ for a solution to a _________ problem: the prevalence of sexually _________ diseases (_________) among _________. Several _________ government-funded _________ used human subjects to research common STDs and treatments. In one such study, American researchers _________ exposed more than _________ human _________ in _________ to _________, gonorrhea, and chancroid to determine the ability of penicillin and other _________ to _________ these _________. Subjects of the study included _________ soldiers, _________, prostitutes, and psychiatric _________ of _________ were _________ that they were _________ part in the study. Researchers _________ subjects to STDs by various _________, from _________ intercourse with infected _________ to _________ subjects with the _________ known to cause the diseases. This latter method involved _________ a small wound on the _________ genitals or elsewhere on the body, and then putting _________ directly into the _________ In _________, a _________. government _________ tasked with investigating the experiment _________ that only some of the _________ were _________ with _________, and _________ subjects _________ by _________, likely as a result of the study.14

Unfortunately, this is one of many horrific _________ of _________ experiments that have _________ basic _________ standards. Even if this study had led to a _________ medical _________ (it did not), few would _________ that its methods were ethically sound or _________ justifiable. But not every case is so clear cut. _________ working in clinical _________ are frequently confronted with ethical _________, such as working with patients who decline a vaccine or life-saving blood transfusion. These are just two _________ of _________ decisions that may _________ with the religious and philosophical _________ of both the _________ and the health-care _________.

No matter how _________ the _________, microbiology _________ and _________ practice must be _________ by a certain set of _________ principles. _________ must be done with integrity. _________ and _________ subjects provide informed _________ (not only agreeing to be _________ or _________ but _________ an _________ of the purpose of the study and any risks _________). Patients’ _________ must be respected. _________ must be approved by an _________ review board. When _________ with _________, accurate _________, honest _________, and _________ are _________. Animals _________ for _________ must be treated _________, and all protocols must be _________ by an institutional animal care and use _________. These are just a few of the _________ principles _________ in the Eye on Ethics _________ throughout this book.

CLINICAL _________

Resolution###

Cora’s _________ samples show no _________ of _________ or _________, as would be _________ with a viral _________. However, there is a high _________ of a particular _________, 14-3-3 _________, in her CSF. An electroencephalogram (_________) of her brain function is also abnormal. The EEG _________ that of a _________ with a neurodegenerative disease like _________ or _________, but _________ rapid _________ decline is not _________ with either of these. Instead, her doctor _________ that _________ has _________ disease (_________), a type of _________ spongiform _________ (TSE).

CJD is an _________ rare disease, with only about _________ cases in the _________ States each year. It is not caused by a _________, fungus, or virus, but rather by prions—which do not fit neatly into any particular category of microbe. Like viruses, _________ are not found on the tree of life because they are _________. Prions are extremely small, about _________ the size of a typical _________. They contain no _________ material and are _________ solely of a type of _________ protein.

CJD can have several different _________. It can be _________ through _________ to the brain or nervous-system _________ of an infected person or animal. Consuming meat from an infected animal is one way such exposure can occur. There have also been _________ cases of exposure to CJD through contact with contaminated _________ equipment15 and from _________ and _________ donors who unknowingly had CJD.16 _________ In _________ cases, the disease _________ from a specific _________ mutation that can _________ be _________. However, in approximately _________ of _________ with _________, the cause of the disease is spontaneous (or sporadic) and has no identifiable _________ Based on her _________ and their rapid _________, Cora is diagnosed with sporadic _________.

Unfortunately for Cora, _________ is a fatal disease for which there is no _________ treatment. _________ 90% of patients die within _________ year of diagnosis.19 Her doctors _________ on _________ her _________ and _________ symptoms as her disease progresses. Eight months later, Cora _________. Her _________ diagnosis is confirmed with a _________ autopsy.