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Scientists have studied prokaryotes for centuries, but it wasn't until 1966 that scientist Thomas Brock (1926–) discovered that certain bacteria can live in boiling water. This led many to wonder whether prokaryotes may also live in other extreme environments, such as at the bottom of the ocean, at high altitudes, or i... | {
"Header 1": "**Introduction**",
"token_count": 248,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Identify and describe unique examples of prokaryotes in various habitats on earth
- Identify and describe symbiotic relationships
- Compare normal/commensal/resident microbiota to transient microbiota
- Explain how prokaryotes are classified
All living organisms are classified into th... | {
"Header 1": "**4.1 Prokaryote Habitats, Relationships, and Microbiomes**",
"token_count": 2041,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
As we have learned, prokaryotic microorganisms can associate with plants and animals. Often, this association results in unique relationships between organisms. For example, bacteria living on the roots or leaves of a plant get nutrients from the plant and, in return, produce substances that protect the plant from path... | {
"Header 1": "**4.1 Prokaryote Habitats, Relationships, and Microbiomes**",
"Header 2": "**Symbiotic Relationships**",
"token_count": 2029,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features. Traditionally, the classification of prokaryotes was based on their shape, staining... | {
"Header 1": "**4.1 Prokaryote Habitats, Relationships, and Microbiomes**",
"Header 2": "**Taxonomy and Systematics**",
"token_count": 301,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
*Bergey's Manual of Determinative Bacteriology* is now **[available](https://openstax.org/l/22mandeterbact) [\(https://openstax.org/l/22mandeterbact\)](https://openstax.org/l/22mandeterbact)** online. You can also access a searchable **[database \(https://openstax.org/l/22databmicrefst\)... | {
"Header 1": "**4.1 Prokaryote Habitats, Relationships, and Microbiomes**",
"Header 2": "**Link to Learning**",
"token_count": 1628,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each class within the phylum Proteobacteria: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria
- Give an example of a bacterium in each class of Proteobacteria
In 1987, the American microbiologi... | {
"Header 1": "**4.2 Proteobacteria**",
"token_count": 2013,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**Figure 4.6** *Neisseria meningitidis* growing in colonies on a chocolate agar plate. (credit: Centers for Disease Control and Prevention)
The pathogen responsible for pertussis (whooping cough) is also a member of Betaproteobacteria. The bacterium *Bordetella pertussis*, from the o... | {
"Header 1": "**4.2 Proteobacteria**",
"token_count": 706,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The most diverse class of gram-negative bacteria is **Gammaproteobacteria**, and it includes a number of human pathogens. For example, a large and diverse family, *Pseudomonaceae*, includes the genus *Pseudomonas*. Within this genus is the species *P. aeruginosa*, a pathogen responsible for diverse infections in variou... | {
"Header 1": "**4.2 Proteobacteria**",
"Header 2": "**Gammaproteobacteria**",
"token_count": 1874,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
coli has<br>been a model organism for many studies in genetics and molecular<br>biology |
| Hemophilus | Gram-negative<br>bacillus | Pleomorphic, may appear as coccobacillus, aerobe, or facultative<br>anaerobe; grow on blood agar; path... | {
"Header 1": "**4.2 Proteobacteria**",
"Header 2": "**Gammaproteobacteria**",
"token_count": 1106,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The smallest class of Proteobacteria is **Epsilonproteobacteria**, which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of Epsilonproteobacteria are *Campylobacter* and *Helicobacter*, both of which include human pathog... | {
"Header 1": "**4.2 Proteobacteria**",
"Header 2": "**Epsilonproteobacteria**",
"token_count": 619,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Spirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most **spirochetes** are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult... | {
"Header 1": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 2": "**Spirochetes**",
"token_count": 637,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The gram-negative nonproteobacteria of the genera *Cytophaga*, *Fusobacterium*, and *Bacteroides* are classified together as a phylum and called the **CFB group**. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shap... | {
"Header 1": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 2": "*Cytophaga***,** *Fusobacterium***, and** *Bacteroides*",
"token_count": 2032,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
"Comparative Proteomic Studies in *Rhodospirillum rubrum* Grown Under Different Nitrogen Conditions." *Journal of Proteome Research* 7 no. 8 (2008):3267–3275.
Another large, diverse group of phototrophic bacteria compose the phylum **Cyanobacteria**; they get their bluegreen color from the chlorophyll contained in th... | {
"Header 1": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 2": "*Cytophaga***,** *Fusobacterium***, and** *Bacteroides*",
"token_count": 1356,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each category of high G+C and low G+C gram-positive bacteria
- Identify similarities and differences between high G+C and low G+C bacterial groups
- Give an example of a bacterium of high G+C and low G+C group commonly associated with each category
Prok... | {
"Header 1": "4.4 Gram-Positive Bacteria",
"token_count": 332,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The name Actinobacteria comes from the Greek words for *rays* and *small rod*, but Actinobacteria are very diverse. Their microscopic appearance can range from thin filamentous branching rods to coccobacilli. Some Actinobacteria are very large and complex, whereas others are among the smallest independently living orga... | {
"Header 1": "4.4 Gram-Positive Bacteria",
"Header 2": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 2032,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Although less common in the United States, tuberculosis is still extremely common in many parts of the world, including Nigeria. Marsha's work there in a medical lab likely exposed her to *Mycobacterium tuberculosis*, the bacterium that causes tuberculosis.
Marsha's doctor ordered her to stay at home, wear a respirat... | {
"Header 1": "4.4 Gram-Positive Bacteria",
"Header 2": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 2024,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
epidermidis*, whose main habitat is the human skin, is thought to be nonpathogenic for humans with healthy immune systems, but in patients with immunodeficiency, it may cause infections in skin wounds and prostheses (e.g., artificial joints, heart valves)*. S. epidermidis* is also an important cause of infections assoc... | {
"Header 1": "4.4 Gram-Positive Bacteria",
"Header 2": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 1997,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of deeply branching bacteria
- Give examples of significant deeply branching bacteria
On a phylogenetic tree (see **[A Systematic Approach](#page-32-0)**), the trunk or root of the tree represents a common ancient evolutionary ancestor, often called the la... | {
"Header 1": "**4.5 Deeply Branching Bacteria**",
"token_count": 1106,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each category of Archaea
- Explain why archaea might not be associated with human microbiomes or pathology
- Give common examples of archaea commonly associated with unique environmental habitats
Like organisms in the domain Bacteria, organisms of the d... | {
"Header 1": "**4.5 Deeply Branching Bacteria**",
"Header 2": "**4.6 Archaea**",
"token_count": 1219,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane. They can l... | {
"Header 1": "**4.5 Deeply Branching Bacteria**",
"Header 2": "**Euryarchaeota**",
"token_count": 1972,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
- Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
- Some pho... | {
"Header 1": "**4.5 Deeply Branching Bacteria**",
"Header 2": "**Euryarchaeota**",
"token_count": 2008,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Although bacteria and viruses account for a large number of the infectious diseases that afflict humans, many serious illnesses are caused by eukaryotic organisms. One example is malaria, which is caused by *Plasmodium*, a eukaryotic organism transmitted through mosquito bites. Malaria is a major cause of morbidity (il... | {
"Header 1": "**Introduction**",
"token_count": 424,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Summarize the general characteristics of unicellular eukaryotic parasites
- Describe the general life cycles and modes of reproduction in unicellular eukaryotic parasites
- Identify challenges associated with classifying unicellular eukaryotes
- Explain the taxonomic scheme used for uni... | {
"Header 1": "**5.1 Unicellular Eukaryotic Parasites**",
"token_count": 2030,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The protists are a **polyphyletic** group, meaning they lack a shared evolutionary origin. Since the current taxonomy is based on evolutionary history (as determined by biochemistry, morphology, and genetics), protists are scattered across many different taxonomic groups within the domain Eukarya. Eukarya is currently ... | {
"Header 1": "**5.1 Unicellular Eukaryotic Parasites**",
"Header 2": "**Taxonomy of Protists**",
"token_count": 1996,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**[Figure 5.10](#page-213-0)** and **[Figure 5.11](#page-214-0)** illustrate the life cycles of cellular and plasmodial slime molds, respectively.
**Figure 5.9** (a) The cellular slime mold *Dictyostelium discoideum* can be grown on agar in a Petri dish. In this image, individual amoebo... | {
"Header 1": "**5.1 Unicellular Eukaryotic Parasites**",
"Header 2": "**Taxonomy of Protists**",
"token_count": 2020,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**Figure 5.16** A saprobic oomycete, or water mold, engulfs a dead insect. (credit: modification of work by Thomas Bresson)
#### **Link to Learning**
Explore the procedures for detecting the presence of an apicomplexan in a public water supply, at **... | {
"Header 1": "**5.1 Unicellular Eukaryotic Parasites**",
"Header 2": "**Taxonomy of Protists**",
"token_count": 1501,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Explain why we include the study of parasitic worms within the discipline of microbiology
- Compare the basic morphology of the major groups of parasitic helminthes
- Describe the characteristics of parasitic nematodes, and give an example of infective eggs and infective larvae
- Descri... | {
"Header 1": "**5.2 Parasitic Helminths**",
"token_count": 1031,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Phylum **Platyhelminthes** (the platyhelminths) are flatworms. This group includes the flukes, tapeworms, and the turbellarians, which include planarians. The flukes and tapeworms are medically important parasites (**[Figure 5.20](#page-223-0)**).
The **flukes** (trematodes) are nonsegmented flatworms that have an or... | {
"Header 1": "**5.2 Parasitic Helminths**",
"Header 2": "**Clinical Focus**",
"Header 3": "**Platyhelminths (Flatworms)**",
"token_count": 2038,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
(credit: Centers for Disease Control and Prevention)
An eradication campaign led by WHO, the CDC, the United Nations Children's Fund (UNICEF), and the Carter Center (founded by former U.S. president Jimmy Carter) has been extremely successful in reducing cases of dracunculiasis. This has been possible because diagnos... | {
"Header 1": "**5.2 Parasitic Helminths**",
"Header 2": "**Clinical Focus**",
"Header 3": "**Platyhelminths (Flatworms)**",
"token_count": 318,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Explain why the study of fungi such as yeast and molds is within the discipline of microbiology
- Describe the unique characteristics of fungi
- Describe examples of asexual and sexual reproduction of fungi
- Compare the major groups of fungi in this chapter, and give examples of each
-... | {
"Header 1": "**5.3 Fungi**",
"token_count": 294,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Fungi have well-defined characteristics that set them apart from other organisms. Most multicellular fungal bodies, commonly called molds, are made up of filaments called **hyphae**. Hyphae can form a tangled network called a **mycelium** and form the **thallus** (body) of fleshy fungi. Hyphae that have walls between t... | {
"Header 1": "**5.3 Fungi**",
"Header 2": "**Characteristics of Fungi**",
"token_count": 1302,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The fungi are very diverse, comprising seven major groups. Not all of the seven groups contain pathogens. Some of these groups are generally associated with plants and include plant pathogens. For example, Urediniomycetes and Ustilagomycetes include the plant rusts and smuts, respectively. These form reddish or dark ma... | {
"Header 1": "**5.3 Fungi**",
"Header 2": "**Fungal Diversity**",
"token_count": 1870,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Explain why algae are included within the discipline of microbiology
- Describe the unique characteristics of algae
- Identify examples of toxin-producing algae
- Compare the major groups of algae in this chapter, and give examples of each
- Classify algal organisms according to major g... | {
"Header 1": "**5.4 Algae**",
"token_count": 643,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Although the algae and protozoa were formerly separated taxonomically, they are now mixed into supergroups. The algae are classified within the Chromalveolata and the Archaeplastida. Although the Euglenozoa (within the supergroup Excavata) include photosynthetic organisms, these are not considered algae because they fe... | {
"Header 1": "**5.4 Algae**",
"Header 2": "**Algal Diversity**",
"token_count": 1538,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Explain why lichens are included in the study of microbiology
- Describe the unique characteristics of a lichen and the role of each partner in the symbiotic relationship of a lichen
- Describe ways in which lichens are beneficial to the environment
No one has to worry about getting s... | {
"Header 1": "**5.5 Lichens**",
"token_count": 216,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
A **lichen** is a combination of two organisms, a green alga or cyanobacterium and an ascomycete fungus, living in a symbiotic relationship. Whereas algae normally grow only in aquatic or extremely moist environments, lichens can potentially be found on almost any surface (especially rocks) or as **epiphytes** (meaning... | {
"Header 1": "**5.5 Lichens**",
"Header 2": "**Characteristics**",
"token_count": 2047,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Public health measures in the developed world have dramatically reduced mortality from viral epidemics. But when epidemics do occur, they can spread quickly with global air travel. In 2009, an outbreak of H1N1 influenza spread across various continents. In early 2014, cases of Ebola in Guinea led to a massive epidemic ... | {
"Header 1": "**Introduction**",
"token_count": 345,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the general characteristics of viruses as pathogens
- Describe viral genomes
- Describe the general characteristics of viral life cycles
- Differentiate among bacteriophages, plant viruses, and animal viruses
- Describe the characteristics used to identify viruses as obligate i... | {
"Header 1": "**Introduction**",
"Header 2": "**6.1 Viruses**",
"token_count": 1159,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Viruses can infect every type of host cell, including those of plants, animals, fungi, protists, bacteria, and archaea. Most viruses will only be able to infect the cells of one or a few species of organism. This is called the **host range**. However, having a wide host range is not common and viruses will typically on... | {
"Header 1": "**Introduction**",
"Header 2": "**Hosts and Viral Transmission**",
"token_count": 2029,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
At the tips of these spikes are structures that allow the virus to attach and enter a cell, like the influenza virus hemagglutinin spikes (H) or enzymes like the neuraminidase (N) influenza virus spikes that allow the virus to detach from the cell surface during release of new virions. Influenza viruses are often ident... | {
"Header 1": "**Introduction**",
"Header 2": "**Hosts and Viral Transmission**",
"token_count": 2025,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the lytic and lysogenic life cycles
- Describe the replication process of animal viruses
- Describe unique characteristics of retroviruses and latent viruses
- Discuss human viruses and their virus-host cell interactions
- Explain the process of transduction
- Describe the repl... | {
"Header 1": "**Introduction**",
"Header 2": "**6.2 The Viral Life Cycle**",
"token_count": 2016,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
After binding to host receptors, animal viruses enter through endocytosis (engulfment by the host cell) or through membrane fusion (viral envelope with the host cell membrane). Many viruses are host specific, meaning they only infect a certain type of host; and most viruses only infect certain types of cells within tis... | {
"Header 1": "**Introduction**",
"Header 2": "**6.2 The Viral Life Cycle**",
"token_count": 2035,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
To establish a systemic infection, the virus must enter a part of the vascular system of the plant, such as the phloem. The time required for systemic infection may vary from a few days to a few weeks depending on the virus, the plant species, and the environmental conditions. The virus life cycle is complete when it i... | {
"Header 1": "**Introduction**",
"Header 2": "**6.2 The Viral Life Cycle**",
"token_count": 1350,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Unlike bacteria, many of which can be grown on an artificial nutrient medium, viruses require a living host cell for replication. Infected host cells (eukaryotic or prokaryotic) can be cultured and grown, and then the growth medium can be harvested as a source of virus. Virions in the liquid medium can be separated fro... | {
"Header 1": "**6.3 Isolation, Culture, and Identification of Viruses**",
"Header 2": "**Isolation of Viruses**",
"token_count": 2044,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Harvesting tissue or organs from a dying patient without consent is not only considered unethical but illegal, regardless of whether such an act could save other patients' lives. Is it ethical, then, for scientists to continue to use Lacks's tissues for research, even though they were obtained illegally by today's stan... | {
"Header 1": "**6.3 Isolation, Culture, and Identification of Viruses**",
"Header 2": "**Isolation of Viruses**",
"token_count": 2039,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe viroids and their unique characteristics
- Describe virusoids and their unique characteristics
- Describe prions and their unique characteristics
Research attempts to discover the causative agents of previously uninvestigated diseases have led to the discovery of nonliving di... | {
"Header 1": "**6.4 Viroids, Virusoids, and Prions**",
"token_count": 1864,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
| Disease | Mechanism(s) of Transmission[10] |
|-------------------------------------------------|---------------------------------------------------------------------------------------------... | {
"Header 1": "**6.4 Viroids, Virusoids, and Prions**",
"token_count": 598,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Resolution**
A few days later, David's doctor receives the results of the immunofluorescence test on his skin sample. The test is negative for rabies antigen. A second viral antigen test on his saliva sample also comes back negative. Despite these results, the doctor decides to continue David's current course ... | {
"Header 1": "**6.4 Viroids, Virusoids, and Prions**",
"Header 2": "**Clinical Focus**",
"token_count": 249,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **[6.1 Viruses](#page-251-0)**
- Viruses are generally ultramicroscopic, typically from 20 nm to 900 nm in length. Some large viruses have been found.
- **Virions** are acellular and consist of a nucleic acid, DNA or RNA, but not both, surrounded by a protein **capsid**. There may also be a phospholipid membrane... | {
"Header 1": "**6.4 Viroids, Virusoids, and Prions**",
"Header 2": "**Summary**",
"token_count": 745,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The earth is estimated to be 4.6 billion years old, but for the first 2 billion years, the atmosphere lacked oxygen, without which the earth could not support life as we know it. One hypothesis about how life emerged on earth involves the concept of a "primordial soup." This idea proposes that life began in a body of w... | {
"Header 1": "**Introduction**",
"token_count": 289,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Identify common elements and structures found in organic molecules
- Explain the concept of isomerism
- Identify examples of functional groups
- Describe the role of functional groups in synthesizing polymers
Biochemistry is the discipline that studies the chemistry of life, and its o... | {
"Header 1": "**7.1 Organic Molecules**",
"token_count": 2042,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Certain species of molds, yeast, and bacteria, such as *Rhizopus*, *Yarrowia*, and *Lactobacillus* spp., respectively, can only metabolize one type of optical isomer; the opposite isomer is not suitable as a source of nutrients. Another important reason to be aware of optical isomers is the therapeutic use of these typ... | {
"Header 1": "**7.1 Organic Molecules**",
"token_count": 1314,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Give examples of monosaccharides and polysaccharides
- Describe the function of monosaccharides and polysaccharides within a cell
The most abundant biomolecules on earth are **carbohydrates**. From a chemical viewpoint, carbohydrates are primarily a combination of carbon and water, an... | {
"Header 1": "**7.2 Carbohydrates**",
"token_count": 1567,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
Describe the chemical composition of lipids
- Describe the unique characteristics and diverse structures of lipids
- Compare and contrast triacylglycerides (triglycerides) and phospholipids.
- Describe how phospholipids are used to construct biological membranes.
Although they are com... | {
"Header 1": "**7.3 Lipids**",
"token_count": 1996,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**Figure 7.16** Cholesterol and hopene (a hopanoid compound) are molecules that reinforce the structure of the cell membranes in eukaryotes and prokaryotes, respectively.
#### **Link to Learning**
#### **Liposomes**
This **[video \(https://openstax.... | {
"Header 1": "**7.3 Lipids**",
"token_count": 383,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the fundamental structure of an amino acid
- Describe the chemical structures of proteins
- Summarize the unique characteristics of proteins
At the beginning of this chapter, a famous experiment was described in which scientists synthesized amino acids under conditions simula... | {
"Header 1": "**7.4 Proteins**",
"token_count": 2032,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
(credit: modification of work by National Human Genome Research Institute)
• What can happen if a protein's primary, secondary, tertiary, or quaternary structure is changed?
#### **Micro Connections**
#### **Primary Structure, Dysfunctional Proteins, and Cystic Fibrosis**
Proteins associated with biological mem... | {
"Header 1": "**7.4 Proteins**",
"token_count": 720,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
• Describe examples of biosynthesis products within a cell that can be detected to identify bacteria
Accurate identification of bacterial isolates is essential in a clinical microbiology laboratory because the results often inform decisions about treatment that directly affect patient o... | {
"Header 1": "**7.5 Using Biochemistry to Identify Microorganisms**",
"token_count": 1898,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**Figure 7.28** Exposure to *Pseudomonas aeruginosa* in the water of a pool or hot tub can sometimes cause a skin infection that manifests as "hot tub rash." (credit: modification of work by "Lsupellmel"/Wikimedia Commons)
*Go back to the [previous](#page-307-1) Clinical Focus box.* ... | {
"Header 1": "**7.5 Using Biochemistry to Identify Microorganisms**",
"token_count": 2029,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Throughout earth's history, microbial metabolism has been a driving force behind the development and maintenance of the planet's biosphere. Eukaryotic organisms such as plants and animals typically depend on organic molecules for energy, growth, and reproduction. Prokaryotes, on the other hand, can metabolize a wide ra... | {
"Header 1": "**Introduction**",
"token_count": 206,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Organisms can be identified according to the source of carbon they use for metabolism as well as their energy source. The prefixes auto- ("self") and hetero- ("other") refer to the origins of the carbon sources various organisms can use. Organisms that convert inorganic carbon dioxide (CO2) into organic carbon compound... | {
"Header 1": "**8.1 Energy, Matter, and Enzymes**",
"Header 2": "**Classification by Carbon and Energy Source**",
"token_count": 632,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile **electron carriers**, molecules that bind to and shuttle high-... | {
"Header 1": "**8.1 Energy, Matter, and Enzymes**",
"Header 2": "Energy Carriers: NAD<sup>+</sup>, NADP<sup>+</sup>, FAD, and ATP",
"token_count": 944,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
A substance that helps speed up a chemical reaction is a **catalyst**. Catalysts are not used or changed during chemical reactions and, therefore, are reusable. Whereas inorganic molecules may serve as catalysts for a wide range of chemical reactions, proteins called **enzyme**s serve as catalysts for biochemical react... | {
"Header 1": "**8.1 Energy, Matter, and Enzymes**",
"Header 2": "**Enzyme Structure and Function**",
"token_count": 1854,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe why glycolysis is not oxygen dependent
- Define and describe the net yield of three-carbon molecules, ATP, and NADH from glycolysis
- Explain how three-carbon pyruvate molecules are converted into two-carbon acetyl groups that can be funneled into the Krebs cycle.
- Define and ... | {
"Header 1": "**8.2 Catabolism of Carbohydrates**",
"token_count": 1257,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
When we refer to glycolysis, unless otherwise indicated, we are referring to the EMP pathway used by animals and many bacteria. However, some prokaryotes use alternative glycolytic pathways. One important alternative is the **Entner-Doudoroff (ED) pathway**, named after its discoverers Nathan Entner and Michael Doudoro... | {
"Header 1": "**8.2 Catabolism of Carbohydrates**",
"Header 2": "**Other Glycolytic Pathways**",
"token_count": 327,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Glycolysis produces pyruvate, which can be further oxidized to capture more energy. For pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the **transition reaction**, also called the **bridge reaction** (see **[Appe... | {
"Header 1": "**8.2 Catabolism of Carbohydrates**",
"Header 2": "**Transition Reaction, Coenzyme A, and the Krebs Cycle**",
"token_count": 918,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Compare and contrast the electron transport system location and function in a prokaryotic cell and a eukaryotic cell
- Compare and contrast the differences between substrate-level and oxidative phosphorylation
- Explain the relationship between chemiosmosis and proton motive force
- Des... | {
"Header 1": "**8.3 Cellular Respiration**",
"token_count": 2024,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Define fermentation and explain why it does not require oxygen
- Describe the fermentation pathways and their end products and give examples of microorganisms that use these pathways
- Compare and contrast fermentation and anaerobic respiration
Many cells are unable to carry out respi... | {
"Header 1": "**8.4 Fermentation**",
"token_count": 1990,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
| Pathway | End Products | Example Microbes | Commercial Products |
|-------------------------------|--------------------------------------------------------------------------------|--... | {
"Header 1": "**8.4 Fermentation**",
"token_count": 1278,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe how lipids are catabolized
- Describe how lipid catabolism can be used to identify microbes
- Describe how proteins are catabolized
- Describe how protein catabolism can be used to identify bacteria
Previous sections have discussed the catabolism of glucose, which provides en... | {
"Header 1": "**8.5 Catabolism of Lipids and Proteins**",
"token_count": 251,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Triglycerides are a form of long-term energy storage in animals. They are made of glycerol and three fatty acids (see **[Figure 7.12](#page-303-1)**). Phospholipids compose the cell and organelle membranes of all organisms except the archaea. Phospholipid structure is similar to triglycerides except that one of the fat... | {
"Header 1": "**8.5 Catabolism of Lipids and Proteins**",
"Header 2": "**Lipid Catabolism**",
"token_count": 658,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Proteins are degraded through the concerted action of a variety of microbial **protease** enzymes. Extracellular proteases cut proteins internally at specific amino acid sequences, breaking them down into smaller peptides that can then be taken up by cells. Some clinically important pathogens can be identified by their... | {
"Header 1": "**8.5 Catabolism of Lipids and Proteins**",
"Header 2": "**Protein Catabolism**",
"token_count": 720,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the function and locations of photosynthetic pigments in eukaryotes and prokaryotes
- Describe the major products of the light-dependent and light-independent reactions
- Describe the reactions that produce glucose in a photosynthetic cell
- Compare and contrast cyclic and nonc... | {
"Header 1": "**8.6 Photosynthesis**",
"token_count": 1433,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
For photosynthesis to continue, the electron lost from the reaction center pigment must be replaced. The source of this electron (H<sub>2</sub>A) differentiates the **oxygenic photosynthesis** of plants and cyanobacteria from **anoxygenic photosynthesis** carried out by other types of bacterial phototrophs (**Figure 8.... | {
"Header 1": "**8.6 Photosynthesis**",
"Header 2": "**Oxygenic and Anoxygenic Photosynthesis**",
"token_count": 777,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules (having lifespans of millionths of a second), photoautotrophs have the fuel needed to build multicarbon carbohydrate molecules, which can survive for hundreds of millions of years, for long-term energy stor... | {
"Header 1": "**8.6 Photosynthesis**",
"Header 2": "**Light-Independent Reactions**",
"token_count": 563,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Define and describe the importance of microorganisms in the biogeochemical cycles of carbon, nitrogen, and sulfur
- Define and give an example of bioremediation
Energy flows directionally through ecosystems, entering as sunlight for phototrophs or as inorganic molecules for chemoautot... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"token_count": 326,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Carbon is one of the most important elements to living organisms, as shown by its abundance and presence in all organic molecules. The carbon cycle exemplifies the connection between organisms in various ecosystems. Carbon is exchanged between heterotrophs and autotrophs within and between ecosystems primarily by way o... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"Header 2": "**Carbon Cycle**",
"token_count": 1285,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Sulfur is an essential element for the macromolecules of living organisms. As part of the amino acids cysteine and methionine, it is involved in the formation of proteins. It is also found in several vitamins necessary for the synthesis of important biological molecules like coenzyme A. Several groups of microbes are r... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"Header 2": "Sulfur Cycle",
"token_count": 300,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Beyond their involvement in the carbon, nitrogen, and sulfur cycles, prokaryotes are involved in other biogeochemical cycles as well. Like the carbon, nitrogen, and sulfur cycles, several of these additional biogeochemical cycles, such as the iron (Fe), manganese (Mn), and chromium (Cr) cycles, also involve redox chemi... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"Header 2": "**Other Biogeochemical Cycles**",
"token_count": 1360,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **[8.1 Energy, Matter, and Enzymes](#page-325-0)**
- **Metabolism** includes chemical reactions that break down complex molecules (**catabolism**) and those that build complex molecules (**anabolism**).
- Organisms may be classified according to their source of carbon. **Autotrophs** convert inorganic carbon dio... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"Header 2": "**Summary**",
"token_count": 1999,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Lipases and phospholipases act as virulence factors for certain pathogenic microbes.
- Fatty acids can be further degraded inside the cell through **β-oxidation**, which sequentially removes twocarbon acetyl groups from the ends of fatty acid chains.
- Protein degradation involves extracellular **proteases** that degra... | {
"Header 1": "**8.7 Biogeochemical Cycles**",
"Header 2": "**Summary**",
"token_count": 791,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
We are all familiar with the slimy layer on a pond surface or that makes rocks slippery. These are examples of biofilms—microorganisms embedded in thin layers of matrix material (**[Figure 9.1](#page-368-1)**). Biofilms were long considered random assemblages of cells and had little attention from researchers. Recently... | {
"Header 1": "**Introduction**",
"token_count": 276,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Define the generation time for growth based on binary fission
- Identify and describe the activities of microorganisms undergoing typical phases of binary fission (simple cell division) in a growth curve
- Explain several laboratory methods used to determine viable and total cell counts... | {
"Header 1": "**9.1 How Microbes Grow**",
"token_count": 1681,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Microorganisms grown in closed culture (also known as a batch culture), in which no nutrients are added and most waste is not removed, follow a reproducible growth pattern referred to as the **growth curve**. An example of a batch culture in nature is a pond in which a small number of cells grow in a closed environment... | {
"Header 1": "**9.1 How Microbes Grow**",
"Header 2": "**The Growth Curve**",
"token_count": 2035,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The enlarged view shows the square within which bacteria (red cells) are counted. If the coverslip is 0.2 mm above the grid and the square has an area of 0.04 mm<sup>2</sup> , then the volume is 0.008 mm<sup>3</sup> , or 0.000008 mL. Since there are 10 cells inside the square, the density of bacteria is 10 cells/0.0000... | {
"Header 1": "**9.1 How Microbes Grow**",
"Header 2": "**The Growth Curve**",
"token_count": 2015,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
**Figure 9.13** In the spread plate method of cell counting, the sample is poured onto solid agar and then spread using a sterile spreader. This process is repeated for each serial dilution prepared. The resulting colonies are counted and provide an estimate of the number of cells in th... | {
"Header 1": "**9.1 How Microbes Grow**",
"Header 2": "**The Growth Curve**",
"token_count": 1615,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Binary fission is the most common pattern of cell division in prokaryotes, but it is not the only one. Other mechanisms usually involve asymmetrical division (as in budding) or production of spores in aerial filaments.
In some cyanobacteria, many nucleoids may accumulate in an enlarged round cell or along a filament,... | {
"Header 1": "**9.1 How Microbes Grow**",
"Header 2": "**Alternative Patterns of Cell Division**",
"token_count": 2037,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Pathogens embedded within biofilms exhibit a higher resistance to antibiotics than their free-floating counterparts. Several hypotheses have been proposed to explain why. Cells in the deep layers of a biofilm are metabolically inactive and may be less susceptible to the action of antibiotics that disrupt metabolic ac... | {
"Header 1": "**9.1 How Microbes Grow**",
"Header 2": "**Alternative Patterns of Cell Division**",
"token_count": 215,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Interpret visual data demonstrating minimum, optimum, and maximum oxygen or carbon dioxide requirements for growth
- Identify and describe different categories of microbes with requirements for growth with or without oxygen: obligate aerobe, obligate anaerobe, facultative anaerobe, aero... | {
"Header 1": "**9.2 Oxygen Requirements for Microbial Growth**",
"token_count": 2038,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
The organism will not grow outside the range of oxygen levels found between the minimum and maximum permissive oxygen concentrations.
- Would you expect the oldest bacterial lineages to be aerobic or anaerobic?
- Which bacteria grow at the top of a thioglycolate tube, and which grow at... | {
"Header 1": "**9.2 Oxygen Requirements for Microbial Growth**",
"token_count": 600,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Aerobic respiration constantly generates reactive oxygen species (ROS), byproducts that must be detoxified. Even organisms that do not use aerobic respiration need some way to break down some of the ROS that may form from atmospheric oxygen. Three main enzymes break down those toxic byproducts: superoxide dismutase, pe... | {
"Header 1": "**9.2 Oxygen Requirements for Microbial Growth**",
"Header 2": "**Detoxification of Reactive Oxygen Species**",
"token_count": 1190,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Illustrate and briefly describe minimum, optimum, and maximum pH requirements for growth
- Identify and describe the different categories of microbes with pH requirements for growth: acidophiles, neutrophiles, and alkaliphiles
- Give examples of microorganisms for each category of pH re... | {
"Header 1": "**9.3 The Effects of pH on Microbial Growth**",
"token_count": 1954,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Illustrate and briefly describe minimum, optimum, and maximum temperature requirements for growth
- Identify and describe different categories of microbes with temperature requirements for growth: psychrophile, psychrotrophs, mesophile, thermophile, hyperthermophile
- Give examples of m... | {
"Header 1": "**9.3 The Effects of pH on Microbial Growth**",
"Header 2": "**9.4 Temperature and Microbial Growth**",
"token_count": 2010,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
For example, amplification of nucleic acids in the polymerase chain reaction (PCR) depends on the thermal stability of *Taq* polymerase, an enzyme isolated from *T. aquaticus*. Degradation enzymes from thermophiles are added as ingredients in hot-water detergents, increasing their effectiveness.
- What temperature re... | {
"Header 1": "**9.3 The Effects of pH on Microbial Growth**",
"Header 2": "**9.4 Temperature and Microbial Growth**",
"token_count": 865,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Most natural environments tend to have lower solute concentrations than the cytoplasm of most microorganisms. Rigid cell walls protect the cells from bursting in a dilute environment. Not much protection is available against high osmotic pressure. In this case, water, following its concentration gradient, flows out of ... | {
"Header 1": "**9.5 Other Environmental Conditions that Affect Growth**",
"Header 2": "**Osmotic and Barometric Pressure**",
"token_count": 1138,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
• Identify and describe culture media for the growth of bacteria, including examples of all-purpose media, enriched, selective, differential, defined, and enrichment media
The study of microorganisms is greatly facilitated if we are able to culture them, that is, to keep reproducing pop... | {
"Header 1": "**9.5 Other Environmental Conditions that Affect Growth**",
"Header 2": "**9.6 Media Used for Bacterial Growth**",
"token_count": 798,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Case in Point**
#### **The End-of-Year Picnic**
The microbiology department is celebrating the end of the school year in May by holding its traditional picnic on the green. The speeches drag on for a couple of hours, but finally all the faculty and students can dig into the food: chicken salad, tomatoes, oni... | {
"Header 1": "Compare the compositions of **[EZ medium \\(https://openstax.org/l/](https://openstax.org/l/22EZMedium) [22EZMedium\\)](https://openstax.org/l/22EZMedium)** and **[sheep blood \\(https://openstax.org/l/22bloodagar\\)](https://openstax.org/l/22bloodagar)** agar. **Link to Learning**",
"token_count": 1... |
Children inherit some characteristics from each parent. Siblings typically look similar to each other, but not exactly the same—except in the case of identical twins. How can we explain these phenomena? The answers lie in heredity (the transmission of traits from one generation to the next) and genetics (the science of... | {
"Header 1": "**Biochemistry of the Genome**",
"Header 2": "**Introduction**",
"token_count": 277,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the discovery of nucleic acid and nucleotides
- Explain the historical experiments that led to the characterization of DNA
- Describe how microbiology and microorganisms have been used to discover the biochemistry of genes
- Explain how scientists established the link between D... | {
"Header 1": "**10.1 Using Microbiology to Discover the Secrets of Life**",
"token_count": 706,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
Despite the discovery of DNA in the late 1800s, scientists did not make the association with heredity for many more decades. To make this connection, scientists, including a number of microbiologists, performed many experiments on plants, animals, and bacteria.
#### **Mendel's Pea Plants**
While Miescher was isolat... | {
"Header 1": "**10.1 Using Microbiology to Discover the Secrets of Life**",
"Header 2": "**Foundations of Genetics**",
"token_count": 2025,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
} |
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