Preface

Welcome to Microbiology, an OpenStax resource. This textbook was written to increase student access to high-quality learning materials, maintaining highest standards of academic rigor at little to no cost.

About OpenStax

OpenStax is a nonprofit based at Rice University, and it’s our mission to improve student access to education. Our first openly licensed college textbook was published in 2012, and our library has since scaled to over 20 books for college and AP® Courses used by hundreds of thousands of students. Our adaptive learning technology, designed to improve learning outcomes through personalized educational paths, is being piloted in college courses throughout the country. Through our partnerships with philanthropic foundations and our alliance with other educational resource organizations, OpenStax is breaking down the most common barriers to learning and empowering students and instructors to succeed.

About OpenStax Resources

Customization

Microbiology is licensed under a Creative Commons Attribution 4.0 International (CC BY) license, which means that you can distribute, remix, and build upon the content, as long as you provide attribution to OpenStax and its content contributors.

Because our books are openly licensed, you are free to use the entire book or pick and choose the sections that are most relevant to the needs of your course. Feel free to remix the content by assigning your students certain chapters and sections in your syllabus, in the order that you prefer. You can even provide a direct link in your syllabus to the sections in the web view of your book.

Instructors also have the option of creating a customized version of their OpenStax book. The custom version can be made available to students in low-cost print or digital form through their campus bookstore. Visit your book page on openstax.org for more information.

Errata

All OpenStax textbooks undergo a rigorous review process. However, like any professional-grade textbook, errors sometimes occur. Since our books are web-based, we can make updates periodically when deemed pedagogically necessary. If you have a correction to suggest, submit it through the link on your book page on openstax.org. Subject matter experts review all errata suggestions. OpenStax is committed to remaining transparent about all updates, so you will also find a list of past errata changes on your book page on openstax.org.

Format

You can access this textbook for free in web view or PDF through openstax.org, and for a low cost in print.

About Microbiology

Microbiology is designed to cover the scope and sequence requirements for the single-semester Microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of Microbiology make the material interesting and accessible to students while maintaining the career-application focus and scientific rigor inherent in the subject matter.

Coverage and Scope

The scope and sequence of Microbiology has been developed and vetted with input from numerous instructors at institutions across the US. It is designed to meet the needs of most microbiology courses for non-majors and allied health students. In addition, we have also considered the needs of institutions that offer microbiology to a mixed audience of science majors and non-majors by frequently integrating topics that may not have obvious clinical relevance, such as environmental and applied microbiology and the history of science.

With these objectives in mind, the content of this textbook has been arranged in a logical progression from fundamental to more advanced concepts. The opening chapters present an overview of the discipline, with individual chapters focusing on microscopy and cellular biology as well as each of the classifications of microorganisms. Students then explore the foundations of microbial biochemistry, metabolism, and genetics, topics that provide a basis for understanding the various means by which we can control and combat microbial growth. Beginning with Chapter 15, the focus turns to microbial pathogenicity, emphasizing how interactions between microbes and the human immune system contribute to human health and disease. The last several chapters of the text provide a survey of medical microbiology, presenting the characteristics of microbial diseases organized by body system.

A brief Table of Contents follows. While we have made every effort to align the Table of Contents with the needs of our audience, we recognize that some instructors may prefer to teach topics in a different order. A particular strength of Microbiology is that instructors can customize the book, adapting it to the approach that works best in their classroom.

American Society of Microbiology (ASM) Partnership

Microbiology is produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book has been developed to align to the curriculum guidelines of the American Society for Microbiology.

About ASM

The American Society for Microbiology is the largest single life science society, composed of over 47,000 scientists and health professionals. ASM's mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications, and educational opportunities. It enhances laboratory capacity around the globe through training and resources and provides a network for scientists in academia, industry, and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences and is committed to offering open-access materials through their new journals, American Academy of Microbiology reports, and textbooks.

PART 1: Concepts and Statements

Evolution

  1. Cells, organelles (e.g., mitochondria and chloroplasts) and all major metabolic pathways evolved from early prokaryotic cells.
  2. Mutations and horizontal gene transfer, with the immense variety of microenvironments, have selected for a huge diversity of microorganisms.
  3. Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).
  4. The traditional concept of species is not readily applicable to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer.
  5. The evolutionary relatedness of organisms is best reflected in phylogenetic trees.

Cell Structure and Function

  1. The structure and function of microorganisms have been revealed by the use of microscopy (including bright field, phase contrast, fluorescent, and electron).
  2. Bacteria have unique cell structures that can be targets for antibiotics, immunity and phage infection.
  3. Bacteria and Archaea have specialized structures (e.g., flagella, endospores, and pili) that often confer critical capabilities.
  4. While microscopic eukaryotes (for example, fungi, protozoa and algae) carry out some of the same processes as bacteria, many of the cellular properties are fundamentally different.
  5. The replication cycles of viruses (lytic and lysogenic) differ among viruses and are determined by their unique structures and genomes.

Metabolic Pathways

  1. Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity (e.g., nitrogen fixation, methane production, anoxygenic photosynthesis).
  2. The interactions of microorganisms among themselves and with their environment are determined by their metabolic abilities (e.g., quorum sensing, oxygen consumption, nitrogen transformations).
  3. The survival and growth of any microorganism in a given environment depends on its metabolic characteristics.
  4. The growth of microorganisms can be controlled by physical, chemical, mechanical, or biological means.

Information Flow and Genetics

  1. Genetic variations can impact microbial functions (e.g., in biofilm formation, pathogenicity and drug resistance).
  2. Although the central dogma is universal in all cells, the processes of replication, transcription, and translation differ in Bacteria, Archaea, and Eukaryotes.
  3. The regulation of gene expression is influenced by external and internal molecular cues and/or signals.
  4. The synthesis of viral genetic material and proteins is dependent on host cells.
  5. Cell genomes can be manipulated to alter cell function.

Microbial Systems

  1. Microorganisms are ubiquitous and live in diverse and dynamic ecosystems.
  2. Most bacteria in nature live in biofilm communities.
  3. Microorganisms and their environment interact with and modify each other.
  4. Microorganisms, cellular and viral, can interact with both human and nonhuman hosts in beneficial, neutral or detrimental ways.

Impact of Microorganisms

  1. Microbes are essential for life as we know it and the processes that support life (e.g., in biogeochemical cycles and plant and/or animal microbiota).
  2. Microorganisms provide essential models that give us fundamental knowledge about life processes.
  3. Humans utilize and harness microorganisms and their products.
  4. Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

PART 2: Competencies and Skills

Scientific Thinking

  1. Ability to apply the process of science

    a. Demonstrate an ability to formulate hypotheses and design experiments based on the scientific method.

    b. Analyze and interpret results from a variety of microbiological methods and apply these methods to analogous situations.

  2. Ability to use quantitative reasoning

    a. Use mathematical reasoning and graphing skills to solve problems in microbiology.

  3. Ability to communicate and collaborate with other disciplines

    a. Effectively communicate fundamental concepts of microbiology in written and oral format.

    b. Identify credible scientific sources and interpret and evaluate the information therein.

  4. Ability to understand the relationship between science and society

    a. Identify and discuss ethical issues in microbiology.

Microbiology Laboratory Skills

  1. Properly prepare and view specimens for examination using microscopy (bright field and, if possible, phase contrast).
  2. Use pure culture and selective techniques to enrich for and isolate microorganisms.
  3. Use appropriate methods to identify microorganisms (media-based, molecular and serological).
  4. Estimate the number of microorganisms in a sample (using, for example, direct count, viable plate count, and spectrophotometric methods).
  5. Use appropriate microbiological and molecular lab equipment and methods.
  6. Practice safe microbiology, using appropriate protective and emergency procedures.
  7. Document and report on experimental protocols, results and conclusions.
OpenStax Microbiology Correlation to ASM Curriculum Guidelines
Chapter ASM Curriculum Guidelines
1—An Invisible World 2, 4, 5, 11, 16, 20, 23, 26, 27, 31
2—How We See the Invisible World 6, 31, 32, 33
3—The Cell 1, 2, 5, 9, 16, 21, 25, 31
4—Prokaryotic Diversity 2, 4, 8, 11, 12, 16, 20, 23, 24, 31
5—The Eukaryotes of Microbiology 2, 4, 5, 9, 12, 20, 23, 31
6—Acellular Pathogens 4, 10, 18, 23, 31
7—Microbial Biochemistry 1, 24, 33, 34
8—Microbial Metabolism 1, 11, 12, 13, 22, 24
9—Microbial Growth 12, 13, 29, 31, 33, 34, 35
10—Biochemistry of the Genome 1, 16, 25, 31
11—Mechanisms of Microbial Genetics 1, 2, 15, 16, 17, 31
12—Modern Applications of Microbial Genetics 19, 26, 31
13—Control of Microbial Growth 13, 14, 26, 31, 36, 37
14—Antimicrobial Drugs 3, 7, 14, 15, 23, 26, 31
15—Microbial Mechanisms of Pathogenicity 8, 9, 10, 15, 18, 23, 33
16—Disease and Epidemiology 7, 14, 23, 26, 31
17—Innate Nonspecific Host Defenses 7, 8, 23
18—Adaptive Specific Host Defenses 7, 23, 26, 31
19—Diseases of the Immune System 7, 8, 24
20—Laboratory Analysis of the Immune Response 31, 34
21—Skin and Eye Infections 8, 9, 10, 14, 18, 23, 24, 31
22—Respiratory System Infections 7, 8, 9, 14, 18, 23, 24, 31
23—Urogenital System Infections 7, 8, 9, 12, 14, 18, 22, 23, 24, 31
24—Digestive System Infections 7, 8, 9, 10, 14, 18, 23, 24, 31
25—Circulatory and Lymphatic System Infections 7, 8, 9, 14, 23, 31
26—Nervous System Infections 7, 8, 9, 14, 18, 23, 24, 31

Engaging Feature Boxes

Throughout Microbiology, you will find features that engage students by taking selected topics a step further. Our features include:

Comprehensive Art Program

Our art program is designed to enhance students’ understanding of concepts through clear and effective illustrations, diagrams, and photographs. Detailed drawings, comprehensive lifecycles, and clear micrographs provide visual reinforcement for concepts.

Figure a is an electron micrograph showing a virus on the surface of a bacterial cell. The virus has a large head region, a thick neck and thin spider-like legs attached to the bacterium. Figure b is a drawing that labels the outside of the head as the capsid with the viral genome inside. The neck as the sheath and the legs as tail fibers.

A diagram of a large cell. The outside of the cell is a thin line labeled plasma membrane. A long projection outside of the plasma membrane is labeled flagellum. Shorter projections outside the membrane are labeled cilia. Just under the plasma membrane are lines labeled microtubules and microfilaments. The fluid inside the plasma membrane is labeled cytoplasm. In the cytoplasm are small dots labeled ribosomes. These dots are either floating in the cytoplasm or attached to a webbed membrane labeled rough endoplasmic reticulum. Some regions of the webbed membrane do not have dots; these regions of the membrane are called smooth endoplasmic reticulum. Other structures in the cytoplasm include an oval with a webbed line inside of it; this is labeled the mitochondrion. Spheres in the cytoplasm are labeled peroxisome and lysosome. A pancake stack of membranes is labeled golgi complex. Two short tubes are labeled centrosomes. A large sphere in the cell is labeled nucleus. The outer membrane of this sphere is the nuclear envelope. Holes in the nuclear envelope are called nuclear pores. A smaller sphere in the nucleus is labeled nucleolus.

Table of electron microscopes which use electron beams focused with magnets to produce an image. Magnification: 20 – 100,00× or more. Transmission electron microscopes (TEM) use electron means that pass through a specimen to visual small images; useful to observe small, thin specimens such as tissue sections and subcellular structures. The sample image (Ebola virus) shows a tube shaped into a letter d at one end. Scanning electron microscopes (SEM) use electron beams to visualize surfaces; useful to observe the three-dimensional surface details of specimens. The sample image (Campylobactor jejuni) shows thick three-dimensional spirals.

A diagram of a rod-shaped prokaryotic cell. The thick outer layer is called the capsule, inside of that is a thinner cell wall and inside of that is an even thinner plasma membrane. Inside of the plasma membrane is a fluid called the cytoplasm, little dots called ribosomes, small spheres called inclusions, a small loop of DNA called a plasmid, and a large folded loo of DNA called the nucleoid. Long projections start at the plasma membrane and extend out of the capsule; these are called flagella (singular: flagellum). A shorter projection is labeled pilus. And many very short projections are labeled fimbriae.

A drawing of the plasma membrane. The top of the diagram is labeled outside of cell, the bottom is labeled cytoplasm. Separating these two regions is the membrane which is made of mostly a phospholipid bilayer. Each phospholipid is drawn as a sphere with 2 tails. There are two layers of phospholipids making up the bilayer; each phospholipid layer has the sphere towards the outside of the bilayer and the two tails towards the inside of the bilayer. Embedded within the phospholipid bilayer are a variety of large proteins. Glycolipids have long carbohydrate chains (shown as a chain of hexagons) attached to a single phospholipid; the carbohydrates are always on the outside of the membrane. Glycoproteins have a long carbohydrate chain attached to a protein; the carbohydrates are on the outside of the membrane. The cytoskeleton is shown as a thin layer of line just under the inside of the phospholipid bilayer.

Eggs or gravid proplottidis from an infected individual are passed into the environment; this is the diagnostic stage. Cattle (T. saginata) and pigs (T. solium) become infected by ingesting vegetation contaminated by eggs or gravid proglottids. Oncospheres hatch, penetrating intestinal wall and circulate to musculature. The oncospheres develop into cysticerci in muscles and become infective. Humans are infected by ingesting raw or undercooked infected meat. The scolex attaches to intestine and adults are found in the small intestine.

Materials That Reinforce Key Concepts

Additional Resources

Student and Instructor Resources

We’ve compiled additional resources for both students and instructors, including Getting Started Guides, a test bank, and an instructor answer guide. Instructor resources require a verified instructor account, which can be requested on your openstax.org log-in. Take advantage of these resources to supplement your OpenStax book.

Partner Resources

OpenStax Partners are our allies in the mission to make high-quality learning materials affordable and accessible to students and instructors everywhere. Their tools integrate seamlessly with our OpenStax titles at a low cost. To access the partner resources for your text, visit your book page on openstax.org.​

About the Authors

Senior Contributing Authors

Nina Parker (Content Lead), Shenandoah University* * *

Dr. Nina Parker received her BS and MS from the University of Michigan, and her PhD in Immunology from Ohio University. She joined Shenandoah University's Department of Biology in 1995 and serves as Associate Professor, teaching general microbiology, medical microbiology, immunology, and epidemiology to biology majors and allied health students. Prior to her academic career, Dr. Parker was trained as a Medical Technologist and received ASCP certification, experiences that drive her ongoing passion for training health professionals and those preparing for clinical laboratory work. Her areas of specialization include infectious disease, immunology, microbial pathogenesis, and medical microbiology. Dr. Parker is also deeply interested in the history of medicine and science, and pursues information about diseases often associated with regional epidemics in Virginia.

Mark Schneegurt (Lead Writer), Wichita State University* * *

Dr. Mark A. Schneegurt is a Professor of Biological Sciences at Wichita State University and maintains joint appointments in Curriculum and Instruction and Biomedical Engineering. Dr. Schneegurt holds degrees from Rensselaer Polytechnic Institute and a Ph.D. from Brown University. He was a postdoctoral fellow at Eli Lilly and has taught and researched at Purdue University and the University of Notre Dame. His research focuses on applied and environmental microbiology, resulting in 70+ scientific publications and 150+ presentations.

Anh-Hue Thi Tu (Senior Reviewer), Georgia Southwestern State University* * *

Dr. Anh-Hue Tu (born in Saigon, Vietnam) earned a BS in Chemistry from Baylor University and a PhD in Medical Sciences from Texas A & M Health Science Center. At the University of Alabama–Birmingham, she completed postdoctoral appointments in the areas of transcriptional regulation in Escherichia coli and characterization of virulence factors in Streptococcus pneumoniae and then became a research assistant professor working in the field of mycoplasmology. In 2004, Dr. Tu joined Georgia Southwestern State University where she currently serves as Professor, teaching various biology courses and overseeing undergraduate student research. Her areas of research interest include gene regulation, bacterial genetics, and molecular biology. Dr. Tu's teaching philosophy is to instill in her students the love of science by using critical thinking. As a teacher, she believes it is important to take technical information and express it in a way that is understandable to any student.

Brian M. Forster, Saint Joseph's University* * *

Dr. Brian M. Forster received his BS in Biology from Binghamton University and his PhD in Microbiology from Cornell University. In 2011, he joined the faculty of Saint Joseph’s University. Dr. Forster is the laboratory coordinator for the natural science laboratory-based classes designed for students who are not science majors. He teaches courses in general biology, heredity and evolution, environmental science, and microbiology for students wishing to enter nursing or allied health programs. He has publications in the Journal of Bacteriology, the Journal of Microbiology & Biology Education and Tested Studies for Laboratory Education (ABLE Proceedings).

Philip Lister, Central New Mexico Community College* * *

Dr. Philip Lister earned his BS in Microbiology (1986) from Kansas State University and PhD in Medical Microbiology (1992) from Creighton University. He was a Professor of Medical Microbiology and Immunology at Creighton University (1994-2011), with appointments in the Schools of Medicine and Pharmacy. He also served as Associate Director of the Center for Research in Anti-Infectives and Biotechnology. He has published research articles, reviews, and book chapters related to antimicrobial resistance and pharmacodynamics, and has served as an Editor for the Journal of Antimicrobial Chemotherapy. He is currently serving as Chair of Biology and Biotechnology at Central New Mexico Community College.

Contributing Authors

Summer Allen, Brown University* * *

Ann Auman, Pacific Lutheran University* * *

Graciela Brelles-Mariño, Universidad Nacional de la Plata* * *

Myriam Alhadeff Feldman, Lake Washington Institute of Technology* * *

Paul Flowers, University of North Carolina–Pembroke* * *

Clifton Franklund, Ferris State University* * *

Ann Paterson, Williams Baptist University* * *

George Pinchuk, Mississippi University for Women* * *

Ben Rowley, University of Central Arkansas* * *

Mark Sutherland, Hendrix College* * *

Reviewers

Michael Angell, Eastern Michigan University* * *

Roberto Anitori, Clark College* * *

James Bader, Case Western Reserve University* * *

Amy Beumer, College of William and Mary* * *

Gilles Bolduc, Massasoit Community College* * *

Susan Bornstein-Forst, Marian University* * *

Nancy Boury, Iowa State University* * *

Jennifer Brigati, Maryville College* * *

Harold Bull, University of Saskatchewan* * *

Evan Burkala, Oklahoma State University* * *

Bernadette Connors, Dominican College* * *

Richard J. Cristiano, Houston Community College–Northwest* * *

AnnMarie DelliPizzi, Dominican College* * *

Elisa M. LaBeau DiMenna, Central New Mexico Community College* * *

Diane Dixon, Southeastern Oklahoma State University* * *

Randy Durren, Longwood University* * *

Elizabeth A. B. Emmert, Salisbury University* * *

Karen Frederick, Marygrove College* * *

Sharon Gusky, Northwestern Connecticut Community College* * *

Deborah V. Harbour, College of Southern Nevada* * *

Randall Harris, William Carey University* * *

Diane Hartman, Baylor University* * *

Angela Hartsock, University of Akron* * *

Nazanin Zarabadi Hebel, Houston Community College* * *

Heather Klenovich, Community College of Alleghany County* * *

Kathleen Lavoie, Plattsburgh State University* * *

Toby Mapes, Blue Ridge Community College* * *

Barry Margulies, Towson University* * *

Kevin M. McCabe, Columbia Gorge Community College* * *

Karin A. Melkonian, Long Island University* * *

Jennifer Metzler, Ball State University* * *

Ellyn R. Mulcahy, Johnson County Community College* * *

Jonas Okeagu, Fayetteville State University* * *

Randall Kevin Pegg, Florida State College–Jacksonville* * *

Judy Penn, Shoreline Community College* * *

Lalitha Ramamoorthy, Marian University* * *

Drew Rholl, North Park University* * *

Hilda Rodriguez, Miami Dade College* * *

Sean Rollins, Fitchburg State University* * *

Sameera Sayeed, University of Pittsburgh* * *

Pramila Sen, Houston Community College* * *

Brian Róbert Shmaefsky, Kingwood College* * *

Janie Sigmon, York Technical College* * *

Denise Signorelli, College of Southern Nevada* * *

Molly Smith, South Georgia State College–Waycross* * *

Paula Steiert, Southwest Baptist University* * *

Robert Sullivan, Fairfield University* * *

Suzanne Wakim, Butte Community College* * *

Anne Weston, Francis Crick Institute* * *

Valencia L. Williams, West Coast University* * *

James Wise, Chowan State University* * *

Virginia Young, Mercer University* * *

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

You can also download for free at http://cnx.org/contents/e42bd376-624b-4c0f-972f-e0c57998e765@5.3

Attribution: