Assignment: Biology for a Changing World Chapter 12 & 17 Summary

Michèle Shuster • Janet Vigna • Matthew Tontonoz Biology for a Changing World Fourth Edition Lecture Slides CHAPTER 17 Prokaryotic Diversity Macmillan Learning © 2021 Chapter 17 Prokaryotic Diversity Driving Questions 1. What is the human microbiome, and what is its role in health, disease, and forensics? 2. What are prokaryotes, and why are they classified into two distinct domains of life? 3. What are features of bacteria and archaea? The Human Microbiome (1 of 2) Microbiome: the diversity of microbes living in and on us • Microbial diversity varies by the part of the body where they occur. • Microbes contribute to the immune system and are part of normal physiology. The Human Microbiome (2 of 2) • Each person has a unique combination of microbe species. • Microbes vary from one portion of the body to another. • They even vary from one hand to another. Prokaryotic Cells (1 of 3) Prokaryotes • Unicellular • Lack internal membranebound organelles • DNA is not contained within a nucleus. • Most of the microbes in our microbiome are prokaryotes. Prokaryotic Cells (2 of 3) Size • Approximately 1/100th the size of a eukaryotic cell • Similar to the size of a eukaryotic mitochondrion • 1–10 microns Prokaryotic Cells (3 of 3) • Reproduce quickly • Found in the trillions on humans • Able to share DNA with each other • Sharing DNA helps them to adapt to diverse environments. Microbial Forensics (1 of 3) • We leave traces of microbial diversity on things we touch.

• The microbes we leave can be detectable for up to two weeks. • Investigators can identify suspects and victims of crimes using microbes they find on surfaces. Microbial Forensics (2 of 3) • It is possible to estimate both who touched a surface (like fingerprints) and when they touched it. • When we touch surfaces, we deposit millions of microbes. • Over time, the microbes we leave behind become less common. Microbial Forensics (3 of 3) • To solve crimes, we sometimes need to know the age of a corpse. • After death, bacteria from the environment cause decay. • It is possible to identify when a person died by examining which microbes are present. Prokaryotic Domains •Prokaryotes come from two domains of life. •Bacteria •Archaea •Both are part of the human microbiome. Bacteria (1 of 2) • Most possess a cell wall. • Tremendous genetic diversity • Differences in nutrition, metabolism, structure, and lifestyle Bacteria (2 of 2) • Autotrophs: make their own food from material in nonliving environment • Heterotrophs: rely on other organisms as a food source Bacteria: Autotrophs (1 of 2) Cyanobacteria • largest group • in oceans, freshwater, exposed rocks, and soil • photosynthesize • oldest photosynthetic organisms • Some perform nitrogen fixation. – conversion of atmospheric nitrogen into a form that plants can use for growth Bacteria: Autotrophs (2 of 2) • Some species obtain energy from geological sources. – inorganic gases of hydrothermal vents • These species do not rely on sunlight at all. Bacteria: Heterotrophs • Decomposers (recyclers) – recycle trapped carbon and other elements • Bioremediation – oil spills • Fermenters – Lactobacillus bulgaricus in yogurt Bacteria: Structure (1 of 2) • Spherical (cocci) • Rod-shaped (bacilli) • Spiral (spirochetes) • Flagella: tiny, whiplike structures that project from the cell and help it move Bacteria: Structure (2 of 2) • Pili: shorter, hairlike appendages that enable bacteria to adhere to a surface • Capsule: a sticky outer layer that helps the cell adhere to surfaces to avoid the defenses of the host Bacteria: Symbiosis • Many live in close association, or symbiosis, with other organisms.

• Can be beneficial – such as Vibrio fischeri, bioluminescent, lives and feeds inside the light organs of certain species of squid Bacteria: Pathogens Pathogens • Disease-causing agents • Cause disease by producing toxins that harm their hosts – strains of Escherichia coli secrete a toxin that causes bloody diarrhea, kidney failure, and sometimes death in its host Archaea (1 of 2) • Lack a nucleus like bacteria • As different from bacteria as they are to us • Originally thought to be more ancient than bacteria Archaea (2 of 2) • Genetically distinct from bacteria • Some archaea are “Extremophiles” – hyperthermophiles – methanogens – halophiles • Some archaea are part of the human microbiome. Microbiome Sources • We gain our unique microbiome during the first 1–2 years of life from various sources: • birth • breastfeeding • diet • other environmental sources Microbiomes and Disease (1 of 2) • Microbiomes in primitive societies have more of some disease-causing bacteria. • People in industrialized societies have more heart disease, autoimmune disease, and autism. • These may be associated with the microbiome. Microbiomes and Disease (2 of 2) • Microbiomes in primitive societies have more of some disease-causing bacteria. • People in industrialized societies have more heart disease, autoimmune disease, and autism. • These may be associated with the microbiome. Microbiome Hope • If having the wrong microbiome causes disease, then can changing our microbiome cure disease? • Highly effective treatment for Clostridium difficile infection: • Fecal transplant from the gut of a healthy person to the gut of a sick person Microbiome Hype • Differences in microbiome can be associated with disease. • However, correlation does not mean causation. • For example: • Autistic people have different microbiomes, but they also tend to be picky eaters.

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• Does the microbiome cause autism, or are both caused by other factors? Diet and the Microbiome • Diet: major driver of microbiome compositions • Fiber-rich diet: • promotes healthy microbial diversity • leads to healthy regulation of body systems • Fiber-poor diet: • promotes low microbial diversity • leads to inflammation and disease Summary (1 of 3) What is the human microbiome, and what is its role in health, disease, and forensics? • The human microbiome consists of the microorganisms—bacteria, archaea, protists, and fungi—living on and in us. • Our microbiome begins to be acquired at birth. • Our individual microbiome can be used to identify objects that we have touched, based on the microbial fingerprints that we leave. • Disruptions to our microbiome can lead to disease. • Restoration of our microbiome (e.g., through fecal transplant) can restore a state of health. Summary (2 of 3) What are prokaryotes, and why are they classified into two distinct domains of life? • Prokaryotes are unicellular organisms that lack organelles, have no nucleus, and are found in virtually every environment on Earth. • Genetic analysis has led to the categorization of life prokaryotes into two domains: Bacteria and Archaea. • Both bacteria and archaea have prokaryotic cells, but they otherwise differ in their genetics, biochemistry, and lifestyles. Summary (3 of 3) What are features of bacteria and archaea? • Bacteria are diverse and have many unique adaptations that allow them to live and thrive in many environments. • Some bacteria cause disease, but most are harmless, and many are beneficial. • Some archaea live in some of the most extreme environmental conditions on Earth, whereas others live in more mild conditions. Interpreting Data (1 of 2) It has been suggested that increasing rates of immune disorders, such as asthma and some food allergies, are the result of a reduced exposure to a diversity of “friendly” bacteria in the human microbiome. a. Based on the data shown in the bar chart, which population would you predict to have the lowest rates of asthma and allergies? Note that the Amerindians are from rural communities in Venezuela.

Interpreting Data (2 of 2) b. If your prediction is correct, is that evidence of correlation or causation? c. Design an epidemiological study to test the hypothesis that reduced diversity of the human microbiome is responsible for increasing rates of immune disorders. (Hint: Refer back to Chapter 1 for observational and epidemiological studies). Mini Case (1 of 5) Your friend’s mother has been hospitalized and has developed a Clostridium difficile (C. diff) infection of the colon. This is a common hospital-associated infection, in which the use of antibiotics to treat another infection reduces the normal microbiome of the colon, allowing C. diff to establish itself. Mini Case (2 of 5) Her doctor is recommending a fecal microbial transplant (FMT), in which feces from a healthy donor are transferred into the intestinal tract of a person with C. diff (either by enema or by a tube extending from the nose to the small intestine). Your friend and her mother find this idea to be disgusting, particularly when they realize that the donor fecal material is not sterilized before the transplant. Mini Case (3 of 5) Data from a clinical trial comparing FMT to standard antibiotic therapy with vancomycin are shown in this bar chart. What can you infer about the effectiveness of FMT compared to vancomycin treatment? Mini Case (4 of 5) More results from the clinical trial on FMT is shown in this bar chart. a. What do you observe about the microbial diversity in patients versus donors? b. What do you observe about the microbial diversity in patients before and after treatment? Mini Case (5 of 5) c. What can you infer about how the FMT works? d. Based on your answer to part c, why can’t the donor fecal material be sterilized? e. Based on the data presented, what treatment do you encourage your friend’s mother to choose? Explain your answer. Michèle Shuster • Janet Vigna • Matthew Tontonoz Biology for a Changing World FOURTH EDITION Lecture Slides Chapter 12 Complex Inheritance Macmillan Learning © 2021 Chapter 12 Complex Inheritance Driving Questions 1. How do chromosomes determine sex, and how does sex influence the inheritance of certain traits? 2. What inheritance patterns are observed when alleles are not simply dominant or recessive?

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Assignment: Biology for a Changing World Chapter 12 & 17 Summary