Study Microbes

Here are questions to ask about microbes, based on Microbiology: An Evolving Science

Chapter 7

1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication? What kind of genetic entities are likely to favor one over the other?

2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division? Explain two specific examples.

3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.

4. During resolution of a catenane, how might a major mutation occur affecting the entire genome? How do you think this mutation is prevented?

5. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?

6. What are the relative advantages and limitations of bidirectional versus rolling-circle replication of DNA? Explain in terms of different genome sizes, types, and cell situation when replication occurs.

7. When you sequence a genome, how do you know where the base pairs in the genome are located since the DNA used to sequence the genome is in fragments?

Chapter 8

1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.

2. If Mycoplasma genitalium cannot synthesize its own amino acids, does it have extensive/multiple protein channels (ABC pumps) to let amino acids pass its membrane? If proteins are made of amino acids, though, how did the first M. genitalium’s protein channels come into existence?

3. In tRNA, there are "unusual" bases not found in mRNA How are these bases generated? Do you think they arise from a recently-evolved aspect of tRNA, or do you think they are an ancient phenomenon of the original RNA world? Explain.

4. What kinds of pharmaceutical agents could you design to act on gene promoters? Explain using protein and/or RNA molecules.

5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?

6. How could you sequence the genome of an unculturable microbe?

7. What are the different ways of starting or stopping transcription of a gene?

8. As a peptide is synthesized, what problems may need to be solved in order to complete a protein and enable its function?

Chapter 9 and 10

1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups? Could part of a gene be moved?

2. How are microbial species defined? What is the role of vertical phylogeny; and the role of horizontal gene exchange? Explain why species definition is a problem.

3. Why is competence factor exported out of the cell to bind to ComD externally in transformation of Streptococcus? Why doesn't the molecule bind internally? Doesn't exporting CF waste energy?

4. If a spontaneous mutation occurs to form an apurinic site, transcription and replication are hindered, but what actually happens when the replisome gets to the hole where the base should be?

5. Explain how a DNA sequence inverts during phase variation. Would you expect it to revert at the same rate? Why or why not?

6. Explain the different propagation strategies available to a replicative transposon. What are various ways the transposon could spread within a cell? Among organisms?

7. Explain how the ara operon works, and how it differs from the lac operon.

8. Explain how different mechanisms acting at different levels on DNA and RNA can modulate gene expression over a range of time scales, from multiple generations to within a few seconds.

9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the trp operon.

Ma et al. paper

1. What do bacterial biofilms have in common with multicellular organisms? How do they differ?

2. What are the advantages to bacteria of biofilm formation? What properties do biofilms confer?

3. Where in the body do biofilms form infections? Why?

5. How does the ara promoter work (pBAD)? How was pBAD used to test the role of the psl operon in bioflim development?

6. How was it proved that psl encodes PSL polysaccharide? How does PSL compare in structure with alginate?

Chapter 13

1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?

2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversible. However, there are a couple of steps that are not reversible. How do you think they get reversed for gluconeogenesis?

3. There are 3 main pathways to form pyruvate- EMP, ED and PPS. How and why might a cell switch among these?

4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.

5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose? Explain several reasons.

6. In glycolysis, explain why bacteria have to return the hydrogens from NADH back onto pyruvate to make fermentation products. Why can't NAD+ serve as a terminal electron acceptor, like O₂?

7. Why do environmental factors regulate catabolism? Give examples. Why are amino acids decarboxylated at low pH, and under anaerobiosis?

8. Why does catabolism of benzene derivatives yield less energy than sugar catabolism? Why is benzene-derivative catabolism nevertheless widespread among soil bacteria?

Chapter 14

1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.

2. Explain how cell processes such as ATP synthesis can be powered by either the transmembrane pH difference or by the charge difference across the membrane. Which form of energy is likely to be used at low external pH? At high external pH?

3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.

4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.

5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation. What are some practical consequences for human industry?

6. Is it surprising that an organism may switch between lithotrophy and organotrophy? What enzymes would have to be replaced, and what enzymes could be used in common for both kinds of metabolism?

7. What kind of environments favor methanogenesis? Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?

Chapter 15

1. Why does biosynthesis need both ATP and NADPH? Why couldn't biosynthetic pathways use just ATP, or just NADPH?

2. Compare and contrast fatty acid biosynthesis and amino acid biosynthesis. Which pathway requires more reduction? Which requires a greater number of different enzymes? Why?

3. What forms of nitrogen are available to microbes for assimilation? When fertilizer is spread on farmland to nourish crops, what problem is caused by microbes? What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion? What about N from reduced organic compounds?

4. How are the pathways of amino acid biosynthesis organized? What common routes flow from which core pathways?

5. How and why do bacteria make "secondary products"? What are their functions?

6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?

Chapter 17

1. Explain why the first kinds of metabolism on Earth involved electron donors from the sediment reacting with electron receptors from above. What geolotical and outer-space processed generated these electron donors and electron acceptors?

2. What evidence supports the "RNA world" aspect of the origin of life? What are evolutionary and medical implications of the RNA world model?

3. What is our modern definition of a microbial species? Explain the strengths and limitations of defining microbial species based on common ancestry of DNA sequence.



4. Explain the evolutionary origins of mitochondria and chloroplasts. What evidence do we see in the structures of modern microbes?



5. What is a virulence gene? How do virulence genes evolve? How can we analyze the relationship between virulent and nonvirulent strains of a bacterium?

Chapter 18

1. Compare and contrast the major divisions of bacteria. State an example of a species of each major division.

2. Explain an example of a major division of bacteria whose species show nearly uniform metabolism but differ widely in form. Explain a different example of a division showing a common, distinctive form, but variety of metabolism.

3. Compare and contrast three different types of phototrophy found in bacteria.

4. Explain the pathology of three different gram-positive pathogens.

5. Explain two different examples of bacterial-host mutualism.

6. Students: Place bacterial unknown descriptions here for identification.

a. This bacteria is irregularly shaped with peptidoglycan cell walls and a cytoskeleton containing tubulin (previously thought to only be present in Eukaryotes). They are heterotrophs living in variable environments that are usually low in salt, and most are oligotrophs.
b. This bacteria has a nucleus similar to that of a eukaryotic organism. It is most notable for its unique membrane structure. It has multiple internal membranes, with a double membrane functioning to surround the nucleoid. What am I?!
c. Bacteria in this group are filamentous photoheterotrophs. In the presence of oxygen they conduct nonphotosynthetic heterotrophy. They can be found in microbial mats together with thermophilic cyanobacteria. Some species contain chlorosomes. They are also known as green nonsulfur bacteria.
d. These bacteria are photolithotrophs that deposit sulfur on the cell surface. They use H₂S as an electron donor and are known as green sulfur bacteria. These bacteria also live in strictly anaerobic conditions below the water surface.
e. This bacterium is gram positive but has permanently lost its cell wall and S-layer due to reductive/degenerative evolution. It also has the smallest genome(580 kbp) and it is parasitic.
f. This bacterial species ferments complex carbohydrates and serves as one of the major mutualists of the human gut. Has a Gram-negative structure and is an obligate anaerobe.
g. These bacteria are deep branching and come in a multitude of forms. They can be found living independently or in colonies. Often times, these different forms allow them to fix nitrogen. While these organisms can be found in both aquatic and terrestrial habitats, many species contain gas vesicles to maintain a favorable position in the water column.

Chapter 19

1. Compare and contrast the different major groups of archaea. Which ones grow in extreme heat or cold? Extreme salt? Produce methane?

Archaea which grow in extreme heat or cold are found in both phyla: Crenarchaeota and Euryarchaeota. Desulfurococcales and Sulfolobales are both groups of Crenarchaeota that grow at high temperatres and gain energy by reducing sulfur. Neither of these groups has a cell wall, and each has an S-layer present. Other thermophiles among the Crenarcheota are Thermoproteales, which also reduce sulfur, and Caldisphaerales, which either respire anaerobically or ferment. Yet there are certain Crenarchaeotes which live at psychrophilic temperatures: Cenararchaeum, which grows on deep-water sponges in Antarctic seawater, is a good example. Thermophiles among the eukaryotes include Thermococcales, anaerobic archaea which use sulfur as an electron acceptor, and Archaeoglobales, which reduce sulfate to sulfide and oxidize acetate to carbon dioxide. Thermoplasmatales are similar to Desulfurococcales and Sulfolobales: they have no cell wall. They have no S-layer either, and an amorphous shape.

Methanogens, archaea which produce methane by transferring electrons from H₂ to CO₂, are all Euryarchaeota which live in anaerobic environments such as landfills, rumen, flooded soil, and the human gut. Halophiles are Euryarchaeota which grow in extreme salt; in fact, they grow best at 4.3 M NaCl, at a pH of 7 or higher. The high GC content in their DNA prevents denaturation in high salt, and most are photoheterotrophs, with rhodopsins which capture light energy by a proton-motive force.

Be careful, "Euryarchaeota," not Eukaryotes.

2. Explain how archaea growing in extreme environments require specialized equipment for study.

3. What kinds of archaea grow in "average" environment such as the soil? Or an animal digestive tract?

Archaea identification: What is it?
These archaea were once thought to be extremophiles, but it turns out they are the most abundant archaea in the ocean. Nonetheless, the thermophiles responsible for giving this false impression are found at temperatures of 113degrees. Others are found living in sulfuring springs. When gram stained, these archaea appear gram-negative.

Chapter 20

1. Compare and contrast the major divisions of eukaryotic microbes. Which groups include primary-symbiont algae? Secondary-symbiont algal protists? Single flagellum versus paired flagella? Motility (widespread) versus limited motility?.

2. Describe examples of eukaryotic microbes that have shells or plates of silicate or calcium carbonate.

3. Explain mixotrophy. Why are so many marine protists mixotrophs?

4. Why do eukaryotes show such as wide range of cell size? What selective forces favor large cell size, and what favors small cell size?

Chapter 21

1. Explain what is meant by symbiosis, mutualism, and parasitism. Show with specific examples how mutualism and parasitism have a lot in common, and how there are inbetween cases.

2. Compare and contrast the roles of microbes in the marine and soil ecosystems.

3. How does oxygen availability determine the community structure of the soil habitat? Of the aquatic (freshwater) sediment habitat?

4. Outline the metabolic processes of the bovine rumen microbial ecosystem.

Chapter 22

1. What are the common gases besides CO2 that contribute to global warming? What is the chemical basis for how these gases trap solar radiation as heat?

2. In the last fifty years, most of the wetlands off the coast of Louisiana have been destroyed. Is this destruction responsible for the increased run-off and pollutants in the Gulf of Mexico, as well as the notorious dead zone there Can dead zones ever be fully revived? What are the methods that used that cause the price of restoration to be $1 billion dollars per year?

3. It is interesting that the ocean's microbial communities could be responsible for over half of the biological uptake of atmospheric carbon. How soluble is CO2 is in water? Is it more soluble than oxygen gas in water?

4. How exactly is ammonium nitrate addition related to higher CO2 efflux in wetlands?

5. Iron is limiting in oceans because the iron in the benthos, where it’s abundant, is inaccessible because it’s far away. In the benthic environment then, is iron not limiting because the microbes can access the sediment? What is typically limiting instead?

7. What is the microbial process in which nitrous oxide gas builds up?

Chapter 23

1. What's the point of breeding a gnotobiotic animal? A gnotobiotic animal is an animal that satisfies one of two rules. It is either entirely germ-free, or all of the microbial species that colonize it are known. These animals are used to demonstrate how microbiotic organisms affect their host. They can be developed so that only particular microbiota are present and then observe any changes in the in the organism's function that may occur. In general, gnotobiotic organisms also demonstrate how microbiota are important to organisms as they show signs of poorly developed immune systems, low cardiac output, thin intestinal walls, and an increased susceptibility to pathogens.
Yes, that sounds right.

3. How do defensins tell the difference between “good” bacteria and pathogens?

4. What are the benefits of an acidic skin? Of an acidic vaginal tract?

5. How are mast cells involved in immune response other than being differentiated with other immune cells?

6. Why do you think gnotobiotic animals have a lower cardiac output?

7. Why does an infection site heat up during vasodilation?

8. How do interferons work? How do they connect with the adaptive immune system?

9. Explain the difference between the innate and adaptive immune systems--and explain how they interconnect.

Chapter 24

1. Now that you know more about adaptive immunity, explain some examples of how the innate and adaptive immune systems interconnect. For instance, how does an innate system receiving a signal activate the adaptive immune system? How does an adaptive response to a pathogen activate an innate response component?

2. Explain the difference between the B-cell and T-cell immune systems--and explain how they interconnect.

3. Explain an example of an antigen-presenting cell within the adaptive immune response.

Species to know for Test 3

For each species, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).

Aeromonas hydrophila

Broader Categories: Gram-negative, anaerobic
Genome: Genes that contribute to its toxicity are cytotoxic enterotoxin gene (act), heat labile enterotoxins (Alt), and heat-stable cytotonic enterotoxins (Ast).
Metabolism: Heterotrophic, ferments glucose, digests gelatin, hemoglobin, and elastin.
Habitat: Exists in aerobic and anaerobic environments: aquatic environments, fish guts, food, human bloodstream and organs.
Disease: Causes many diseases in fish and amphibians, since it exists in aquatic environments. Can cause disease in humans, such as septiticemia, meningitis, pneumonia, and gastroenteritis.

Anabaena sp.


Broader Categories: Barrel-shaped cells. Filamentous cyanobacteria (blue-green algae) found as plankton.
Genome: 1 circular chromosome with 5368 protein-coding regions and 6 plasmids (from sequenced PCC 7120 strain).
Metabolism: Photoautotrophic, perform oxygenic photosynthesis. Form heterocysts (specialized nitrogen-fixing cells that convert nitrogen to ammonia) during nitrogen starvation.
Habitat: Freshwater and damp soil. Form symbiotic relationships with certain plants.
Disease: Produce neurotoxins, such as anatoxins (neuromuscular poisons), that are harmful to wildlife and farm animals.

Aquifex sp.

Broader categories: gram-negative, generally rod-shaped, thermophilic, non spore forming, aerobe. Genome: Densely packed genome with overlapping genes. No introns or splicing proteins. Genome is about 1/3 the size of that of E. coli. Metabolism: Autotrophic chemolithotrophs that fix carbon from the environment and draw energy from inorganic chemical sources. Uses oxygen as terminal electron acceptor when it oxidizes hydrogen to form water “aquifex=water forming.” They can also use sulfur or thiosulfate to produce H2S instead of water. Some aquifcales aren’t aerobic, however, and reduce nitrogen instead of oxygen. In this case the reaction ends with H2. Habitat: Near volcanoes or hot springs Diseases Caused: None

Aspergillus sp.

Broader Categories: Over 185 species of this genus Genome: Largely incomplete Metabolism: Highly aerobic. Pathogenic species obtain nutrients from host, while non-pathogenic species obtain nutrients from soil, wood, and plant detritus. Habitat: Grow as molds in oxygen-rich environments and carbon-sources. Some species are capable of living in nutrient-depleted environments as well. Disease: About 20 species are pathogenic in humans and animals. Aspergillus fumigatus and Aspergillus flavus cause invasive pulmonary aspergillosis and is often fatal.

Bacillus anthracis

Broader Categories: Gram-positive, rod-shaped, form endo-spores and biofilms
Genome: 1 circular chromosome with over 5 million b.p. 2 circular plasmids: pxO1 and pxO2. These plasmids encode main virulent factors.
Metabolism: Facultative anaerobe and must grow in medium with essential nutrients including C and N sources. Upon nutrient deprivation, endospores form (requires oxygen to form) and can live in inhospitable envrionments for many years. Can grow into vegetative cells in aqueous environment with adequate nutrients.
Habitat: Live in soils world-wide and is the main habitat.
Disease: Anthrax disease. Infectious endospores harm host by germinating for vegetative growth. During growth the bacteria produce toxins in the body of humans and animals. The slime capsule enables it to resist phagocytosis. 3 main forms of the disease: cutaneous, pulmonary, and gastrointestinal. Can cause death in 2-48 hours.

Bacillus subtilis

Broader Categories: Gram-positive, rod-shaped, form stress-resistant endospores Genome: 1 circular chromosome with 4100 genes coding for proteins. Metabolism: Can grow in aerobic and anaerobic conditions. Uses fermentation and nitrate ammonification to make ATP in the absence of oxygen. Habitat: Soil and vegetation at mesophilic temperatures. Disease: Non-pathogenic. Responsible for spoilage of food, since contamination often results in decomposition, but it rarely causes food-poisoning.

Bacillus thuringiensis

Broader Categories: Gram-positive, spore-forming, rod-shaped Genome: 1 circular chromosome with 5.2-5.8 Megabases. Contains many plasmids. Metabolism: Facultative anaerobe (makes ATP by aerobic respiration if oxygen is present, but can switch to fermentation). Habitat: Soil. It is used in 90% of pesticides. Fends off insects by producing crystal proteins (Cry proteins). Disease: Species-specific, non-pathogenic to humans, making it an environmentally-friendly insecticide. Cry toxin grows and sporulates in alkaline gut o finsect, which aids in its ability to infect the insect gut. The gut breaks down and the insect eventually dies.

Bacteroides thetaiotaomicron

Broader Categories: Gram-negative, anaerobic, human-bacterial symbiosis model Genome: 1 circular chromosome made of d.s. DNA, consists of 4776 proein-coding genes, 90% of which are essential in the binding and import of various polysaccharides. Metabolism: Starch (all 3 forms) is primary carbohydrate used as its source of C and Energy. Polysaccharides bind to the cell surface before undergoing hydrolysis. Habitat: Adult intestine-allows humans to degrade plant polysaccharides Disease: Serious infections include intra-abdominal sepsis and bacteremia. It is resistant to many antimicrobial agents.

Borrelia burgdorferi

Broader Categories: Sprial-shaped with 2 flagella Genome: A linear chromosome with 910,725 b.p. with 853 genes. 17 linear and circular plasmids. Metabolism: Require specific nutritional requirements making it difficult to culture in vitro. Habitat: Live extracellularly and adapts to various host animals (tick, rodents, birds) by regulating various lipoproteins on thier surface. Disease: Lyme disease and recurring fever.

Chlamydia sp.

Broader Categories: Gram-negative, aerobic, coccoid or rod-shaped Genome: C. trachomatis-1,042,519 b.p. with 894 protein-coding sequences (70 genes are not homologous to sequences on the C. pneumoniae genome). C. pneumoniae- 1,230,230 b.p. (186 genes are not homologous to sequences on the C. trachomatis genome) Metabolism: Cannot synthesize its own ATP, so they cannot be grown on artificial medium and require growing cells to remain viable. Habitat: C. trachomatis-human host cells, C. suis- swine host cells, C. muridarum- mice and hamster host cells. Infectious elementary body form induces endocytosis upon contact with host cell. Once inside, the elementary body germinates to vegetative form, and divides every 2-3 hrs. It then reverts back to the elementary form and is released by the cell through exocytosis. Disease: C. trahomatis causes chlamydia and is the most common STD in the world. C. pneumoniae causes pneumonia and bronchitis

Clostridium botulinum

Broader Categories: Gram-positive, rod-shaped, anaerobic, spore-former Genome: Genome size of 4039 kbp, which is larger than most Gram-positive genomes, indicating the extra genomic requirements needed for sporulation and pathogenic toxin production Metabolism: Lie dormant in very adverse environments. Spores can begin to grow in favorable conditions: non-halophilic salinity and anaerobic conditions. Grows at mesophilic temps. Habitat: Soils and improperly canned food products Disease: A-G subtypes produce different botulin toxin- al except C and D subtypes are human pathogens. The toxin prevents propagation of action potentials to the muscle fibers- causing paralysis by inhibiting muscle contraction. Fatalities usually occur due to asphyxiation

Chloroflexus sp.

Corynebacterium diphtheriae

Escherichia coli

Broader Categories: Gram-negative, rod-shaped, aerobic Genome: 1 circular chromosome, (4300 coding sequences) with 1800 known proteins. Some contain circular plasmid. Metabolism: Facultative anaerobe. Uses mixed-acid fermentation in anaerobic conditions. Growth driven by aerobic or anaerobic respiration using a large variety of redox pairs: oxidation of pyruvic acid, formic acid, hydrogen, and amino acids and reduction of oxygen, nitrate, dimethyl sulfoxide, trimethylamine N-oxide. Habitat: Lower intestines of human and mammals, where it aids in digestion processes: vitamin K production, food breakdown and absorption Disease: E. coli O157:H7 (enterohemorrhagic strain) causes food poisoning- leading to bloody diarrhea and kidney failure due to its production of Shiga-like toxin. Also can cause urinary tract infections by ascending infections of the urethra.

Geobacter metallireducens

Broader Categories: Gram-negative, rod-shaped, possesses flagella, and pili Genome: 1 circular chromosome encoding 3621 genes. Plasmid encodes 13 genes, 1 of which is addiction module toxin (gives resistance to bacteria and another encoding plasmid stabilization system protein (allows bacteria to adapt to new environmental conditions) Metabolism: First organism with the ability to oxidize organic compounds and metals (iron, radioactive metals like Uranium, and petroleum compounds) into environmentally benign carbon dioxide while using iron oxide and other available metals an electron acceptors. Habitat: anaerobic conditions in soils and aquatic sediments Disease: Non-pathogenic

Pseudomonas aeruginosa

Broader categories: Gram-negative, rod-shaped, does not produce spores. Habitat: due to its capability to synthesize arginine, P. aeruginosa proliferates in anaerobic conditions. It can be found in environments such as soil, water, humans, animals, plants, sewage, and hospitals. Metabolism: Aerobic respiration. P. aeruginosa can metabolize on hundreds of other things besides arginine, and can respire on nitrate (although it does much better on O2).Genome: a single and supercoiled circular chromosome in the cytoplasm. Disease(s) caused: Causes disease in immuno-compromised patients, such as those with cystic fibrosis, cancer, or AIDS. It further weakens the patient, allowing the patient to become more susceptible to other diseases. Usually this kills the patient. P. aeruginosa forms biofilms in the lung of cystic fibrosis patients; it is the major cause of death in these individuals.

Broader Categories: Gram-negative, rod-shaped, and contains 1 flagella Genome: It contains a 5.2 to 7 million base pairs and a single, supercoiled circular chromosome in the cytoplasm with many plasmids contributing to its pathogenicity. Metabolism: Facultative aerobe, with its preferred metabolism being aerobic respiration by transferring electrons from glucose to oxygen. Habitat: Ubiquitous in that it can live in both human and inanimate environments. This is possible mainly because of the vast array of enzymes that allow uptake of diverse forms of nutrients. Pathogenicity: Disease-causing agent to immuno-compromised individuals (cystic fibrosis patients) or indivuals in a trauma (burn victims). It tends to form biofilms and cause tissue damage through its virulence factors.

Halobacterium sp.

Broader categories: rod-shaped, halophilic, candidate for life on Mars. Genome: 1 large chromosome and 2 plasmids (3 circular replicons). Metabolism: aerobic, but not glucose degradation. Habitat: highly saline lakes. Disease: non-pathogenic

Helicobacter pylori

Broader Categories: Gram-negative, spiral-shaped, 6-8 flagella at one end Genome: Single circular chromosome with genes that encode urease, membrane cytotoxins, and the cag pathogenicity island. Metabolism: Glucose is the only carbohydrate used by H. pylori and is metabolized through the ED pathway. Pyruvate is synthesized from D-amino acids, lactate, L-alanine, and L-serine, rather than glucose. Fermentation of pyruvate yields acetate. Urease converts urea into ammonia and bicarbonate to buffer the low pH of the stomach. Habitat: The lining of the stomach and duodenum, where it is well adapted to a pH of 2 or less. Pathogenicity: Peptic ulcers and gastritis

Lactobacillus sp.

Lactococcus sp.

Broader categories: spherical, gram positive. Genome: 1 circular chromosome with 2, 365, 589 bp, where 86 % of the genome code for protein, 1.4 % for RNA, and 12.6 % for noncoding region. 64.2 % of the genes code for known functional proteins, and 20.1 % of the genes for known protein with unknown function. Metabolism: aerobic or anaerobic, often use lactic acid fermentation. Habitat: plant surfaces, digestive tract of cows. Disease: non-pathogenic.

Leptospira

Broader Categories: spirochete, spiral-shaped with one or both ends usually hooked, of the family Leptospiraceae, and the genus Leptospira. Very thin and must be observed through darkfield microscopy. Genome: Consists of a large chromosome and a small chromosome, with about 4768 total genes. Metabolism: aerobic using oxygen as the final electron acceptor. Energy is gained primarily through long-chain fatty acids. Carbohydrates are not used as a source of carbon, but can be synthesized through the TCA cycle. Habitat: Occupies diverse environments, habitats, and life cycles. Stagnant waters are its natural environment. Prefers slightly alkaline environment. Prefers a temp of 28-30 degrees C bu can grow at temp. as low as 11-13 degrees C. Pathogenicity: Leptospirosis is potentially deadly in both humans and animals. In humans it can cause symptoms of fever, chills, sore muscles, vomiting, jaundice, red eyes, abdominal pain, diarrhea, or rashes. It is typically spread through contact with water, food, or urine of an infected animal.

Methanococcus sp.

Broader categories: gram-negative, cocci-shaped, archaea domain, thermophilic and mesophilic. Genome: 1 circular chromosome with 1 large extra-chromosomal element and 1 small extra-chromosomal element. Metabolism: autotrophic, anaerobic, reduces carbon dioxide with hydrogen gas to generate methane. Habitat: can grow up to pressures of 200 atm, temperature ranges between 48-94 degrees C, with optimal growth at 85 degrees C. Disease: non-pathogenic.

Mycobacterium tuberculosis

Mycoplasma pneumoniae sp.

Broader categories: spherical without a cell wall, highly pathogenic--osmotic instability. Genome: 1 small circular chromosome. Metabolism: major nutrients come from mucosal epithelial cells of the host, many proposed metabolic pathways. Habitat: not found in the environment but can be cultured in medium-rich agar. Disease: highly pathogenic; parasitizes epithelial cells in the respiratory tract.

Nitrospira sp.

Paramecium sp.

Broader categories: Eukaryotic ciliated unicellular organisms. Genome: Linear. Metabolism: Paramecium eject trichocyts to help capture their prey. They commonly eat bacteria, yeasts, algae, and small protozoa. Paramecium are also heterotrophs. Habitat: Aquatic environments, usually in stagnant warm water. Some Paramecium species form symbiotic relationships with green algae or bacteria. The bacteria/algae live in the cytoplasm of the Paramecium and perform photosynthesis. Disease: Non-pathogenic

Plasmodium falciparum

Broader Categories: Protazoan parasite Genome: It contains a 23-megabase nuclear genome consisting of 14 chromosomes, encoding about 5,300 genes, and is the most A/T rich genome sequenced to date Metabolism: Uses intracellular hemoglobin as a food source. Anaerobic glycolisis with pyruvate being converted to lactate. Habitat: Requires both human and mosquito hosts Pathogenicity: Causative agent of malaria

Prochlorococcus sp.

Broader Categories: Single-celled cyanobacteria Genome: It is about 1.67 Mega-base pairs long with 1,694 predicted protein-coding regions Metabolism: photoautotrophic Habitat: Oceans Pathogenicity: Non-pathogenic

Rhodobacter sp.

Broader categories: quorum-sensing bacteria, flagella motility. Genome: unique complexities-2 chromosomes, 1 large and 1 small, circular chromosomes. Metabolism: photosynthesis mostly, also capable of lithotrophy, aerobic, and anaerobic respiration pathways. Habitat: aquatic and marine environments. Disease: non-pathogenic.
Which photosystem does it use? Does it conduct phototrophy anaerobically, or in the presence of oxygen?

Rhodopseudomonas sp.

Rhodospirillum rubrum
Which photosystem does it use?
Rickettsia sp.

Saccharomyces cerevesiae

Broader Categories: Best known as brewer's and baker's yeast, used as a model system due to its short generation time (1.5-2 hrs. at 30 degrees C), can be easily cultured, easily transformed which allows the addition or deletion of genes, and is a eukaryote so it shares much of the non-coding DNA stretches found in higher order eukaryotes Genome: Single, linear, d.s. DNA, with little repeated sequences and less the 5% of the sequences have introns. Metabolism: Heterotrophs that use both aerobic respiration and fermentation and obtain their energy from glucose. Habitat: The natural habitat is the surface of fruits. Industrially, it is used in baking and brewing and is considered an ale yeast, or top yeast. Pathogenicity: Is used as a probiotic in humans. However, new evidence may suggest that the use of S. cerevesiae probiotics could potentially be harmful, causing the infection of S. cerevesiae fungemia.

Salmonella enterica

Broader Categories: Gram-negative, rod-shaped, flagellated Genome: Circular chromosome with a one to a few plasmids (depending on the 1 of 2,000 serovars that comprise S. enterica. Metabolism: aerobic respiration Habitat: Reptile and amphibian microbiota. It is also found in red meat, poultry, and raw egg shells Pathogenicity: Salmonella enterica serovar Typhi is the causative agent of typhoid fever. Salmonella enterica serovar Typhimurium generally causes gastroenteritis. Its major virulent factor is its secreted proteins, such as adhesins that help colonize the host and are involved in biofilm formation.

Serratia marcescens

Broader Categories: Gram-negative, rod-shaped, motile, of the family Enterobacteriaceae. Genome: Singular circular chromosome. Few plasmids Metabolism: Facultative anaerobe, but uses primarily fermentation to obtain Energy. Nitrate is usually the final electron acceptor. Habitat: Found in diverse environments from water and soil to plants and animals. One of the most common contaminant on laboratory Petri dishes. Pathogenicity: A wide variety of diseases can result mainly in immuno-compromised individuals, such as bacteremia, meningitis, urinary tract infections, osteomyelitis, ocular infections, and endocarditis. It is resistant to penicillin and ampicillin, due to R-factors on plasmids encoding genes involved in antibiotic resistance and is able to produce biofilms.

Sinorhizobium meliloti

Staphylococcus epidermidis

Broader Categories: Gram positive, spherical, arrange in grape-like clusters, resistant to all penicillins and methicillin. Genome: The chromosome length is 2,616,530 bp and contains a few plasmids, depending on the strain. Metabolism: Facultative anaerobe that can grow by aerobic respiration or by fermentation. Most strains can reduce nitrate. Habitat: The skin and in mucous membranes of animals. Has the ability to produce slime and biofilms, which enable it to grow on biomedical devices. Pathogenicity: The primary virulence factor is its ability to form biofilms. With the increased use of intravascular catheters, the rate of infection has increased. It is more resistant to antibiotics that most other species.

Staphylococcus aureus

Broader categories: gram positive, spherical, immobile. Genome: 1 circular genome, resistance for antibiotics are encoded by a transposon. Metabolism: EMP and Pentose-Phosphate pathways. Lactate is the end product of anaerobic glucose metabolism. Acetate and carbon dioxide are the end products of aerobic metabolism. Habitat: skin, mucous membranes of animals. Disease: skin infections, invasive diseases, toxic shock syndrome (TSS).

Streptococcus sp.

Broader Categories: Gram positive, spherical, can be found in chains or in pairs, immobile. Genome: 1 circular chromosome. Metabolism: Many species of Streptococcus are facultative anaerobes, while others are obligate anaerobes. Habitat: Part of normal animal flora. Can become pathogenic and infect humans and other animals. They often imitate aspects of their host organism to avoid being detected. Disease: Can cause step throat, necrotizing fasciitis, scarlet fever, rheumatic fever, postpartum fever, and streptococcal toxic shock syndrome. Some species of Streptococcus can cause pneumonia.

Streptomyces sp.

Vibrio cholerae

Broader Categories: Gram-negative, bent rod shaped, one polar flagellum. Genome: Two circular chromosomes. Metabolism: Fermentative and respiratory. Habitat: Aquatic environments. Disease: Responsible for cholera in humans, which is characterized by diarrhea and vomiting leading to dehydration. The bacteria secrete a toxin that ultimately causes an increase in cyclic AMP levels that stimulates ion transport in the cells lining the intestine. This is followed by water leaving the intestinal cells to compensate for the change in osmolarity.

Vibrio fischeri

Broader Categories: Rod shaped, gram-negative. Genome: Two circular chromosomes with 2,284,050 bp and a plasmid. The lux operon controls bioluminescence. Metabolism: Heterotrophic. Habitat: Found in marine environments in a symbiotic relationship or as free-living. It can also be parasitic and saprophytic. Often found in the Hawaiian squid, Euprymna scolopes, where the bacteria bioluminesce in the light organ. The squid protects the bacteria from predators and provides nutrients, while the bacteria’s light eliminates the squid’s shadow, protecting it from predators. Disease: Other Vibrio species can cause human infections.