Humans and the Microbial World - Ch1

microbiology, **need to add previous slides based on lecture

What’s microbiology?

study of life (aka the microbial world) too small to be seen by the unaided eye

anything < 0.1mm requires microscopes to be seen

microorganisms

living cellular organisms that are a part of the microbial world, organisms too small to be seen with the naked eye

• bacteria, archaea, eukarya

Bacteria/bacterium

unicellular prokaryotes

rigid cell wall contains peptidoglycan

moves by flagellum/flagella which are filamentous appendages that extend from the cell

single is bacterium

has many shapes and a specific species has a characteristic shape that it maintains (4 shapes)

utilizes usual sources that humans use for energy AND unusual sources like hydrogen sulfide (H2S) and being photosynthetic

its divided by binary fission: how it reproduces asexually by splitting into 2 identical daughter cells

Archaea/archaeon

unicellular prokaryotes that resemble bacteria, except are unique in that they:

• has motile filamentous appendages that are structurally different than bacteria’s

• has rigid cell walls that lack peptidoglycan

• have characteristic/unique rRNA nucleotide sequences

• can grow in extreme environments

similar to bacteria in that it:

• shares some shapes and energy sources

• divided by binary fission

Eukarya

eukaryotes which include:

• fungi: group of eukaryotes that are unicellular (yeasts) or multicellular (molds)

• algae: photosynthetic uni/multicellular eukaryotes

• protozoa: unicellular eukaryotes that live in both aquatic and terrestrial habitats

• helminths: parasitic worms

Microbe

refers to the general members (everything) of the microbial world

anything <0.1 mm

living (cellular): bacteria, protozoa, fungi, algae AND nonliving (acellular): prions, viroid, viruses

What’s a domain?

Highest level of biological classification

3 __ for all living things is: bacteria, archaea, and eukarya

• subdivided into 2 groups of microorganisms: P and E depending on the cell they are made of

draw out the division of the microbial world

yep

Prokaryote

single celled organism. the single cell is a prokaryotic cell; lacks membrane-bound organelles, no nucleus

• pro: “prior to”

• karyote: “nucleus”

• includes the domains bacteria and archaea

eukaryote

organism composed of one or more eukaryotic cells: cell type known for having membrane-bound nucleus and organelles

• eu “true”

• karyote “nucleus”

• includes the domain: eukarya

Anthoni van Leeuwenhoek

discovered/founder of the microbial world, microbiology born as a science in 1674, Dutch fabric merchant, made simple glass lenses to view fabric, used lens to study a drop of lake water; first glimpses of the microbial world thru a microscope

animalcules

anthoni van leeuwenhoek called microorganisms this, it means small animals because this is what he observed

• A: ratchet bacterium

• B: drawn out to denote its movement

• G: spriochete

• F: rods

Spontaneous Generation

abiogenesis, 1st proposed by Aristotle; thought life comes from non-living things, small animals and insects are so simple (simpler than humans) that they come from _ _

supporters: john needhan

detractors: francesco redi, lazarro spallanzani, louis pasteur, john tyndall

John Needham

English scientist and Catholic priest, supporter of SG proposed by Aristotle

what he did: boiled broths and then subsequently sealed with corks, said that it still produced microorganisms

the flaw: he didn’t boil it for long enough, he covered it after letting it cool down which allowed for air microbes to contaminate it, probably didn’t seal it well enough

Francesco Redi

Italian biologist and physician, disproved SG, rotting meat experiment, uncovered jars had maggots/flies on the meat, gauze-covered jars had maggots/flies on the gauze, covered jars had no maggots/flies

• despite the evidence it took another 200 years for SG to be convincingly disproved

Lazarro Spallanzani

animal physiology and priest, disproved SG, Liquid Sterile, boiled broths longer, sealed the flasks by melting the necks, broths remained sterile

controversy that caused it to be dismissed: sealing prevented entry of “vital force” in the air necessary for spontaneous generation, the vf is oxygen

Louis Pasteur

father of modern microbiology, French chemist, disproved SG by developing the swan-necked flask, demonstrated that microorganisms are still present in the air, oxygen can go in and out even after many years, but the microbes can’t get in there; dust particles are too heavy and get trapped in the neck area, supported biogenesis; production of living things from existing things

• was only contaminated when the flask was tilted allowing the microbes to come in contact with the broth

abiogenesis vs biogenesis

a (without) bio (life) genesis (to create) VS bio (life) genesis (to create)

• production of living things from non-living things VS production of living things from other living things

Golden Age of Microbiology

disproving of SG led to this, 1854-1914, time of great interest in the study of microorganisms

discoveries: microorganisms can cause disease, microbes in the air were called contagions (specific ones caused specific diseases → germ theory of disease)

• work on viruses began; discovery of electron microscope that let us see them

• understanding of microbes led to control efforts to improve human health including vaccines (to prevent diseases), antibiotics (to treat infectious diseases), antimicrobials, modern sanitation

Sub disciplines of microbiology (abt 12)

bacteriology: study of bacteria

virology: study of viruses

mycology: study of fungi

parasitology: study of parasites

forensic microbiology (not fully accepted): utilization of microbiomes during forensic investigations, ex. identical twins, DNA is identical, but the microbes present on the body and in the body are compared → their microbiome

• microbiomes reflect environments you interact with and DNA remains constant

epidemiology: study of infectious diseases/how diseases spread

biotechnology: use of microbiological and biochemical techniques to solve practical problems (often thru genetic engineering) EX: using microbes to make food

food microbiology: utilization of microbes to make food (dairy mbio; utilization of microbes to transform milk into different food products)

agricultural mbio: how microbes affect agriculture

environmental mbio: studies microbes in the environment and their effects including using microorganisms to clean up the environment

aquatic mbio: studies microbes in aquatic environments

microbial ecology: looks at how microbes interact with each other and their environment

genetic engineering

intro of genes into microbes → commercial products, before they couldn’t make that product but us inserting the gene with DNA let it make that product, engineering of DNA to give desired qualities which is done by changing DNA of microorganisms by inserting a gene into that microbe that makes them produce…

• medically important products: insulin (to treat diabetes), vaccines, antibiotics, dietary amino acids

• biological pesticides: bacillus thuringiensis BT toxin

• pest/disease-resistant plants

• industrial products: ethanol = biofuel (10% of standard gasoline is ethanol), solvents

Bacillus Thuringiensis

bacterium that normally lives in the soil, goes thru a process called endospore and produces the BT toxin protein, its toxic to the larvae form of a pest, these pests will feed on plants and will destroy them, if we produce a lot of this toxin and spray them → them ingesting it will degrade the larvae from inside out, it’s not toxic to any other organism other than the pest, it being a protein allows it to degrade in the environment easily, cooking will also denature/destroy the protein

why study microorganisms?

Impact on humans

• Positive: contributions to ecosystem, we could not survive without microorganisms

• Negative: can cause disease, disease causing microbes have killed more people than even been killed in war, incidental or used as weapons in bioterrorism attacks…and can spoil food/crops

Good models for study:

• simpler organism: simpler than eukaryotes: only have a single copy of any gene, a prokaryote, it changes the trait of the whole organism when we change one gene

• same as higher forms of life like:

  • 1. metabolism; glycolysis, pathways of food breakdown

  • 2. genetic properties; DNA, RNA, DNA-replication, transcription and translation

  • 3. building blocks of macromolecules; nucleic acids, proteins, carbohydrates, lipids (fats)

• “what is true of elephants is also true of bacteria, and bacteria are much easier to study” - Dr. Jacques Monod

Host-Microbe Interactions

All surfaces of the human body are populated by microorganisms: 500-1000 species of microbes in/on the body; outnumber cells in the body by 3:1

• beneficial microbes that help protect us in and on the surface of plants, animals aka the microbiome/normal microbiota/normal flora

  • prevents diseases by competing with pathogens that are parasites causing damage to body tissues and leading to disease symptoms

  • pathogens are microbes that can cause disease

  • development of the immune system response

  • e coli lives in the colon/gut and aids in digestion

Microorganisms in the environment

microbes found in:

• air that we breath (50-100 microbes per cubic foot)

• soils (one gram of soil > 10 million microbes)

• bodies of water (oceans, lakes)

• deep in the earth’s crust → polar ice caps

Important for

• nitrogen fixation: only carried out by prokaryotes; take nitrogen from the air and convert it to a form that living organisms can use

• oxygen production through photosynthesis

• building of proteins, dna

• recycling of nutrients

• decomposition of certain material

  • cellulose in the environment and in the digestive tracts of ruminants of cow, sheep, deer

nitrogen fixation

microorganisms participate in the recycling of nutrients

• prokaryotes take N2 in the air → ammonia (NH3) → nitrate (NO3), converting them into usable forms that other organisms can use

this is bcuz

• N2 is the most common gas in our atmosphere, but unusable by most life forms

• nitrogen is important in nucleic acids and proteins

  • important in DNA/RNA and expression of them

  • therefore: we can’t survive without microorganisms

Applications of Microbiology: food production

food production (fermentation)

• baking bread using yeast

• fermentation of grains to produce beer

• fermentation of milk by lactobacillus acidophilus (lactic acid bacteria that breaks down milk to create lactic acid → sour taste) → yogurt, cheeses, buttermilk

• - probiotics are bacteria added to fermented milk products that are advertised as live organisms providing a health benefit

• pickles, sauerkraut, soy sauce, coffee, chocolate, olives

Applications of Microbiology: bio

biodegradation: general breakdown of material by microorganisms, ex. when animals die, they decay and are broken down by microorganisms

bioremediation: use of selected/engineered microbes to degrade environmental pollutants (chemicals toxic to humans), cleaned the following using microbes

• pesticides (PCBs, DDT), trichloroethylene, radioactive wastes, heavy metals

• oil spills; marine bacteria and the gulf of mexico oil spill → microbes eat oil like food and produce CO2 and H2O which are harmless/not toxic/innocuous products

• bacteria that will break it down will feed on that, microbes were already there and used to oil spill as a source of food and increased in numbers, they helped to clean up the gulf

biotechnology: use of microbiological and biochemical (using specific enzymes produced by microorganisms) techniques to solve practical problems

genetic engineering: intro of genes into microbes → commercial products (etc on other slide)

Microbes and Disease

Most microorganisms are not harmful

Some are pathogens; they can cause disease

infectious diseases: important to prevent/treat cuz they can spread

Past deadly diseases:

• Influenza: killed more Americans than died in WWI, WWII, Korean, Vietnam, and Iraq wars combined (US population)

• Black Plague: killed ~1/3 of population of Europe (~25 million individuals), Today <100 people die worldwide

• Smallpox: killed ~10 mil deaths over 4,000 years, IMP: worldwide eradication: no reported cases since 1977

Reduction in diseases due to:

• Modern sanitation: water contaminated by sewage does not give us disease BUT some developing countries are still affected by disease cuz they don’t have modern sanitation

• Vaccination: great way to prevent infectious diseases, less likely to be affected cuz you’re already immune

• Effective antimicrobial treatments

Present and Future challenges

Despite impressive progress, infectious diseases remain a threat

• In U.S. ~750 mil infections/year, ~200k deaths, $$ tens of billions on healthcare

Emerging diseases continue to rise: they’re either brand new or have been around for a long time and were under control but they came back because of a change in the pathogens

Emerging Diseases

Newly Recognized

• West Encephalitis (still ongoing)

  • transmitted through mosquitoes

• COVID-19 (2019): coronavirus disease 2019. major wake up call

  • caused by SARS-CoV-2: severe acute respiratory syndrome coronavirus 2

• Ebola virus (1970 > 2014-2016)

  • largest

• Zika virus (2015)

• Swine Flu (2009): viral disease deadly to pigs

• SARS (2003) - originally found in bats and chickens

1990’s

• Lyme Disease

• Hemolytic Uremic syndrome (E. coli O157:H7)

• Hantavirus pulmonary syndrome

1980’s

• HIV

• Hepatitis C

• Mad Cow Disease

Re-emerging Diseases

not new but showing increased occurrence and wider distribution

can’t seem to get rid of in US:

• pertussis (whooping cough)

• measles (coming back)

• multidrug resistant TB

and others around the world:

• cholera

• malaria

• anthrax

Factors for rise of emerging diseases

changing lifestyles increase opportunities to spread

• closer contact with animals (ex. hantavirus; smelling mice feces leads to lung infection)

evolution of infectious agents previously unable to infect humans (HIV/AIDS, SARS, Ebola Virus, TB)

• they were zoonotic diseases that were formerly in animals and now they affect humans

• increased contact with pathogens led to crossing of species barrier to humans

chronic diseases thought to be caused by environmental stressors may be caused by bacteria

• ex. gastric/peptic ulcers caused by Helicobacter pylori (only bacteria that can inhabit the stomach, now known to cause GU)

  • when people have HP, it can destroy the lining of the stomach leading to ulcers and long term is stomach cancer

• microbes possibly responsible for indigestion, Crohn’s disease, others

Factors for rise of re-emerging diseases

Re-emerging = resurgence of old diseases though to be defeated

1. vaccination becomes a victim of its own success

• parents relaxed about childhood vaccination; it’s working so well that they stopped vaccinating → can spread more easily among children

• lack of firsthand knowledge of dangers of diseases can lead people to fear vaccines more than the diseases

  • measles, mumps, whooping cough

2. pathogens have evolved/can become resistant to antimicrobial medications (ex. tuberculosis [disease caused by mycobacterium tuberculosis], malaria)

3. increased travel and immigration

• many diseases eliminated from developed countries still exist in many parts of the world (malaria, cholera, plague, yellow fever)

4. changes in population

• people are living much longer and are older, so they have weakened immune systems and are therefore more vulnerable to infections (ex. elderly, HIV/AIDS)

Members of Microbial World

major groups of the microbial world

• present in all environments on earth

• <1% of all microbial species can be grown and studied in lab

extra stuff: multicellular helminths; parasitic worms, huge and long, their eggs are microscopic

• all living things classified into 3 domains: bacteria, archaea, eukarya; organisms in each domain share certain important properties

Microorganisms

two basic types of microorganisms (microbes)

Prokaryotes: no membrane bound organelles, no nucleus

Eukaryotes: membrane bound organelles, nucleus

Are foundation for all life on Earth - all life depends on their activities

Includes:

Organisms

• bacteria, archaea, fungi, protozoa, algae, helminths

Acellular infectious agents

• viruses, viroids, prions

Sizes in the microbial world

Tremendous range in size

• smallest virus ~1/1milnth size of largest eukaryotic cell

• largest bacterium ~600 micrometer x 80 micrometer - visible to the naked eye bcuz its almost 1meter (0.6 micrometer)

Scientific Names

Binomial system of nomenclature

• Two word naming system

  • First = genus

    • always capitalized (Escherichia → Theodor Escherich, who discovered bacterium)

    • groups of microbes are often informally referred to by resemblances of their genus, and not italicized (Staphylococcus → staphylococci)

  • Second - specific epithet/species

    • not capitalized (coli)

    • strain: variations that occur in species, but not enough to separate them, and noted of offspring when genetic difference is important; E. coli B, E. coli K12

  • Abbreviated: E. coli

  • full name always italicized or underlined

  • names derived from

    • discoverer, location, shape/arrangement of bacteria, color of bacterial growth

Staphylococcus Aureus

genus:

• staphylo: bunch of grapes → desc. its growth

• coccus: berry → desc. its shape (spherical cell)

species:

• aureus: golden → desc. its color on nutrient agar plate

shape of bacteria and archaea

Coccus: spherical that may be flattened or slightly oval on one side

Rod or bacillus: rod or cylinder-shaped cell

• if short enough to be confused with coccus; “coccobacillus” NOT genus Bacillus even though they’re rod shaped as well

Vibrio: short, curved rod

Spirillum: a curved rod long enough to be spiral-shaped

Spirochete: long, helical-shaped cell with flexible cell wall and unique mechanism of motility

pleomorphic

when a bacterium characteristically varies in their shape, usually in cells that don’t have a cell wall

pleo: many, morphic: shape

binary fission

bacteria and archaea divide by this, how it reproduces asexually by enlarging and by splitting into 2 identical daughter cells, forms characteristic bacterial grouping/arrangements depending on if they divide on:

One Plane

• pairs called diplo cocci: cocci that remain in 2’s, characteristic of Neisseria gonorrhoeae

• chains called strepto cocci: characteristic of Strepto coccus (twisted chain)

Perpendicular Plane 2-3 planes

• packets → cubical, categorized by

  • Sarcina: packet of 8

  • tetrad: packet of 4, characteristic of Micrococcus

Random/several planes

• clusters called staphylo, characteristic of Staphylo coccus (bunch of grapes)

Rods

rod shaped bacteria can be grouped as well dependent on their attachment

• single bacillus: separate

  • as some bacteria have tendency to separate during binary fission, like E. coli

• diplo bacilli: two rods attached to each other

• strepto bacilli: a chain of rat shaped cells

  • genus: Streptobacillus

Fungi/fungus

diverse group of eukaryotes that are unicellular (yeasts) or multicellular (molds)

• hyphae/hypha: microscopic filament of mold that branches and twists to form mycelium

• mycelium: what is seen on food mold, alongside what’ll become →

• conidia: spores, microscopic reproductive forms, spores: reproductive unit capable of giving rise to a new individual without sx fusion

  • easily airborne; how they spread so easily

• some fungi make macroscopic structures known as mushrooms

HIV

human immunodeficiency virus type 1; causes AIDs, originally found in chimpanzees and primates, HIV on the surface of a CD4 cell

haemophilus influenzae

bacterium

genus: haemo (blood) philus (loving)

• requires blood components for growth

species: influenza, as this bacterium was mistakenly thought to cause the disease; actually caused by a virus

red mold

fungi, mold that grows on bread

Amoeba

a protozoan

volvox

very common algae

Saccharomyces cereviseae

fungus

genus: saccharo (sugar) myces (fungus)

species: cereviseae (beer)

→ fungi/yeast is used to make beer

Shigella dystenteriae

bacterium

genus: honors Kiyoshi Shiga (one who discovered the bacterium)

species: derived from “dysentery” → mucus/blood diarrhea disease caused by bacterium

Protists

a eukaryotic organism other than a plant, animal, or fungus that can be uni/multicellular; algae and protozoa are referred to as this

Algae/alga

photosynthetic uni/multicellular eukaryotes

• photosynthesis occur in chloroplast (chlorophyll-containing organelle)

• found near surface of salt/fresh water, or moist terrestrial habitats

• rigid cell wall that is chemically different from bacteria and archaea

• also move by flagella that is structurally complex and unrelated to prokaryotes

Protozoa/zoan

unicelluar eukaryotes that live in both aquatic and terrestrial habitats

• complex organisms that are much larger than prokaryotes

• lack rigid cell wall

• motile and ingest organic material as food sources

Helminths

parasitic worms that live at the expense of a host

• adult worms are macroscopic

• considered part of microbial world bcuz of their microscopic larval forms and eggs → diagnosis of diseases

• includes roundworms, tapeworms, flukes

Prion

acellular infectious agent consisting only of protein

• misfolded version of protein that cause other normal proteins to fold upon contact

  • bind to form fibrils: thread-life structures that group together/congregate in cells

  • eventually kills the cells

  • forms spaces in affected tissue

• cause spongiform encephalopathies; named after sponge-like appearance of affected brain tissue

  • encephalo: brain

  • patho: disease

  • most well known: bovine spongiform encephalopathy (BSE) or Mad Cow Disease

Viroid

acellular infectious agent consisting only of RNA

Virus

acellular infectious agent consisting of nucleic acid surrounded by a protein coat

• requires a host cell: living cell a __infects, in order to duplicate

• all forms of life can be infected by a __

endospores

discovered by Ferdinand Cohn who was a German botanist

a survival form that some bacteria make when conditions become harsh

• its heat resistant cuz it has a very tough protective structure, so it can survive things that would normally kill a bacterial cell such as

  • high heat, drying out, some chemicals, radiation

• its not a NEW bacterium; its a bacterial cell that’s broken down leaving an endospore and then when conditions become normal it can germinate and become an active/normal bacterial cell again

microbiome

beneficial microorganisms permanently residing in our body/total genetic content of microbial community

• <1% can be grown in lab, 99% identified only through their genetic sequence

• aka normal microbiota/normal flora

• prevents disease by competing for residency with pathogens

• composition of this can affect brain chemistry and behavior alongside weight changes

• helps with developing the immune system response

  • keeps our immune system on alert

  • early exposure lessens likelihood of allergies, asthma, etc.

• helps in digestion; E coli

• all human body surfaces populated with microorganisms

  • 500-1000 species of microbes in/out of body

  • outnumber body cells 3:1

cyanobacteria

microorganism responsible for most of the oxygen production

found in the surfaces of our oceans

cellulose

microorganisms are important as they aid in decomposition of certain material such as __: an important component of plants

• humans and other animals cant digest it

• microorganisms in both the environment and guts of animals do

  • why leaves and fallen trees do not pile up in the environments