1.1 Microbio

Microorganism:

Microorganism:

A microscopic organism consisting of a single cell or cell cluster, also including the viruses, which are not cellular. (Brock 13th ed.)

Microscopic =

= too small to see with the naked eye (~0.5 mm). Includes: Bacteria, Archaea, Microbial Eukaryotes, viruses, and prions

Microbiology =

The study of microorganisms. Microbiology is focused on the study of organisms unified only by their small size. As such, most subdisciplines within biology also have subdisciplines within microbiology: microbial ecology, microbial genetics, microbial physiology

How many microbes exist?

Bacteria: ~1030 on Earth; ~1 μm long 1030 cells x 10-6 m/cell = ~1024 m = ~1021 km Earth to moon = ~384,403 km 1021 km/3.85 km = ~2.615 Earth-Moon units Viruses: ~1031 on Earth; ~10 nm long 1020 km/3.85 km =~2.614 Earth-Moon units Microbes comprise ~50% of the Earth’s biomass

Microbes are ubiquitous

Thrive in environments inhospitable for eukaryotes

The main role of Bacteria and Archaea is to act as catalysts of biogeochemical cycles

- Microorganisms catalyze reactions that cycle C, N, S, Fe, O, P and possibly all other elements through the biosphere - Biogeochemical cycles make life on Earth possible

Prokaryotes Bacteria & Archaea

Greek pro-, before; + Greek karutos, having nuts (from karuon, nut; see karyo-)

Lack eukaryotic-style organelles Bacteria and Archaea perform glycolysis, fermentation, citric acid cycle, electron transport, photosynthesis, DNA replication, transcription, and translation

Eukaryotes Plants, Animals, Fungi, Protista

Greek eu-, true or genuine; + Greek karutos, having nuts (from karuon, nut; see karyo-)

The term prokaryote is obsolete

Microbiologists do not care for the term prokaryote

- Electron microscopy in 1962*

- Originally used to describe organisms without: - Membrane bound nucleus

- Some bacteria have a membrane bound nucleoid - Membrane bound organelles

- Some bacteria have membrane bound structures that perform specific tasks - A cytoskeleton

- Bacteria and Archaea have a cytoskeleton

As we learn more about Bacteria and Archaea, the term prokaryote makes little sense

Textbooks emphasize that prokaryotes lack eukaryotic organelles

Advances in microscopy revealed that some bacteria have membrane bound compartments, which were not detected by 1960’s electron microscopy

Microbiology changed the world

- Disproved Spontaneous Generation

- Cell Theory

- Germ Theory of Disease

- Infectious Disease

- Changed how biologists organized all living things on the planet

- Three Domain Tree of Life

- Microbiome - Human associated microbes influence homeostasis

Spontaneous Generation

Living organisms could arise directly and rapidly from nonliving material

Pure observation & speculation

No experimentation Not science

vital forces

Ancient civilizations from all over the world believed in some version of spontaneous generation

European scientists were strongly influence by the ancient Greeks

Francesco Redi (1668)

Had an experiment with flies where he had unsealed jar with rotten meat, sealed jar, and gauze. When flies couldn’t reach no eggs. Critics claimed that fresh air was required for life.

Lazzaro Spallanzini

Heated broth, left flask open and found microbes. Did it with closed flask and no growth. Critics claimed that heating destroyed the vital force; life required fresh air.

Who discovered microorganisms?

Antoni van Leeuwenhoek

Kingdom System

- Good for naming organisms

- Changed over time

- Two ® Three ® Four ® Five (added fungi)

- Biologists had issues with tiny single celled organisms - Protista

- Primarily unicellular eukaryotes

- Monera

- Bacteria & blue-green algae

- Linnaeus (1707-1778

- Taxonomy

- Genus & species

- Latin binomial

• Canis familiaris - Adopted a system for grouping similar species

- Plants

- Animals

- Minerals

- Studying nature would provide answers to the big questions

Monera

-Cells without nuclei

-Greek for solitary, single

-Bacteria

-Blue-green algae - Photosynthetic bacteria

Why were plants and animals on top of kingdom system

They were thought to be superior than monera

Bacteria were assumed to be related to plants

because some were photosynthetic, and most have cell walls; plants are photosynthetic and have cell walls; bacteria are not plants and plants are eukaryotes

Cells and organisms have become highly specialized over the last 3.5 billion years

Origin of life on Earth was marked by the origin of the first prokaryotic cells.

2nd Type of Prokaryote - 1976

- A new type of prokaryote was found

- Methanogen

- Produce methane (CH4)

- Anaerobes

- Sequence of ribosomal RNA (rRNA) demonstrated that they were unique

- Archaea: different type of prokaryote

- Physiologically, structurally & biochemically unique

- Archae (ancient)bacteria (obsolete term)

- Kingdom Monera became obsolete

cows fart methane because of

anaerobes (methanogen)

After discovery of archae bacteria how were things organized

kingdom system was changed to three domain system: Bacteria, archaea, and eukarya. Within domains there are kingdoms.

We determine where something belongs in three domain system using

ribosomal RNA

First cells appeared

3.8 billion years ago and were prokaryotes

LUCA

last common ancestor (3.8 bya)

Second division in three domain system led to

division between archaea and eukarya

Current scientific data supports the contention that

life first diverged into bacteria and a common ancestor of archaea and eukaryotes

What prokaryote are humans most related to

archaea

Microbiome -

the combined DNA of the microorganisms in a particular environment

- Microbiologist do not how to “culture” the majority of microorganisms

- But we know they exist since microbial DNA can be isolated and sequence

- Animals including humans are full of microbes

~30 trillion human cells

~39 trillion bacterial cells (more microorganisms than our own cells)

Microbiome colonizes

- GI tract

- Vagina

- Ear canal

- Oral cavity

- Distal urethra

- External skin surface

- Upper respiratory system

Colonized within hours after birth; acquire microorganisms during vaginal birth

Intestinal microbiome

- 1013 - 1014 microbes per gram of intestinal content

- Microbiome estimated to weigh 10 lbs

- Diverse ecosystem

- Majority cannot be cultured

- Anaerobes & facultative anaerobes

- Healthy and chronically ill individuals have different intestinal microbial communities

- Raises the question: can some chronic illness be mediated or reversed by manipulating the intestinal microbiom

HUman microbiome project

Attempt to identify all human associated microorganism

Many experiments with “germ free” mice

- Receive massive antibiotic treatments after birth

- Eat sterile food & drink sterile water

- Raised in sterile environments

- Germ free mice are inoculated with individual or multiple species of Bacteria / Archaea

- Investigate the effect of manipulating the intestinal microbiome on illness

- Compare with conventionally raised mice

Microbiome transplantation with germ free mice The experiment that launched the microbiome phenomenon

- Adult germ-free mice received the cecum microbiome from either obese or lean mice

- Germ free mice that received the microbiota from obese mice had a significantly greater increase in body fat

- Two weeks

Mice received the same quantity of food

Cecum microbes altered the physiology of the mice

Germ-free mice received microbes from lean mice and

did have an increase in body fat but did not become obese

Firmicutes / Bacteroidetes Ratio Hypothesis

Human gut microbiome is dominated (>90%) by bacterial phyla (Large groups of organisms): Firmicutes and Bacteroidetes

- Hypothesis proposes that Firmicutes are more effective in extracting energy from food than Bacteroidetes

- Firmicutes assist humans in the absorption of calories and the subsequent weight gain

- Bacteroidetes consume carbohydrates and keep most of the calories

High fat diets have greater Firmicutes and lower Bacteroidetes

– associated with obesity

High fiber diets have greater Bacteroidetes and lower Firmicutes

-associate with being lean

Connection between gut microflora and physiology

- Morbidly obese and slender individuals have different intestinal microbial communities

- Healthy and chronically ill individuals have different intestinal microbial communities

- Unfortunately, the relationships are not well understood

Microbiota dysbiosis affects physiology

“Imbalance” in the gut microbial community that is associated with disease

Fecal microbiota transplant (FMT)

Transplantation of fecal bacteria from a healthy individual into a recipient Clostridioides difficile colitis (can form endospores). They are harmless and everyone has them. when dysbiosis occurs the endospores can germinate and make it harmful.

Two medical treatments involving the microbiome

Fecal microbiota transplant (FMT)

Children born via C-section can be swabbed with vaginal microflora - Not actually approved; sparse data - Infection risk

How does FMT resolve clostridioides difficile

induces C. Difficile to form benign endospores

no dates just remmeber people

n/a

Louis pasteur

Disproved spontaneous pasteurization. broth is in swan-necked flasks

Boil-->incubate-->no growth (germs trapped)

Tilted falsk-->incubated-->growth

Pasteurization

the process of treating a substance with heat to destroy or slow the growth of pathogens

71.7ºC (161ºF)

15 - 20 sec

Ferdinand Cohn

- Discovered bacterial spores

- Survival structure

- Resistant to heat and

disinfectants

- Bacillus can switch between

vegetative and endospore state

- Pioneer of modern bacteriology

- Work on life cycle of endospore-

forming Bacillus

- Heating killed vegetative cells

- Spores were not killed by boiling

- Laid technical and theoretical groundwork for field of

bacteriology

- Early taxonomy

- Cotton plugs

- Believed all bacteria were plants

- Bacteria and plants both have cell walls

- Commonly accepted belief until the mid-20 th century

John Tyndall

- Tyndallization

- Boiling for 15 min for

three consecutive days

- Eliminated spores

contamination

Cell theory

- Cells are the

fundamental

units of life

- All living things

are composed

of cells

- All cells come from pre-existing cells

- Spontaneous generation was not valid

- Spontaneous generation was not valid

At the start of the 19th century the

possible explanations for disease

includedincluded

– Poverty

– Bad luck

– Bad blood

– Miasma or contagion

– Curses, hexes or witchcraft

– Invisible organisms (ca 1546)

– Laziness, sloppiness, apathy, sloth

Pure observation & speculation

No experimentation

- Foreigners

- Immigrants

- Minority groups

Robert Hooke

First to use the term cell

- 1665

- Plant cells like the small rooms

used by monks

- Observed fungi and other types

of microorganism

Robert Hooke

Antoni van Leeuwenhoek

- Discovered microorganisms

- ca. 1674

- Animalcules

“the number of these animals in

the scurf of a man¢s teeth, are so

many that I believe they exceed

the number of men in the

kingdom....I found too many living

animals therein, that I guess there

might have been in a quantity of

matter no bigger than the 1/100 of

a [grain of] sand.

”

Leeuwenhoek’s observations

Leeuwenhoek documented

the common bacterial

morphologies and accurately

estimated their sizes. He also

observed motile rods: they

“swim about among one another

gently like a swarm of

mosquitoes in the air...”

For the next 200 years,

biologists knew that

microorganisms existed,

but do not know how to

classify them and most

believed that they were

not important

Some biologists argued that

microorganisms were too

small to be truly alive

The "germs" develop into

macro-organisms

“Germinated” into macro-

organisms by some unknown

process

Others speculated that

microorganisms were

immature or primitive macro-

organisms

Microorganism are

described as "germs" in

late 17 th century; derived

from germination:

progenitor of something

else

All unscientific speculation – No experimentation

Biologists find "germs" everywhere

- Fresh water Ocean Air

- Soil Skin Intestines

- Plants Sewage Feces

In the late 18 th century "germs" are associated with

unsanitary conditions and disease

- soil, mud, sewage, feces

- 1796 definition of "germ" includes the phrase

"seed of a disease"

Not clear if "germs" were

the cause or the result of

disease

No experimentation

Speculation

Ignaz Semmelweis ca. 1847

- Physician in a Viennese maternity hospital

- Babies were delivered by physicians

- High mortality rate

- Babies delivered by midwives

- Low mortality rate

- Hypothesis

- "germs" from autopsy cadavers infected the

pregnant women during delivery

- Experiment

- Physicians were to wash hands in antiseptic

solution

- Mortality significantly decreased

John Snow

Founder of Epidemiology

- 1854 London cholera epidemic

- Blamed on miasma

- Analyzed death records, obtained

information on victims

- Interviewed survivors

- Concluded water from a single pump was the source

of the contagion

- Recommended closing the contaminated water pump

- Significantly reduced number of cases

Memorial & pub on Broadwick Street

(Was called Broad street in 1854)

Documented that water companies

pumped from sewage contaminated

areas of the Thames river

Vibrio cholerae

Cholera was caused by a poison in human feces

Robert Koch isolated and named Vibrio cholerae in 1882

Florence Nightingale

Crimean War

- Sanitarian Movement

- Cleanliness eliminated miasma/contagion

- Filth causes disease

- Social hygiene

- Hospitals should be scrupulously clean

- Sewers

- Whitewash

- Punctual meals

- Clean uniforms

- Clean bandages

- Bury dead dogs

- Bathe frequently

- Chlorinated lime & bleach

Joseph Lister

-Apply carbolic acid to surgical

instruments, bandages and

wounds

- Phenol

- Antiseptics

- Medical hygiene

- Observed a decline in post-

operative infections

1865

1827 - 1912

Koch’s Postulates

1. Find evidence of a

particular microbe in every

case of a disease

2. Isolate that microbe from

an infected subject and

grow it in pure culture

3. Inoculate a susceptible

healthy subject with the

laboratory isolate and

observe the resultant

disease

4. Reisolate the infectious

agent from the test subject

Robert Koch

- Proved the germ theory of disease

- Anthrax - Bacillus anthracis

- Tuberculosis - Mycobacterium

tuberculosis

- Isolation of microbes and pure

cultures

- Aseptic technique

- Use of solid growth medium

- Inferred a colony grew from a

single cell

- Development of Koch’s postulates

- Experiments conducted on

volunteers recruited from

prisons

Pasteur developed vaccines based on weakened, or

attenuated, microbes for...

- Rabies virus

- Anthrax - Bacillus anthracis

- Diptheria – Corynebacterium diphtheriae

- Chicken cholera - Pasteurella multocida

- Koch proved that tuberculosis was caused by

Mycobacterium tuberculosis

- Impetuous for government public health agencies

The initial investigations into antimicrobial agents,

antibiotics and immunology can all be traced to the work

of Pasteur and Koch.

19 th medical research often involved vulnerable

populations: prisoners, orphans, mentally ill and indigent.

In 1900, upper respiratory diseases and gastroenteritis were the

leading causes of death.

Heart disease, cancer and stroke

became more common since medical science treated infectious

diseases effectively and Americans lived longer.

How did tyndallization eliminate bacterial contamination for the 19th century canned food industry?

Boiling treatments were conducted on three successive days.