Preface 序言
Microbial World around Us
Chapter Objective:
1. How has Microbiology, as a subject,
developed so far?
2. What may microbiology do for your
career? And your life?
Bacteria-what comes to your mind first?
 Diseases: infections 传染?
 Food Spoilage
Facts: among all bacteria disease...
1%
95%
4%
Human disease
Plant disease
Non-pathogens
Microbiology in post-genome period
 Most standard microbe strains have been
sequenced
 2011: Earth Microbiome Project (EMP)

全球最大微生物基因组研究项目, 华大基因
 New challenge




Antibiotics resistance
Evolution of new viruses: HIV
Food-born disease
Bioremediation
传统抗生素耐药性
G. Taubes, Science. 2008, 321: 356-361
What is microorganism?
 Microorganism
Tiny creatures not seen with unaided eye
 Single or clusters, include non-cellular life forms
(viruses and prions)
Microorganisms - Microbes – Germs

 Microbiology

1.
2.
Bio-: life; -ology: study of
Basic science: provides tools for probing the processes
of life.
Applied science: deals with many important practical
problems in medicine, agriculture, and industry.
What is Life 生命是什么?
 Hallmarks / Characteristics of Life
1.
2.
3.
4.
5.
6.
Metabolism 代谢
Growth 生长
Differentiation 分化
Communication 交流
Movement 运动
Evolution 进化
Different from plant & animal cells
1. Very small 微小
 bacteria 0.5-5 μm
2. Highly diverse 形态多样
 All kinds of morphology
3. Leading an independent living 独立生活
Diverse morphology of microorganisms
A single plant or animal cell cannot have
an independent existence.
A single plant or animal cell cannot have an
independent existence.
Free-living cells
Free-living cells: A single microbial cell can have
an independent existence.
Five Characteristics of Microbes
1.
Small size but big area
体积小，面积大
2. Strong absorption and fast metabolism
吸收多，转化快
3. Fast growth and rapid reproduction
生长旺，繁殖快
4. Powerful adaptations and easy mutation
适应强，易变异
5. Wide distribution and variable classes
分布广，种类多
Relative Size of Microbes
Category of Microorganisms 微生物分类
 THREE categories and TEN groups :
1.
Prokaryotes原核生物: include eubacteria & archaea
①
②
③
④
⑤
⑥
2.
3.
Bacteria 细菌
Actinomycetes 放线菌
Cyanobacteria 蓝细菌 (blue algae, 蓝藻)
Mycoplasma 支原体
Rickettsia 立克次体
Chlamydia 衣原体
Eukaryotes 真核生物
① Fungi 真菌
② Macro algae 显微藻类 (not included in our content)
③ Protozoa 原生动物 (not included in our content)
Acellular microorganisms 非细胞微生物

Viruses 病毒: Neither prokaryotes nor eukaryotes
Organisms & branch study of Microbiology
1. Bacteria 细菌
 Bacteriology
2. Protozoans 原生动物
 Protozoology
3. Algae 藻
 Phycology
4. Parasites 寄生物
 Parasitology
5. Yeasts & Molds酵母,霉菌  Mycology真菌学
 Fungi 真菌
6. Viruses
 Virology
Microbes and Disease
 Origin & development of microbiology
 Napoleon in Russia
 Typhus 斑疹伤寒, tetanus 破伤风, etc.
intimately connected
Warfare
Why?
Infectious diseases
Poor sanitation, people movement,
malnutrition → outbreaks
The Black Plague
黑死病,鼠疫


Recurrence of plague
in Naples in 1656
Gene mutation saved
Europe:

Delta 32
细菌美女？二战后日本731部队的变态计划
 鼠疫等生化武器
1.
中国“圆木”
 携带病菌的中国受害者
2. “满洲”PX:
 45公斤带病菌跳蚤，相当于1.45亿只
3. 日本美女
Infections disease in Human
Infectious diseases as cause of death worldwide in 1998
Historical Perspectives - 3 Phases of
Microbiology Development
1. Beginning of Microbiologly
2. Transition Period
3. Golden Age of Microbiology
Phase 1: Beginning of Microbiology
 1665 Robert Hooke
 “little boxes” – “cells”
 Cell Theory 细胞学说
 Microscope: an important tool for
microbiology
Anton van
Leeuwenhoek

Lens
Specimen
mount
First microbiologist 1st person to
actually see living
microorganisms
Screw plate
Focusing screw
Elevating screw
A Modern Bright-Field Microscope
Phase 2: Transition Period
 What life was like at that time
1. Spontaneous Generation 自然发生说
 Maggots蛆-nonliving things, flies-manure
2. Biogenesis 生物发生说 - Germ Theory
of Disease
 Life from pre-existing Life
Essence of scientific method - Logic reasoning
1. Build on established
scientific fact
2. Formulate a hypothesis
3. Test it with
an experiment
Francesco Redi: disprove Spontaneous
Generation
 1668: Fly - meat experiment
 Maggots only appeared in the open jar
Phase 3: Golden age of microbiology
→ Modern microbiology
Father of modern microbiology:
Louis Pasteur
Father of bacteriology:
Robert Koch
Sterilizing the contents of the flask
Sterile 消毒
If the flask remains upright, no microbial growth will occur
If microbes trapped in the neck reach the sterile liquid, growth will occur
Pasteur’s Credits
1. Cultivation 培养 of Viruses & Bacteria
 Cultivation in an appropriate, sterile medium → basis of
microbiology
2. Vaccines 疫苗
 Attenuation减毒: cholera霍乱, rabies狂犬病
3. Aseptic Technique 无菌操作
4. Fermentation - exclude oxygen from wine 发酵
 Aerobic vs. Anaerobic
5. Pasteurization 巴斯德消毒
“There are science and the
applications of science, separate yet
bound together as the fruit of the
tree.”
- Louis Pasteur, describing how pure
and practical science are related
A Case of "Microbes Revenge"
 During his investigation on bacteria,
two of Pasteur's daughters and his
father died of Typhoid fever 伤寒
Robert Koch – Microbial Etiology
微生物病原学
 1876: 1st proved bacteria caused
disease
 Established “scientific rules”
 Show a cause-effect relationship between
a microbe and a disease: anthrax
 Koch‘s Postulates
 1905: Nobel Prize in Physiology or
Medicine
Koch’s Work with anthrax (1)
 Method

Microscopic observation
 Results

Bacterial cells were observed in the blood of
animals with the disease
 Conclusion

The disease might be caused by this
bacterium
 Criticism

The bacterium might as well be a result of
the disease
Koch’s Work with anthrax (2)
 Method


Transfer of disease with blood among animals
Observe with microscope of the artificially infected animals
 Results


Blood containing the bacterium could cause disease in healthy
animals and newly infected animal’s blood contained the
bacterial cells
Highly repeatable
 Conclusion

The bacteria in the blood of infected animals can cause
disease in healthy animals
 Criticism

How do you know it is the bacteria not something else in the
blood caused the infection?
Koch’s Work with anthrax (3)

Method




Results



Isolated bacteria caused disease in healthy animals
The same bacteria were isolated from dead animals
Conclusion


Culture of the bacterium in nutrient broth
Transfer of disease by the isolated bacteria
Microscopic observation
The bacterial cells in the blood of infected animals are
indeed the reason for the disease
Germ theory of disease established
The same pathogen must be present
in every case of the disease
Koch’s
Postulatesanthrax in
cattle
The pathogen must be isolated from the
diseased host and grown in pure culture
Koch’s
Postulatesanthrax in
cattle
Koch and wife
1905-Nobel Prize
The pathogen causes the same disease
in healthy lab animals
Koch’s
Postulatesanthrax in
cattle
The pathogen is re-isolated and shown to
be the same pathogen
Koch’s
Postulatesanthrax in
cattle
Koch‘s Postulates 科赫原则
1. Isolate the suspected agent from a
disease victim;
2. Grow the agent in pure culture;
3. Infect a healthy host and show that
the organism produces the classical
clinical disease;
4. Isolate the "same" organism from
the new victim.
Scheme of Koch’s postulates
Koch’s other contributions
 Development of pure culture technique 纯培养技术
 Potato slice
 Solid medium: gelatin明胶 vs. agar琼脂培养基

Fannie Eilshemius: 1st to use Agar to solidify culture media–
Woman in Microbiology
 Demonstration of causal agent of tuberculosis肺结核
 Microscopy
 Differential staining鉴别染色法 of bacteria & human tissues
 Pure culture isolation of bacteria
 Animal inoculation
 Cholera 霍乱: Vibrio cholerae
Differential staining of bacteria and human tissues
对人体组织和细菌的鉴别染色法
Cells of M. tuberculosis stain blue in a lung tissue sample whereas the tissue stains brown.
Koch’s Work on M. tuberculosis culture

TB growing on a glass
plate of coagulated blood
serum inside a glass box
在玻璃盒中用凝固血清培
养基培养结核分枝杆菌

A colony of M. tuberculosis
appears as long "cordlike"
forms when taken from a
glass plate
结核杆菌的绳索状细菌菌落
Exceptions to Koch‘s Postulates
1. Some organisms never been grown in
pure culture on artificial media
 Treponema pallidum梅毒螺旋体– Syphilis梅毒
 Mycobacterium lepra 麻风分支杆菌– Leprosy
2. Morally unacceptable on “human
guinea pig”?
 Ex: Does HIV cause AID’s
Treponema pallidum苍白梅毒螺旋体- Syphilis梅毒
Mycobacterium lepra麻风分枝杆菌 – Leprosy麻风
E. Jenner: Immune to smallpox 天花
 Ancient China → India
 "if you want to marry a woman who will never
be scarred by the 'POX', marry a milkmaid"
Critical thinking questions:
1. What do you think of Jenner using a
child to test his theory on? How about
today?
2. What shall we do with the remaining
smallpox virus? Your vote?
Ignaz Philipp Semmelweis: Defender of Motherhood
Lister Introduces Antisepsis 消毒
1865, Joseph Lister: aseptic technique: antisepsis with phenol 石碳酸
Conquest of Yellow Fever by Major Walter Reed
- Role of mosquito
The Scientific Method
Observations
Questions
Hypothesis
Design experiments
Results
Rejects
Accepts
Modifies
Achievement by the Golden Age of
Microbiology
 By 1930’s




Grow most agents
Purify agents
Observe agents (Light and TEM)
Vaccines (prevent some diseases)
 Bacteria, Viruses, Parasites, Molds
landmarks in microbiology
Some landmarks in microbiology in the past 65 years
Highlights in the History of Microbiology
1674
1796
1847
1859
1865
1876
1881
1892
1894
1929
1977
Leuwenhoek discovers microorganisms
Jenner creates a vaccine for smallpox
Semmelweiss establishes the causes of childbed fever
Pasteur disproves spontaneous generation of microorganisms
Lister introduces antiseptic techniques
Koch proves specific microorganisms cause specific diseases
Koch uses agar to obtain a pure culture
Iwanowski discovers viruses
Ehrlich articulates the principle of selective toxicity
Fleming discovers penicillin
Carl Woese discovers the archaea
Partial Nobel Prizes Awarded for Research in Microbiology
Date Scientist
Research
1901
E. Von Behring (GR)
Diphtheria antitoxin 白喉抗毒素
1902
R. Ross (GB)
Cause and transmission of malaria 疟疾
1905
R. Koch (GR)
Tuberculosis research 结核病
1908
P. Ehrlich, E. Metchnikoff
Work on immunity
1945
A.Fleming, Chain (GB), Florey (AU) Discovery of penicillin and its therapeutic value
1962
F. Crick (GB), J. Watson (US)
Discoveries concerning the structure of DNA
1980
B. Benacerraf, G. Snell (US),
J. Dausset (F), P. Berg (US),
W.Gilbert (US)&F.Sanger (GB)
Discovery of histocompatibility antigenes
Development of rDNA technology ,
Sequencing techniques (Chemistry Prize)
1984
C. Milstein (GB) G. Kohler
(GR) N.K. Jerne (D)
Technique for formation of monoclonal
antibodies 单克隆抗体
1989
J.M. Bishop; H.E. Varmus (US) Discovery of oncogenes 致癌基因,
Discovery of catalytic RNA
S. Altman; T.R. Cech (US)
1993
K. B. Mullis (US)
M. Smith (US)
R.J. Sharp (US)
Invention of the polymerase chain reaction
Development of site-directed mutagenesis 定向
突变
Discovery of split genes 断裂基因
1997
S. Prusiner (US)
Discovery of prions 朊病毒
FYI
- Beriberi 脚气病
In 1911, the Polish chemist
Casimir Funk isolated an active substance from
rice husks and proposed that it prevents
beriberi, a disease of the muscular and nervous
systems. “Nonsense,” he was told, “Spend your
time more profitably – look for a
microorganism!” Today we know that Funk was
correct: Beriberiis a nutritional disease caused
by a vitamin deficiency. But at that time, the
scientific community scoffed at his idea. Why
do you think that happen?
Impact of microorganism on human life
Agriculture
Disease
Food
Microbiology
Bioterrorism
Energy/environment
Biotechnology
New Challenges
in Microbiology
Recent outbreaks of epidemics










2014: Ebola virus 埃博拉病毒,1976, mortality 50-90%
Mad Cow Disease疯牛病: Europe, US
2001: Bacillus anthrax, bio-terrorism , US
2003, Monkey pox 猴痘: Mortality 10%
2003 Spring: SARS
2004: Avian Influenza禽流感
Oct 2004, Plague青海鼠疫, mortality50-100%
Encephalitis B 乙型脑炎, Jan 2005
……
Bioterrorism: 鼠疫、炭疽、霍乱、O157: H7, 天花、马
尔堡、SARS
微生物与食品安全

食物类型与污染特点：
速食食品——李斯特氏菌；海产品——弧菌
鸡蛋和禽类——沙门氏菌； 禽类——弯曲菌

细菌病原：


近年：肠出血性大肠杆菌O157：H7、单增李斯特氏菌、多
重耐药性沙门氏菌、空肠弯曲菌、变形杆菌、肉毒杆菌、
金黄色葡萄球菌
真菌毒素：

黄曲霉毒素、伏马毒素、赭曲霉毒素、杂色曲霉素、岛青
霉素、黄天精、桔青霉素、层青霉素、单端孢霉素类、玉
米赤霉烯酮

藻类毒素：微囊藻毒素

其他：河豚毒素、朊病毒
Food born disease in the USA

1/6 population every year, death: 3000
2011，the first 5 pathogens：
引发疾病病原
（%）
入院治疗的病原
（%）
致死病原
（%）
诺瓦病毒
58
26
11
非伤寒沙门菌
Salmonella, nontyphoidal
产气荚膜梭菌
11
35
28
15
6
病 原
Norovirus
Clostridium perfringens
弯曲菌
Campylobacter spp.
金黄色葡萄球菌
Staphylococcus aureus
10
9
3
大肠杆菌O157
E. coli (STEC) O157
单增李斯特菌
4
弓形虫
8
19
Listeria monocytogenes
Toxoplasma gondii
24
2003:出口日本277批不合格食品的原因
不合格原因
不合格
（批）
构成
(%)
农残
兽残
毒素
食品添加剂
微生物
水产品及制品
83
29.96
1
35
10
30
21
8
水果蔬菜及制品
64
23.10
25
26
9
2
花生等农产品
24
8.66
11
糖果、蜜饯等
21
7.58
1
禽、蛋奶制品
15
5.41
米面制品
14
松茸、蘑菇
5
重金属
其他
2
20
1
3
10
5.05
17
1
11
3.97
11
2
肉类
7
2.52
4
1
2
冷冻食品
6
2.16
1
3
2
蜂蜜
5
1.81
调味料
4
1.44
3
1
容器、器皿
9
3.24
3
其他
14
5.05
2
合计
277
100
40
4
1
5
5
7
44
15
127
2
5
46
5
22
出口食品不合格：以检测项目统计
微生物
二氧化硫
甜蜜素
毒死蜱
丁酰肼
氯氰菊酯
贝类毒素
抗菌素
有毒鱼种
以上项目合计
不合格批
构成比（%）
49
17.68
38
29
18
11
11
10
9
8
183
13.71
10.47
6.49
3.97
3.97
3.61
3.25
2.89
66.6
Amount and Cultivability of
Microorganisms in Nature
Environment
Soil
Lakes/rivers
Groundwater
Marine (surface)
Marine (depth)
Sediments
Counts
1011-12/kg
109-10/L
7-8
10 /L
11-13
10 /L
107-8/L
109-12/kg
Cultivability
0.01-0.1%
0.01-0.1%
<1%
0.001-0.1%
ND
0.01-0.1%
From: N. Pace
Microbes on Human Body
How many microbes?
What their function?
What the relationship?
Human
Body
Bio-refinery（生物炼制）
Fuels
Solvent
Plastics
Bulk chemicals
Biomass
Fine chemicals
Fibres
Oils
MGF and Cell Factory Project
 Goal:

Ideal platform with fewer genes for
establishing cell-factory system, less regulation
 Japan: ‘Minimum genome factory’ (MGF) in
2001

Escherichia coli K-12
 EU: “Cell factory” project from 1998 to
2002 in the Fifth Framework Programme.


B. subtilis
About 3000 genes (except 271 essential genes)
have been disrupted or deleted singly.
Where will microbiology go?
Careers as a Microbiologist
B.A., B.S.
Research associate
Food, industrial, or environmental microbiologist, quality
assurance technologist
Clinical or veterinary microbiologists
M.A., M.S.
Supervisor or laboratory manager, instructor
Ph.D., M.D.
Scientist, University or college professor, research director,
consultant, infectious disease specialist
Key Points
1. What is microorganism and their major
categories
2. The individuals, with discoveries & time
frame, covered in microbiology history.
3. 5 major characteristics of microorganism