Chapter 13: Microbe Human Interactions, Infections, Disease, and Epidemiology

where do microbiomes exist

everywhere microbes and other organisms interact, not just on humans

what is the human microbiome

all microbes that share our body space, either externally or internally

what is special about the human microbiome

each person’s is unique due to environmental factors

what is the human microbiome project

characterization of the microbes that share our body space

how many microbes are living within humans

100 trillion microbes are living in or on us

how many of microbes are in the GI tract

95 million

ratio of microbes

there are more bacterial genes living on or in you then those that make you up, almost 150:1

what are most microbes living within us

most are prokaryotic

viruses vs bacteria in microbiome

viruses out number bacteria 5:1

when does the development of a microbiome begin

microbiota begins developing in utero with the rest developing at birth and changes as we age

what happens by age 3

we develop an adultlike community of microbes

what characteristics are attributed to the microbiota we develop by age 3

they are rich in diversity, containing mutualistic and commensal microbes

what can provide different sets of data on developing microbiomes

age, environmental factors, and method of investigation

what does a baby’s GI tract microbiota depend on

breastmilk and formula until solid foods are introduced

what happens as the microbiome of a person ages

there is an expansion of bacteriodetes at the expense of firmicutes and reduction in richness

reduction in richness of an aging microbiome

reduction of important secondary metabolite producing microbes

what can causes to microbiome aging be due to

significant changes in lifestyle

what do significant lifestyle changes include

decreased locomotion, nutritional changes, chronic consumption of medications, and residential status

what are free of microbiomes

internal tissues (brain, blood, CSF, muscles)

what are constantly in contact with the environment and exposed to microbes

surface tissues (skin and mucous membranes), epithelial tissue lines surface and internal GI tracts and most microbes are here along with the breathing aspect/system

what is different of an individual’s microbiome

it is relatively stable over time and is highly variable between individuals

what makes a microbiome unique

rarer microbiota that can even causes changes

what are the 5 major bacteria phyla common to human skin, intestinal tract, and other mucosal surfaces

actinobacteria, bacteroidetes, firmicutes, fusobacteria, and proteobacteria along with a number of archaea, fungi, and viruses

where are the different body regions where colonizing microbes are found

skin microbiome, respiratory microbiome, gut microbiome, and in females the urogenital tract

what inputs affect the microbiome

genetics, environment, diet, lifestyle, hormones, and industry

what do microbes do in the nose

mucus production and antimicrobial chemicals

what do microbes do in the mouth

assist digestion and ward off pathogens

what do microbes do in the lungs

lubricate pulmonary tissues

what do microbes do in the stomach

prevent gastric complications

what do microbes do in the colon

digestion of complex carbohydrates

what do microbes do in reproductive organs

maintain pH and H2O production to kill microbes

what do microbes do in the skin

fortify immune system and scent production

what kind of environment does skin entail

an inhospitable environment due to slightly acidic pH, high NaCl, many areas being low in moisture and oily lubricant sebum and antimicrobial peptides

what kind of inhospitable environments are there in skin

successful vs nonsuccessful

why does skin have an inhospitable environment

because it is affected by the outside environment due to constant exposure

why is the environment of the skin not consistent throughout the whole body

because skin can be broken into oil, moist,and dry regions which changes the microbes present

what are three environment niches of skin

different communities live in different areas due to environmental niches such as dry (greatest microbial diversity), moist, and dry (containing sebum allowing for the lowest microbial diversity)

what does eubiosis mean

healthy/balanced

what does dysbiois mean

disrupted gut

what do oil glands secrete

complex lipids degraded by gram positive bacteria, cutibacterium acnes

what does cutibacterium acnes do

convert lipids secreted by oil glands to unsaturated fatty acids; some are volatile and have a strong odor but are usually harmless

acne

attributed in dysbiosis of cutibacterium acnes, and a subset of people with acne scarring have an over abundance of this

what can you tell from data collected of skin types

whether people are living in mega cities or rural cities

what does the nasal microbiome do

interacts directly with the environment and is the 1st area where air is brought in with no gas exchange, but traps microbes

what kind of microbes live in the nasal microbiome

transient

what does the nasal microbiome vary in

seasonally in abundance and diversity, the higher abundance of microbes is due to being airs first passage

what are the two major differing microbiome regions in the respiratory tract

upper respiratory tract and lower respiratory tract

upper respiratory tract

nostrils, sinuses, pharynx, and oropharynx

lower respiratory tract

larynx below the vocal cords, trachea, bronchi, and lungs

what is special about microbes in the respiratory tract

moving further away from the nose reduces the amount of the microbes, and there should be no travel of microbes to the alveoli because it can block gas exchange

what is the goal of the respiratory tract

to remove microbes as you travel down the respiratory tract

what is cystic fibrosis beneficial to

microbes which become damaging

within hours of birth, what happens to the oral cavity

it is colonized by microorganisms

what is the mouth full of

microenvironments

what do microenvironments provide

wide variety of habitats for microbes

where do anaerobes become dominant

between the teeth and gums

what happens as teeth grow

epithelial surfaces change which enable microbes to attach to oral surfaces and contribute to the formation of dental plaque, caries, gingivitis, and periodontal diseases

what does plaque lead to

dysbiosis of the mouth

what is the pH of the gut microbiome like

the stomach is super acidic and the duodenum is the site of acid neutralization and the acid out of the stomach and buffers with in mix

how are most microbes killed in the stomach

by acidic conditions, though there are a few exceptions

how do some microbes survive in the stomach

if they pass through the stomach quickly

how does the microbiome community vary

by contributions from the stomach and large intestine

microbiomes in the colon and large intestine

95 percent of the microbiome is in the colon and large intestine and species richness is in the large intestine as they facilitate absorption, immune system, make precursors, and modulation of CNS

what does gut microbiota convert food into

calories we can use

what do overweight and obese people have

higher relative concentrations of gut bacteria belonging to the phylum firmicutes compared to bacteria belonging to the phylum bacteroidetes

where should attention be directed to in gut microbiome

refocused attention from the individual species that constitute the gut microbiome to the metabolome (products these microorganisms secrete)

what do many bacteria ferment

complex polysaccharides into short-chain fatty acids, some of which promote weight gain

dysbiosis of large intestine

can lead to obesity, but the use of mice and gut microbiomes have led to research to cures, as gut microbiomes reflect body size not food ingested

large intestine (colon)

largest microbial population of body, diverse and abundant, many contributions to host, some microbes essential for health and homeostasis

what do antibiotics due to the gut microbial community

disrupt it

what happens following antibiotic treatment

people are at higher risk of GI tract infections and colonization resistance

what is colonization resistance based on

competitive exclusion

what does the microbiome release

toxic peptides that target pathogens, and antibiotics can disrupt microbes that regulate the immune system and inflammatory response

what does gut microbiota affect

our central nervous system as seen by studies in which specific behavioral traits differ when comparing GF mice and conventional mice

what are three ways the microbiome can influence the CNS

immune system inputs, via enteric nervous system which is connected to the CNS by the vagus nerve which transmits signals to the brain, and through soluble microbial products like short chain fatty acids

what does loss of microbiome diversity lead to

dysbiosis and variety of diseases

what does the placenta do

cleanses, placenta allows nothing bad to get to the fetus but stuff can still make it through and damage the placenta

what are germ free mice

mice that are born by C section and raised in sterility

what can germ free mice be used for

to study effects of microbes on animal health by comparing germ free animals to normal animals

how are germ free mice important to studies

as they are born through C section and raised in sterility, they offer a blank slate because there is no exposure to microbial environment and differences can be seen in different types of mice and gut dysbiosis as they serve as a control and can test for gut microbes and how they interact with there things because they’re microbe free except for those in utero

what is epidemiology

epic meaning on or upon and demon meaning people and population which translates to the study of that which befalls men

epidemiology definition

the study of how diseases affect whole communities and populations using science that evaluates occurrence, determinants, distributions, and control of health and diseases in a defined human population

where is the CDC

located in Atlanta, GA

what does the CDC function as a national focus for

developing and applying disease prevention and control, environmental health, and health promotion and education activities

what is the World Health Organization

an international counterpart to CDC that is located in Geneva Switzerland

sporadic disease

occurs occasionally and at irregular intervals and is hard and unpredictable, for example tetanus which is less protected against

endemic disease

maintains a relatively steady low level frequency at a moderately regular interval for example common colds are not virulent enough to be of drastic imprints as they are always around and not eliminated

hyperendemic diseases

gradually increase in frequency above the endemic level but not to the epidemic levels, for example flu strains are all year around but are hard to spread in the summer but in the winter it increases to regular intervals (hyper)

outbreak

sudden, unexpected occurrence of diseases, usually in a limited segment of population, they are not low or unsteady and are sudden, for example E.coli

epidemic

outbreak affecting many people at once, along with a sudden increase in occurrence above expected number, based on how long it lasts

pandemic

increase in disease occurrence within a large population over at least two countries

why in particular is pandemic an anthropocentric term

there is a vague definition as epidemiologists in different countries have different regulations

what is an infectious disease

disease resulting from an infection by microbial agents

what is a communicable disease

can be transmitted from one host to another

what do patterns of epidemic disease concern

how does it move with in a population and how does it infect

what are the two types of epidemics

common source and propagated

common source epidemic

single common contaminated source (food), a huge onset of people get it right away, then it drops off quickly, for example E.coli which is not human to human

propagated epidemic

one infected individual into a susceptible group, infection propagated to others, they are communicable and have a longer peak and take longer to move out

how do epidemiologists determine if an outbreak, epidemics, or pandemic is occurring

measuring disease frequency at time intervals

statistics

mathematics dealing with collection, organization, and interpretation of numerical data