microbes that are normally not pathogenic may prove to be opportunistic pathogens should the opportunity present itself. 

 virulence

Understanding how the gut microbiota, serotonin, and the brain-gut axis is critical as we developing new ways to treat mood disorders. Probiotics designed to improve the gut microbiota may be a useful therapy aimed at improving serotonin levels. 
and addressing related health issues. 

Dysbiosis and antibiotics

Your gut microbiota (microbiome/gut flora)
​are the microbes that live in your digestive tract.
This microbiota influences our resistance to pathogens, the health of intestinal tissues, the production of important molecules, and emotional health via the gut–brain axis.
Your colon contains the most microbes with between 300 and 1000 different species present, most of them anaerobic bacteria.  99% of your gut bacteria come from about 30 or 40 species.
55% of your poo is bacteria.

pathogenic
gut microbes

the gut - brain axis

 compare Ro to Rt
Rt = the effective reproduction number (also called Re or just R)

chapters 11 & 12

Serotonin
 your gut microbiota produces over 90% of the body's serotonin. 
Gut bacteria modulate tryptophan supplies needed for serotonin production.
Serotonin produced in the gut influence your brain via your Vagus nerve.
 The Vagus nerve is a communication highway between the gut and the brain. 

Escherichia, Enterococcus, Candida, and Streptococcus ​have been found to produce serotonin in your gut. 

pathogenicity vs virulence

other Ro values:
Chickenpox – 10-12
Polio – 10-12
HIV/AIDS – 2-5
SARS – 0.19-1.08
MERS – 0.3-0.8
Common Cold – 2-3
Ebola – 1.56-1.9

ex:

pathogens more easily transmitted from host to host become common in a population

gut microbes and your health

        a
1. Virulence Factors:

Definition:
Virulence factors are molecules or structures that a pathogen uses to invade, colonize, and cause damage to the host. 
Examples:

Adhesins: Allow pathogens to attach to host cells (e.g., fimbriae in bacteria). 
Invasion factors: Help pathogens enter host cells. 
Toxins: Damage host cells or tissues (e.g., exotoxins and endotoxins). 
Capsules: Protect pathogens from the host's immune system. 
Spike proteins: Facilitate entry into host cells. 
Immune evasion factors: Allow pathogens to evade the host's immune response. 

Function:
Virulence factors enable pathogens to:

Colonize the host. 
Infect host cells. 
Evade the host's immune system. 
Cause damage to the host. 

           the host-microbe
     relationship is complex
bacteria, viruses, fungi, parasites
 interact with hosts in ways that             aren't always negative: 
 1. commensalistic: microbes                                              benefit                                                  without                                                causing harm
2. mutualistic: host and microbes
                           both benefit
3. parasitic: microbes harm the
                       host

pathogenicity

 gut microbes
      normal   v   pathogenic   

microbes have a preference for which cells/tissues/organisms they colonize. 

virulence and transmission

                                   host factors are characteristics of the host that influence
                                   its susceptibility or resistance to infection including:

a. Immune status: weakened immune systems/immunocompromised individuals                                                  cause hosts to be more susceptible to infection
b. Genetics: specific genes can confer resistance or susceptibility to specific pathogens
c. Age: very young and very old people are often more vulnerable to infections
d. Nutrition: malnutrition weakens immune systems
e. Co-infections: being already sick impairs a host's ability to fight off other pathogens
f. Gut microbiome: the gut microbiome can influence susceptibility to certain
​                                         infections

 Dysbiosis
is an imbalance in the gut microbiota.
it's been linked to mood/mental health disorders due to its negative impact on serotonin levels

        an attenuated pathogen
is a weakened form of a disease-causing microorganism. its been altered so that it can still stimulate an immune response but its
virulence has been so reduced it will not cause disease  

normal
​gut microbes 

the incidence of a microbe invading a host does not guarantee it will cause disease

Dysbiosis

R0 =
the reproduction rate
of a pathogen
Ro quantifies the contagiousness and transmissibility of pathogens.

the immune response

the measles virus
 R0 = 12-18
each person with measles, on average, infects 12-18 other people

virulence and the host
​|it's not just about the pathogen...

the host matters too