NORMAL HUMAN MICROBIOTA AND NOSOCOMIAL INFECTION
● Escherichia coli, Bacteroides, Fusobacterium, Lactobacillus,
The Human Microbiome
● The microbiome is the genetic material of all microorganisms living in
the human body.
● There are roughly 1.3 bacterial cells for every human cell in the body.
● This microbial community is first established in utero.
● More microorganisms are acquired from the environment and this
community remains' throughout the rest of the individual’s lifespan.
● Everyone has a unique microbiome signature.
● Normal microbiota permanently colonize the host and do not
cause disease under normal conditions
● Distribution and composition of normal microbiota are
determined by many factors
○ Nutrients
○ Physical and chemical factors
○ Host defenses
○ Mechanical factors
● Transient microbiota may be present for days, weeks, or
months
Skin
● Propionibacterium, Staphylococcus, Corynebacterium,
Micrococcus, Acinetobacter, Brevibacterium; Candida (fungus),
and Malassezia (fungus)
● Most of the microbes in direct contact with skin don’t become
residents because secretions from sweat and oil glands have
antimicrobial properties.
● Keratin is a resistant barrier, and the low p H of the skin inhibits
many microbes.
● The skin has a relatively low moisture content so most microbes
will not be able to colonize it effectively
Eyes (Conjunctiva)
● Staphylococcus epidermidis, S. aureus, diphtheroids,
Propionibacterium, Corynebacterium, streptococci, and
Micrococcus
● The conjunctiva, a continuation of the skin or mucous membrane,
contains basically the same microbiota found on the skin.
● Tears and blinking eliminate some microbes or inhibit others from
colonizing.
Nose and Throat (Upper Respiratory System)
● Staphylococcus aureus, S. epidermidis, and aerobic diphtheroids
in the nose; S. epidermidis, S. aureus, diphtheroids,
Streptococcus pneumoniae, Haemophilus, and Neisseria in the
throat.
● Although some normal microbiota are potential pathogens, their
ability to cause disease is reduced by microbial antagonism.
● Nasal secretions kill or inhibit many microbes, and mucus and
ciliary action remove many microbes.
Mouth
● Streptococcus, Lactobacillus, Actinomyces, Bacteroides,
Veillonella, Neisseria, Haemophilus, Fusobacterium, Treponema,
Staphylococcus, Corynebacterium, and Candida (fungus)
● Abundant moisture, warmth, and the constant presence of food
make the mouth an ideal environment that supports very large
and diverse microbial populations on the tongue, cheeks, teeth,
and gums.
● Biting, chewing, tongue movements, and salivary flow dislodge
microbes. Saliva contains several antimicrobial substances.
● - FISH uses fluorescent DNA probes
Large Intestine
Enterococcus, Bifidobacterium, Enterobacter, Citrobacter,
Proteus, Klebsiella, and Candida (fungus)
● The large intestine contains the largest numbers of resident
microbiota in the body because of its available moisture and
nutrients.
● Mucus and periodic shedding of the lining prevent many
microbes from attaching to the lining of the gastrointestinal tract,
and the mucosa produces several antimicrobial chemicals.
Urinary and Reproductive Systems
● Staphylococcus, Micrococcus, Enterococcus, Lactobacillus,
Bacteroides, Aerobic Diphtheroids, Pseudomonas, Klebsiella,
and Proteus in urethra; Lactobacilli, Streptococcus, Clostridium,
Candida albicans (fungus).
● The lower urethra in both sexes has a resident population; the
vagina has an acid-tolerant population of microbes because of
the nature of its secretions.
● Mucus and periodic shedding of the lining prevent microbes from
attaching to the lining; urine flow mechanically removes
microbes, and the p H of urine and urea are antimicrobial.
● Cilia and mucus expel microbes from the cervix of the uterus into
the vagina, and the acidity of the vagina inhibits or kills microbes.
Connections between Birth and the Microbiome
● Infants born via C-section tend to have different gut microbiomes
than those born via vaginal birth.
● Infants are exposed to the mother’s vaginal microbes at birth and
this normalizes their own microbiome development during their
first year of life.
● Infants who are born via C-section tend not to have this exposure
and are therefore more likely to become afflicted with dysbiosis
(an imbalance in the gut microbial community that is associated
with disease).
Why does this guy get a free pass?
Why does lactobacillus get a free pass?
its a good bacteria found in yakult, they take up space and leave no room
for bad bacteria (they are very competitive)
Relationships between the Normal Microbiota and the Host
● Normal microbiota protect the host by:
○ Competing for nutrients
○ Producing substances harmful to invading microbes
○ Affecting pH and available oxygen
● Symbiosis is the relationship between normal microbiota and the
host
○ Commensalism: one organism benefits, and the other
is unaffected
○ Mutualism: both organisms benefit
○ Parasitism: one organism benefits at the expense of
the other
● Microbial antagonism (competitive exclusion) is a competition
between microbes
Commensalism

● No cell cultures are involved in this whole process, you just

obtain the sample, extract the DNA material, an proceed
- Can help promote the development of intestinal layers (the mucosa
● Can be used on soil samples, water samples, etc.
(epithelium, lamina propria, and muscular mucosae), the submucosa, the
muscularis propria (inner circular muscle layer, intermuscular space, and
Healthcare-Associated Infections (HAI)
outer longitudinal muscle layer), and the serosa)
● Acquired while receiving treatment in a health care facility
○ Also known as nosocomial infections
Human Microbiome Project
● HAIs result from:
● A United States NIH (National Institutes of Health) research
○ Microorganisms in the hospital environment
initiative launched in 2007 with the goal of improving
○ Weakened status of the host
understanding of the relationship between the microbiome and
○ Chain of transmission in a hospital
human health and disease.
● Compromised host - an individual whose resistance to infection
● Uses whole genome sequencing and metagenomics to
is impaired by disease, therapy, or burns
characterize microbial communities via culture-independent
methods.
● - Most of the information provided comes directly from
institutions participating in this intiative

Microorganisms Involved in Healthcare-Associated Infections

- Antimicrobial assay performed in lab would be a way to check this, just

figure out the overall number of bacteria you have in your sample
- Metagenomic sequencing uses ALL sequences in a sample, allows the
assessment of proportions of specific metabolic genes and microbial
families based on markers in contigs
Control of Healthcare-Associated Infections
1. Universal precautions
● Standard precaution - basic, minimum practices (e.g.
handwashing, cough etiquette)
● Transmission-based precautions - supplemental to standard
precautions; designed for known or suspected infections
○ Contact precautions
○ Droplet precautions
○ Airborne precaution

2. Reduce number of pathogens

● Handwashing
● Disinfecting tubs used to bathe patients
● Cleaning instruments scrupulously
● Using disposable bandages and intubation
● Establishment of infection control committees