Human Microbiome + Infection

Microbiota

Collection of microbes found in a specified environment

Prokaryotes, eukaryotes, viruses

Microbes include __ (bacteria, archaea), __ (microbial parasites and fungi), and __ embedded in the microbiota

Resident, transient, carrier

__ are more or less permanent microbiota

__ microbiota establish a niche only briefly

Bacteria in the __ state are potentially disease-causing that are resident in some individuals

Skin, respiratory, vagina, oral, GI

Body locations colonized by microbiota include

__, __ tract (trach-bron-alv), __/opening urethra, __ cavity, and __ tract (stom-col-rect)

Blood, fluids, peritoneum, disease

In healthy individuals, sterile environments free of bacteria and fungi are:

• __

• Body __ - urine, pleural fluid, cerebrospinal fluid

• Enclosed body cavities (i.e. __)

• If microorganisms are at any of these, indicates __

Cervix, vagina

Humans (newborns) acquire microbiota during passage through the __ and __

16 rRNA

Bacterial diversity of microbiota are analyzed by __ (#) __ sequencing

30s, genus

16 rRNA is a component of __ bacterial ribosomal unit, and has hypervariable regions used for phylogenetic classification to the __ level

Staphylococcus Aureus (Staph A)

Potential pathogen present on skin of many individuals

Abundant, few, limited, high

GI tract microbiota

• Oral Cavity - Saliva __ in microorganisms, mainly bacteria

• Stomach - __ bacteria due to acidic pH, mainly H. pylori

• Small intestine - __ numbers of bacteria

• Colon - Very __ numbers of microorganisms, mainly E. coli, C. diff

Intestinal

There is a significant difference in __ (gut variant) microbiota based on diet of individual hosts or oral antibiotic use

Exclusionary Effect

Healthy gut microbiota outcompete and reduce the presence of potential pathogens in a host

Upper respiratory tract microbiota (URT)

• Nares are similar to the skin (HIGH microorganism count)

• Majority of healthy population are colonized with potential respiratory pathogens (i.e. Staphylococcus aureus)

Lower respiratory tract microbiota (LRT)

Few bacteria populated due to function of cilia on the epithelium

microbes from upper migrate here

Last centimeter, disease

Urinary system is mostly sterile except for the __ __ of the urethra. Bacteria to urinary tract is thus deemed a __ state.

Acidic, stable, large

The microbiota of vagina in adulthood thrive in a slightly __ environment

Microbiota is __ in pregnancy

Post menopause period has a __ impact on microbiome

Fungi, yeast

In many individuals, __ Candida albicans is normal component of vaginal microbiota. Disturbances in this balance can lead to __ infection symptoms.

Bacterial Vaginosis

Shift in pH and changes in population of bacteria in vaginal region

Bacteriophages

Viruses that infect bacteria

Virome

All viral DNA in a specified environment

Human Virome

All viruses on the human body not causing disease

Fossil Viruses

Remainder of provirus integrated in human genome

Dark Matter

Unidentified DNA that appears to be viral in origin

Bacteriophages, non-disease

Most of the human virome is probably…

Eukaryotic viruses in virome include both pathogenic, latent infections, and __ __ causing viruses

Infection

Multiplication of the organism in a host, not necessarily disease

Carriers

Individuals with subclinical infection (no symptoms)

Non-Communicable Infections

Infections not transmitted from human to human

• Opportunistic infections, ingestion of pre-formed toxins, zoonotic from animals

Communicable Infections

Microorganism transmitted from human to human (directly or vector)

• Influenza, COVID-19, malaria, insect vectors

Animals, carriers, living

3 reservoirs of pathogens

• (1) __ , (2) human __, (3) non-__ (water, food)

Vertical, horizontal

__ transmission is an infection transmission from mother to fetus/infant

where as __ transmission is an infection transmission from one person to another OR from animal/environment to individual

Skin-to-skin, sexual, respiratory, objects, salivary, food/water, vector, blood

Horizontal Transmission methods

• __to__ : Group A strep and impetigo, dermatophyte fungi for ringworm

• __: Neisseria gonorrhoeae, HIV

• __: Influenza virus, rhinoviruses, TB

• Contact with __: May lead to transmission of some respiratory infections

• __: Rabies virus, EBV

• __/__ borne: Vibrio cholera, polio, fecal-oral

• __ borne: Malaria, insect

• __borne and other fluids: Hepatitis C, HIV

Pathogens, virulence

__ are a microbe with potential to cause disease

__ is a variation in ability of microbe to cause disease

Incubation Period

Time from infection to symptoms

endemic, epidemic, pandemic, epidemic

__ is a disease present in population at low and constant level, constant presence

__ is a disease present in specific population at level higher than usual, outbreak

__ is a widespread __ through defined geographic region, even worldwide