Microbiota and Their Functions in the Body

Microbiota

• Microbiota are microorganisms, primarily bacteria, fungi, protozoa, and viruses, that live in the human body.
• They are essential for the human body, and are continuously present.
• In a healthy individual, microbiota are harmless and can be beneficial.
• They are also known as commensals or microflora.
• The human body contains roughly 100 trillion microbes.
• There are approximately 2.5 kg of microbes in the human body, mostly in the colon.
• There are about 5000 different species of microbes in the gut alone.
• The gut microbiota weighs about 2 kg.

Learning Objectives

• Students should be able to define and explain the functions of normal microbiota.
• Define permanent and temporary microbiota.
• Explain the importance of permanent microbiota.
• Understand microbiota in differing parts of the body.
• Describe the role of normal microbiota in host defense and disease.

Microbiota in the Gut

• The gut microbiota primarily includes bacteria, viruses, fungi, and parasites.

The Human Microbiome

• 25 known phyla (~2000 genera ~5000 species)
• 80% mappability of metagenomes
• 316 million genes
• ~20% sequences not matching microbial genomes
• Functional unknowns (~40% genes without a match in functional databases)

Stuff about Microbiota

• A fetus is sterile at birth, then acquires normal microbiota from its mother, air, and environment.
• Internal organs (spleen, liver, pancreas, bladder, CSF, blood) are generally sterile unless during infections.
• Microbiota vary between individuals based on age, sex, hormonal status, hygiene, diet, and geography.
• A reduction in resident microbiota allows opportunistic microbes to cause infection.
• Human body microbiota is part of natural resistance and forms at birth.

Why Should We Know About Microbiota?

• Understand possible infections resulting from injury.
• Learn about the source and significance of microorganisms from infection sites.

Transient Microbiota

• Microbes temporarily living on or within the human body.
• Attract to moist, warm areas in the external environment.
• These microbes may be washed away by bathing, unable to compete with resident flora, killed by resident flora substances or unable to survive the pH levels of the site.
• They may be flushed away by bodily secretions (tears, sweat, urine, feces).

Where Can We Find Microbiota?

• Skin, Eyes and Ears,Respiratory Tract, Oral Cavity (Mouth), Gastrointestinal Tract, Urogenital Tract.

Skin Microbiota

• Skin acquires transient bacteria from the environment.
• Transients can be washed off, die due to dry conditions, acidic pH, and sweat/oil production.
• Resident bacteria are found in any skin layer, including hair follicles, sweat and sebaceous glands.
• Aerobic bacteria are present in the outer layer (e.g., Staphylococcus epidermidis, Staphylococcus aureus).
• Anaerobic bacteria are present in deeper layers (e.g., Cutibacterium acnes).
• The presence of skin microbiota is generally harmless but may lead to bloodstream infections.

Eyes Microbiota

• Conjunctiva of the eye primarily contains S. epidermidis, followed by S. aureus, C. diphtheroids, and S. pneumoniae.
• Some skin normal flora exist present at fewer amounts, and tears, mucus, and oil protect the conjunctiva from colonization by more bacteria.

Ears Microbiota

• Middle and inner ear is usually sterile.
• Outer ear and auditory canal contains the same skin flora.
• Microbes can enter middle ear from coughs, sneezes, and nose blowing, causing infections.

Respiratory Tract Microbiota

• The upper respiratory tract (nasal cavity, pharynx, larynx, trachea) has many microorganisms.
• Some are normal flora; some are opportunistic, and others (e.g. C. diphtheroids) are carried.
• The lower respiratory tract is usually sterile, due to mucus membranes that remove microbes.

Oral Cavity (Mouth) Microbiota

• Contains both aerobic and anaerobic bacteria.
• Common types include C. diphtheroides, S. aureus, S. epidermidis.
• Yeasts, molds, protozoa, and viruses can also be present.
• Poor hygiene promotes bacterial growth causing dental caries, gingivitis.
• Dental surgery can create a risk of bloodstream infection (endocarditis).

Gastrointestinal Tract Microbiota

• Stomach has few bacteria due to acidity and gastric enzymes.
• Small intestine has few normal flora in the upper part, due to bile killing the bacteria, while the lower part has more.
• Colon is full of bacteria, mostly anaerobic.
• Many fungi, protozoa, and viruses can also be present.
• Some normal flora can cause urinary infections if they travel to other areas (e.g., E. coli).

Urogenital Tract Microbiota

• Kidneys, ureters, and urinary bladder are sterile.
• Lower urethra and external openings have bacteria, yeast, and viruses, similar to skin flora.
• Genital areas are mostly sterile, with the exception of the vagina.
• Lactobacillus spp. maintains an acidic pH to prevent opportunistic infections (fungal vaginitis: Candida albicans, or bacterial vaginosis: Bacteroides spp., Gardnerella vaginalis).

Normal Flora in the Vagina

• Includes various types of bacteria, such as Actinomyces, Staphylococcus, Streptococcus, Corynebacterium, Klebsiella, Proteus, Pseudomonas, Bacteroides, Lactobacillus, Mycoplasma.
• The yeast-like fungus Candida albicans is a common overgrowth.

Sterile Body Zones

• Middle ear, lungs, pleura, paranasal sinuses, blood, endocardium, fallopian tubes, cerebrospinal fluid, meninges, liver, gallbladder, bones/joints, kidneys, ureters, bladder, prostate, epididymis.

Beneficial Functions of Normal Flora

• Protect organs from invading pathogens.
• Stimulate immune system development in newborns.
• Provide nutrients (e.g., vitamin K) aiding digestion and absorption.

Importance of Microbiome

• Microorganisms play a role in many processes including weight control, inflammatory bowel disease, general immune response, and infectious disease resistance.

Harmful Effects of Normal Flora

• Displaced normal flora can become pathogenic, causing infections in other parts of the body (e.g., bloodstream infections, antibiotic-therapy-related infections, cancer).
• Food substances can be converted by normal microbiota into carcinogens.
• Immunocompromised individuals may experience overgrowth of normal flora, causing infections.

Colonization Resistance

• Normal microbiota protects against the overgrowth of harmful microbes.
• Preventing Clostridioides difficile overgrowth during antibiotic therapy.
• Fecal transplants from healthy individuals can cure intractable colitis.

This quiz explores the essential role of microbiota within the human body, focusing on their functions and significance in health. Students will learn about the different types of microbiota, their locations, and their impact on host defense and disease. Test your understanding of this fascinating aspect of human biology!