Notes
Human Microbiome
Sections
Overview
The normal human flora comprises bacteria and yeasts; moreover, bacterial cells outnumber the host's cells by 10:1.
Microorganisms of the normal flora are "commensals" because they benefit the host, but do not harm it.
Individual's specific microbiome is influenced by hygiene, diet, water sources, drugs and medications, and exposure to environmental toxins.
The normal flora impacts human health and disease:
– The microbiome guides immune system development.
– Protects against colonization by pathogenic microbes; and, in the gut, contributes to digestion and metabolism.
– The human microbiome is also associated with pathology.
Opportunistic pathogens are members of the normal flora that cause disease in immunosuppressed individuals or if the microbes move to a new anatomical niche.
Strict pathogens are micro-organisms that always cause disease.
Dysbiosis, aka, dysbacteriosis, occurs when disruption of the normal flora allows pathogenic microbes to flourish.
– For example, some antibiotics kill off protective microbes in the gut, therefore facilitating overgrowth of toxin-producing microbes.
Holobiont
Comprises the human host plus its microbiome; this is sometimes referred to as a "superorganism."
The core microbiome comprises those microorganisms present in more than 95% of individuals at specific anatomical sites.
The secondary microbiome comprises the microorganisms that are more variable among individuals.
Skin
Staphylococcus epidermidis, which is the predominant bacteria found on the skin in most individuals.
Staphylococcus aureus is also common.
Propionibacterium acnes are anaerobic bacteria that reside within the follicles of the dermis, and cause acne.
Candida albicans is a common yeast; as an opportunistic pathogen, it can cause systemic infections.
Be aware that S. epidermidis and S. aureus are significant opportunistic pathogens if they gain entry to the bloodstream.
– For example, both are associated with bacterial endocarditis, particularly when prosthetic valves are involved.
Commonly colonized by Staphylococcus aureus.
– Some authors suggest that asymptomatic nasal colonization of methicillin-resistant Staphylococcus aureus (MRSA) may be a risk factor for MRSA infection.
Oral Cavity
The oral cavity microbiome is varied, and includes hundreds of species; furthermore, there are distinct microbial communities found on the teeth, tongue, lips, etc.
Viridans streptococci are predominant in the mouth.
The gingival crevices are home to several anaerobic bacteria, including Bacteroides, Prevotella, Fusobacterium, Clostridium, Peptostreptococcus, and, Actinomyces israelii.
Throat
The microbiome of the throat comprises viridans streptococci, Neisseria species, and Staphylococcus epidermidis.
– These strains provide colonization resistance to more pathogenic species such as Streptococcus pyogenes and Neisseria meningitides.
Gastrointestinal tract
The diet significantly influences the gut microbiome.
Microbes of the gut contribute to digestion, particularly of carbohydrates, and produce vitamins and energy sources for the human host.
Historically, the stomach was assumed to be a sterile environment, due to its highly acidic nature. However, advances in molecular genetics have shown this to be untrue.
The stomach microbiome is, in fact, quite diverse. In healthy individuals, the stomach is dominated the bacterial phyla Proteobacteria, Firmicutes, Bacteriodetes, and Actinobacteria.
The microbiome of the stomach is easily affected by diet and medications.
Colonization by the pathogenic bacteria Helicobacter pylori is a significant result of dysbiosis, and causes chronic gastric inflammation, ulcers, and stomach cancer.
The microbiome of the small intestine is difficult to assess, and appears to fluctuate with dietary intake; furthermore, it is thought to be less populated than the large intestine.
– Streptococcus species and Veillonella species are likely members of the small intestine's core microbiome.
The large intestine is a significant reservoir of bacteria; up to 30% of the solid mass of feces comprises bacteria.
– Bacteriodes fragilis, Escherichia coli, Fusobacterium, Peptostreptococcus, and Enterococci.
– Be aware that these normal inhabitants of the colon are pathogenic in other areas; for example, Enterococcus faecialis is associated with endocarditis.
– When the colon microbiome is disturbed, Clostridium difficile can flourish, causing colitis and diarrhea.
Vagina
Adult vagina is home to Lactobacilli, which maintain the protective acidic pH; be aware that the presence of Lactobacilli appears to fluctuate with estrogen levels.
Group B streptococci are found in 10-20% of women; though non-pathogenic in the vagina, these bacteria can cause neonatal infections if transmitted during childbirth.
Staphylococcus aureus is present in ~5% of women, and is a risk factor for Toxic Shock Syndrome; interestingly, Lactobacilli reduce the virulence of Staphylococcus aureus.
Urinary Tract
The urinary tract was long thought to be sterile. However, advanced molecular methods indicate that the urinary tract is likely inhabited by a core microbiome.
Appears to vary by both age and sex.
Microbes from other regions of the body, particularly Escherichia coli, can lead to urinary tract infections.
Additional pathologies associated with dysbiosis.
- Irritable bowel syndrome, inflammatory bowel disease, and allergy are associated with reduced microbiome diversity.
- Some studies report a correlation between obesity and gut microbes, which differentially metabolize carbohydrates.
- Some cardiovascular diseases are related to gut dysbiosis via changes in metabolism and/or blood pressure.
Future research on the role of microbiome disturbance in human disease may have significant impact on how we treat some of these diseases.