The Microbe-Human Ecosystem

Human Microbiome

  • Human Microbiome: Includes archaea, bacteria, fungi, and viruses found in areas like the mouth, skin, digestive system, and urogenital tract.
  • Humans are composed of both human and microbial cells; microbial cells are estimated to be as numerous as human cells, comprising approximately 0.5-1 lbs of body mass.

Terminology

  • Microbiome: The community of microorganisms in a specific environment.
  • Microbiota: All the microorganisms present within a particular environment.
  • Holobionts: Hosts and their associated microbes living together in symbiosis and evolving together.
  • Microbial niches vary based on body location, age, sex, diet, and environment.

Human Microbiome Specifics

  • Human Microbiome: The community of microorganisms existing in and on the human body, including all genomic content of the microbiota.
  • Human Microbiota: All the individual microorganisms residing in and on the human body.
  • Commensals: Microorganisms that inhabit the human body without causing harm; however, this relationship is complex.

Human Microbiome Project (NIH)

  • Funded by the National Institute of Health (NIH) from 2007-2016.
  • Aim: To characterize the human microbiome and understand its role in health and disease.
  • Goals Completed:
    • Sequenced >3,000 isolate genomes.
    • Characterized human body site microbiomes (oral, nasal, skin, gastrointestinal, urogenital) using 16S rRNA gene and metagenome sequencing.
    • Developed tools and standards for analysis.
    • Characterized microbiome in pregnancy stages and diseases (e.g., ulcerative colitis, Crohn’s disease, obesity, type II diabetes).

Human Microbiome Composition

  • Known:

    • 25 Phyla
    • 2,000 Genera
    • ~5,000 Species
    • ~80% Metagenome mappability
    • 316 million genes

  • Unknown:

    • 19 Undetected unknowns (low abundance)
    • Hidden taxa & strain-level diversity
    • ~20% sequences not matching microbial genomes
    • Functional unknowns: ~40% of genes without a match in functional databases

Human Gut Microbiome Database

  • A collection of >200,000 high-quality genomes from human gut microbiomes (Unified Human Gastrointestinal Genome (UHGG) collection).
  • >70% of these genomes lack cultured representatives.
  • >40% of genes lack function assignments.

Normal Microbiota

  • Animals, including humans, are nearly germ-free in utero.
  • Microorganisms begin colonization in and on the body soon after birth.
  • Normal Microbiota: Microorganisms that establish permanent colonies inside or on the body without producing disease (e.g., Staphylococcus on epidermis and mucus membranes, Escherichia coli in colon).
  • Transient Microbiota: Microbes that are present for various periods and then disappear; they colonize briefly but cannot become permanent due to host defenses.

Benefits of Normal Microbiota

  1. Synthesize and excrete vitamins (Vitamin K and Vitamin B12).
  2. Prevent colonization by pathogens by competing for attachment sites or essential nutrients.
  3. May antagonize other bacteria through the production of substances that inhibit or kill non-indigenous species (nonspecific fatty acids, peroxides, bacteriocins).
  4. Stimulate the development of certain tissues (e.g., intestines, certain lymphatic tissues, capillary density).
  5. Stimulate the production of cross-reactive antibodies; low levels of antibodies against normal flora components can cross-react with related pathogens, preventing infection or invasion.

Microbial Antagonism

  • Normal microbiota can prevent pathogens from causing infection by competing for nutrition.
  • Affecting conditions such as pH or available oxygen; decreased oxygen slows the growth of facultative anaerobic pathogens.
  • Produce substances harmful to invading organisms (interference competition).
  • Bacteroidales produce bacteriocins.

Correlation of Microbiome Changes with Illness

  • Research has characterized microbial diversity and shown correlations with illnesses.
  • Current research focuses on mechanisms (how?) and therapeutics.
  • Dysbiosis: An imbalance of the “normal” flora in a human microbiome.

Development of a Stable Microbiome

  • Microbiota community is not static in early life; it begins developing at birth and changes with age.
  • A stable microbial community is typically adopted by age 3.
  • Developing a diverse microbiome is important.

Early Colonization

  • Newborn colonization is important.
  • Vaginal birth exposes newborns to microbes from the mother’s birth canal, while cesarean delivery exposes them to microbes from initial caretakers.
  • Bifidobacteria transport polymeric sugars (oligosaccharides) from human breast milk directly across their plasma membrane.
  • Fermentation of these sugars provides the infant with calories and lowers gut pH, limiting pathogen growth.

Adult Human Microbiota

  • Relatively stable over time, changing only due to physical or lifestyle changes.
  • Variable from person to person and at different sites within a person.
  • Common bacteria include six major phyla: Actinobacteriota, Bacteroidetes, Firmicutes, Fusobacteriota, Proteobacteria, Verrucomicrobiota.
  • Some archaea, fungi, and viruses are also present.

Microbiota Variation by Body Site

  • Internal organs and tissues (brain, blood, cerebrospinal fluid, muscles) are normally free of microorganisms.
  • Surface tissues (skin and mucous membranes) are constantly in contact with the environment and are colonized by various microbes.

Individual Microbiomes

  • Microbiomes are unique to each individual.
  • Examples include the oral cavity, skin, vagina, oesophagus, colon, and hair.
  • The presence or absence of H. pylori in the stomach can also influence the microbiome.

Skin Environment

  • Slightly acidic pH.
  • High concentration of NaClNaCl.
  • Some areas lack moisture.
  • Some areas are bathed in oily lubricant sebum and antimicrobial peptides.
  • Some microbes are temporarily present but unable to multiply on the skin.
  • Three environmental niches: dry (greatest microbial diversity), moist, and sebaceous.

Human Skin Microbiome

  • Adapted to nutrient limitation.
  • Microorganisms can produce molecules that inhibit colonization of others.
  • Adult skin microbiota remains stable.
  • Skin diseases are associated with altered microorganism communities.
  • Dominant bacteria: Propionibacterium acnes, Staphylococcus epidermidis, and Staphylococcus aureus.

Skin Microbiome Composition by Location

  • Similarities of skin microbial communities are more dependent on the site than the individual.
    • Examples: Antecubital crease, back, nare, and plantar heel.

Skin Microbiome Details

  • Microorganisms and mites (arthropods) colonize hair follicles and glands.
  • Commensal fungus, Malassezia spp., grows as branching hyphae and individual cells.
  • Odors are produced by microorganisms, with > 10610^6 cells per cm2cm^2.

Factors Influencing The Skin Microbiome

  • Intrinsic:
    • Age, sex, hormones: greater fungal diversity pre-puberty; sebum production increases bacterial abundance during puberty.
    • Genetics and ethnicity: Skin microbiome differs between different ethnic groups.
  • Extrinsic:
    • Hygiene, use of lotions, UV exposure, cosmetics.
    • Cosmetics can reduce abundance and diversity of microorganisms.
    • Frequency of bathing and products used impact microorganism presence.
    • Disrupting the microbiome can cause inflammation, irritation, dryness, itchiness, dermatitis.

Skin as an Active Immune Organ

  • The skin's function can change with the presence of commensal microbiota.
  • Keratinocytes and dermal appendages release antimicrobial peptides and proteins (AMPs), providing defense against pathogenic microbes.
  • Dry and sebaceous sites are predominantly colonized by Cutibacterium acnes, while moist sites and the foot are mainly colonized by Corynebacterium tuberculostearicum.
  • Skin-microbial interactions promote innate immune function.

Normal Skin Flora

Classes and Organisms:
* Aerobic cocci:
* Organisms include Staphylococcus aureus, S. saprophyticus, S. epidermidis, Micrococcus luteus, M. roseus, M. varians.
* Found on all body sites, especially intertriginous areas.
* Aerobic coryneform bacteria:
* Organisms include Corynebacterium minutissimum, C. lipophilicus, C. xerosis, C. jeikeium, Brevibacterium epidermidis.
* Found in intertriginous areas (e.g., axillae, groin, toe webs).
* Anaerobic coryneform bacteria:
* Organisms include Propionibacterium acnes, P. granulosum, P. avidum.
* Found in sebaceous glands and follicles.
* Gram-negative bacteria:
* Organisms include Acinetobacter spp.
* Found in axillae, perineum, antecubital fossa.
* Yeast:
* Organisms include Malassezia furfur.
* Found on skin rich in sebaceous glands (e.g., scalp).
* S. epidermidis is the most common coccus on human skin.

Staphylococcus epidermidis

  • Most common coccus that colonizes the skin and is a key component of healthy skin.
  • Generally non-pathogenic.
  • Modulates keratinocyte gene expression, stimulating antimicrobial peptide release.
  • Secretes products of fermentation called short-chain fatty acids.
  • Binds to the pattern recognition receptor TLR-2.
  • Exhibits bacterial interference, inhibiting growth of pathogens via bacteriocins that are proteases targeting adhesins that S. aureus needs for host attachment.

Dysbiosis and Atopic Dermatitis

  • Dysbiosis of the skin microbiome contributes to atopic dermatitis.
  • Currently affects 15% of US children.
  • A 2-fold increase has been observed in the last 30 years in western countries.

AD Microbiome Progression Hypothesis

  • Microbial diversity decreases during AD flares, with the proportion of Staphylococcus increasing.
  • Disease severity correlates with these changes.

Staphylococcus aureus and AD Flares

  • Staphylococcus aureus increases during AD flares.
    *

Regulation of Staphylococcus aureus

  • Repression:
    • Antibiotic production by other bacteria.
    • Serine protease from S. epidermidis induces keratinocytes to produce AMPs.
  • Promotion:
    • Propionibacterium acnes produces coproporphyrin III that promotes S. aureus aggregation and biofilm formation.

Probiotic Soaps

  • Probiotic soaps containing Lactobacillus spp. and Bifidobacterium spp. can reduce the risk of atopic dermatitis.
  • The use of these skin probiotics has been shown to be transient (2 weeks after treatment).

Link Between Skin and Gut Microbiome

  • Connections via blood and lymph, as well as immune imbalances.
  • Healthy state vs. Dysbiotic state:
    • In dysbiosis, there is:
      • Reduced mucous
      • Reduced IgA
      • Reduced AMP production
      • High Th2 cytokine immune cell response
  • The immune response promotes the growth of S. aureus.

Families and Microbiomes

  • Families have more similar microbiomes due to host genetics and environment.
  • Cohabitation is significantly associated with skin microbiome composition.
  • Use of skincare products, pets, allergies, and alcohol consumption shape the skin microbiome.
  • Identical twins have more similar skin microbiomes.
  • Humans may share microbiome members with their dogs.

Environmental Effects on Skin Microbiome

  • Swimming in ocean water affects the skin microbiome, causing temporary changes and introducing some potential pathogens.
  • Soap helps lift dirt and bacteria off the skin, reducing the abundance of pathogens.

Anti-Bacterial Soap Adverse Effects

  • Environmental exposure to triclosan (a main ingredient in anti-microbial soap) helps bacterial populations develop resistance mutations to triclosan and other important antibiotics.

Microbiome of the Eye and External Ear

  • Eye:
    • A small number of bacteria are found on the conjunctiva.
    • The predominant bacterium is Staphylococcus epidermidis.
  • External Ear:
    • Similar to skin flora, with nonpathogenic staphylococci and Corynebacterium spp. predominating.

Respiratory Tract

  • Upper Respiratory Tract: Nostrils, sinuses, pharynx, and oropharynx colonized by a diverse group of microbes.
  • Lower Respiratory Tract: Larynx below the vocal cords, trachea, bronchi, and lungs.
    • Not sterile as previously thought.

Lower Respiratory Tract Microbiome

  • Difficult to sample lungs without contamination from the upper respiratory tract.
  • Microbes are introduced principally from the oropharynx.
  • Not stable, rather a fluid microbial community (migration and clearance).
  • Microbial dysbiosis in the lung is linked to cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD), with evidence for dysbiosis and pathogens causing disease via inflammation.

Oral Microbiome

  • Soon after birth, the mouth is colonized by microorganisms from the surrounding environment.
  • Anaerobes become dominant due to the anoxic nature of the space between the teeth and gums.
  • As teeth grow, Streptococcus parasanguinis and S. mutans attach to enamel surfaces; S. salivarius attaches to the buccal (inside the cheeks) and gum epithelial surfaces and colonizes the saliva.
    • These bacteria produce a glycocalyx and various other adherence factors that enable them to attach to oral surfaces.
    • They contribute to dental plaque, caries, gingivitis, and periodontal disease.

Key Factors Influencing the Oral Microbiome

  • A) Age (time):
    • Changes in host and habits.
    • Horizontal transfer of microorganisms.
    • Micro-evolution.
    • Changes in diversity.
  • B) Host & Environment:
    • Genetic factors.
    • Immune system.
    • Environment, diet & habits.
    • Changes in host defenses.
  • C) Habitat (Examples: Tongue, Teeth & Gingival Crevice, Buccal Mucosa, Saliva):
  • D) Biofilm Maturation:
  • E) Variables within the habitat:
    • Oxygen (redox).
    • Surface.
    • Nutrition.
    • pH.
    • Oral hygiene.
    • Salivary flow and GCF (Gingival Crevicular Fluid).
    • Shedding or not.
    • Density.
    • Environment.
    • Microbial interactions.
    • Immune response of the host.

Oral Microbiome and Systemic Diseases

  • Several oral and systemic diseases are associated with the oral microbiome, including:
    • Alzheimer's disease (Spirochaetes, Porphyromonas gingivalis)
    • Cardiovascular disease (Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia, Prevotella nigrescens, Campylobacter rectus)
    • Cystic fibrosis (Streptococcus oralis, other Streptococci)
    • Esophageal cancer (Tannerella forsythia, Porphyromonas gingivalis, Neisseria, Streptococcus pneumoniae)
    • Colorectal cancer (Fusobacterium nucleatum, Lactobacillus, Rothia)
    • Periodontitis (Red complex - Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Archaeological methanogens, Proteobacteria
    • Caries (Streptococcus mutans, Lactobacillus, non-mutans Streptococci)
    • Diabetes (Aggregatibacter, Neisseria, Gemella, Porphyromonas, Filifactor, Eubacterium)
    • Pancreatic cancer (Leptotrichia, Porphyromonas gingivalis, Aggregatibacter actinomycetemocomitans)
    • Rheumatoid arthritis (Veillonella, Atopobium, Prevotella, Leptotrichia, Lactobacillus salivarius, Cryptobacterium curtum, Porphyromonas gingivalis, Haemophilus, Neisseria, Rothia mucilaginosa, Rothia dentocariosa, Rothia aeria)

Dental Caries Development

  • Early Colonizers: Mainly health-associated streptococci (e.g., S. sanguinis and S. gordonii).
  • Diet: Sucrose leads to glucan production by S. mutans, resulting in robust biofilm formation, acid tolerance, and acid production.
  • Late Colonizers: Acid-tolerant and acid-producing bacteria (e.g., Lactobacillus and Veillonella spp.).
  • Poor oral hygiene and high-sugar diets contribute to dental caries.
  • Fluoride inhibits glucan production and promotes enamel remineralization.
  • Probiotics, vaccines, polyol gums, antimicrobial peptides, and phage can be used to antagonize S. mutans and other cariogenic taxa.

Kissing and Oral Microbiota

  • Kissing for 10 seconds transfers an average of 80 million bacteria.
  • Couples who kiss more often have more similar oral microbiota, especially on the tongue surface.

Genitourinary Tract

  • Kidneys, ureter, and urinary bladder are normally free (or nearly free) of microbes.
  • Distal portions of the urethra contain few microbes (S. epidermidis, Enterococcus faecalis, and Corynebacterium spp.).
  • Intestinal dysbiosis is linked to UTI prevalence.
    • Female genital tract contains a complex microbiota that changes due to the menstrual cycle, with acid-tolerant lactobacilli predominating.