The Microbiome Overview

Overview of the Microbiome

• Microbiome consists of various microbes in a system, including bacteria, viruses, fungi, and protozoa.
• Contains genetic material from all microbes in and on the human body, with about 200 times more genes than the human genome.
• Total weight can reach up to 2 kg.

Microbiome vs. Microbiota

• Microbiota includes prokaryotes and eukaryotes, comprising microbial structures, metabolites, and movable genetic elements.
• The microbiome encompasses a broader range, including elements not found in microbiota like phages, plasmids, free DNA, prions, and viroids.

Human Microbiome Project

• Aims to catalog all microorganisms in the human body, extending the Human Genome Project.
• Sponsored by the National Institutes of Health (NIH) in the USA.
• Studies major microbial sites in 300 healthy individuals, including skin, mouth, nose, colon, and vagina.

Personalization of Microbiome

• Microbiomes of individuals can differ 80-90%, despite human genomes being 99.9% identical.
• The human gut microbiome contains approximately 3.3 million genes compared to 22,000 human genes.

Development of the Microbiome

• At birth, neonates are microbe-free; rapid colonization occurs through contact with the birth canal and caregivers.
• Types of feeding (breast vs. bottle) lead to different developments in microflora.

Benefits of the Microbiome

• Established resident flora provides a barrier against external pathogens and opportunistic infections.
• Bacterial interference may occur through competition for nutrients, receptor binding, and production of inhibitory substances (e.g., fatty acids, bacteriocins).
• Normal flora prevents harmful microbial invasion by competing for resources and maintaining low pH environments.

Functions of Gut Bacteria

• Help harvest nutrients from food, breaking down carbohydrates that humans cannot digest, contributing to approximately 30% of caloric intake.
• Produce vitamin K for normal blood clotting.
• Generate signaling chemicals that regulate hunger, satiety, and neurotransmitters like serotonin.

Factors Affecting the Microbiome

• Diet: Long-term dietary habits can alter gut microbiome; plant-rich diets enhance microbial diversity, while limited diets reduce it.
• Age: Aging is associated with decreased microbial diversity, linked to increased inflammation and frailty.
• Lifestyle Influences:
  • Cohabitation with pets: Exposure to pets can reduce allergy development and modify gut microbiome.
  • Exercise: Promotes microbial health and reduces inflammation.
  • Sleep deprivation: Correlates with adverse changes in the gut microbiome.
  • Stress: Increases intestinal permeability, altering microbiome composition.
  • Occupational factors and social environment can also impact the microbiome.

Definition and Composition of the Microbiome

• The microbiome is a functional collection of diverse microbes, including bacteria, viruses, fungi, and protozoa, present in a system.
• It contains genetic material from all microbes associated with the human body, with the number of genes being 200 times greater than those in the human genome.
• The total weight of the microbiome can reach up to 2 kg.

Differences between Microbiome and Microbiota

• Microbiota, defined in 2020 by a panel of over 100 experts, refers to the microbial structures, metabolites, and movable genetic elements, including both prokaryotes and eukaryotes.
• Microbiomes encompass a broader range than microbiota.

Development of the Microbiome

• At birth, neonates are microbe-free, but rapid colonization occurs through contact with the birth canal, caregivers, and the hospital environment.
• Different feeding methods (breast vs. bottle) contribute to distinct microbial flora.
• Example of early colonizers: Streptococcus haemolyticus within 4-12 hours after birth and persistent S. aureus found in about 20% of individuals.

Microbial Flora in the Eye

• Bacterial presence on the eye surface is minimal due to effective natural defenses.
• Key defense components include lysozyme, antimicrobial peptides, and immunoglobulins.
• Common bacterial species found in the eye include Propionibacterium, Corynebacteria, Staphylococcus, and Streptococcus.

Gut Microbial Flora

• Microbial flora in the gastrointestinal tract can weigh approximately 1 kg and constitutes 60% of the dry mass of feces.
• Lactobacillus species aid in acid fermentation, resulting in a low pH, thus protecting against harmful microbes.

Benefits of Gut Bacteria

• Gut bacteria assist in nutrient harvesting, breaking down carbohydrates that humans cannot digest, contributing to 30% of processed calories.
• They produce vitamin K, essential for normal blood clotting.
• Gut microbiota also generate signaling molecules that influence hunger signals and produce neurotransmitters like serotonin.
• They play a crucial role in balancing beneficial and harmful bacteria, impacting immune functions and metabolism.

Factors Affecting the Microbiome

• Various factors influence normal flora composition, including:
  • Sex
  • Diet: Long-term diets can significantly alter the gut microbiome; plant-rich diets boost microbial diversity.
  • Age: Increased age leads to reduced microbial diversity, linked to inflammation and frailty.
  • Lifestyle Choices:
    • Cohabitation with pets: Exposure to dogs can positively affect the gut microbiome and reduce allergy risks.
    • Exercise: Known to lower inflammation levels.
    • Sleep deprivation: Correlates negatively with a healthy microbiome.
    • Stress: Increases intestinal permeability, altering the microbiome.
    • Occupation: Differences in microbiomes seen between farmers and office workers.

Effects of Antibiotics

• Antibiotics can disrupt both targeted pathogens and normal microbiota, leading to significant shifts in microbial composition across gut, vaginal, and skin flora.
• Early antibiotic administration may hinder the development of normal microflora and the immune system, potentially increasing susceptibility to allergies and autoimmune disorders.

Probiotics and Prebiotics

• Prebiotics: Specific non-digestible carbohydrates that serve as nourishment for beneficial microbes, stimulating their growth.
• Probiotics: Live microorganisms that may confer health benefits upon consumption, such as Bifidobacterium and Lactobacillus species.

Microbiome Overview

• Includes entities like phages, viruses, plasmids, free DNA, prions, and viroids that are NOT part of the microbiota.
• The human microbiome project aims to catalog all microorganisms in the human body, extending the human genome project and funded by NIH, USA.
• Study involved 300 healthy individuals across major microbial sites: skin, mouth, nose, colon, and vagina.

Personalization of Microbiomes

• Individual microbiomes are highly personalized with estimates stating 80-90% differences across individuals.
• Human genomes are 99.9% identical whereas the gut microbiome consists of about 3.3 million genes compared to 22,000 human genes.

Normal Microbial Flora

• Normal flora includes both resident and transient microorganisms.
• Resident flora can multiply, while transient flora usually cannot.
• The human body provides diverse habitats suitable for different microbial populations.

Microbiome Development

• At birth, the neonate starts microbe-free; rapid colonization occurs via the birth canal and environment.
• Breastfeeding or bottle-feeding leads to distinct microflora development.
• Early colonizers include a-haemolytic Streptococcus within hours post-birth.
• Coagulase-negative Staphylococcus can inhibit the colonization of more harmful microbes like S. aureus.

Microbiota of the Feet

• Foot microbiota are distinct, harboring more fungal species than other body areas.
• Common bacteria include Corynebacteriaceae, Micrococcaceae, and Propionibacteriaceae, with fungi such as Malassezia, Cryptococcus, Aspergillus, Trichophyton, and Candida.

Nasal Microbiota

• Microbial composition of the nose resembles that of skin.
• Approximately 20-30% of the population are carriers of S. Lactobacillus species, which contribute to low pH via acid fermentation.

Benefits of Gut Bacteria

• Gut bacteria assist in digesting nutrients humans cannot, accounting for 30% of caloric processing.
• They produce vitamin K essential for blood clotting and signaling molecules related to hunger and satiety.
• Gut flora play roles in immune response and metabolic functions, maintaining a balance between good and bad bacteria.

Factors Affecting Microbiomes

• Diet significantly influences gut microbiome diversity; plant-rich diets enhance microbial variety.
• Aging correlates with decreased microbial diversity, linked with inflammation and frailty.
• Lifestyle factors including cohabitation with pets can reduce allergies and alter gut microbiome.

Pathogenic Microorganisms

• Opportunistic pathogens like Candida albicans and Staphylococcus aureus can cause infections under conducive conditions.
• Candidates for infection include: poor hygiene, tight clothing, and corticosteroid use increase vulnerability.
• S. aureus is noted for conditions such as Scalded Skin Syndrome, Toxic Shock Syndrome, and MRSA prevalence.

Pseudomonas aeruginosa

• Ubiquitous in various habitats, particularly in human and animal impacted environments.
• It poses significant risks for immunocompromised individuals and can cause severe infections like microbial keratitis in contact lens wearers.

Terms to Know

• Pathogenic: capable of causing disease.
• Non-pathogenic: not capable of causing disease.
• Contamination: presence of infectious agents.
• Colonization: establishment of microorganisms.
• Infection: invasion leading to disease.
• Opportunistic pathogen: causes disease when host is compromised.

What is the Microbiome?

• Defined as a functional collection of diverse microbes, including bacteria, viruses, fungi, and protozoa.
• Contains genetic material from all microbes in and on the human body.
• The human microbiome’s gene count is 200 times that of the human genome.
• Microbiome can weigh up to 2 kg.

Microbiome vs Microbiota

• Microbiota: Includes prokaryotes and eukaryotes, consisting of microbial structures, metabolites, and movable genetic elements.
• Microbiome: A broader concept, containing additional elements not found in microbiota such as phages, viruses, plasmids, free DNA, prions, and viroids.

Human Microbiome Project

• Aims to catalog all microorganisms in the human body.
• An extension of the Human Genome Project, funded by the National Institutes of Health (NIH) in the U.S.
• Studies major microbial sites across 300 healthy individuals, including skin, mouth, nose, colon, and vagina.

Personalization of the Microbiome

• Microbiomes are highly personalized, with estimates indicating 80-90% difference between individuals.
• Despite human genomes being 99.9% identical, gut microbiomes contain approximately 3.3 million genes compared to 22,000 human genes.

Normal Microbial Microflora

• Normal flora includes both resident and transient microflora on human skin and mucous membranes.
• Resident microflora: Permanently found, re-established if removed, plays a role in microbial antagonism.
• Transient microflora: Temporarily present, influenced by the environment, not usually replicating significantly.

Development of the Microbiome

• At birth, neonates are free of microbes; rapid colonization begins with contact from the birth canal and caregivers.
• Breastfeeding establishes different microbial populations compared to bottle-feeding.
• Bifidobacterium is predominant in breast-fed infants, making up 90-99% of fecal bacteria.

Microbial Populations of the Body

• Normal microbiota may include pathogens even without causing symptoms.
• Pathogens are specific microorganisms that can cause diseases such as Yersinia pestis (bubonic plague) or Treponema pallidum (syphilis).
• Variability in skin characteristics affects microbial populations.

Beneficial Microbes and Pathogens

• Many beneficial microbes can behave as potential pathogens under certain conditions.
• Pathogens differ in virulence; some strains cause milder diseases compared to others.
• Meningitis can be caused by various pathogens including bacteria and viruses, highlighting the complexity of microbial diseases.

This quiz introduces the concept of the microbiome, focusing on its definition, development, and the difference between resident and transient microflora. Explore how various microbes function collectively within biological systems, enhancing your understanding of this essential biological component.