Human Microbiome Notes

Human Microbiome Overview

Chapter Overview

  • Focus on how individuals acquire their personal microbiome.

Primary Learning Objectives

  • Describe microbial diversity across various human body sites.

  • Explain the acquisition of a human microbiome.

  • Predict how medical interventions may alter the resident microbiome.

  • Reminder: Chapter 15 homework due on 10/20/25 at 8:00 am.

Fun Facts about the Human Microbiome

  • Bacterial Cells in the Body: There are approximately 10 times more bacterial cells than human cells in the human body (Human Microbiome Project, NIH).

  • Microbial Cell Count: The human body contains between 10 to 100 trillion microbial cells (Human Microbiome Project, NIH).

  • Bacterial Genes: There are about 1000 times more bacterial genes than human genes within the human genome (Human Microbiome Project, NIH).

  • Body Mass Contribution: Microbes constitute 1-3% of body mass, which equates to approximately 4.5 lbs in an individual weighing 150 lbs (Human Microbiome Project, NIH).

  • Microbial Functions: Microbes perform essential functions, including:

    • Producing vitamins.

    • Producing anti-inflammatory compounds.

    • Educating immune cells (Human Microbiome Project, NIH).

Definition of Human Microbiome

  • The collection of microbes (including their genes) inhabiting the human body is collectively referred to as the human microbiome. This includes not only bacteria but also viruses and other microorganisms.

Major Microbial Groups by Body Site

  • Mouth, Pharynx, Respiratory System:

    • Streptococcus viridans

    • Neisseria sicca

    • Candida albicans

    • Streptococcus salivarius

  • Stomach:

    • Helicobacter pylori

  • Intestines:

    • Bacteroides fragilis

    • Streptococcus thermophilus

    • Lactobacillus casei

    • Escherichia coli

    • Lactobacillus gasseri

    • Lactobacillus reuteri

    • Bacteroides thetaiotaomicron

  • Skin:

    • Pityrosporum ovale

    • Staphylococcus epidermidis

    • Corynebacterium jeikeium

    • Trichosporon

    • Staphylococcus haemolyticus

  • Urogenital Tract:

    • Ureaplasma parvum

    • Corynebacterium aurimucosum

Gut Microbiome Characteristics

  • Diversity and Distinction: The gut microbiome is characterized as distinct and diverse, predominantly consisting of mutualistic or commensal microbes rather than pathogens.

  • Key Functions:

    • Protects against pathogens.

    • Extracts essential nutrients from food.

    • Synthesizes vitamins for the host.

    • Aids in the function of the immune system.

Microbial Diversity - Comparison Studies

Research Context

  • Research by Lozupone et al. (2012) examines differences in microbial diversity between tongue-scrape samples and fecal samples.

  • Sample Information: Three samples taken from three different individuals are analyzed.

  • Data Presentation: Stacked colored bars used to show the percentage of the sample identified in various microbial groups, categorized by either phylum or functional group.

Insights from Variations in Diversity

  • The analysis reveals the differences in taxonomic diversity at the phylum level between tongue and fecal samples. This understanding contributes to the broader context of how microbiomes can be compared across different sites in the human body.

Factors Affecting Microbiome Acquisition

Timing and Modality of Delivery

  • Most Important Factor: The mode of delivery (vaginal vs. cesarean) is crucial in seeding the infant's microbiome.

    • Vaginally delivered infants acquire microbiota from the mother’s vaginal and fecal microbiome.

    • Infants delivered via cesarean receive their microbiota from the mother’s skin microbiome.

    • Referenced by Maria Gloria Dominguez-Bello, Rutgers University.

Comparative Study between Infants and Mothers

  • Dominguez-Bello et al. (2010) compares the microbiome of infants to their mothers, where each dot in presented figures represents microbiome composition in samples. Dots that are closer together signify more similarity in composition.

Vaginal Seeding Interventions

  • Vaginal seeding of infants is noted as beneficial, promoting microbiomes with fewer health risk factors, according to research by Hourigan, Dominguez-Bello, and Mueller (2022).

Impact of Antibiotics on Microbiome

Research Findings on Antibiotic Use

  • Antibiotics Effect: Use of antibiotics disrupts the normal gut microbiome, leading to decreased diversity—a state known as dysbiosis, which is defined as a shift from “normal” microbiome composition to an “abnormal” one.

  • Associated Risks: Early-life antibiotic usage correlates with increased risks of:

    • Obesity

    • Allergies

    • Autoimmunity

    • Inflammatory bowel disease (IBD).

  • The recovery from antibiotic-induced dysbiosis can take years and may be incomplete.

Experimental Design by Suez et al. (2018)

  • Examined various recovery methods following antibiotic use:

    • Administered antibiotics to study participants.

    • Employed three different recovery interventions:

    1. Fecal microbiota transplant (FMT) from the participant's own sample.

    2. Introduction of probiotics post-antibiotics (which included 11 strains like Lactobacillus and Bifidobacterium).

    3. No intervention (spontaneous recovery).

  • Compared results against a control group that did not receive antibiotics.

Key Findings from Suez et al. Study

  1. Post-antibiotic microbiomes were significantly different from the no-antibiotic control group.

  2. The probiotic intervention did not lead to recovery within the study period.

  3. FMT provided the most significant recovery to baseline microbiome composition, highlighting the importance of this method in restoring gut diversity post-antibiotic treatment.