FP - Human Gut Microbiome Flashcards
Where are microbes found in the human body? (5)
- Oral cavity
- Respiratory tract
- Skin
- Urogenital tract
- Gastrointestinal tract
Where do the majority of microbes reside in the human body?
95% of total microbes live in the large intestine (Colon).
What is the composition of the human microbiome? (4)
Bacteria - Major component
Archaea - Not present in everyone
Eukarya - Active role is not fully understood
Viruses - Diversity is underestimated
The human microbiome by the numbers (4)
- 1:1 ratio of human cells to bacteria
- Microbiota weighs approximately 1kg
- Each microbiome is unique (hundreds of species (100-800)
- ~10,000,000 non-redundant microbial genes (10x human genes)
How does the gut microbiome diversity compare with other environments?
- Lower diversity: Plant rhizosphere, soil, sediments
- Similar diversity: Freshwater
- Higher diversity: Other animal parts, including the proximal gut.
What are the main features of the gut microbiome composition by section? (3)
- Stomach: pH 4-5 (can be as low as 1), Oxygen +++, 10³ microbes, Transit time: 60 mins
- Small intestine: pH 5-7.4, Oxygen ++, 10⁴-10⁸ microbes, Transit time: 255 mins
- Large intestine: pH 7.0, Oxygen +, 10⁸-10¹¹ microbes, Transit time: 24-34 hours.
What are the predominant microbial families in the small intestine and colon?
Small intestine: Lactobacillaceae (P: Firmicutes), Enterobacteriaceae (P: Proteobacteria)
Colon: Bacteroidaceae, Prevotellaceae, Rikenellaceae (P: Bacteroidetes), Lachnospiraceae, Ruminococcaceae (P: Firmicutes).
What is the role of mucus in the Gut?
Mucus limits the diffusion of antimicrobial peptides
- Microbes can grow without too much prevention
How have microbes adapted to the intestinal environment? (3)
- The mammalian large intestine is anaerobic; >99% are strict anaerobes.
- Some facultative aerobes exist (e.g., Escherichia coli).
- Aerotolerant microbes (e.g., Bacteroides spp.) can survive in low oxygen but cannot grow.
What are some key functions of the gut microbiome? (6)
- Metabolizes undigested food compounds for additional energy.
- Synthesizes vitamins and amino acids for the host.
- Inhibits pathogen colonization.
- Trains the immune system and adjusts inflammatory responses.
- Contributes to energy homeostasis.
- Stimulates intestine maturation after birth.
Where does the microbiome originate from? (3)
- The fetus is mostly sterile; the microbiome is first established during birth.
- Vaginal delivery: Resembles mother’s vaginal microbiome.
- Cesarean section: Resembles mother’s skin microbiome (lower diversity).
What factors influence the establishment of the gut microbiome in early life? (4)
- Skin-to-skin contact: Initial colonization by facultative anaerobes (Proteobacteria).
- Oxygen reduction: Allows strict anaerobes (e.g., Clostridia, Bifidobacteria) to colonize.
- Breast milk: Contains bacteria; promotes Bifidobacteria growth (metabolizes human milk oligosaccharides).
- Exposure (siblings, pets, solid food): Shift towards Bacteroides and Firmicutes.
What shapes the human microbiome’s diversity? (4)
- The microbiome resembles an adult’s by age 3, but functional potential continues to develop.
- Dominated by Firmicutes and Bacteroidetes.
- Inter-individual variability is greater than intra-individual variability.
- Higher microbe sharing within families and households.
What are the three enterotypes of the adult gut microbiome? (3)
Enterotype 1: Bacteroides
Enterotype 2: Prevotella
Enterotype 3: Ruminococcus
What evidence exists for heritability in the gut microbiome? (4)
- Study of over 1000 UK individuals, including 416 twin pairs.
- Higher similarity in microbiota of monozygotic (MZ) twins.
- 8.8% of gut microbial taxa are heritable.
- Christensenellaceae is the most heritable taxon
