Microbiome Composition and Major Bacterial Phyla

Understanding Microbial Taxonomy

The human microbiome is composed of diverse microorganisms classified into hierarchical taxonomic groups. From broadest to most specific, these include: Kingdom → Phylum → Class → Order → Family → Genus → Species. Understanding this classification helps us comprehend the complex relationships and functions within our microbial communities.

The composition varies dramatically between body sites, individuals, and populations, but certain patterns emerge that are consistent across healthy humans. Most human-associated bacteria belong to just a few major phyla, despite the enormous diversity of microbial life on Earth.

The "Big Four" Bacterial Phyla

Four phyla dominate the human microbiome, accounting for over 90% of all bacterial sequences in healthy individuals:

Firmicutes

Abundance: 40-60% of gut bacteria

Key genera: Lactobacillus, Clostridium, Enterococcus, Streptococcus
Functions: Short-chain fatty acid production, immune modulation
Characteristics: Gram-positive, often spore-forming
Clinical relevance: High F/B ratio linked to obesity

Bacteroidetes

Abundance: 20-40% of gut bacteria

Key genera: Bacteroides, Prevotella, Xylanibacter
Functions: Complex carbohydrate breakdown, vitamin synthesis
Characteristics: Gram-negative, excellent fiber digesters
Diet correlation: Higher in plant-rich diets

Actinobacteria

Abundance: 3-15% of gut bacteria

Key genera: Bifidobacterium, Propionibacterium, Corynebacterium
Functions: Pathogen resistance, immune development
Characteristics: Gram-positive, high GC content
Life stage: Dominant in breastfed infants

Proteobacteria

Abundance: 1-10% of gut bacteria

Key genera: Escherichia, Klebsiella, Pseudomonas, Helicobacter
Functions: Various metabolic processes, some pathogenic
Characteristics: Gram-negative, metabolically diverse
Health marker: Elevated levels may indicate inflammation

Minor but Important Phyla

While less abundant, these phyla play crucial roles in human health:

Verrucomicrobia

Key species: Akkermansia muciniphila
Function: Mucin degradation, gut barrier maintenance
Health significance: Associated with metabolic health and weight control
Abundance: 1-4% of gut microbiome

Fusobacteria

Key species: Fusobacterium nucleatum
Locations: Oral cavity, some gut presence
Clinical relevance: Linked to colorectal cancer when overgrown
Characteristics: Gram-negative, strictly anaerobic

The Firmicutes/Bacteroidetes Ratio

Clinical Significance: The F/B ratio is one of the most studied aspects of microbiome composition, serving as a biomarker for metabolic health, obesity, and dietary patterns.

Condition	F/B Ratio	Implications
Healthy lean individuals	Balanced (1:1 to 2:1)	Optimal metabolic function
Obesity	High (>3:1)	Increased energy harvest
Inflammatory bowel disease	Variable, often low	Reduced beneficial functions
High-fiber diet	Lower	Enhanced fiber fermentation

Site-Specific Composition

Microbial composition varies dramatically across body sites:

Gut Microbiome

Dominant: Firmicutes, Bacteroidetes
Environment: Anaerobic, nutrient-rich
Diversity: Highest bacterial diversity
Stability: Relatively stable in healthy adults

Skin Microbiome

Dominant: Actinobacteria, Firmicutes, Proteobacteria
Environment: Dry, acidic, exposed to UV
Variation: Different by body site (oily vs. dry areas)
Key species: Staphylococcus epidermidis

Oral Microbiome

Dominant: Firmicutes, Bacteroidetes, Proteobacteria
Environment: Various niches (teeth, tongue, saliva)
Biofilms: Complex structured communities
Health impact: Links to cardiovascular disease

Vaginal Microbiome

Dominant: Lactobacillus species (healthy state)
Environment: Acidic, hormone-influenced
Variation: Changes with menstrual cycle
Protection: Maintains acidic pH against pathogens

Functional Groups and Guilds

Beyond taxonomy, microbes can be grouped by their functions:

Primary Fermenters

Break down complex polysaccharides into simpler compounds:

Bacteroides species: Degrade plant polysaccharides
Ruminococcus species: Cellulose and resistant starch degradation
Prevotella species: Protein and complex carbohydrate metabolism

Secondary Fermenters

Process products of primary fermentation:

Faecalibacterium prausnitzii: Produces butyrate from acetate
Eubacterium rectale: Butyrate production from sugars
Roseburia species: Cross-feeding and SCFA production

Mucin Degraders

Specialized in breaking down host-derived mucins:

Akkermansia muciniphila: Primary mucin degrader
Bacteroides thetaiotaomicron: Mucin utilization in nutrient-poor conditions
Ruminococcus gnavus: Mucin degradation and inflammation

Core vs. Variable Microbiome

Core Microbiome

Species found in most healthy individuals:

Faecalibacterium prausnitzii
Bacteroides uniformis
Eubacterium rectale
Ruminococcus bromii
Bifidobacterium adolescentis

Significance: Likely essential for basic human health functions

Variable Microbiome

Species that vary between individuals:

Diet-specific bacteria
Geographic variants
Age-related species
Host genetic influences
Environmental exposures

Significance: Reflects personal history and environment

Measuring Microbiome Composition

Several methods are used to analyze microbial composition:

Method	Target	Resolution	Advantages
16S rRNA sequencing	Bacterial identification	Genus level	Cost-effective, standardized
Whole genome shotgun	All microbes + functions	Species/strain level	Functional information included
Metatranscriptomics	Active gene expression	Functional activity	Real-time activity measurement
Culturomics	Cultivable bacteria	Individual isolates	Live bacteria for experiments

Important Note: Microbiome composition is highly individual and dynamic. What's "normal" varies widely between healthy individuals, making personalized approaches increasingly important in microbiome research and therapy.