🧫 Non-Human Microbiomes

Every animal has its own unique microbiome — the community of microorganisms living in its gut. These microbial systems vary depending on:

• 🥩 Diet (meat, plants, or mixed)
• 🧠 Evolution and digestion (gut anatomy, enzyme types, passage time)

Microbiomes adapt to what an organism eats and how it digests food. By studying microbial DNA in feces, scientists can predict both the animal’s diet and sometimes even its species.

🦓 Aalborg Zoo Study

Researchers sampled feces from 54 mammal species in Aalborg Zoo to compare microbiomes.

Findings:

• 🐅 Carnivores form one cluster — low microbial diversity (fewer bacteria needed to digest meat efficiently).
• 🐒 Primates and 🐄 Herbivores/Ruminants form separate clusters — higher diversity to handle complex plant matter.
• 🧬 Omnivores (like humans) are in-between.

Diversity pattern: Carnivores < Omnivores < Herbivores

More plant material → more enzymes needed → more microbes required.

🌍 Industrial vs. Traditional Humans

Tribal or rural populations have higher gut diversity than people in industrialized societies. Reasons:

• Faster gut passage time (<24 h vs. 3–4 days)
• More natural, fiber-rich diets
• Less processed food

Industrial diets extract more energy but reduce diversity, similar to carnivore systems.

🧍‍♂️ Captivity Effects

When animals live in captivity:

• Their microbiomes shift toward human-like compositions.
• Alpha diversity (number of microbial species) drops due to less varied diets.
• Wild animals generally show higher microbial diversity.

However, roughly 50% of the wild microbiome persists even after several generations in captivity — showing partial resilience.

Main taxa affected: Firmicutes and Bacteroidetes, two key bacterial groups for gut health and metabolism.

💊 Antibiotics & Aging

• Antibiotics reduce microbial diversity dramatically, often irreversibly.
• Aging naturally decreases diversity as well. → Antibiotics should be used only when necessary, not preventively.

🪰 Microbiome Development in Flies

Houseflies (Musca domestica) show stage-specific microbiome patterns:

• Egg → Larva → Pupa → Adult → back to Egg Each stage has distinct microbial profiles. → Microbiome composition changes with life stage in all animals, not just humans.

🧬 Forensic Microbiology 🔍

Microbes help determine time of death:

• Different bacterial species decompose fat, muscle, and bone at specific rates.
• By measuring their abundance, forensic scientists can estimate how long a body has been decomposing.

Example: Firmicutes species involved in fat and bone decay act as biological clocks for investigators.

🦅 Scavengers & “Refrigeration Zone” Hypothesis

Scavengers (like vultures) eat decaying meat full of pathogens. Their adaptations:

• 🧪 Very acidic stomachs (low pH)
• Longer residence time in stomach → kills pathogens
• Acid-tolerant (acidophilic) gut microbes

Some animals bury food (“refrigeration zone hypothesis”) to store it safely for later. → These species’ microbiomes are distinct and useful for conservation biology.

🦬 Conservation & Rewilding Projects

Microbiome studies guide wildlife management:

• 🪴 Identify diet composition via DNA traces from feces.
• 🦠 Measure parasite loads to assess health.
• 🐎 Ongoing work in horses, bison, and moose tracks exposure to parasites and diet adaptation.
• Rewilding programs use microbiome data to ensure animals’ gut profiles resemble wild ones before release.

⚗️ Synthetic Microbiomes

Researchers are building artificial microbial communities for biotechnology:

• 🧯 Applications: biogas plants, cellulose degradation, methane/ethanol production
• Challenges:
  • 🧫 Contamination by unwanted microbes
  • 🦠 Phage infections wiping out monocultures
  • ⚖️ Maintaining balance and diversity

A guiding rule from engineering:

KISS – “Keep It Simple, Stupid” But in microbiology, simple doesn’t work. Synthetic systems need complexity and diversity to stay stable — mimicking natural ecosystems.

🧩 Key Takeaways