🧬 Introduction: What Is a Microbiome?

A microbiome is the total community of microorganisms (bacteria, fungi, archaea, viruses) living in a specific environment — from our gut to the ocean floor. When combined with its host, they form one integrated unit called the Holobiont.

• Host + microbiota = Holobiont → A co-evolved ecological and evolutionary system.
• These microbes aren’t just passengers — they affect the host’s physiology and evolution.
• Example: Coral holobiont 🪸 = coral + symbiotic algae + bacteria → vital for coral health.

💡 Key point: Humans are “partly microbial” — about 37% of our 23,000 genes have bacterial origins.

🌎 Animals in a Bacterial World

Microbes dominate all ecosystems and respond quickly to environmental changes. They can act as bioindicators for:

• Human and animal health
• Soil and wetland quality
• Water eutrophication
• Engineered systems (e.g., wastewater treatment)

➡️ Microbiomes can reflect ecosystem performance, similar to biological quality indicators.

🔄 Microbial–Host Coevolution

There are two perspectives:

🧠 Implication: The theory you choose changes how you interpret evolution, health, and ecology.

🧫 Studying Microbiomes: Methods & Multi-Omics

Progression of methods:

1. Culturing – Only a small fraction of microbes can be grown in lab.
2. 16S rRNA sequencing – Identifies “who’s there.”
3. Shotgun metagenomics – Reveals “what they can do.”
4. Multi-omics – Combines genomics, transcriptomics, proteomics, and metabolomics to understand function.

Microbial relationships are visualized with co-occurrence networks, showing which microbes coexist or compete. But to truly understand interactions, we need model experiments testing hypotheses from these networks.

🧍‍♂️ The Human Microbiome

Your microbiome is 80–90% unique to you, and microbes outnumber your cells 10–100:1. They live everywhere:

• 🦷 Oral – Streptococcus, Veillonella, Neisseria
• 💧 Reproductive tract – Lactobacillus prevents infections
• 🍼 Human milk – Staphylococcus, Streptococcus, Bifidobacteria
• 🧴 Skin – S. epidermidis, Corynebacterium, P. acnes
• 🍽️ Gut – the largest and most studied ecosystem

🧠 The Human Gut Microbiome

• Changes through pregnancy (↑ Proteobacteria & Actinobacteria)
• Varies across age and diet
• The Firmicutes/Bacteroidetes ratio is key:

🧪 Influenced by diet and substances:

• Increased by 🥛 dairy, 🌶️ capsaicin, and PPI use
• Reduced by 🍇 resveratrol, 🫐 cranberry, 🕒 melatonin, pea fiber

🧩 Gut-Brain Axis

Microbes produce Short-Chain Fatty Acids (SCFAs) during fermentation → these signal to the brain, influencing mood, cognition, and neurological health. Also, some bacteria (like Corynebacterium) can make serotonin (5-HT) 💭.

🧪 Ulcerative Colitis & Microbiome Research

Master project (AAU + Hospital collaboration):

• Sampling from biopsies, saliva, blood, feces
• Combining 16S rRNA, metagenomics, and metabolomics
• Aim: correlate microbial shifts with disease severity (MAYO score, calprotectin)

💩 Fecal & Vaginal Microbiota Transplants (FMT/VMT)

FMT: Restores healthy gut microbes in patients with dysbiosis (e.g., C. difficile infection).

• Tested in Randomized Controlled Trials (RCTs)VMT: Emerging research for restoring vaginal flora balance.

Healthy microbiota = beneficial Lactobacillus and Bifidobacterium Pathogenic state = overgrowth of E. coli, Clostridium difficile, Candida albicans, etc.

🐘 Other Microbiomes (Animals, Environmental, Synthetic)

🦓 Animal Gut Microbiomes

Study across 54 mammals shows:

• Clear groupings by diet and gut morphology (carnivores, ruminants, etc.)
• Ruminants (e.g., cows) and carnivores have distinctive microbial clusters
• Captivity reduces diversity, especially in carnivores
• Zoos across the world (France, USA, Switzerland) provided samples
• Some species (giraffes, zebras, horses) share ~50% of gut microbes
• Wild animals often have unique microbes missing in captivity

🧩 Microbiome composition reflects diet, behavior, and conservation status.

⚰️ Cadaver Microbiomes

After death:

• Early decay: ↑ Clostridiaceae, Corynebacteriaceae
• Late decay: ↑ Firmicutes
• Bone decomposition linked with Peptostreptococcaceae Used in forensic science to estimate time since death ⏳

🦅 Scavengers & Insects

• Scavengers: low stomach pH → acid-loving microbes (Lactobacillus)
• Hoarders: bury food → “refrigeration zone” keeps pathogens down
• Bone-degraders: Firmicutes
• Saprophagous insects (like carrion beetles, black soldier flies) → rich in Wohlfahrtiimonadaceae

🌿 Conservation Applications

Gut microbiome can:

• Reveal animal health and welfare
• Track diet (e.g., moose, bison)
• Monitor parasites
• Evaluate readiness for rewilding or conservation programs

🧪 Synthetic Microbiomes – “Building the Ark”

Scientists design synthetic microbial communities (consortia) for:

• Gut model systems
• Agriculture and industrial use
• Learning from probiotics

Challenges: microbial competition, phage attacks, instability, and invasion by outsiders. 🧠 Lesson: ecosystems are complex — no “KISS” (Keep It Simple, Stupid) approach works here.