Other meanings of Microbiome
Biology
The microbiome is the community of microorganisms—bacteria, archaea, fungi, viruses, and protozoa—that inhabit a particular environment, such as the human gut, soil, or ocean. These microbial communities play critical roles in health, disease, and ecosystem function, and are studied through advanced sequencing and bioinformatics.
The term microbiome was coined by Nobel laureate Joshua Lederberg to describe the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space. It is often used interchangeably with microbiota, though strictly microbiota refers to the microorganisms themselves, while microbiome includes their genomes and the surrounding environmental conditions. The human microbiome project, launched in 2007, aimed to characterize the microbial communities at various body sites, revealing that the gut alone harbors over 1,000 bacterial species.1
Beyond humans, the microbiome concept applies to any habitat: soil, oceans, plants, animals, and built environments. Each microbiome is shaped by physical and chemical factors, and in turn influences nutrient cycling, host physiology, and ecosystem resilience. The study of these communities relies on metagenomics, which sequences DNA directly from environmental samples, and bioinformatics to assemble and analyze the data.2
The human microbiome is essential for digestion, vitamin synthesis, immune system development, and protection against pathogens. The gut microbiome, dominated by Bacteroidetes and Firmicutes, ferments dietary fibers into short-chain fatty acids that nourish colon cells and regulate metabolism. Disruptions in this community, termed dysbiosis, have been linked to obesity, inflammatory bowel disease, allergies, and even neurological conditions via the gut-brain axis.3
Each body site has a distinct microbial signature: the skin is rich in Staphylococcus and Propionibacterium, the oral cavity in Streptococcus, and the vagina in Lactobacillus. The composition is influenced by genetics, diet, antibiotics, and lifestyle. Fecal microbiota transplantation (FMT) has proven highly effective for recurrent Clostridioides difficile infection, restoring a healthy community and highlighting the therapeutic potential of microbiome manipulation.4
Soil microbiomes are among the most diverse on Earth, with a single gram containing up to 10 billion microorganisms. They drive nutrient cycling, decompose organic matter, and support plant growth through symbiotic relationships like mycorrhizal fungi and nitrogen-fixing bacteria. The ocean microbiome, dominated by Prochlorococcus and Pelagibacter, produces half of the planet's oxygen and forms the base of marine food webs.
Extreme environments host specialized microbiomes: hydrothermal vent communities rely on chemosynthesis, while microbes in deep subsurface rocks survive on hydrogen and carbon dioxide. These extremophiles offer insights into the limits of life and potential for biotechnology, such as enzymes that function at high temperatures or pressures. The plant microbiome, particularly the root-associated rhizosphere, is crucial for crop health and sustainable agriculture.5
The field of microbiome research was revolutionized by high-throughput sequencing, which allows culture-independent analysis of microbial communities. The Human Microbiome Project used 16S rRNA gene sequencing to identify bacteria, while metagenomics provides functional gene content. Metatranscriptomics and metabolomics reveal active gene expression and metabolic products, offering a dynamic view of microbial activity.1
Bioinformatics tools like QIIME and Mothur process massive datasets, and machine learning is increasingly used to associate microbial signatures with disease. However, challenges remain: distinguishing correlation from causation, standardizing protocols, and integrating multi-omic data. The development of gnotobiotic animal models, raised germ-free and colonized with defined communities, has been instrumental in testing causal hypotheses.6
Beyond the well-known gut microbiome, the microbiome of the built environment—homes, hospitals, and offices—affects human exposure to microbes and potential pathogens. Studies have shown that opening windows increases microbial diversity indoors, and that each person sheds a unique microbial cloud detectable in a room.7
The microbiome also plays a role in forensics: the post-mortem microbiome changes predictably, aiding in estimating time of death. Additionally, the 'hologenome' concept posits that the host and its microbiome together form a unit of natural selection, influencing evolution. The microbiome of the placenta was once thought sterile, but recent evidence suggests a low-abundance community, though this remains debated. Finally, the gut microbiome of insects like termites enables cellulose digestion, and the microbiome of the Hawaiian bobtail squid provides bioluminescence for camouflage—a classic model of symbiosis.8
The microbiome is a dynamic and complex field, with ongoing research revealing new dimensions of its impact on life.
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