Microbial dark matter

Microbial dark matter comprises microbial lineages known mainly from environmental genetic sequences rather than cultured representatives. Their diversity and biology are inferred largely from genomes recovered directly from samples.

Metagenomics: The study of genetic material recovered directly from environmental or host-associated samples. Sequencing mixed samples exposes microbial genomes without isolating their organisms.
Ribosomal Database Project: A curated resource for ribosomal RNA sequences and related microbial taxonomy. Its sequence collections helped map microbial diversity beyond organisms grown in laboratories.
Microbial taxonomy: The classification and naming of bacteria, archaea, and other microorganisms. Dark-matter lineages challenge classification built around cultured organisms.
Biogeochemical cycle: The movement of chemical elements through organisms and the physical environment. Dark-matter genomes can identify previously unknown participants in elemental cycling.
Microbial cultivation: The growth of microorganisms under controlled laboratory conditions. Cultivation can test genomic predictions that sequence data alone cannot confirm.
Metagenome-assembled genome: A reconstructed genome assembled from DNA sequences in a metagenomic dataset. These reconstructions provide much of the genomic evidence for uncultured lineages.
Human Microbiome Project: A United States research initiative that characterized microbial communities associated with the human body. Its genome catalogs included many organisms without cultured representatives.
Horizontal gene transfer: The transfer of genetic material between organisms outside parent-to-offspring inheritance. Gene exchange can complicate evolutionary relationships inferred from microbial genomes.
Nitrogen cycle: The biological and chemical transformations that move nitrogen among atmospheric, inorganic, and organic forms. Uncultured microbes may carry genes for nitrogen transformations in ecosystems.
Synthetic microbial ecology: The experimental construction and study of simplified microbial communities. Defined communities could reveal how uncultured lineages interact with known microbes.

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