Biological dark matter refers to uncharacterized microbial sequences in metagenomic data

Viral communities of the human gut: metagenomic analysis of composition and dynamics. 2017. https://doi.org/10.1186/s13100-017-0095-y

The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal. Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning.

Probing periodontal microbial dark matter using metataxonomics and metagenomics. 2020. https://doi.org/10.1111/prd.12349

AbstractOur view of the periodontal microbial community has been shaped by a century or more of cultivation‐based and microscopic investigations. While these studies firmly established the infection‐mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the “great plate count anomaly”, in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as “microbial dark matter”. The discovery that DNA was an effective tool to “see” microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability‐driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open‐ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.

Global Distribution Patterns of Dark Matter Fungi in Cold Seep: A Metagenomic Meta-Analysis. 2025. https://doi.org/10.3390/jof11120878

Deep-sea cold seep ecosystems, known for their unique geochemical niches and chemosynthetic communities, harbor numerous “dark matter fungi (DMF)” that remain understudied compared to their bacterial and archaeal counterparts. Integrating 105 metagenomic datasets from 12 global cold seep sites, this study systematically elucidated the diversity, biogeography, and assembly mechanisms of cold seep fungal communities. Our analysis revealed highly diverse and abundant fungi, spanning 21 phyla and 928 genera, characterized by the absolute dominance of Ascomycota and a pervasive presence of unclassified DMF. Crucially, the fungal communities exhibited significant geographical and seep-type heterogeneity, with peak abundance notably in methane seep environments. Further analyses revealed that fungal community diversity and structure are influenced by both spatial and biological factors. Moreover, assembly exhibits multi-scale characteristics: dispersal limitation is the primary determinant globally, while local-scale structure is jointly driven by environmental variables and biological interactions with key chemosynthetic genes. These findings establish the macro-biogeographical pattern of deep-sea cold seep fungi, underscoring their tight coupling with core energy metabolism and providing essential data for future research and potential utilization.

Biological dark matter. https://en.wikipedia.org/wiki/Biological_dark_matter

organisms. Sequences that are believed to be derived from unknown microbes are referred to as the microbial dark matter, the dark virome, or dark matter fungi Biological dark matter is an informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganisms whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fal Biological dark matter is an informal term for unclassified or poorly understood genetic material.…