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 microorganism whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fall under the three existing domains of life: Bacteria, Archaea and Eukaryota; thus, it has been suggested that a possible fourth domain of life may yet be discovered, although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA (so-called "junk DNA") and non-coding RNA produced by known organisms.
Genomic dark matter
Much of the genomic dark matter is thought to originate from ancient transposable elements and from other low-complexity repetitive elements. Uncategorized genetic material is found in humans and many other species. Their phylogenetic novelty could indicate the cellular organisms or viruses from which they evolved.
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. Such sequences are not rare. It has been estimated that in material from humans, between 40 and 90% of viral sequences are from dark matter. Human blood contains over three thousand different DNA sequences which cannot yet be identified.
Algorithms have been developed that examine sequences for similarities to bacterial 16S RNA sequences, K-mer similarities to known viruses, specific features of codon usage, or for inferring the existence of proteins. These approaches have suggested, for example, the existence of a novel bacteriophage of the microviridae family, and a novel bacterioidales-like phage. Other studies have suggested the existence of 264 new viral genera, discovered in publicly available databases, and a study of human blood suggested that 42% of people have at least one previously unknown virus each, adding up to 19 different new genera. A comprehensive study of DNA sequences from multiple human samples inferred the existence of 4,930 species of microbes of which 77% were previously unreported. Health-related findings include a prophage that might be associated with cirrhosis of the liver, and seven novel sequences from children with type-1 diabetes that have characteristics of viruses. Although they might exist, no organisms that clearly cause human disease have been discovered in the dark matter.
- List of unsolved problems in biology
- Microbiological culture – Method of allowing microorganisms to multiply in a controlled medium
- Microbiome – Microbial community assemblage and activity
- Shadow biosphere – Hypothetical biosphere of Earth
- Taxonomy – Science of naming, defining and classifying organisms
- Xenobiology – Science of synthetic life forms
- Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (March 2011). "Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees". PLOS ONE. 6 (3): e18011. Bibcode:2011PLoSO...618011W. doi:10.1371/journal.pone.0018011. PMC 3060911. PMID 21437252.
- Colin Barras (18 March 2011). "Biology's 'dark matter' hints at fourth domain of life". New Scientist.
- Lopez P, Halary S, Bapteste E (October 2015). "Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life". Biology Direct. 10: 64. doi:10.1186/s13062-015-0092-3. PMC 4624368. PMID 26502935.
- Colin Barras (11 November 2015). "Mystery microbes in our gut could be a whole new form of life". New Scientist.
- Carey N (2015). Junk DNA: A Journey Through the Dark Matter of the Genome. Columbia University Press. ISBN 9780231170840.
- Kolata G (5 September 2012). "Bits of Mystery DNA, Far From 'Junk', Play Crucial Role". The New York Times. Retrieved 2015-09-09.
- Boyle R (6 September 2012). "Inside the Mysterious Dark Matter of the Human Genome". Popular Science. Retrieved 2015-09-09.
- Pugh BF, Voss K (13 September 2013). "Scientists Discover the Origins of Genomic "Dark Matter"". Penn State Science. Archived from the original on 2015-09-08. Retrieved 2015-09-09.
- "Scientists shed some light on biological "dark matter"". Ecole Polytechnique Federale de Lausanne. 20 January 2014. Retrieved 2015-09-09.
- van Bakel H, Nislow C, Blencowe BJ, Hughes TR (May 2010). Eddy SR (ed.). "Most "dark matter" transcripts are associated with known genes". PLOS Biology. 8 (5): e1000371. doi:10.1371/journal.pbio.1000371. PMC 2872640. PMID 20502517.
- de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD (December 2011). "Repetitive elements may comprise over two-thirds of the human genome". PLOS Genetics. 7 (12): e1002384. doi:10.1371/journal.pgen.1002384. PMC 3228813. PMID 22144907.
- Maumus F, Quesneville H (2014). "Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter". PLOS ONE. 9 (4): e94101. Bibcode:2014PLoSO...994101M. doi:10.1371/journal.pone.0094101. PMC 3978025. PMID 24709859.
- Barras C (March 18, 2011). "Biology's 'dark matter' hints at fourth domain of life". New Scientist. Reed Business Information Ltd. 209 (2805): 16. Bibcode:2011NewSc.209Q..16B. doi:10.1016/S0262-4079(11)60657-X. Retrieved August 23, 2015.
- Kemsley T (13 July 2015). "New Study on "Dark Matter" of Biology Fills in Major Holes in Tree of Life". Nature World News. Retrieved 2015-09-09.
- Huang WE, Song Y, Xu J (January 2015). "Single cell biotechnology to shed a light on biological 'dark matter' in nature". Microbial Biotechnology. 8 (1): 15–16. doi:10.1111/1751-7915.12249. PMC 4321360. PMID 25627841.
- Lok C (16 June 2015). "Mining the microbial dark matter". Nature News. Retrieved 2015-09-09.
- Check-Hayden E (14 July 2013). "Researchers glimpse microbial 'dark matter'". Nature News. Retrieved 2015-09-09.
- Gronstal AL (4 November 2011). "Studying Biology's Dark Matter". NASA Astrobiology Institute. Retrieved 2015-09-09.
- Rinke C (2015). "What is Microbial Dark Matter and why should we explore it?". Microbial Dark Matter. Retrieved 2015-09-09.
- Lok C (June 2015). "Mining the microbial dark matter". Nature. 522 (7556): 270–73. Bibcode:2015Natur.522..270L. doi:10.1038/522270a. PMID 26085253.
- Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA (October 2015). "The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome". mBio. 6 (5): e01578-15. doi:10.1128/mBio.01578-15. PMC 4620475. PMID 26489866.
- Ryberg M, Nilsson RH (2018). "New light on names and naming of dark taxa". MycoKeys. 30 (30): 31–39. doi:10.3897/mycokeys.30.24376. PMC 5904500. PMID 29681731.
- Aggarwala V, Liang G, Bushman FD (2017). "Viral communities of the human gut: metagenomic analysis of composition and dynamics". Mobile DNA. 8: 12. doi:10.1186/s13100-017-0095-y. PMC 5627405. PMID 29026445.
- Kramná L, Kolářová K, Oikarinen S, Pursiheimo JP, Ilonen J, Simell O, Knip M, Veijola R, Hyöty H, Cinek O (May 2015). "Gut virome sequencing in children with early islet autoimmunity". Diabetes Care. 38 (5): 930–33. doi:10.2337/dc14-2490. PMID 25678103.
- Krishnamurthy SR, Wang D (July 2017). "Origins and challenges of viral dark matter". Virus Research. 239: 136–42. doi:10.1016/j.virusres.2017.02.002. PMID 28192164.
- Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, Martin L, Neff NF, Okamoto J, Wong RJ, Kharbanda S, El-Sayed Y, Blumenfeld Y, Stevenson DK, Shaw GM, Wolfe ND, Quake SR (September 2017). "Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA". Proceedings of the National Academy of Sciences of the United States of America. 114 (36): 9623–28. doi:10.1073/pnas.1707009114. PMC 5594678. PMID 28830999.
- Bowman JS (2018). "Identification of Microbial Dark Matter in Antarctic Environments". Frontiers in Microbiology. 9: 3165. doi:10.3389/fmicb.2018.03165. PMC 6305705. PMID 30619224.
- Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F (July 2017). "VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data". Microbiome. 5 (1): 69. doi:10.1186/s40168-017-0283-5. PMC 5501583. PMID 28683828.
- Bzhalava Z, Tampuu A, Bała P, Vicente R, Dillner J (September 2018). "Machine Learning for detection of viral sequences in human metagenomic datasets". BMC Bioinformatics. 19 (1): 336. doi:10.1186/s12859-018-2340-x. PMC 6154907. PMID 30249176.
- Barrientos-Somarribas M, Messina DN, Pou C, Lysholm F, Bjerkner A, Allander T, Andersson B, Sonnhammer EL (January 2018). "Discovering viral genomes in human metagenomic data by predicting unknown protein families". Scientific Reports. 8 (1): 28. Bibcode:2018NatSR...8...28B. doi:10.1038/s41598-017-18341-7. PMC 5758519. PMID 29311716.
- Ogilvie LA, Bowler LD, Caplin J, Dedi C, Diston D, Cheek E, Taylor H, Ebdon JE, Jones BV (2013). "Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences". Nature Communications. 4: 2420. Bibcode:2013NatCo...4.2420O. doi:10.1038/ncomms3420. PMC 3778543. PMID 24036533.
- Roux S, Hallam SJ, Woyke T, Sullivan MB (July 2015). "Viral dark matter and virus-host interactions resolved from publicly available microbial genomes". eLife. 4. doi:10.7554/eLife.08490. PMC 4533152. PMID 26200428.
- Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A (March 2017). "The blood DNA virome in 8,000 humans". PLOS Pathogens. 13 (3): e1006292. doi:10.1371/journal.ppat.1006292. PMC 5378407. PMID 28328962.
- Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N (January 2019). "Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle". Cell. 176 (3): 649–662.e20. doi:10.1016/j.cell.2019.01.001. PMC 6349461. PMID 30661755.
- Cinek O, Kramna L, Lin J, Oikarinen S, Kolarova K, Ilonen J, Simell O, Veijola R, Autio R, Hyöty H (November 2017). "Imbalance of bacteriome profiles within the Finnish Diabetes Prediction and Prevention study: Parallel use of 16S profiling and virome sequencing in stool samples from children with islet autoimmunity and matched controls". Pediatric Diabetes. 18 (7): 588–98. doi:10.1111/pedi.12468. PMID 27860030. S2CID 19106167.