Biological dark matter explained

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,[1] although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA (so-called "junk DNA")[2] [3] [4] and non-coding RNA produced by known organisms.[5] [6] [7]

Genomic dark matter

See main article: Junk DNA. Much of the genomic dark matter is thought to originate from ancient transposable elements and from other low-complexity repetitive elements.[8] [9] Uncategorized genetic material is found in humans and many other species.[10] [11] Their phylogenetic novelty could indicate the cellular organisms or viruses from which they evolved.[12]

Unclassified microorganisms

Up to 99% of all living microorganisms cannot be cultured,[13] [14] [15] [16] [17] so few functional insights exist about the metabolic potential of these organisms.

Sequences that are believed to be derived from unknown microbes are referred to as the microbial dark matter,[18] the dark virome,[19] or dark matter fungi.[20] 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.[21] [22] [23] Human blood contains over three thousand different DNA sequences which cannot yet be identified.[24] A mycological study from 2023 found that dark matter fungi seem to dominate the fungal kingdom. [25]

Algorithms have been developed that examine sequences for similarities to bacterial 16S RNA sequences,[26] K-mer similarities to known viruses,[27] specific features of codon usage,[28] or for inferring the existence of proteins.[29] These approaches have suggested, for example, the existence of a novel bacteriophage of the microviridae family, and a novel bacterioidales-like phage.[30] Other studies have suggested the existence of 264 new viral genera, discovered in publicly available databases,[31] 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.[32] 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.[33] 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.[34] Although they might exist, no organisms that clearly cause human disease have been discovered in the dark matter.

In February 2023, scientists reported the findings of unusual DNA strands from the microorganisms in "dark microbiome" in the driest non-polar desert on the Earth.[35] [36]

Notes and References

  1. Lopez P, Halary S, Bapteste E . Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life . Biology Direct . 10 . 64 . October 2015 . 26502935 . 4624368 . 10.1186/s13062-015-0092-3 . free .
  2. Book: Carey. Nessa . vanc . Nessa Carey. Junk DNA: A Journey Through the Dark Matter of the Genome. 2015. Columbia University Press. 9780231170840.
  3. News: Kolata . Gina . vanc . Bits of Mystery DNA, Far From 'Junk', Play Crucial Role . The New York Times . 5 September 2012 . 2015-09-09 .
  4. News: Boyle . Rebecca . vanc . Inside the Mysterious Dark Matter of the Human Genome . Popular Science . 6 September 2012 . 2015-09-09 .
  5. News: Pugh BF, Voss K . Scientists Discover the Origins of Genomic "Dark Matter" . Penn State Science . 13 September 2013 . 2015-09-09 . 2015-09-08 . https://web.archive.org/web/20150908030948/http://science.psu.edu/news-and-events/2013-news/Pugh9-2013 . dead .
  6. News: Scientists shed some light on biological "dark matter" . Ecole Polytechnique Federale de Lausanne . 20 January 2014 . 2015-09-09 .
  7. van Bakel H, Nislow C, Blencowe BJ, Hughes TR . Most "dark matter" transcripts are associated with known genes . PLOS Biology . 8 . 5 . e1000371 . May 2010 . 20502517 . 2872640 . 10.1371/journal.pbio.1000371 . Eddy . Sean R. . free .
  8. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD . Repetitive elements may comprise over two-thirds of the human genome . PLOS Genetics . 7 . 12 . e1002384 . December 2011 . 22144907 . 3228813 . 10.1371/journal.pgen.1002384 . free .
  9. Maumus F, Quesneville H . Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter . PLOS ONE . 9 . 4 . e94101 . 2014 . 24709859 . 3978025 . 10.1371/journal.pone.0094101 . 2014PLoSO...994101M . free .
  10. Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA . 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 . March 2011 . 21437252 . 3060911 . 10.1371/journal.pone.0018011 . 2011PLoSO...618011W . free .
  11. Biology's 'dark matter' hints at fourth domain of life . Reed Business Information Ltd. . New Scientist . 209 . 2805 . 16 . March 18, 2011 . August 23, 2015 . Barras . Colin . vanc . 2011NewSc.209Q..16B . 10.1016/S0262-4079(11)60657-X .
  12. News: Kemsley . Tamarra . vanc . New Study on "Dark Matter" of Biology Fills in Major Holes in Tree of Life . Nature World News . 13 July 2015 . 2015-09-09 .
  13. Huang WE, Song Y, Xu J . Single cell biotechnology to shed a light on biological 'dark matter' in nature . Microbial Biotechnology . 8 . 1 . 15–16 . January 2015 . 25627841 . 4321360 . 10.1111/1751-7915.12249 .
  14. News: Lok . Corie . vanc . Mining the microbial dark matter . Nature News . 16 June 2015 . 2015-09-09 .
  15. News: Check-Hayden . Erika . vanc . Researchers glimpse microbial 'dark matter' . Nature News . 14 July 2013 . 2015-09-09 .
  16. News: Gronstal . Aaron L. . vanc . Studying Biology's Dark Matter . NASA Astrobiology Institute . 4 November 2011 . 2015-09-09 .
  17. Web site: What is Microbial Dark Matter and why should we explore it? . Rinke . Chris . vanc . Microbial Dark Matter . 2015 . 2015-09-09 . 2018-10-22 . https://web.archive.org/web/20181022071834/http://microbialdarkmatter.org/index.php/11-intro/2-what-is-microbial-dark-matter-and-why-should-we-explore-it . dead .
  18. Lok C . Mining the microbial dark matter . Nature . 522 . 7556 . 270–73 . June 2015 . 26085253 . 10.1038/522270a . 2015Natur.522..270L . free .
  19. Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA . 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 . October 2015 . 26489866 . 4620475 . 10.1128/mBio.01578-15 .
  20. Ryberg M, Nilsson RH . New light on names and naming of dark taxa . MycoKeys . 30 . 30 . 31–39 . 2018 . 29681731 . 5904500 . 10.3897/mycokeys.30.24376 . free .
  21. Aggarwala V, Liang G, Bushman FD . Viral communities of the human gut: metagenomic analysis of composition and dynamics . Mobile DNA . 8 . 12 . 2017 . 29026445 . 5627405 . 10.1186/s13100-017-0095-y . free .
  22. Kramná L, Kolářová K, Oikarinen S, Pursiheimo JP, Ilonen J, Simell O, Knip M, Veijola R, Hyöty H, Cinek O . Gut virome sequencing in children with early islet autoimmunity . Diabetes Care . 38 . 5 . 930–33 . May 2015 . 25678103 . 10.2337/dc14-2490 . free .
  23. Krishnamurthy SR, Wang D . Origins and challenges of viral dark matter . Virus Research . 239 . 136–42 . July 2017 . 28192164 . 10.1016/j.virusres.2017.02.002 .
  24. David K. Stevenson . 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 . 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 . September 2017 . 28830999 . 5594678 . 10.1073/pnas.1707009114 . 2017PNAS..114.9623K . free .
  25. Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K . How, not if, is the question mycologists should be asking about DNA-based typification . MycoKeys . 30 . 96 . 143–157 . 2023. 10.3897/mycokeys.96.102669 . 37214179 . 10194844 . 10138/357843 . free . free .
  26. Bowman JS . Identification of Microbial Dark Matter in Antarctic Environments . Frontiers in Microbiology . 9 . 3165 . 2018 . 30619224 . 6305705 . 10.3389/fmicb.2018.03165 . free .
  27. Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F . VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data . Microbiome . 5 . 1 . 69 . July 2017 . 28683828 . 5501583 . 10.1186/s40168-017-0283-5 . free .
  28. Bzhalava Z, Tampuu A, Bała P, Vicente R, Dillner J . Machine Learning for detection of viral sequences in human metagenomic datasets . BMC Bioinformatics . 19 . 1 . 336 . September 2018 . 30249176 . 6154907 . 10.1186/s12859-018-2340-x . free .
  29. Barrientos-Somarribas M, Messina DN, Pou C, Lysholm F, Bjerkner A, Allander T, Andersson B, Sonnhammer EL . Discovering viral genomes in human metagenomic data by predicting unknown protein families . Scientific Reports . 8 . 1 . 28 . January 2018 . 29311716 . 5758519 . 10.1038/s41598-017-18341-7 . 2018NatSR...8...28B .
  30. Ogilvie LA, Bowler LD, Caplin J, Dedi C, Diston D, Cheek E, Taylor H, Ebdon JE, Jones BV . Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences . Nature Communications . 4 . 2420 . 2013 . 24036533 . 3778543 . 10.1038/ncomms3420 . 2013NatCo...4.2420O .
  31. Roux S, Hallam SJ, Woyke T, Sullivan MB . Viral dark matter and virus-host interactions resolved from publicly available microbial genomes . eLife . 4 . July 2015 . 26200428 . 4533152 . 10.7554/eLife.08490 . free .
  32. Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A . The blood DNA virome in 8,000 humans . PLOS Pathogens . 13 . 3 . e1006292 . March 2017 . 28328962 . 5378407 . 10.1371/journal.ppat.1006292 . free .
  33. 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 . Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle . Cell . 176 . 3 . 649–662.e20 . January 2019 . 30661755 . 6349461 . 10.1016/j.cell.2019.01.001 .
  34. Cinek O, Kramna L, Lin J, Oikarinen S, Kolarova K, Ilonen J, Simell O, Veijola R, Autio R, Hyöty H . 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 . November 2017 . 27860030 . 10.1111/pedi.12468 . 19106167 . free .
  35. News: Achenbach . Joel . Strange DNA found in the desert offers lessons in the hunt for Mars life . 21 February 2023 . . 21 February 2023 .
  36. Azua-Bustos, Armando . et al. . Dark microbiome and extremely low organics in Atacama fossil delta unveil Mars life detection limits . 21 February 2023 . . 14 . 808 . 808 . 10.1038/s41467-023-36172-1 . 36810853 . 9944251 . 2023NatCo..14..808A .

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