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Hologenomics

January 01, 1970

Hologenomics is the omics study of hologenomes. A hologenome is the whole set of genomes of a holobiont, an organism together with all co-habitating microbes, other life forms, and viruses.[1] While the term hologenome originated from the hologenome theory of evolution, which postulates that natural selection occurs on the holobiont level,[2] hologenomics uses an integrative framework to investigate interactions between the host and its associated species. Examples include gut microbe[3] or viral[4] genomes linked to human or animal genomes for host-microbe interaction research.[5] Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges.[6]

History edit

The origins of hologenomics revolves around the hologenome theory of evolution, which describes individual multicellular organisms, microbes, and viruses establishing symbiotic relationships and undergoing coevolution together.[2][7] Richard Jefferson introduced the term 'hologenome' to describe the host-symbiont genome as an evolutionary unit.[8] Prior to this, Lynn Margulis used the term 'holobiont' to describe hosts and their associated species as an ecological unit.[9]

Eukaryotes-prokaryotes coevolution edit

 
Distinct microbial communities in sponges converge to have common functionality despite retaining phylogenetic differences.[10]

Earliest evidence of multicellular-unicellular interactions are seen in sponges, which are a well studied hologenomic system. Porifera are often described as holobionts because they harbor a wide range of bacteria, archaea and algae. Microbial communities present have been observed in facilitating metabolic functions and immune responses.[10] Offspring inherit these microbial colonies via vertical and/or horizontal transmission.[10] Symbiont colonies are transferred through parental gametes in vertical transmission, whereas offspring acquire same colonies from their environment in horizontal transmission. Vertical transmission is also seen in terrestrial organisms like C. ocellatus, where gammaproteobacteria in the parental gut is vertically transferred through egg contamination.[11]

Criticism edit

The hologenome theory evolution is not fully accepted, and research in microbial-host phylogenetics is ongoing. Rather than the selection of corals with certain symbiotic microbial communities, coral bleaching may simply be a result of environmental stressors, and bacterial presence in bleached coral may be explained simply as opportunistic colonization.[12] Ubiquity testing also revealed many different bacterial and algal symbionts that are not associated with a single species of coral,[13] suggesting that hologenomics just identifies and validates mechanistic interactions between pathogens, microbes, and their hosts. [14]

Examples of discoveries with hologenomic approaches edit

  • Nanopore sequencing - Profiling organelle genomes in the holobiont C. ashmeadii revealed that Rhodospirillaceae was dominant among six putative endosymbionts.[15]
  • 16S rRNA sequencing - Sponge-specific microbial communities were profiled with rRNA and rRNA gene sequencing, providing insight into bacterial diversity and activity of those communities.[16]
  • Metagenomic DNA - Gene profiles of sponge microbiomes were compared to surrounding planktonic communities.[17] Core function genes of microbial symbionts expressed consistent patterns of phylogeny and function that differ from planktonic samples, demonstrating host-symbiont co-evolution.[17]

Applications edit

Medicine edit

It's hypothesized the continued incidence non-infectious diseases is a result of modernization reducing the diversity of symbiotic microbes.[14] The human microbiome has also been correlated to numerous etiologies of non-communicable disease, such as brain disorders,[18] cancer,[19][20] and heart disease.[21] Interactions between human microbiome and human health are complex and suggest a hologenomic approach.

Disease biomarkers can be found by investigating lifestyle, genomic differences, and mRNA/protein/metabolite profiles of the patient and their microbiota.[14] For investigating microbiomes and specifically microbiota subcommunities that may contribute to a disease phenotype, longitudinal studies are recommended as everyone has a personalized microbiome with small differences in microbiome phylotypes.[14] A personalized plan managing a person’s microbiome can then be developed, with prebiotics nurturing beneficial endogenous microbes, and probiotics manipulating a person’s hologenome.[22]

Immunology edit

Conditional mutualism, where parasites have mutualistic effects under certain environmental/ecological conditions, have been found with holobiont-holobiont interactions.[23] Maturation of mammalian host immune systems has been known to involve gastrointestinal flora.[24] Understanding microorganism recognition of foreign pathogenic invasion and how host immunity favors the most ideal symbiont may aid in discovering novel therapeutic treatments to combat evolving diseases.

See also edit

References edit

  1. ^ Rosenberg, Eugene; Zilber-Rosenberg, Ilana (2018-04-25). "The hologenome concept of evolution after 10 years". Microbiome. 6 (1): 78. doi:10.1186/s40168-018-0457-9. ISSN 2049-2618. PMC 5922317. PMID 29695294.
  2. ^ a b Number 6 in a series of 7 VHS recordings, A Decade of PCR: Celebrating 10 Years of Amplification, Cold Spring Harbor Laboratory Press, 1994. ISBN 0-87969-473-4.
  3. ^ Denman, Stuart E.; McSweeney, Christopher S. (2015-02-16). "The Early Impact of Genomics and Metagenomics on Ruminal Microbiology". Annual Review of Animal Biosciences. 3 (1): 447–465. doi:10.1146/annurev-animal-022114-110705. ISSN 2165-8102. PMID 25387109.
  4. ^ Patowary, Ashok; Chauhan, Rajendra Kumar; Singh, Meghna; KV, Shamsudheen; Periwal, Vinita; KP, Kushwaha; Sapkal, Gajanand N.; Bondre, Vijay P.; Gore, Milind M. (2012-01-01). "De novo identification of viral pathogens from cell culture hologenomes". BMC Research Notes. 5: 11. doi:10.1186/1756-0500-5-11. ISSN 1756-0500. PMC 3284880. PMID 22226071.
  5. ^ Miller, William B. Jr. (2013). The Microcosm Within: Evolution and Extinction in the Hologenome. Universal-Publishers. ISBN 978-1612332772.
  6. ^ Webster, Nicole S.; Thomas, Torsten (2016-05-04). "The Sponge Hologenome". mBio. 7 (2): e00135–16. doi:10.1128/mBio.00135-16. ISSN 2150-7511. PMC 4850255. PMID 27103626.
  7. ^ Rosenberg, Eugene; Zilber-Rosenberg, Ilana (2018-04-25). "The hologenomce concept of evolution after 10 years". Microbiome. 6 (1): 78. doi:10.1186/s40168-018-0457-9. ISSN 2049-2618. PMC 5922317. PMID 29695294.
  8. ^ Number 6 in a series of 7 VHS recordings, A Decade of PCR: Celebrating 10 Years of Amplification, Cold Spring Harbor Laboratory Press, 1994. ISBN 0-87969-473-4.
  9. ^ Margulis, University of Massachusetts Amherst Massachusetts Lynn; Margulis, Lynn; Fester, René (1991). Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis. MIT Press. ISBN 978-0-262-13269-5.
  10. ^ a b c Webster, Nicole S.; Thomas, Torsten (2016-05-04). "The Sponge Hologenome". mBio. 7 (2): e00135-16. doi:10.1128/mBio.00135-16. ISSN 2150-7511. PMC 4850255. PMID 27103626.
  11. ^ Kaiwa, Nahomi; Hosokawa, Takahiro; Kikuchi, Yoshitomo; Nikoh, Naruo; Meng, Xian Ying; Kimura, Nobutada; Ito, Motomi; Fukatsu, Takema (2010-06-01). "Primary Gut Symbiont and Secondary, Sodalis-Allied Symbiont of the Scutellerid Stinkbug Cantao ocellatus". Applied and Environmental Microbiology. 76 (11): 3486–3494. Bibcode:2010ApEnM..76.3486K. doi:10.1128/AEM.00421-10. ISSN 0099-2240. PMC 2876435. PMID 20400564.
  12. ^ Ainsworth, T. D.; Fine, M.; Roff, G.; Hoegh-Guldberg, O. (2008). "Bacteria are not the primary cause of bleaching in the Mediterranean coral Oculina patagonica". The ISME Journal. 2 (1): 67–73. doi:10.1038/ismej.2007.88. ISSN 1751-7362. PMID 18059488. S2CID 1032896.
  13. ^ Hester, Eric R.; Barott, Katie L.; Nulton, Jim; Vermeij, Mark JA; Rohwer, Forest L. (May 2016). "Stable and sporadic symbiotic communities of coral and algal holobionts". The ISME Journal. 10 (5): 1157–1169. doi:10.1038/ismej.2015.190. ISSN 1751-7370. PMC 5029208. PMID 26555246.
  14. ^ a b c d Theis, Kevin R. (2018-04-10). "Hologenomics: Systems-Level Host Biology". mSystems. 3 (2). doi:10.1128/mSystems.00164-17. ISSN 2379-5077. PMC 5895875. PMID 29657963.
  15. ^ Sauvage, Thomas; Schmidt, William E.; Yoon, Hwan Su; Paul, Valerie J.; Fredericq, Suzanne (2019-11-13). "Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery". BMC Genomics. 20 (1): 850. doi:10.1186/s12864-019-6248-2. ISSN 1471-2164. PMC 6854639. PMID 31722669.
  16. ^ Kamke, Janine; Taylor, Michael W.; Schmitt, Susanne (2017-01-07). "Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons". The ISME Journal. 4 (4): 498–508. doi:10.1038/ismej.2009.143. ISSN 1751-7370. PMID 20054355.
  17. ^ a b Fan, Lu; Reynolds, David; Liu, Michael; Stark, Manuel; Kjelleberg, Staffan; Webster, Nicole S.; Thomas, Torsten (2012-07-03). "Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts". Proceedings of the National Academy of Sciences. 109 (27): E1878–E1887. doi:10.1073/pnas.1203287109. ISSN 0027-8424. PMC 3390844. PMID 22699508.
  18. ^ Zhu, Sibo; Jiang, Yanfeng; Xu, Kelin; Cui, Mei; Ye, Weimin; Zhao, Genming; Jin, Li; Chen, Xingdong (2020-01-17). "The progress of gut microbiome research related to brain disorders". Journal of Neuroinflammation. 17 (1): 25. doi:10.1186/s12974-020-1705-z. ISSN 1742-2094. PMC 6969442. PMID 31952509.
  19. ^ Xavier, Joao B.; Young, Vincent B.; Skufca, Joseph; Ginty, Fiona; Testerman, Traci; Pearson, Alexander T.; Macklin, Paul; Mitchell, Amir; Shmulevich, Ilya; Xie, Lei; Caporaso, J. Gregory (2020-03-01). "The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View". Trends in Cancer. 6 (3): 192–204. doi:10.1016/j.trecan.2020.01.004. ISSN 2405-8033. PMC 7098063. PMID 32101723.
  20. ^ Helmink, Beth A.; Khan, M. A. Wadud; Hermann, Amanda; Gopalakrishnan, Vancheswaran; Wargo, Jennifer A. (2019-03-06). "The microbiome, cancer, and cancer therapy". Nature Medicine. 25 (3): 377–388. doi:10.1038/s41591-019-0377-7. ISSN 1546-170X. PMID 30842679. S2CID 71145949.
  21. ^ Trøseid, Marius; Andersen, Geir Øystein; Broch, Kaspar; Hov, Johannes Roksund (2020-02-01). "The gut microbiome in coronary artery disease and heart failure: Current knowledge and future directions". eBioMedicine. 52: 102649. doi:10.1016/j.ebiom.2020.102649. ISSN 2352-3964. PMC 7016372. PMID 32062353.
  22. ^ Young, Vincent B. (2017-03-15). "The role of the microbiome in human health and disease: an introduction for clinicians". BMJ. 356: j831. doi:10.1136/bmj.j831. ISSN 0959-8138. PMID 28298355. S2CID 2443057.
  23. ^ Dheilly, Nolwenn Marie (2014-07-03). "Holobiont–Holobiont Interactions: Redefining Host–Parasite Interactions". PLOS Pathogens. 10 (7): e1004093. doi:10.1371/journal.ppat.1004093. ISSN 1553-7374. PMC 4081813. PMID 24992663.
  24. ^ Belkaid, Yasmine; Hand, Timothy W. (2014-03-27). "Role of the Microbiota in Immunity and Inflammation". Cell. 157 (1): 121–141. doi:10.1016/j.cell.2014.03.011. ISSN 0092-8674. PMC 4056765. PMID 24679531.


 

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January 01, 1970
hologenomics, omics, study, hologenomes, hologenome, whole, genomes, holobiont, organism, together, with, habitating, microbes, other, life, forms, viruses, while, term, hologenome, originated, from, hologenome, theory, evolution, which, postulates, that, natu. Hologenomics is the omics study of hologenomes A hologenome is the whole set of genomes of a holobiont an organism together with all co habitating microbes other life forms and viruses 1 While the term hologenome originated from the hologenome theory of evolution which postulates that natural selection occurs on the holobiont level 2 hologenomics uses an integrative framework to investigate interactions between the host and its associated species Examples include gut microbe 3 or viral 4 genomes linked to human or animal genomes for host microbe interaction research 5 Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges 6 Contents 1 History 2 Eukaryotes prokaryotes coevolution 3 Criticism 4 Examples of discoveries with hologenomic approaches 5 Applications 5 1 Medicine 5 2 Immunology 6 See also 7 ReferencesHistory editThe origins of hologenomics revolves around the hologenome theory of evolution which describes individual multicellular organisms microbes and viruses establishing symbiotic relationships and undergoing coevolution together 2 7 Richard Jefferson introduced the term hologenome to describe the host symbiont genome as an evolutionary unit 8 Prior to this Lynn Margulis used the term holobiont to describe hosts and their associated species as an ecological unit 9 Eukaryotes prokaryotes coevolution edit nbsp Distinct microbial communities in sponges converge to have common functionality despite retaining phylogenetic differences 10 Earliest evidence of multicellular unicellular interactions are seen in sponges which are a well studied hologenomic system Porifera are often described as holobionts because they harbor a wide range of bacteria archaea and algae Microbial communities present have been observed in facilitating metabolic functions and immune responses 10 Offspring inherit these microbial colonies via vertical and or horizontal transmission 10 Symbiont colonies are transferred through parental gametes in vertical transmission whereas offspring acquire same colonies from their environment in horizontal transmission Vertical transmission is also seen in terrestrial organisms like C ocellatus where gammaproteobacteria in the parental gut is vertically transferred through egg contamination 11 Criticism editThe hologenome theory evolution is not fully accepted and research in microbial host phylogenetics is ongoing Rather than the selection of corals with certain symbiotic microbial communities coral bleaching may simply be a result of environmental stressors and bacterial presence in bleached coral may be explained simply as opportunistic colonization 12 Ubiquity testing also revealed many different bacterial and algal symbionts that are not associated with a single species of coral 13 suggesting that hologenomics just identifies and validates mechanistic interactions between pathogens microbes and their hosts 14 Examples of discoveries with hologenomic approaches editNanopore sequencing Profiling organelle genomes in the holobiont C ashmeadii revealed that Rhodospirillaceae was dominant among six putative endosymbionts 15 16S rRNA sequencing Sponge specific microbial communities were profiled with rRNA and rRNA gene sequencing providing insight into bacterial diversity and activity of those communities 16 Metagenomic DNA Gene profiles of sponge microbiomes were compared to surrounding planktonic communities 17 Core function genes of microbial symbionts expressed consistent patterns of phylogeny and function that differ from planktonic samples demonstrating host symbiont co evolution 17 Applications editMedicine edit It s hypothesized the continued incidence non infectious diseases is a result of modernization reducing the diversity of symbiotic microbes 14 The human microbiome has also been correlated to numerous etiologies of non communicable disease such as brain disorders 18 cancer 19 20 and heart disease 21 Interactions between human microbiome and human health are complex and suggest a hologenomic approach Disease biomarkers can be found by investigating lifestyle genomic differences and mRNA protein metabolite profiles of the patient and their microbiota 14 For investigating microbiomes and specifically microbiota subcommunities that may contribute to a disease phenotype longitudinal studies are recommended as everyone has a personalized microbiome with small differences in microbiome phylotypes 14 A personalized plan managing a person s microbiome can then be developed with prebiotics nurturing beneficial endogenous microbes and probiotics manipulating a person s hologenome 22 Immunology edit Conditional mutualism where parasites have mutualistic effects under certain environmental ecological conditions have been found with holobiont holobiont interactions 23 Maturation of mammalian host immune systems has been known to involve gastrointestinal flora 24 Understanding microorganism recognition of foreign pathogenic invasion and how host immunity favors the most ideal symbiont may aid in discovering novel therapeutic treatments to combat evolving diseases See also editPangenome SuperorganismReferences edit Rosenberg Eugene Zilber Rosenberg Ilana 2018 04 25 The hologenome concept of evolution after 10 years Microbiome 6 1 78 doi 10 1186 s40168 018 0457 9 ISSN 2049 2618 PMC 5922317 PMID 29695294 a b Number 6 in a series of 7 VHS recordings A Decade of PCR Celebrating 10 Years of Amplification Cold Spring Harbor Laboratory Press 1994 ISBN 0 87969 473 4 Denman Stuart E McSweeney Christopher S 2015 02 16 The Early Impact of Genomics and Metagenomics on Ruminal Microbiology Annual Review of Animal Biosciences 3 1 447 465 doi 10 1146 annurev animal 022114 110705 ISSN 2165 8102 PMID 25387109 Patowary Ashok Chauhan Rajendra Kumar Singh Meghna KV Shamsudheen Periwal Vinita KP Kushwaha Sapkal Gajanand N Bondre Vijay P Gore Milind M 2012 01 01 De novo identification of viral pathogens from cell culture hologenomes BMC Research Notes 5 11 doi 10 1186 1756 0500 5 11 ISSN 1756 0500 PMC 3284880 PMID 22226071 Miller William B Jr 2013 The Microcosm Within Evolution and Extinction in the Hologenome Universal Publishers ISBN 978 1612332772 Webster Nicole S Thomas Torsten 2016 05 04 The Sponge Hologenome mBio 7 2 e00135 16 doi 10 1128 mBio 00135 16 ISSN 2150 7511 PMC 4850255 PMID 27103626 Rosenberg Eugene Zilber Rosenberg Ilana 2018 04 25 The hologenomce concept of evolution after 10 years Microbiome 6 1 78 doi 10 1186 s40168 018 0457 9 ISSN 2049 2618 PMC 5922317 PMID 29695294 Number 6 in a series of 7 VHS recordings A Decade of PCR Celebrating 10 Years of Amplification Cold Spring Harbor Laboratory Press 1994 ISBN 0 87969 473 4 Margulis University of Massachusetts Amherst Massachusetts Lynn Margulis Lynn Fester Rene 1991 Symbiosis as a Source of Evolutionary Innovation Speciation and Morphogenesis MIT Press ISBN 978 0 262 13269 5 a b c Webster Nicole S Thomas Torsten 2016 05 04 The Sponge Hologenome mBio 7 2 e00135 16 doi 10 1128 mBio 00135 16 ISSN 2150 7511 PMC 4850255 PMID 27103626 Kaiwa Nahomi Hosokawa Takahiro Kikuchi Yoshitomo Nikoh Naruo Meng Xian Ying Kimura Nobutada Ito Motomi Fukatsu Takema 2010 06 01 Primary Gut Symbiont and Secondary Sodalis Allied Symbiont of the Scutellerid Stinkbug Cantao ocellatus Applied and Environmental Microbiology 76 11 3486 3494 Bibcode 2010ApEnM 76 3486K doi 10 1128 AEM 00421 10 ISSN 0099 2240 PMC 2876435 PMID 20400564 Ainsworth T D Fine M Roff G Hoegh Guldberg O 2008 Bacteria are not the primary cause of bleaching in the Mediterranean coral Oculina patagonica The ISME Journal 2 1 67 73 doi 10 1038 ismej 2007 88 ISSN 1751 7362 PMID 18059488 S2CID 1032896 Hester Eric R Barott Katie L Nulton Jim Vermeij Mark JA Rohwer Forest L May 2016 Stable and sporadic symbiotic communities of coral and algal holobionts The ISME Journal 10 5 1157 1169 doi 10 1038 ismej 2015 190 ISSN 1751 7370 PMC 5029208 PMID 26555246 a b c d Theis Kevin R 2018 04 10 Hologenomics Systems Level Host Biology mSystems 3 2 doi 10 1128 mSystems 00164 17 ISSN 2379 5077 PMC 5895875 PMID 29657963 Sauvage Thomas Schmidt William E Yoon Hwan Su Paul Valerie J Fredericq Suzanne 2019 11 13 Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery BMC Genomics 20 1 850 doi 10 1186 s12864 019 6248 2 ISSN 1471 2164 PMC 6854639 PMID 31722669 Kamke Janine Taylor Michael W Schmitt Susanne 2017 01 07 Activity profiles for marine sponge associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons The ISME Journal 4 4 498 508 doi 10 1038 ismej 2009 143 ISSN 1751 7370 PMID 20054355 a b Fan Lu Reynolds David Liu Michael Stark Manuel Kjelleberg Staffan Webster Nicole S Thomas Torsten 2012 07 03 Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts Proceedings of the National Academy of Sciences 109 27 E1878 E1887 doi 10 1073 pnas 1203287109 ISSN 0027 8424 PMC 3390844 PMID 22699508 Zhu Sibo Jiang Yanfeng Xu Kelin Cui Mei Ye Weimin Zhao Genming Jin Li Chen Xingdong 2020 01 17 The progress of gut microbiome research related to brain disorders Journal of Neuroinflammation 17 1 25 doi 10 1186 s12974 020 1705 z ISSN 1742 2094 PMC 6969442 PMID 31952509 Xavier Joao B Young Vincent B Skufca Joseph Ginty Fiona Testerman Traci Pearson Alexander T Macklin Paul Mitchell Amir Shmulevich Ilya Xie Lei Caporaso J Gregory 2020 03 01 The Cancer Microbiome Distinguishing Direct and Indirect Effects Requires a Systemic View Trends in Cancer 6 3 192 204 doi 10 1016 j trecan 2020 01 004 ISSN 2405 8033 PMC 7098063 PMID 32101723 Helmink Beth A Khan M A Wadud Hermann Amanda Gopalakrishnan Vancheswaran Wargo Jennifer A 2019 03 06 The microbiome cancer and cancer therapy Nature Medicine 25 3 377 388 doi 10 1038 s41591 019 0377 7 ISSN 1546 170X PMID 30842679 S2CID 71145949 Troseid Marius Andersen Geir Oystein Broch Kaspar Hov Johannes Roksund 2020 02 01 The gut microbiome in coronary artery disease and heart failure Current knowledge and future directions eBioMedicine 52 102649 doi 10 1016 j ebiom 2020 102649 ISSN 2352 3964 PMC 7016372 PMID 32062353 Young Vincent B 2017 03 15 The role of the microbiome in human health and disease an introduction for clinicians BMJ 356 j831 doi 10 1136 bmj j831 ISSN 0959 8138 PMID 28298355 S2CID 2443057 Dheilly Nolwenn Marie 2014 07 03 Holobiont Holobiont Interactions Redefining Host Parasite Interactions PLOS Pathogens 10 7 e1004093 doi 10 1371 journal ppat 1004093 ISSN 1553 7374 PMC 4081813 PMID 24992663 Belkaid Yasmine Hand Timothy W 2014 03 27 Role of the Microbiota in Immunity and Inflammation Cell 157 1 121 141 doi 10 1016 j cell 2014 03 011 ISSN 0092 8674 PMC 4056765 PMID 24679531 nbsp This genetics article is a stub You can help Wikipedia by expanding it vte Retrieved from https en wikipedia org w index php title Hologenomics amp oldid 1188176402, wikipedia, wiki, book, 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