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Hologenomics

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Hologenomicsis theomicsstudy ofhologenomes.A hologenome is the whole set ofgenomesof aholobiont,an organism together with all co-habitatingmicrobes,other life forms, andviruses.[1]While the term hologenome originated from thehologenome theory of evolution,which postulates thatnatural selectionoccurs on the holobiont level,[2]hologenomics uses an integrative framework to investigate interactions between thehostand its associatedspecies.Examples includegut 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 ofmarine sponges.[6]

History

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The origins of hologenomics revolves around the hologenome theory of evolution, which describes individualmulticellular organisms,microbes, and viruses establishingsymbiotic relationshipsand undergoingcoevolutiontogether.[2][7]Richard Jeffersonintroduced the term 'hologenome' to describe the host-symbiont genome as an evolutionary unit.[8]Prior to this,Lynn Margulisused the term 'holobiont' to describe hosts and their associated species as an ecological unit.[9]

Eukaryotes-prokaryotes coevolution

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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.Poriferaare often described as holobionts because they harbor a wide range ofbacteria,archaeaandalgae.Microbial communities present have been observed in facilitatingmetabolicfunctions andimmuneresponses.[10]Offspring inherit these microbial colonies viaverticaland/orhorizontal transmission.[10]Symbiontcoloniesare transferred through parentalgametesin vertical transmission, whereasoffspringacquire same colonies from their environment in horizontal transmission. Vertical transmission is also seen interrestrialorganisms likeC. ocellatus,wheregammaproteobacteriain the parental gut is vertically transferred through egg contamination.[11]

Criticism

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The hologenome theory evolution is not fully accepted, and research inmicrobial-host phylogeneticsis ongoing. Rather than the selection of corals with certain symbiotic microbial communities,coral bleachingmay simply be a result ofenvironmental stressors,and bacterial presence in bleached coral may be explained simply as opportunisticcolonization.[12]Ubiquity testing also revealed many differentbacterialandalgalsymbionts that are not associated with a single species of coral,[13]suggesting that hologenomics just identifies and validates mechanistic interactions betweenpathogens,microbes, and their hosts.[14]

Examples of discoveries with hologenomic approaches

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  • Nanopore sequencing- Profiling organelle genomes in the holobiontC. ashmeadiirevealed thatRhodospirillaceaewas dominant among six putativeendosymbionts.[15]
  • 16S rRNAsequencing - 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 spongemicrobiomeswere 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

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Medicine

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It's hypothesized the continued incidencenon-infectious diseasesis a result ofmodernizationreducing the diversity of symbiotic microbes.[14]The human microbiome has also been correlated to numerousetiologiesofnon-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.

Diseasebiomarkerscan be found by investigating lifestyle, genomic differences, andmRNA/protein/metaboliteprofiles of the patient and their microbiota.[14]For investigating microbiomes and specifically microbiota subcommunities that may contribute to a diseasephenotype,longitudinal studiesare recommended as everyone has a personalized microbiome with small differences in microbiomephylotypes.[14]A personalized plan managing a person’s microbiome can then be developed, withprebioticsnurturing beneficial endogenous microbes, andprobioticsmanipulating a person’s hologenome.[22]

Immunology

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Conditionalmutualism,whereparasiteshave 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 involvegastrointestinalflora.[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

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References

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  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.ISSN2049-2618.PMC5922317.PMID29695294.
  2. ^abNumber 6 in a series of 7 VHS recordings,A Decade of PCR: Celebrating 10 Years of Amplification,Cold Spring Harbor Laboratory Press, 1994.ISBN0-87969-473-4.
  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.ISSN2165-8102.PMID25387109.
  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.ISSN1756-0500.PMC3284880.PMID22226071.
  5. ^Miller, William B. Jr. (2013).The Microcosm Within: Evolution and Extinction in the Hologenome.Universal-Publishers.ISBN978-1612332772.
  6. ^Webster, Nicole S.; Thomas, Torsten (2016-05-04)."The Sponge Hologenome".mBio.7(2): e00135–16.doi:10.1128/mBio.00135-16.ISSN2150-7511.PMC4850255.PMID27103626.
  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.ISSN2049-2618.PMC5922317.PMID29695294.
  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.ISBN0-87969-473-4.
  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.ISBN978-0-262-13269-5.
  10. ^abcWebster, Nicole S.; Thomas, Torsten (2016-05-04)."The Sponge Hologenome".mBio.7(2): e00135-16.doi:10.1128/mBio.00135-16.ISSN2150-7511.PMC4850255.PMID27103626.
  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.ISSN0099-2240.PMC2876435.PMID20400564.
  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.ISSN1751-7362.PMID18059488.S2CID1032896.
  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.ISSN1751-7370.PMC5029208.PMID26555246.
  14. ^abcdTheis, Kevin R. (2018-04-10)."Hologenomics: Systems-Level Host Biology".mSystems.3(2).doi:10.1128/mSystems.00164-17.ISSN2379-5077.PMC5895875.PMID29657963.
  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.ISSN1471-2164.PMC6854639.PMID31722669.
  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.ISSN1751-7370.PMID20054355.
  17. ^abFan, 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.ISSN0027-8424.PMC3390844.PMID22699508.
  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.ISSN1742-2094.PMC6969442.PMID31952509.
  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.ISSN2405-8033.PMC7098063.PMID32101723.
  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.ISSN1546-170X.PMID30842679.S2CID71145949.
  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.ISSN2352-3964.PMC7016372.PMID32062353.
  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.ISSN0959-8138.PMID28298355.S2CID2443057.
  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.ISSN1553-7374.PMC4081813.PMID24992663.
  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.ISSN0092-8674.PMC4056765.PMID24679531.


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