Bik Holly M.

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Last Name
Bik
First Name
Holly M.
ORCID
0000-0002-4356-3837

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  • Article
    RCN4GSC Workshop Report : managing data at the interface of biodiversity and (meta)genomics, March 2011
    (Genomic Standards Consortium, 2012-07-28) Robbins, Robert J. ; Amaral-Zettler, Linda A. ; Bik, Holly M. ; Blum, Stan D. ; Edwards, James ; Field, Dawn ; Garrity, George M. ; Gilbert, Jack A. ; Kottmann, Renzo ; Krishtalka, Leonard ; Lapp, Hilmar ; Lawrence, Carolyn ; Morrison, Norman ; O Tuama, Eamonn ; Parr, Cynthia Sims ; San Gil, Inigo ; Schindel, David ; Schriml, Lynn M. ; Vieglas, David ; Wooley, John
    Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.
  • Article
    Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution
    (Public Library of Science, 2021-08-19) Leray, Matthieu ; Wilkins, Laetitia G. E. ; Apprill, Amy ; Bik, Holly M. ; Clever, Friederike ; Connolly, Sean R. ; De León, Marina E. ; Duffy, J. Emmett ; Ezzat, Leïla ; Gignoux-Wolfsohn, Sarah ; Herre, Edward Allen ; Kaye, Jonathan Z. ; Kline, David ; Kueneman, Jordan G. ; McCormick, Melissa K. ; McMillan, W. Owen ; O’Dea, Aaron ; Pereira, Tiago J. ; Petersen, Jillian M. ; Petticord, Daniel F. ; Torchin, Mark ; Vega Thurber, Rebecca ; Videvall, Elin ; Wcislo, William T. ; Yuen, Benedict ; Eisen, Jonathan A.
    Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.