The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology and human health. This dynamic research program integrates the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and underlying mechanisms of biomedical importance. Projects span all evolutionary time scales, ranging from deep phylogenetic divergence of ancient eukaryotic and prokaryotic lineages, to ecological analyses of how members of diverse communities contribute and respond to environmental change.

Recent Submissions

  • Identifying contamination with advanced visualization and analysis practices : metagenomic approaches for eukaryotic genome assemblies 

    Delmont, Tom O.; Eren, A. Murat (PeerJ, 2016-03-29)
    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target ...
  • Association of cesarean delivery and formula supplementation with the intestinal microbiome of 6-week-old infants 

    Madan, Juliette C.; Hoen, Anne G.; Lundgren, Sara N.; Farzan, Shohreh F.; Cottingham, Kathryn L.; Morrison, Hilary G.; Sogin, Mitchell L.; Li, Hongzhe; Moore, Jason H.; Karagas, Margaret R. (American Medical Association, 2016-01-11)
    The intestinal microbiome plays a critical role in infant development, and delivery mode and feeding method (breast milk vs formula) are determinants of its composition. However, the importance of delivery mode beyond the ...
  • Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis 

    Zozaya, Marcela; Ferris, Michael J.; Siren, Julia D.; Lillis, Rebecca; Myers, Leann; Nsuami, M. Jacques; Eren, A. Murat; Brown, Jonathan; Taylor, Christopher M.; Martin, David H. (BioMed Central, 2016-04-19)
    The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from male to female ...
  • Bacterial diversity and community composition from seasurface to subseafloor 

    Walsh, Emily A.; Kirkpatrick, John B.; Rutherford, Scott D.; Smith, David; Sogin, Mitchell L.; D'Hondt, Steven (Nature Publishing Group, 2015-10-02)
    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the ...
  • Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii 

    Green, Hyatt C.; Fisher, Jenny C.; McLellan, Sandra L.; Sogin, Mitchell L.; Shanks, Orin C. (2015-12-16)
    The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial ...
  • Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis Lung Disease 

    Hogan, Deborah A.; Willger, Sven D.; Dolben, Emily L.; Hampton, Thomas H.; Stanton, Bruce A.; Morrison, Hilary G.; Sogin, Mitchell L.; Czum, Julianna; Ashare, Alix (Public Library of Science, 2016-03-04)
    Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate ...
  • Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium 

    Davies, Neil; Field, Dawn; Gavaghan, David; Holbrook, Sally J.; Planes, Serge; Troyer, Matthias; Bonsall, Michael; Claudet, Joachim; Roderick, George; Schmitt, Russell J.; Amaral-Zettler, Linda A.; Berteaux, Veronique; Bossin, Hervé C.; Cabasse, Charlotte; Collin, Antoine; Deck, John; Dell, Tony; Dunne, Jennifer A.; Gates, Ruth D.; Harfoot, Mike; Hench, James L.; Hopuare, Marania; Kirch, Patrick; Kotoulas, Georgios; Kosenkov, Alex; Kusenko, Alex; Leichter, James J.; Lenihan, Hunter; Magoulas, Antonios; Martinez, Neo; Meyer, Chris; Stoll, Benoit; Swalla, Billie; Tartakovsky, Daniel M.; Teavai Murphy, Hinano; Turyshev, Slava; Valdvinos, Fernanda; Williams, Rich; Wood, Spencer; IDEA Consortium (BioMed Central, 2016-03-17)
    Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to ...
  • A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge 

    Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A. (Nature Publishing Group, 2016-03-03)
    The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active ...
  • Extensive modulation of the fecal metagenome in children With Crohn’s disease during exclusive enteral nutrition 

    Quince, Christopher; Ijaz, Umer Zeeshan; Loman, Nick; Eren, A. Murat; Saulnier, Delphine; Russell, Julie; Haig, Sarah J.; Calus, Szymon T.; Quick, Joshua; Barclay, Andrew H.; Bertz, Martin; Blaut, Michael; Hansen, Richard; McGrogan, Paraic; Russell, Richard K.; Edwards, Christine A.; Gerasimidis, Konstantinos (Nature Publishing Group, 2015-11-03)
    Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn’s disease (CD). Fecal ...
  • Mobile genetic elements : in silico, in vitro, in vivo 

    Arkhipova, Irina R.; Rice, Phoebe A. (2015-11-30)
    Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function, and evolution. ...
  • The obese gut microbiome across the epidemiologic transition 

    Dugas, Lara R.; Fuller, Miles; Gilbert, Jack A.; Layden, Brian T. (BioMed Central, 2016-01-11)
    The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing ...
  • Microbial diversity - exploration of natural ecosystems and microbiomes 

    Gibbons, Sean M.; Gilbert, Jack A. (2015-09-29)
    Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to ...
  • A simple novel device for air sampling by electrokinetic capture 

    Gordon, Julian; Gandhi, Prasanthi; Shekhawat, Gajendra; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (BioMed Central, 2015-12-27)
    A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use ...
  • The biogeography of the Plastisphere : implications for policy 

    Amaral-Zettler, Linda A.; Zettler, Erik R.; Slikas, Beth; Boyd, Gregory D.; Melvin, Donald W.; Morrall, Clare E.; Proskurowski, Giora; Mincer, Tracy J. (Ecological Society of America, 2015-12)
    Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid-ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) ...
  • Microbial gene abundance and expression patterns across a river to ocean salinity gradient 

    Fortunato, Caroline S.; Crump, Byron C. (Public Library of Science, 2015-11-04)
    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. ...
  • Anvi’o : an advanced analysis and visualization platform for ‘omics data 

    Eren, A. Murat; Esen, Ozcan C.; Quince, Christopher; Vineis, Joseph H.; Morrison, Hilary G.; Sogin, Mitchell L.; Delmont, Tom O. (PeerJ, 2015-10-08)
    Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively ...
  • Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica 

    Delmont, Tom O.; Eren, A. Murat; Vineis, Joseph H.; Post, Anton F. (Frontiers Media, 2015-10-26)
    Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis ...
  • Chemical dispersants can suppress the activity of natural oil-degrading microorganisms 

    Kleindienst, Sara; Seidel, Michael; Ziervogel, Kai; Grim, Sharon L.; Loftis, Kathy; Harrison, Sarah; Malkin, Sairah Y.; Perkins, Matthew J.; Field, Jennifer; Sogin, Mitchell L.; Dittmar, Thorsten; Passow, Uta; Medeiros, Patricia M.; Joye, Samantha B. (2015-09)
    During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil ...
  • Lifestyle evolution in cyanobacterial symbionts of sponges 

    Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; Haber, Markus; Blom, Jochen; Marshall, Christopher W.; Gilbert, Jack A.; Hentschel, Ute; Steindler, Laura (American Society for Microbiology, 2015-06-02)
    The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The ...

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