Eisen
Jonathan A.
Eisen
Jonathan A.
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ArticleMIxS-BE : a MIxS extension defining a minimum information standard for sequence data from the built environment(Nature Publishing Group, 2013-10-24) Glass, Elizabeth M. ; Dribinsky, Yekaterina ; Yilmaz, Pelin ; Levin, Hal ; Van Pelt, Robert ; Wendel, Doug ; Wilke, Andreas ; Eisen, Jonathan A. ; Huse, Susan M. ; Shipanova, Anna ; Sogin, Mitchell L. ; Stajich, Jason ; Knight, Rob ; Meyer, Folker ; Schriml, Lynn M.The need for metadata standards for microbe sampling in the built environment.
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ArticleAncestral absence of electron transport chains in Patescibacteria and DPANN(Frontiers Media, 2020-08-17) Beam, Jacob P. ; Becraft, Eric D. ; Brown, Julia M. ; Schulz, Frederik ; Jarett, Jessica K. ; Bezuidt, Oliver ; Poulton, Nicole J. ; Clark, Kayla ; Dunfield, Peter F. ; Ravin, Nikolai V. ; Spear, John R. ; Hedlund, Brian P. ; Kormas, Konstantinos Ar. ; Sievert, Stefan M. ; Elshahed, Mostafa S. ; Barton, Hazel A. ; Stott, Matthew B. ; Eisen, Jonathan A. ; Moser, Duane P. ; Onstott, Tullis C. ; Woyke, Tanja ; Stepanauskas, RamunasRecent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
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ArticleNatural 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.
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ArticleInsights into the phylogeny and coding potential of microbial dark matter(Nature Publishing Group, 2013-07-14) Rinke, Christian ; Schwientek, Patrick ; Sczyrba, Alexander ; Ivanova, Natalia N. ; Anderson, Iain J. ; Cheng, Jan-Fang ; Darling, Aaron ; Malfatti, Stephanie A. ; Swan, Brandon K. ; Gies, Esther A. ; Dodsworth, Jeremy A. ; Hedlund, Brian P. ; Tsiamis, Georgios ; Sievert, Stefan M. ; Liu, Wen-Tso ; Eisen, Jonathan A. ; Hallam, Steven J. ; Kyrpides, Nikos C. ; Stepanauskas, Ramunas ; Rubin, Edward M. ; Hugenholtz, Philip ; Woyke, TanjaGenome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
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ArticleForensic analysis of the microbiome of phones and shoes(BioMed Central, 2015-05-12) Lax, Simon ; Hampton-Marcell, Jarrad T. ; Gibbons, Sean M. ; Colares, Georgia Barguil ; Smith, Daniel ; Eisen, Jonathan A. ; Gilbert, Jack A.Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.