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  • 1
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    Microbial diversity - exploration of natural ecosystems and microbiomes (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Current Opinion in Genetics & Development 35 (2015): 66-72, doi:10.1016/j.gde.2015.10.003.
    Description: 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 multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world.
    Description: S.M.G. was supported by an EPA STAR Graduate Fellowship and by NIH training grant 5T-32EB-009412.
    Description: 2016-11-18
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 2
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    Aquarium microbiome response to ninety-percent system water change : clues to microbiome management (2015)
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    Publication Date: 2022-05-25
    Description: Author Posting. © John Wiley & Sons, 2015. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Zoo Biology 34 (2015): 360-367, doi:10.1002/zoo.21220.
    Description: The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health.
    Description: Sean Gibbons was supported by an EPA STAR Graduate Fellowship.
    Description: 2016-05-28
    Keywords: Aquatic microbes ; Aquarium life support ; Veterinary ; Dysbiosis ; Fish health
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 3
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    Athletic equipment microbiota are shaped by interactions with human skin (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.
    Description: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
    Description: MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Gym microbiome ; Athletic equipment ; Microbiology ; Niche communities ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 21, doi:10.1186/s40168-015-0082-9.
    Description: 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.
    Description: This work was enabled by the generous support of the Alfred P Sloan foundation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. S.M.G. was supported by an EPA STAR Graduate Fellowship and by a National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Forensic microbiology ; Source-sink dynamics ; Shoe microbiome ; Phone microbiome ; Microbial time series
    Repository Name: Woods Hole Open Access Server
    Type: Article
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    Format: application/vnd.ms-excel
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  • 5
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    Ecological succession and viability of human-associated microbiota on restroom surfaces (2014)
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    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology (2014), doi:10.1128/AEM.03117-14.
    Description: Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in 4 public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late successional community developed within 5-8 hours on restroom floors, and showed remarkable stability over weeks to months. Despite late successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human-exclusion. MRSA-associated virulence genes were found on floors, but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophage, human papilloma and herpes viruses, were significantly correlated with bacteria abundances, and showed an unexpectedly low virus-to-bacteria ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.
    Description: S.M.G. was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5T-32EB-009412. We acknowledge funding from the Alfred P Sloan Foundation’s Microbiology of the Built Environment Program.
    Description: 2015-05-14
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 6
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    Disturbance regimes predictably alter diversity in an ecologically complex bacterial system (2017)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e01372-16, doi:10.1128/mBio.01372-16.
    Description: Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
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    Invasive plants rapidly reshape soil properties in a grassland ecosystem (2017)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 2 (2017): e00178-16, doi:10.1128/mSystems.00178-16.
    Description: Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales.
    Description: Sean Gibbons was supported by an EPA STAR Graduate Fellowship and National Institutes of Health training grant 5T-32EB-009412. Other funding for this project was provided by MPG Ranch and DOE contract DE-AC02-06CH11357.
    Keywords: 16S RNA ; Copiotroph ; Metagenomics ; Oligotroph ; Plant invasions ; Plant-microbe interactions ; Soil bacteria ; Soil fungi ; Soil microbiology
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    A communal catalogue reveals Earth’s multiscale microbial diversity (2017)
    Nature Research
    In:  Nature, 551 (7681). pp. 457-463.
    Details
    Publication Date: 2020-02-06
    Description: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/nature24621
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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