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  • 1
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    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (2011)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Biotechnology 29 (2011): 415-420, doi:10.1038/nbt.1823.
    Description: Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The “environmental packages” apply to any sequence whose origin is known and can therefore be used in combination with MIMARKS or other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we establish the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
    Description: See Supplementary Note
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
    Format: application/vnd.ms-excel
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  • 2
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    Tools for the microbiome : nano and beyond (2016)
    American Chemical Society
    Details
    Publication Date: 2022-05-25
    Description: © American Chemical Society, 2015. This article is posted here by permission of American Chemical Society; copying and redistribution for non-commercial research and education purposes only. The definitive version was published in ACS Nano 10 (2016): 6-37, doi:10.1021/acsnano.5b07826.
    Description: The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
    Description: This research was supported by the Office of Naval Research Grant #N000141410051 (P.S.W., G.C.L.W., and T.Y.), the Genomic Science Program of the U.S. DOE-OBER,
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Current understanding of the human microbiome (2018)
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    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Medicine 24 (2018): 392–400, doi:10.1038/nm.4517.
    Description: Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.
    Description: Many of the studies described here in our laboratories were supported by the NIH, NSF, DOE, and the Alfred P. Sloan Foundation.
    Description: 2018-10-10
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 4
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    Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys (2017)
    American Society for Microbiology
    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 mSystems 1 (2015): e00009-15, doi:10.1128/mSystems.00009-15.
    Description: Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.
    Description: J.A.F. and A.P. are supported by the Gordon and Betty Moore Foundation (GMBF3779) and NSF grant 1136818. A.P. is supported by an NSF Graduate Fellowship. A.A. is supported by NSF grant OCE-1233612. J.K.J. is supported by the Microbiomes in Transition Initiative LDRD Program at the Pacific Northwest National Laboratory, a multiprogram national laboratory operated by Battelle for the DOE under contract DE-AC06-76RL01830. J.A.G. is supported by the U.S. Department of Energy under contract DE-AC02-06CH11357. J.G.C., J.A.G., and R.K. are supported by the Alfred P. Sloan Foundation. R.K. is supported by the Howard Hughes Medical Institute.
    Keywords: Microbial ecology ; Marker genes ; Primers ; 16S ; ITS
    Repository Name: Woods Hole Open Access Server
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  • 5
    Electronic Resource
    Electronic Resource
    Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 51 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Pseudomonas fluorescens SBW25, a plant growth promoting bacterium, has been widely studied due to its potential as an inoculum for improving crop yields. Environmental inoculants are usually applied on seeds or directly to soil and to effectively promote plant growth they need to be viable and active. However, it is difficult to study the physiological status of specific microorganisms in complex environments, such as soil. In this study, our aim was to use molecular tools to specifically monitor the physiological status of P. fluorescens SBW25 in soil and in pure cultures incubated under different nutritional conditions. The cells were previously tagged with marker genes (encoding green fluorescent protein and bacterial luciferase) to specifically track the cells in environmental samples. The physiological status of the cells was determined using the viability stains 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) and propidium iodide (PI), which stain active and dead cells, respectively. Luciferase activity was used to monitor the metabolic activity of the population. Most of the cells died after incubation for nine days in nutrient rich medium. By contrast when incubated under starvation conditions, most of the population was not stained with CTC or PI (i.e. intact but inactive cells), indicating that most of the cells were presumably dormant. In soil, a large fraction of the SBW25 cell population became inactive and died, as determined by a decline in luciferase activity and CTC-stained cells, an increase in PI-stained cells, and an inability of the cells to be cultured on agar medium. However, approximately 60% of the population was unstained, presumably indicating that the cells entered a state of dormancy in soil similar to that observed under starvation conditions in pure cultures. These results demonstrate the applicability of this approach for monitoring the physiological status of specific cells under stress conditions, such as those experienced by environmental inoculants in soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.07.007
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  • 6
    Electronic Resource
    Electronic Resource
    Flow cytometric and microscopic analysis of GFP-tagged Pseudomonas fluorescens bacteria (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 22 (1997), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The gene encoding the green fluorescent protein (GFP) from the jellyfish Aequorea victoria was assembled into an expression cassette for bacteria by fusing it to the T7 gene10 ribosome binding site and the strong, constitutive promoter PpsbA from Amaranthus hybridus. By using Tn5-based transposon delivery systems, Pseudomonas fluorescens bacteria were chromosomally tagged with gfp. We demonstrate that expression of a single copy gfp gene is sufficient to permit the visualization of bacteria by epifluorescence and laser confocal microscopy and detection by flow cytometry. The green fluorescent phenotype was detectable in all growth phases even under nutrient-limited conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1997.tb00352.x
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  • 7
    Electronic Resource
    Electronic Resource
    Specific monitoring by PCR amplification and bioluminescence of firefly luciferase gene-tagged bacteria added to environmental samples (1994)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 15 (1994), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract The firefly luciferase gene, luc, was demonstrated to hold promise as a specific marker for monitoring of genetically modified bacteria in the environment. PCR amplification and bioluminescence procedures were modified and compared for environmental monitoring of luc-tagged bacteria, using Escherichia coli as a model. The methods were used to track luc-tagged bacterial cells added to intact sediment core microcosms. Detection limits for the luc-tagged cells were the following, expressed as cells per 0.5 g of sediment: 102, by PCR amplification; 103, by whole cell luminescence; and 103−104, by measurement of luminescence in cell extracts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1994.tb00243.x
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  • 8
    Electronic Resource
    Electronic Resource
    Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 42 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L (chromosomally tagged with the firefly luciferase gene, luc) was inoculated into 4-chlorophenol-contaminated soil to assess the impact of bioaugmentation with a biodegrading strain on the indigenous microbiota. Simultaneously, the impact of 4-chlorophenol alone, or inoculation with A. chlorophenolicus into non-contaminated soil, was addressed. Using terminal restriction fragment length polymorphism (T-RFLP) several significant changes were detected in community fingerprint patterns obtained from soil microcosms treated under the different conditions. The relative abundances of some populations, as judged by the relative intensity of terminal restriction fragments, were significantly impacted by either 4-chlorophenol, A. chlorophenolicus inoculation, or by a combination of both inoculation and 4-chlorophenol contamination. Some populations were significantly stimulated and others were significantly repressed when compared to control soil with no additions. For several peaks, the positive or negative impact imposed by the treatments increased over the 13-day incubation period. Some members of the bacterial community were specifically sensitive to A. chlorophenolicus inoculation or to 4-chlorophenol contamination, whereas other populations remained relatively unaffected by any of the treatments. The A. chlorophenolicus inoculum was also monitored by T-RFLP and was found to have a significantly higher relative abundance in soil contaminated with 4-chlorophenol. These results were substantiated by a high correlation to luciferase activity measurements and the number of colony forming units of the inoculum. Therefore, the A. chlorophenolicus A6L population was positively stimulated by the presence of the 4-chlorophenol substrate (180 μg g−1 soil) that it catabolized during the first 8 days of the incubation period as a carbon and energy source. Together, these results demonstrate that specific populations in the soil bacterial community rapidly fluctuated in response to specific disturbances and the resulting shifts in the community may therefore represent an adjustment in community structure favoring those populations best capable of responding to novel stress scenarios.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb01028.x
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  • 9
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    Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome (2020)
    Frontiers Media
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    Publication Date: 2020-08-26
    Electronic ISSN: 1664-302X
    Topics: Biology
    Published by Frontiers Media
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  • 10
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    Tackling soil diversity with the assembly of large, complex metagenomes (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-03-14
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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