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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)
    In:  EPIC3Nature Biotechnology, 29(5), pp. 415-420, ISSN: 1087-0156
    Details
    Publication Date: 2020-02-12
    Description: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting 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 genome sequence of known origin and can be used in combination with MIMARKS and 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 present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 2
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    Soil bacterial diversity is associated with human population density in urban greenspaces (2018)
    Details
    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 American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science and Technology 52 (2018): 5115–5124, doi:10.1021/acs.est.7b06417.
    Description: Urban greenspaces provide extensive ecosystem services, including pollutant remediation, water management, carbon maintenance, and nutrient cycling. However, while the urban soil microbiota underpin these services, we still have limited understanding of the factors that influence their distribution. We characterized soil bacterial communities from turf-grasses associated with urban parks, streets and residential sites across a major urban environment, including a gradient of human population density. Bacterial diversity was significantly positively correlated with the population density; and species diversity was greater in park and street soils, compared to residential soils. Population density and greenspace type also led to significant differences in the microbial community composition that was also significantly correlated with soil pH, moisture and texture. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in high density population areas had fewer interactions, while abundant bacteria in high moisture soils had more interactions. These results indicate the significant influence of changes in urban demographics and land-use on soil microbial communities. As urbanization is rapidly growing across the planet, it is important to improve our understanding of the consequences of urban zoning on the soil microbiota.
    Description: This study is supported by the Earth Microbiome Project (http://www.earthmicrobiome.org/) and the China Scholarship Council (http://en.csc.edu.cn/).
    Description: 2019-04-06
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 3
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    Existing climate change will lead to pronounced shifts in the diversity of soil prokaryotes (2018)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 3 (2018): e00167-18, doi:10.1128/mSystems.00167-18.
    Description: Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.
    Description: This work was supported by the Strategic Priority Research Program (XDB15010101, XDA05050404) of the Chinese Academy of Sciences, the National Program on Key Basic Research Project (2014CB954002, 2014CB954004), the National Natural Science Foundation of China (41701298, 41371254), the “135” Plan and Frontiers Projects of Institute of Soil Science (ISSASIP1641), and the National Science and Technology Foundation project (2015FY110100). J.A.G. was supported by the U.S. Dept. of Energy under contract DE-AC02-06CH11357. N.F. was supported by a grant from the National Science Foundation (DEB-0953331). K.S.P. and J.L. were supported by the National Science Foundation (DMS-1069303), the Gordon and Betty Moore Foundation (grant no. 3300), the Gladstone Institutes, and a gift from the San Simeon Fund.
    Keywords: Soil bacterial diversity ; Niche modeling ; Climate change ; Microbial biogeography ; Biogeography ; Diversity ; Soil microbiology
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Toward interoperable bioscience data (2012)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Genetics 44 (2012): 121-126, doi:10.1038/ng.1054.
    Description: To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.
    Description: The authors also acknowledge the following funding sources in particular: UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/I000771/1 to S.-A.S. and A.T.; UK BBSRC BB/I025840/1 to S.-A.S.; UK BBSRC BB/I000917/1 to D.F.; EU CarcinoGENOMICS (PL037712) to J.K.; US National Institutes of Health (NIH) 1RC2CA148222-01 to W.H. and the HSCI; US MIRADA LTERS DEB-0717390 and Alfred P. Sloan Foundation (ICoMM) to L.A.-Z.; Swiss Federal Government through the Federal Office of Education and Science (FOES) to L.B. and I.X.; EU Innovative Medicines Initiative (IMI) Open PHACTS 115191 to C.T.E.; US Department of Energy (DOE) DE-AC02- 06CH11357 and Arthur P. Sloan Foundation (2011- 6-05) to J.G.; UK BBSRC SysMO-DB2 BB/I004637/1 and BBG0102181 to C.G.; UK BBSRC BB/I000933/1 to C.S. and J.L.G.; UK MRC UD99999906 to J.L.G.; US NIH R21 MH087336 (National Institute of Mental Health) and R00 GM079953 (National Institute of General Medical Science) to A.L.; NIH U54 HG006097 to J.C. and C.E.S.; Australian government through the National Collaborative Research Infrastructure Strategy (NCRIS); BIRN U24-RR025736 and BioScholar RO1-GM083871 to G.B. and the 2009 Super Science initiative to C.A.S.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Microbial diversity - exploration of natural ecosystems and microbiomes (2016)
    Details
    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
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  • 6
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    Stool consistency as a major confounding factor affecting microbiota composition : an ignored variable? (2016)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of BMJ Publishing Group for personal use, not for redistribution. The definitive version was published in Gut 65 (2016): 1-2, doi:10.1136/gutjnl-2015-310043.
    Description: 2016-07-17
    Keywords: Microbiome ; Therapy ; Biomarker ; Gut-transit time
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 7
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    A simple novel device for air sampling by electrokinetic capture (2016)
    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): 79, doi:10.1186/s40168-015-0141-2.
    Description: 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 of a novel device, which has no technical complexity and is easily deployable. An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
    Description: This work was partly supported by Breakout Labs, a program of the Thiel Foundation, and partly from personal funds from Julian Gordon and Prasanthi Gandhi. This work was supported in part by the US Dept. of Energy under Contract DE-AC02-06CH11357.
    Keywords: Atomic force microscopy ; Reverse transcriptase PCR ; Air sampling ; Field study ; Aerosol ; Nanoparticles ; Aerobiome ; Amplicon sequencing ; Bacteria ; Molds
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    The obese gut microbiome across the epidemiologic transition (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Emerging Themes in Epidemiology 13 (2016): 2, doi:10.1186/s12982-015-0044-5.
    Description: 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 within the gastrointestinal tract of humans, has now been implicated in the obesity epidemic. Importantly, this bacterial community is impacted by external environmental factors through a variety of undefined mechanisms. We focus this review on how the external environment may impact the gut microbiota by considering, the host’s geographic location ‘human geography’, and behavioral factors (diet and physical activity). Moreover, we explore the relationship between the gut microbiota and obesity with these external factors. And finally, we highlight here how an epidemiologic model can be utilized to elucidate causal relationships between the gut microbiota and external environment independently and collectively, and how this will help further define this important new factor in the obesity epidemic.
    Description: BTL is supported by the Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development, Career Development (Grant no. 1IK2BX001587-01).
    Keywords: Obesity ; Gut microbiome ; Geographical differences
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Metagenomic analysis of basal ice from an Alaskan glacier (2018)
    BMC
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 6 (2018): 123, doi:10.1186/s40168-018-0505-5.
    Description: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska. DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome. Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.
    Description: This work was supported in part by funding from the Ministry of Science and Technology of China (2016YFC0206300 and 2015CB553402), the National Natural Science Foundation of China (21750005, 31470532, 91543102, and 31711530153), the Beijing Nova Program (Z171100001117011), the Tsinghua University Initiative Scientific Research Program (20161080152), the NASA ASTEP Program (NNX11AJ89G), the Tsinghua University-Peking University Center for Life Sciences (CLS), and the Beijing Advanced Innovation Center for Structural Biology.
    Keywords: Microbiome ; Metagenomics ; Glacier ; Basal ice layer
    Repository Name: Woods Hole Open Access Server
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  • 10
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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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