The Earth Microbiome project: successes and aspirations

Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob

doi:10.1186/s12915-014-0069-1

Title: The Earth Microbiome project: successes and aspirations

Abstract

Here, the Earth Microbiome Project (EMP) was launched in August 2010, with the ambitious aim of constructing a global catalogue of the uncultured microbial diversity of this planet. The primary vision of the Earth Microbiome Project, to process the microbial diversity and functional potential from approximately 200,000 environmental samples, marks it as an undertaking so massive that it was at first considered to be pure folly (as late as 2012, Jonathan Eisen was quoted in Nature as saying ‘Knight and Gilbert literally talk about sampling the entire planet. It is ludicrous and not feasible - yet they are doing it’ [1]).

Authors:

Gilbert, Jack A. ^[1]; Jansson, Janet K. ^[2]; Knight, Rob ^[3]

Argonne National Lab. (ANL), Lemont, IL (United States); Univ. of Chicago, Chicago, IL (United States); Zhejiang Univ., Hangzhou (China)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Univ. of Colorado, Boulder, CO (United States); Howard Hughes Medical Institute, Boulder, CO (United States)

Publication Date:: Fri Aug 22 00:00:00 EDT 2014

Research Org.:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1467640

Grant/Contract Number:: AC02-06CH11357

Resource Type:: Accepted Manuscript

Journal Name:: BMC Biology

Additional Journal Information:: Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1741-7007

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Earth Microbiome Project; Human Microbiome Project; Quantitative Insight Into Microbial Ecology; John Templeton Foundation; Freshwater Lake Sediment

Citation Formats


                    Gilbert, Jack A., Jansson, Janet K., and Knight, Rob. The Earth Microbiome project: successes and aspirations.  United States: N. p., 2014. 
Web.  doi:10.1186/s12915-014-0069-1.

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                    Gilbert, Jack A., Jansson, Janet K., & Knight, Rob. The Earth Microbiome project: successes and aspirations.  United States.  https://doi.org/10.1186/s12915-014-0069-1

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                    Gilbert, Jack A., Jansson, Janet K., and Knight, Rob. Fri .  
"The Earth Microbiome project: successes and aspirations".  United States.  https://doi.org/10.1186/s12915-014-0069-1.  https://www.osti.gov/servlets/purl/1467640.

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@article{osti_1467640,

  title        = {The Earth Microbiome project: successes and aspirations},

  author       = {Gilbert, Jack A. and Jansson, Janet K. and Knight, Rob},

  abstractNote = {Here, the Earth Microbiome Project (EMP) was launched in August 2010, with the ambitious aim of constructing a global catalogue of the uncultured microbial diversity of this planet. The primary vision of the Earth Microbiome Project, to process the microbial diversity and functional potential from approximately 200,000 environmental samples, marks it as an undertaking so massive that it was at first considered to be pure folly (as late as 2012, Jonathan Eisen was quoted in Nature as saying ‘Knight and Gilbert literally talk about sampling the entire planet. It is ludicrous and not feasible - yet they are doing it’ [1]).},

  doi          = {10.1186/s12915-014-0069-1},

  journal      = {BMC Biology},

  number       = 1,

  volume       = 12,

  place        = {United States},

  year         = {Fri Aug 22 00:00:00 EDT 2014},

  month        = {Fri Aug 22 00:00:00 EDT 2014}

}

Copy to clipboard

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Works referenced in this record:

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
journal, January 2014

Piombino, Paola; Genovese, Alessandro; Esposito, Silvia
PLoS ONE, Vol. 9, Issue 1
DOI: 10.1371/journal.pone.0085611

Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

Gibbons, S. M.; Caporaso, J. G.; Pirrung, M.
Proceedings of the National Academy of Sciences, Vol. 110, Issue 12
DOI: 10.1073/pnas.1217767110

Distinct microbial communities associated with buried soils in the Siberian tundra
journal, December 2013

Gittel, Antje; Bárta, Jiří; Kohoutová, Iva
The ISME Journal, Vol. 8, Issue 4
DOI: 10.1038/ismej.2013.219

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
journal, January 2010

Gilbert, Jack A.; Meyer, Folker; Jansson, Janet
Standards in Genomic Sciences, Vol. 3, Issue 3
DOI: 10.4056/aigs.1443528

Human and Environmental Impacts on River Sediment Microbial Communities
journal, May 2014

Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita
PLoS ONE, Vol. 9, Issue 5
DOI: 10.1371/journal.pone.0097435

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011
journal, November 2011

Gilbert, Jack A.; Bailey, Mark; Field, Dawn
Standards in Genomic Sciences, Vol. 5, Issue 2
DOI: 10.4056/sigs.2134923

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
journal, December 2011

McDonald, Daniel; Price, Morgan N.; Goodrich, Julia
The ISME Journal, Vol. 6, Issue 3
DOI: 10.1038/ismej.2011.139

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion
Standards in Genomic Sciences, Vol. 3, Issue 3
DOI: 10.4056/sigs.1433550

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
journal, September 2011

Zinger, Lucie; Amaral-Zettler, Linda A.; Fuhrman, Jed A.
PLoS ONE, Vol. 6, Issue 9
DOI: 10.1371/journal.pone.0024570

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
journal, July 2012

McDonald, Daniel; Clemente, Jose C.; Kuczynski, Justin
GigaScience, Vol. 1, Issue 1
DOI: 10.1186/2047-217X-1-7

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
Nature Methods, Vol. 7, Issue 5
DOI: 10.1038/nmeth.f.303

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013

Fierer, N.; Ladau, J.; Clemente, J. C.
Science, Vol. 342, Issue 6158
DOI: 10.1126/science.1243768

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
journal, November 2009

Chen, Vincent B.; Davis, Ian W.; Richardson, David C.
Protein Science, Vol. 18, Issue 11
DOI: 10.1002/pro.250

EMPeror: a tool for visualizing high-throughput microbial community data
journal, November 2013

Vázquez-Baeza, Yoshiki; Pirrung, Meg; Gonzalez, Antonio
GigaScience, Vol. 2, Issue 1
DOI: 10.1186/2047-217X-2-16

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
journal, July 2013

Rubin, Benjamin E. R.; Gibbons, Sean M.; Kennedy, Suzanne
PLoS ONE, Vol. 8, Issue 7
DOI: 10.1371/journal.pone.0070460

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
journal, March 2014

Scott, Nicole M.; Hess, Matthias; Bouskill, Nick J.
Frontiers in Microbiology, Vol. 5
DOI: 10.3389/fmicb.2014.00108

Microbes en masse: The sequencing machine
journal, July 2012

Gewin, Virginia
Nature, Vol. 487, Issue 7406
DOI: 10.1038/487156a

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014

Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio
The ISME Journal, Vol. 8, Issue 7
DOI: 10.1038/ismej.2013.254

Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes
journal, November 2003

Zehr, Jonathan P.; Crumbliss, Lori L.; Church, Matthew J.
BioTechniques, Vol. 35, Issue 5
DOI: 10.2144/03355st08

The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change
journal, April 2021

Fouquier, Jennifer; Moreno Huizar, Nancy; Donnelly, Jody
mSystems, Vol. 6, Issue 2
DOI: 10.1128/msystems.00848-20

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
text, January 2011

Amaral-Zettler, Linda A.; Huse, Susan M.; Horner-Devine, M. Claire
Public Library of Science
DOI: 10.7892/boris.91392

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
journal, November 2009

Chen, Vincent B.; Davis, Ian W.; Richardson, David C.
Protein Science, Vol. 18, Issue 11
DOI: 10.1002/pro.250

Microbes en masse: The sequencing machine
journal, July 2012

Gewin, Virginia
Nature, Vol. 487, Issue 7406
DOI: 10.1038/487156a

Distinct microbial communities associated with buried soils in the Siberian tundra
journal, December 2013

Gittel, Antje; Bárta, Jiří; Kohoutová, Iva
The ISME Journal, Vol. 8, Issue 4
DOI: 10.1038/ismej.2013.219

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014

Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio
The ISME Journal, Vol. 8, Issue 7
DOI: 10.1038/ismej.2013.254

Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
journal, September 2020

Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R.
Scientific Reports, Vol. 10, Issue 1
DOI: 10.1038/s41598-020-71922-x

Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

Gibbons, S. M.; Caporaso, J. G.; Pirrung, M.
Proceedings of the National Academy of Sciences, Vol. 110, Issue 12
DOI: 10.1073/pnas.1217767110

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013

Fierer, N.; Ladau, J.; Clemente, J. C.
Science, Vol. 342, Issue 6158
DOI: 10.1126/science.1243768

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
journal, March 2014

Scott, Nicole M.; Hess, Matthias; Bouskill, Nick J.
Frontiers in Microbiology, Vol. 5
DOI: 10.3389/fmicb.2014.00108

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
journal, January 2010

Gilbert, Jack A.; Meyer, Folker; Jansson, Janet
Standards in Genomic Sciences, Vol. 3, Issue 3
DOI: 10.4056/aigs.1443528

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion
Standards in Genomic Sciences, Vol. 3, Issue 3
DOI: 10.4056/sigs.1433550

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011
journal, November 2011

Gilbert, Jack A.; Bailey, Mark; Field, Dawn
Standards in Genomic Sciences, Vol. 5, Issue 2
DOI: 10.4056/sigs.2134923

Works referencing / citing this record:

The gut microbiome of nonhuman primates: Lessons in ecology and evolution
journal, June 2018

Clayton, Jonathan B.; Gomez, Andres; Amato, Katherine
American Journal of Primatology, Vol. 80, Issue 6
DOI: 10.1002/ajp.22867

Composition and stability of the vervet monkey milk microbiome
journal, May 2019

Petrullo, Lauren; Jorgensen, Matthew J.; Snyder‐Mackler, Noah
American Journal of Primatology, Vol. 81, Issue 10-11
DOI: 10.1002/ajp.22982

The gut microbiome in human neurological disease: A review: Gut Microbiome
journal, March 2017

Tremlett, Helen; Bauer, Kylynda C.; Appel-Cresswell, Silke
Annals of Neurology, Vol. 81, Issue 3
DOI: 10.1002/ana.24901

Edaphic and host plant factors are linked to the composition of arbuscular mycorrhizal fungal communities in the root zone of endangered Ulmus chenmoui Cheng in China
journal, July 2019

Song, Juan; Chen, Long; Chen, Fengmao
Ecology and Evolution, Vol. 9, Issue 15
DOI: 10.1002/ece3.5446

Innovation Rather than Improvement: A Solvable High-Dimensional Model Highlights the Limitations of Scalar Fitness
journal, January 2018

Tikhonov, Mikhail; Monasson, Remi
Journal of Statistical Physics, Vol. 172, Issue 1
DOI: 10.1007/s10955-018-1956-6

Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
journal, February 2020

Jo, Jihoon; Oh, Jooseong; Park, Chungoo
Journal of Microbiology, Vol. 58, Issue 3
DOI: 10.1007/s12275-020-9525-5

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses
journal, February 2018

Afrin, Tanzila; Kounosu, Asuka; Billah, Mohammad-Masum
Applied Entomology and Zoology, Vol. 53, Issue 2
DOI: 10.1007/s13355-018-0551-2

Strategies to improve reference databases for soil microbiomes
journal, December 2016

Choi, Jinlyung; Yang, Fan; Stepanauskas, Ramunas
The ISME Journal, Vol. 11, Issue 4
DOI: 10.1038/ismej.2016.168

Cohesion: a method for quantifying the connectivity of microbial communities
journal, July 2017

Herren, Cristina M.; McMahon, Katherine D.
The ISME Journal, Vol. 11, Issue 11
DOI: 10.1038/ismej.2017.91

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
journal, July 2016

Gohl, Daryl M.; Vangay, Pajau; Garbe, John
Nature Biotechnology, Vol. 34, Issue 9
DOI: 10.1038/nbt.3601

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017

Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
Nature Biotechnology, Vol. 35, Issue 8
DOI: 10.1038/nbt.3893

Stability of peatland carbon to rising temperatures
journal, December 2016

Wilson, R. M.; Hopple, A. M.; Tfaily, M. M.
Nature Communications, Vol. 7, Article No. 13723
DOI: 10.1038/ncomms13723

An assessment of US microbiome research
journal, January 2016

Stulberg, Elizabeth; Fravel, Deborah; Proctor, Lita M.
Nature Microbiology, Vol. 1, Issue 1
DOI: 10.1038/nmicrobiol.2015.15

Microbial diversity knows no borders
journal, January 2018

Pike, Lindsay J.; Viciani, Elisa; Kumar, Nitin
Nature Reviews Microbiology, Vol. 16, Issue 2
DOI: 10.1038/nrmicro.2017.166

Microbial succession on decomposing root litter in a drought-prone Scots pine forest
journal, May 2019

Herzog, Claude; Hartmann, Martin; Frey, Beat
The ISME Journal, Vol. 13, Issue 9
DOI: 10.1038/s41396-019-0436-6

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
journal, May 2019

Youngblut, Nicholas D.; Reischer, Georg H.; Walters, William
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-10191-3

Vertical transmission of sponge microbiota is inconsistent and unfaithful
journal, July 2019

Björk, Johannes R.; Díez-Vives, Cristina; Astudillo-García, Carmen
Nature Ecology & Evolution, Vol. 3, Issue 8
DOI: 10.1038/s41559-019-0935-x

Detecting macroecological patterns in bacterial communities across independent studies of global soils
journal, November 2017

Ramirez, Kelly S.; Knight, Christopher G.; de Hollander, Mattias
Nature Microbiology, Vol. 3, Issue 2
DOI: 10.1038/s41564-017-0062-x

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data
journal, January 2020

Chong, Jasmine; Liu, Peng; Zhou, Guangyan
Nature Protocols, Vol. 15, Issue 3
DOI: 10.1038/s41596-019-0264-1

Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial
journal, July 2018

Stull, Valerie J.; Finer, Elijah; Bergmans, Rachel S.
Scientific Reports, Vol. 8, Issue 1
DOI: 10.1038/s41598-018-29032-2

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae
journal, August 2016

Marcelino, Vanessa Rossetto; Verbruggen, Heroen
Scientific Reports, Vol. 6, Issue 1
DOI: 10.1038/srep31508

Scaling laws predict global microbial diversity
journal, May 2016

Locey, Kenneth J.; Lennon, Jay T.
Proceedings of the National Academy of Sciences, Vol. 113, Issue 21
DOI: 10.1073/pnas.1521291113

Caenorhabditis elegans responses to bacteria from its natural habitats
journal, June 2016

Samuel, Buck S.; Rowedder, Holli; Braendle, Christian
Proceedings of the National Academy of Sciences, Vol. 113, Issue 27
DOI: 10.1073/pnas.1607183113

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space
journal, March 2019

Helbert, William; Poulet, Laurent; Drouillard, Sophie
Proceedings of the National Academy of Sciences, Vol. 116, Issue 13
DOI: 10.1073/pnas.1815791116

Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis
journal, March 2019

Helber, Stephanie B.; Steinert, Georg; Wu, Yu-Chen
FEMS Microbiology Ecology, Vol. 95, Issue 4
DOI: 10.1093/femsec/fiz026

Biophysical processes supporting the diversity of microbial life in soil
journal, August 2017

Tecon, Robin; Or, Dani
FEMS Microbiology Reviews, Vol. 41, Issue 5
DOI: 10.1093/femsre/fux039

On the maverick Planctomycetes
journal, July 2018

Wiegand, Sandra; Jogler, Mareike; Jogler, Christian
FEMS Microbiology Reviews, Vol. 42, Issue 6
DOI: 10.1093/femsre/fuy029

The sponge microbiome project
journal, August 2017

Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon
GigaScience, Vol. 6, Issue 10
DOI: 10.1093/gigascience/gix077

Genomes OnLine database (GOLD) v.7: updates and new features
journal, October 2018

Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
Nucleic Acids Research, Vol. 47, Issue D1
DOI: 10.1093/nar/gky977

DPSN: standardizing the short names of amplicon-sequencing primers to avoid ambiguity
posted_content, January 2020

Tan, Yuxiang; Tian, Yixia; Chen, Junyu
bioRxiv
DOI: 10.1101/2020.01.23.916429

TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology
posted_content, October 2018

Valente Pires, Douglas Eduardo; Oliveira, Francislon Silva; Correa, Felipe Borim
BioRxiv
DOI: 10.1101/263293

An expectation-maximization-like algorithm enables accurate ecological modeling using longitudinal metagenome sequencing data
posted_content, January 2018

Li, Chenhao; Chng, Kern Rei; Av-Shalom, Tamar V.
bioRxiv
DOI: 10.1101/288803

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California
posted_content, May 2018

Ul-Hasan, Sabah; Bowers, Robert M.; Figueroa-Montiel, Andrea
bioRxiv
DOI: 10.1101/324442

Vertical transmission of sponge microbiota is inconsistent and unfaithful
posted_content, January 2019

Björk, Johannes R.; Diéz-Vives, Cristina; Astudillo-García, Carmen
bioRxiv
DOI: 10.1101/425009

The Impact of Uremia and Intestinal Dysbiosis on Hepatic Drug Metabolism in a Rat Model of Progressive Chronic Kidney Disease
posted_content, January 2019

Hartjes, Emily D.; Lim, Yong Jin; Velenosi, Thomas J.
BioRxiv
DOI: 10.1101/531939

Clonal reconstruction from time course genomic sequencing data
posted_content, November 2019

Ismail, Wazim Mohammed; Tang, Haixu
bioRxiv
DOI: 10.1101/832063

Host genetics and geography influence microbiome composition in the sponge Ircinia campana
journal, July 2019

Griffiths, Sarah M.; Antwis, Rachael E.; Lenzi, Luca
Journal of Animal Ecology, Vol. 88, Issue 11
DOI: 10.1111/1365-2656.13065

Validation of a universal set of primers to study animal‐associated microeukaryotic communities
journal, July 2019

del Campo, Javier; Pons, Maria J.; Herranz, Maria
Environmental Microbiology, Vol. 21, Issue 10
DOI: 10.1111/1462-2920.14733

Selection for novel metabolic capabilities in Salmonella enterica
journal, March 2019

Warsi, Omar; Lundin, Erik; Lustig, Ulrika
Evolution, Vol. 73, Issue 5
DOI: 10.1111/evo.13713

Impacts of indoor surface finishes on bacterial viability
journal, May 2019

Hu, Jinglin; Ben Maamar, Sarah; Glawe, Adam J.
Indoor Air, Vol. 29, Issue 4
DOI: 10.1111/ina.12558

Puberty and the Evolution of Developmental Science
journal, March 2019

Worthman, Carol M.; Dockray, Samantha; Marceau, Kristine
Journal of Research on Adolescence, Vol. 29, Issue 1
DOI: 10.1111/jora.12411

Coral-the world's most diverse symbiotic ecosystem
journal, October 2015

Blackall, Linda L.; Wilson, Bryan; van Oppen, Madeleine J. H.
Molecular Ecology, Vol. 24, Issue 21
DOI: 10.1111/mec.13400

First Release of the Bacterial Biobank of the Urban Environment (BBUE)
journal, October 2018

Antelo, Verónica; Salazar, Cecilia; Martínez, Arací
Microbiology Resource Announcements, Vol. 7, Issue 16
DOI: 10.1128/mra.01201-18

Extreme Dysbiosis of the Microbiome in Critical Illness
journal, August 2016

McDonald, Daniel; Ackermann, Gail; Khailova, Ludmila
mSphere, Vol. 1, Issue 4
DOI: 10.1128/msphere.00199-16

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
journal, November 2017

Videvall, Elin; Strandh, Maria; Engelbrecht, Anel
mSystems, Vol. 2, Issue 6
DOI: 10.1128/msystems.00132-17

The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont
journal, December 2019

Luter, Heidi M.; Whalan, Steve; Andreakis, Nikos
mSystems, Vol. 4, Issue 6
DOI: 10.1128/msystems.00743-19

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
journal, January 2016

Leung, Elo; Huang, Amy; Cadag, Eithon
BMC Bioinformatics, Vol. 17, Issue 1
DOI: 10.1186/s12859-016-0887-y

MMinte: an application for predicting metabolic interactions among the microbial species in a community
journal, September 2016

Mendes-Soares, Helena; Mundy, Michael; Soares, Luis Mendes
BMC Bioinformatics, Vol. 17, Issue 1
DOI: 10.1186/s12859-016-1230-3

Limitations of a metabolic network-based reverse ecology method for inferring host–pathogen interactions
journal, May 2017

Takemoto, Kazuhiro; Aie, Kazuki
BMC Bioinformatics, Vol. 18, Issue 1
DOI: 10.1186/s12859-017-1696-7

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture
journal, July 2017

Azman, Syafiq Kamarul; Anwar, Muhammad Zohaib; Henschel, Andreas
BMC Bioinformatics, Vol. 18, Issue 1
DOI: 10.1186/s12859-017-1763-0

Difficulty in inferring microbial community structure based on co-occurrence network approaches
journal, June 2019

Hirano, Hokuto; Takemoto, Kazuhiro
BMC Bioinformatics, Vol. 20, Issue 1
DOI: 10.1186/s12859-019-2915-1

Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation
journal, July 2017

Oliveira, Jorge S.; Araújo, Wydemberg J.; Figueiredo, Ricardo M.
BMC Microbiology, Vol. 17, Issue 1
DOI: 10.1186/s12866-017-1077-4

The impact of skin care products on skin chemistry and microbiome dynamics
journal, June 2019

Bouslimani, Amina; da Silva, Ricardo; Kosciolek, Tomasz
BMC Biology, Vol. 17, Issue 1
DOI: 10.1186/s12915-019-0660-6

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
journal, May 2016

Flygare, Steven; Simmon, Keith; Miller, Chase
Genome Biology, Vol. 17, Issue 1
DOI: 10.1186/s13059-016-0969-1

Heritable components of the human fecal microbiome are associated with visceral fat
journal, September 2016

Beaumont, Michelle; Goodrich, Julia K.; Jackson, Matthew A.
Genome Biology, Vol. 17, Issue 1
DOI: 10.1186/s13059-016-1052-7

Tiny microbes, enormous impacts: what matters in gut microbiome studies?
journal, October 2016

Debelius, Justine; Song, Se Jin; Vazquez-Baeza, Yoshiki
Genome Biology, Vol. 17, Issue 1
DOI: 10.1186/s13059-016-1086-x

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
journal, September 2017

McIntyre, Alexa B. R.; Ounit, Rachid; Afshinnekoo, Ebrahim
Genome Biology, Vol. 18, Issue 1
DOI: 10.1186/s13059-017-1299-7

Microbial community dynamics in mesophilic and thermophilic batch reactors under methanogenic, phenyl acid-forming conditions
journal, May 2020

Prem, Eva Maria; Stres, Blaz; Illmer, Paul
Biotechnology for Biofuels, Vol. 13, Issue 1
DOI: 10.1186/s13068-020-01721-z

Tentacle: distributed quantification of genes in metagenomes
journal, September 2015

Boulund, Fredrik; Sjögren, Anders; Kristiansson, Erik
GigaScience, Vol. 4, Issue 1
DOI: 10.1186/s13742-015-0078-1

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database
journal, May 2016

Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys
GigaScience, Vol. 5, Issue 1
DOI: 10.1186/s13742-016-0126-5

Context and the human microbiome
journal, November 2015

McDonald, Daniel; Birmingham, Amanda; Knight, Rob
Microbiome, Vol. 3, Issue 1
DOI: 10.1186/s40168-015-0117-2

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
journal, February 2018

Louca, Stilianos; Doebeli, Michael; Parfrey, Laura Wegener
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0420-9

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
journal, September 2018

Lager, Susanne; de Goffau, Marcus C.; Sovio, Ulla
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0529-x

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data
journal, August 2019

Li, Chenhao; Chng, Kern Rei; Kwah, Junmei Samantha
Microbiome, Vol. 7, Issue 1
DOI: 10.1186/s40168-019-0729-z

CoNet app: inference of biological association networks using Cytoscape
journal, January 2016

Faust, Karoline; Raes, Jeroen
F1000Research, Vol. 5
DOI: 10.12688/f1000research.9050.1

The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics
journal, January 2018

Shaaban, Heba; Westfall, David A.; Mohammad, Rawhi
Gates Open Research, Vol. 2
DOI: 10.12688/gatesopenres.12772.1

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples
journal, August 2017

Deck, John; Gaither, Michelle R.; Ewing, Rodney
PLOS Biology, Vol. 15, Issue 8
DOI: 10.1371/journal.pbio.2002925

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem
journal, September 2015

Rodríguez-Marconi, Susana; De la Iglesia, Rodrigo; Díez, Beatriz
PLOS ONE, Vol. 10, Issue 9
DOI: 10.1371/journal.pone.0138837

DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017

Goodwin, Kelly D.; Thompson, Luke R.; Duarte, Bernardo
Frontiers in Marine Science, Vol. 4
DOI: 10.3389/fmars.2017.00107

Back to the Future of Soil Metagenomics
journal, February 2016

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.00073

Predicting the HMA-LMA Status in Marine Sponges by Machine Learning
journal, May 2017

Moitinho-Silva, Lucas; Steinert, Georg; Nielsen, Shaun
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.00752

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities
journal, July 2017

Gravuer, Kelly; Eskelinen, Anu
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.01271

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution
journal, May 2018

Ingala, Melissa R.; Simmons, Nancy B.; Wultsch, Claudia
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.00803

Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens
journal, May 2018

Leung, Jacqueline M.; Graham, Andrea L.; Knowles, Sarah C. L.
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.00843

The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
journal, January 2019

Rocca, Jennifer D.; Simonin, Marie; Blaszczak, Joanna R.
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.03272

Simultaneous Metabarcoding of Eukaryotes and Prokaryotes to Elucidate the Community Structures within Tardigrade Microhabitats
journal, March 2020

Arakawa, Kazuharu
Diversity, Vol. 12, Issue 3
DOI: 10.3390/d12030110

Microbial and Phenyl Acid Dynamics during the Start-up Phase of Anaerobic Straw Degradation in Meso- and Thermophilic Batch Reactors
journal, December 2019

Prem, Eva Maria; Markt, Rudolf; Lackner, Nina
Microorganisms, Vol. 7, Issue 12
DOI: 10.3390/microorganisms7120657

Community-level cohesion without cooperation
journal, June 2016

Tikhonov, Mikhail
eLife, Vol. 5
DOI: 10.7554/elife.15747

Swarm v2: highly-scalable and high-resolution amplicon clustering
journal, January 2015

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher
PeerJ, Vol. 3
DOI: 10.7717/peerj.1420

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens
journal, January 2015

Luter, Heidi M.; Widder, Stefanie; Botté, Emmanuelle S.
PeerJ, Vol. 3
DOI: 10.7717/peerj.1435

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
journal, January 2017

Ijaz, Ali Z.; Jeffries, Thomas C.; Ijaz, Umer Z.
PeerJ, Vol. 5
DOI: 10.7717/peerj.3827

Generalized joint attribute modeling for biodiversity analysis: median‐zero, multivariate, multifarious data
journal, January 2017

Clark, James S.; Nemergut, Diana; Seyednasrollah, Bijan
Ecological Monographs, Vol. 87, Issue 1
DOI: 10.1002/ecm.1241

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities
journal, November 2016

Shulse, Christine N.; Maillot, Brianne; Smith, Craig R.
MicrobiologyOpen, Vol. 6, Issue 2
DOI: 10.1002/mbo3.428

Making big data smart—how to use metagenomics to understand soil quality
journal, March 2017

Vestergaard, Gisle; Schulz, Stefanie; Schöler, Anne
Biology and Fertility of Soils, Vol. 53, Issue 5
DOI: 10.1007/s00374-017-1191-3

A perspective on inter-kingdom signaling in plant–beneficial microbe interactions
journal, January 2016

Rosier, Amanda; Bishnoi, Usha; Lakshmanan, Venkatachalam
Plant Molecular Biology, Vol. 90, Issue 6
DOI: 10.1007/s11103-016-0433-3

MetaG: a graph-based metagenomic gene analysis for big DNA data
journal, July 2016

Chowdhury, Linkon; Khan, Mohammad Ibrahim; Deb, Kaushik
Network Modeling Analysis in Health Informatics and Bioinformatics, Vol. 5, Issue 1
DOI: 10.1007/s13721-016-0132-7

A communal catalogue reveals Earth’s multiscale microbial diversity
journal, November 2017

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
Nature, Vol. 551, Issue 7681
DOI: 10.1038/nature24621

Diversity, structure and convergent evolution of the global sponge microbiome
journal, June 2016

Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel
Nature Communications, Vol. 7, Issue 1
DOI: 10.1038/ncomms11870

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)
journal, December 2019

Rosado, Daniela; Xavier, Raquel; Severino, Ricardo
Scientific Reports, Vol. 9, Issue 1
DOI: 10.1038/s41598-019-55314-4

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia
journal, December 2016

Mello, Bruno L.; Alessi, Anna M.; McQueen-Mason, Simon
Scientific Reports, Vol. 6, Issue 1
DOI: 10.1038/srep38781

A parallel computational framework for ultra-large-scale sequence clustering analysis
journal, July 2018

Zheng, Wei; Mao, Qi; Genco, Robert J.
Bioinformatics, Vol. 35, Issue 3
DOI: 10.1093/bioinformatics/bty617

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance
journal, October 2015

Kato, Hiromi; Mori, Hiroshi; Maruyama, Fumito
DNA Research, Vol. 22, Issue 6
DOI: 10.1093/dnares/dsv023

Forest microbiome: diversity, complexity and dynamics
journal, November 2016

Baldrian, Petr
FEMS Microbiology Reviews
DOI: 10.1093/femsre/fuw040

MMinte: An application for predicting metabolic interactions among the microbial species in a community
posted_content, June 2016

Mendes-Soares, Helena; Mundy, Michael; Mendes-Soares, Luis
bioRxiv
DOI: 10.1101/059550

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples
journal, November 2018

Casimiro-Soriguer, Carlos S.; Loucera, CArlos; Florido, Javier Perez
Biology Direct
DOI: 10.1101/476853

HOPS: Automated detection and authentication of pathogen DNA in archaeological remains
posted_content, January 2019

Hübler, Ron; Key, Felix M.; Warinner, Christina
bioRxiv
DOI: 10.1101/534198

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring
journal, November 2018

Siegenthaler, Andjin; Wangensteen, Owen S.; Soto, Ana Z.
Molecular Ecology Resources, Vol. 19, Issue 1
DOI: 10.1111/1755-0998.12956

Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny
journal, November 2019

Gogarten, Jan F.; Calvignac‐Spencer, Sébastien; Nunn, Charles L.
Molecular Ecology Resources, Vol. 20, Issue 1
DOI: 10.1111/1755-0998.13101

LUCAS Soil, the largest expandable soil dataset for Europe: a review: LUCAS Soil, pan-European open-access soil dataset
journal, November 2017

Orgiazzi, A.; Ballabio, C.; Panagos, P.
European Journal of Soil Science, Vol. 69, Issue 1
DOI: 10.1111/ejss.12499

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability
journal, March 2016

Derycke, S.; De Meester, N.; Rigaux, A.
Molecular Ecology, Vol. 25, Issue 9
DOI: 10.1111/mec.13597

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats
journal, March 2018

Schuelke, Taruna; Pereira, Tiago José; Hardy, Sarah M.
Molecular Ecology, Vol. 27, Issue 8
DOI: 10.1111/mec.14539

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
journal, August 2017

Smits, Samuel A.; Leach, Jeff; Sonnenburg, Erica D.
Science, Vol. 357, Issue 6353
DOI: 10.1126/science.aan4834

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome
journal, May 2017

Neilson, Julia W.; Califf, Katy; Cardona, Cesar
mSystems, Vol. 2, Issue 3
DOI: 10.1128/mSystems.00195-16

The microbiome and ophthalmic disease
journal, November 2018

Baim, Adam D.; Movahedan, Asadolah; Farooq, Asim V.
Experimental Biology and Medicine, Vol. 244, Issue 6
DOI: 10.1177/1535370218813616

GLOSSary: the GLobal Ocean 16S subunit web accessible resource
journal, November 2018

Tangherlini, M.; Miralto, M.; Colantuono, C.
BMC Bioinformatics, Vol. 19, Issue S15
DOI: 10.1186/s12859-018-2423-8

Genetic influences on the human oral microbiome
journal, August 2017

Demmitt, Brittany A.; Corley, Robin P.; Huibregtse, Brooke M.
BMC Genomics, Vol. 18, Issue 1
DOI: 10.1186/s12864-017-4008-8

Clonal reconstruction from time course genomic sequencing data
journal, December 2019

Ismail, Wazim Mohammed; Tang, Haixu
BMC Genomics, Vol. 20, Issue S12
DOI: 10.1186/s12864-019-6328-3

The ocean sampling day consortium
journal, June 2015

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo
GigaScience, Vol. 4, Issue 1
DOI: 10.1186/s13742-015-0066-5

Taxa-function robustness in microbial communities
journal, March 2018

Eng, Alexander; Borenstein, Elhanan
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0425-4

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
journal, February 2017

Foster, Zachary S. L.; Sharpton, Thomas J.; Grünwald, Niklaus J.
PLOS Computational Biology, Vol. 13, Issue 2
DOI: 10.1371/journal.pcbi.1005404

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome
journal, March 2018

McCall, Laura-Isobel; Tripathi, Anupriya; Vargas, Fernando
PLOS Neglected Tropical Diseases, Vol. 12, Issue 3
DOI: 10.1371/journal.pntd.0006344

Research priorities for harnessing plant microbiomes in sustainable agriculture
text, January 2017

Alison, Bennett,; Mustafa, Morsy,; E., Leach, Jan
The University of North Carolina at Chapel Hill University Libraries
DOI: 10.17615/bt3a-tr35

Toward a global platform for linking soil biodiversity data
journal, July 2015

Ramirez, Kelly S.; Döring, Markus; Eisenhauer, Nico
Frontiers in Ecology and Evolution, Vol. 3
DOI: 10.3389/fevo.2015.00091

Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model
journal, October 2016

Deines, Peter; Bosch, Thomas C. G.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01610

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys
journal, March 2017

Thijs, Sofie; Op De Beeck, Michiel; Beckers, Bram
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.00494

A Risky Business? Habitat and Social Behavior Impact Skin and Gut Microbiomes in Caribbean Cleaning Gobies
journal, April 2019

Xavier, Raquel; Mazzei, Renata; Pérez-Losada, Marcos
Frontiers in Microbiology, Vol. 10
DOI: 10.3389/fmicb.2019.00716

Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition
journal, November 2019

Gowers, Glen-Oliver. F.; Vince, Oliver; Charles, John-Henry
Genes, Vol. 10, Issue 11
DOI: 10.3390/genes10110902

Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling
journal, June 2019

Rampelotto, Pabulo H.; Sereia, Aline F. R.; de Oliveira, Luiz Felipe V.
International Journal of Molecular Sciences, Vol. 20, Issue 12
DOI: 10.3390/ijms20123099

A Descriptive Review on the Prevalence of Gastrointestinal Disturbances and Their Multiple Associations in Autism Spectrum Disorder
journal, December 2019

Lefter, Radu; Ciobica, Alin; Timofte, Daniel
Medicina, Vol. 56, Issue 1
DOI: 10.3390/medicina56010011

Characterizing the Composition of the Pediatric Gut Microbiome: A Systematic Review
journal, December 2019

Deering, Kane E.; Devine, Amanda; O’Sullivan, Therese A.
Nutrients, Vol. 12, Issue 1
DOI: 10.3390/nu12010016

Microbial succession on decomposing root litter in a drought-prone Scots pine forest
text, January 2019

Herzog, Claude; Hartmann, Martin; Frey, Beat
ETH Zurich
DOI: 10.3929/ethz-b-000361643

Cyanobacterial endobionts within a major marine planktonic calcifier ( Globigerina bulloides , Foraminifera) revealed by 16S rRNA metabarcoding
journal, January 2017

Bird, Clare; Darling, Kate F.; Russell, Ann D.
Biogeosciences, Vol. 14, Issue 4
DOI: 10.5194/bg-14-901-2017

VSEARCH: a versatile open source tool for metagenomics
text, January 2016

Rognes, Torbjorn; Flouri, Tomas; Nichols, Ben
Karlsruhe
DOI: 10.5445/ir/1000062113

Swarm v2: highly-scalable and high-resolution amplicon clustering
posted_content, July 2015

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher
PeerJ Preprints
DOI: 10.7287/peerj.preprints.1222

Assessing alignment-based taxonomic classification of ancient microbial DNA
journal, January 2019

Eisenhofer, Raphael; Weyrich, Laura Susan
PeerJ, Vol. 7
DOI: 10.7717/peerj.6594

Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies
journal, January 2019

Ravenscraft, Alison; Berry, Michelle; Hammer, Tobin
Ecological Monographs, Vol. 89, Issue 2
DOI: 10.1002/ecm.1346

Comparative Metagenomics
book, December 2017

Maltez Thomas, Andrew; Prata Lima, Felipe; Maria Silva Moura, Livia
Comparative Genomics
DOI: 10.1007/978-1-4939-7463-4_8

Advancements in Microbial Genome Sequencing and Microbial Community Characterization
book, January 2019

Reddy, Bhaskar
Microbial Genomics in Sustainable Agroecosystems
DOI: 10.1007/978-981-13-8739-5_5

Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies
journal, August 2017

Pascoe, Emily L.; Hauffe, Heidi C.; Marchesi, Julian R.
The ISME Journal, Vol. 11, Issue 12
DOI: 10.1038/ismej.2017.133

Minimum Information about a Biosynthetic Gene cluster
journal, August 2015

Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin
Nature Chemical Biology, Vol. 11, Issue 9
DOI: 10.1038/nchembio.1890

Patterns of protist diversity associated with raw sewage in New York City
journal, July 2019

Maritz, Julia M.; Ten Eyck, Theresa A.; Elizabeth Alter, S.
The ISME Journal, Vol. 13, Issue 11
DOI: 10.1038/s41396-019-0467-z

Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease
journal, October 2018

Quintanilla, Elena; Ramírez-Portilla, Catalina; Adu-Oppong, Boahemaa
Scientific Reports, Vol. 8, Issue 1
DOI: 10.1038/s41598-018-33007-8

Diversity of macaque microbiota compared to the human counterparts
journal, October 2018

Chen, Zigui; Yeoh, Yun Kit; Hui, Mamie
Scientific Reports, Vol. 8, Issue 1
DOI: 10.1038/s41598-018-33950-6

Sequence clustering in bioinformatics: an empirical study
journal, September 2018

Zou, Quan; Lin, Gang; Jiang, Xingpeng
Briefings in Bioinformatics
DOI: 10.1093/bib/bby090

Consistent and correctable bias in metagenomic sequencing experiments
posted_content, July 2019

McLaren, Michael R.; Willis, Amy D.; Callahan, Benjamin J.
eLife
DOI: 10.1101/559831

Cultivating microbial dark matter in benzene-degrading methanogenic consortia: Microbes involved in anaerobic benzene activation
journal, December 2015

Luo, Fei; Devine, Cheryl E.; Edwards, Elizabeth A.
Environmental Microbiology, Vol. 18, Issue 9
DOI: 10.1111/1462-2920.13121

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments: Metagenome-based surveillance and diagnostic approaches
journal, September 2017

Doyle, Conor J.; O'Toole, Paul W.; Cotter, Paul D.
Environmental Microbiology, Vol. 19, Issue 11
DOI: 10.1111/1462-2920.13859

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes : Archaeal occurrence in high-altitude lakes
journal, January 2016

Ortiz-Alvarez, Rudiger; Casamayor, Emilio O.
Environmental Microbiology Reports, Vol. 8, Issue 2
DOI: 10.1111/1758-2229.12370

The ecologist's field guide to sequence‐based identification of biodiversity
journal, May 2016

Creer, Simon; Deiner, Kristy; Frey, Serita
Methods in Ecology and Evolution, Vol. 7, Issue 9
DOI: 10.1111/2041-210x.12574

Microbial assemblages reflect environmental heterogeneity in alpine streams
journal, May 2019

Hotaling, Scott; Foley, Mary E.; Zeglin, Lydia H.
Global Change Biology, Vol. 25, Issue 8
DOI: 10.1111/gcb.14683

Towards a macroscope: Leveraging technology to transform the breadth, scale and resolution of macroecological data
journal, November 2019

Dornelas, Maria; Madin, Elizabeth M. P.; Bunce, Michael
Global Ecology and Biogeography, Vol. 28, Issue 12
DOI: 10.1111/geb.13025

Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin
journal, August 2017

Longo, Ana V.; Zamudio, Kelly R.
Molecular Ecology, Vol. 26, Issue 18
DOI: 10.1111/mec.14220

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics
journal, May 2018

Cardona, Cesar; Lax, Simon; Larsen, Peter
mSystems, Vol. 3, Issue 3
DOI: 10.1128/msystems.00052-18

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota
journal, December 2018

Popovic, Ana; Bourdon, Celine; Wang, Pauline W.
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0612-3

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
journal, January 2016

Ramiro-Garcia, Javier; Hermes, Gerben D. A.; Giatsis, Christos
F1000Research, Vol. 5
DOI: 10.12688/f1000research.9227.1

Two dynamic regimes in the human gut microbiome
journal, February 2017

Gibbons, Sean M.; Kearney, Sean M.; Smillie, Chris S.
PLOS Computational Biology, Vol. 13, Issue 2
DOI: 10.1371/journal.pcbi.1005364

16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)
journal, January 2018

Bird, Clare; Darling, Kate F.; Russell, Ann D.
PLOS ONE, Vol. 13, Issue 1
DOI: 10.1371/journal.pone.0191653

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
text, January 2018

Louca, Stilianos; Doebeli, Michael; Parfrey, Laura W.
BioMed Central
DOI: 10.14288/1.0364063

Earth BioGenome Project: Sequencing life for the future of life.
journalarticle, January 2018

Lewin, Harris A.; Robinson, Gene E.; Kress, W. John
Proceedings of the National Academy of Sciences
DOI: 10.17863/cam.30734

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.
text, January 2015

Ziesemer, Kirsten A.; Mann, Allison E.; Sankaranarayanan, Krithivasan
Apollo - University of Cambridge Repository
DOI: 10.17863/cam.33198

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium
journal, November 2016

Chase, Alexander B.; Arevalo, Philip; Polz, Martin F.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01874

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body
journal, December 2019

Pausan, Manuela R.; Csorba, Cintia; Singer, Georg
Frontiers in Microbiology, Vol. 10
DOI: 10.3389/fmicb.2019.02796

PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults
journal, March 2019

Febvre, Hallie; Rao, Sangeeta; Gindin, Melinda
Nutrients, Vol. 11, Issue 3
DOI: 10.3390/nu11030666

First release of the bacterial biobank of the urban environment (BBUE)
text, January 2018

Antelo, Verónica; Salazar, Cecilia; Martínez, Arací
ETH Zurich
DOI: 10.3929/ethz-b-000304430

A communal catalogue reveals Earths multiscale microbial diversity
text, January 2017

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
ETH Zurich
DOI: 10.3929/ethz-b-000431177

Metabarcoding analysis of the Pacific harbor seal diet in Mexico
journal, July 2019

Brassea-Pérez, Elizabeth; Schramm, Yolanda; Heckel, Gisela
Marine Biology, Vol. 166, Issue 8
DOI: 10.1007/s00227-019-3555-8

Environmental sustainability: challenges and viable solutions
journal, December 2018

Arora, Naveen Kumar; Fatima, Tahmish; Mishra, Isha
Environmental Sustainability, Vol. 1, Issue 4
DOI: 10.1007/s42398-018-00038-w

The past, present and future of microbiome analyses
journal, September 2016

White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.
Nature Protocols, Vol. 11, Issue 11
DOI: 10.1038/nprot.2016.148

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems
journal, March 2018

Khaliq, Ihsanul; Hardy, Giles E. St J.; White, Diane
FEMS Microbiology Ecology, Vol. 94, Issue 5
DOI: 10.1093/femsec/fiy048

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain
journal, November 2016

Kwon, Min Jung; Beulig, Felix; Ilie, Iulia
Global Change Biology, Vol. 23, Issue 6
DOI: 10.1111/gcb.13558

Microbiomes in light of traits: A phylogenetic perspective
journal, November 2015

Martiny, J. B. H.; Jones, S. E.; Lennon, J. T.
Science, Vol. 350, Issue 6261
DOI: 10.1126/science.aac9323

Interactions between species introduce spurious associations in microbiome studies
journal, January 2018

Menon, Rajita; Ramanan, Vivek; Korolev, Kirill S.
PLOS Computational Biology, Vol. 14, Issue 1
DOI: 10.1371/journal.pcbi.1005939

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
collection, January 2018

Lager, Susanne; De Goffau, Marcus C.; Sovio, Ulla
Apollo - University of Cambridge Repository
DOI: 10.17863/cam.26436

Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight
journal, June 2019

Richardson, Elisabeth; Dacks, Joel B.
Microorganisms, Vol. 7, Issue 6
DOI: 10.3390/microorganisms7060178

Swarm v2: highly-scalable and high-resolution amplicon clustering
posted_content, July 2015

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher
PeerJ Preprints
DOI: 10.7287/peerj.preprints.1222v1

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis
journal, January 2018

Porter, Teresita M.; Hajibabaei, Mehrdad
Molecular Ecology, Vol. 27, Issue 2
DOI: 10.1111/mec.14478

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
journal, February 2019

Chen, Zigui; Hui, Pak Chun; Hui, Mamie
mSystems, Vol. 4, Issue 1
DOI: 10.1128/msystems.00271-18

HOPS: automated detection and authentication of pathogen DNA in archaeological remains
journal, December 2019

Hübler, Ron; Key, Felix M.; Warinner, Christina
Genome Biology, Vol. 20, Issue 1
DOI: 10.1186/s13059-019-1903-0

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples
journal, August 2019

Casimiro-Soriguer, Carlos S.; Loucera, Carlos; Perez Florido, Javier
Biology Direct, Vol. 14, Issue 1
DOI: 10.1186/s13062-019-0246-9

CoNet app: inference of biological association networks using Cytoscape
journal, January 2016

Faust, Karoline; Raes, Jeroen
F1000Research, Vol. 5
DOI: 10.12688/f1000research.9050.2

Earth BioGenome Project: Sequencing life for the future of life
journal, April 2018

Lewin, Harris A.; Robinson, Gene E.; Kress, W. John
Proceedings of the National Academy of Sciences, Vol. 115, Issue 17
DOI: 10.1073/pnas.1720115115

Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers
journal, June 2017

McIntyre, Alexa B. R.; Ounit, Rachid; Afshinnekoo, Ebrahim
Genome Biology
DOI: 10.1101/156919

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
journal, May 2016

Lan, Yemin; Rosen, Gail; Hershberg, Ruth
Microbiome, Vol. 4, Issue 1
DOI: 10.1186/s40168-016-0162-5

Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny
text, January 2019

Gogarten, Jan F.; Calvignac-Spencer, Sébastien; Nunn, Charles L.
Robert Koch-Institut
DOI: 10.25646/6621

Biophysical processes supporting the diversity of microbial life in soil
text, January 2017

Robin, Tecon,; Dani, Or,
ETH Zurich
DOI: 10.3929/ethz-b-000219910

Interactions between species introduce spurious associations in microbiome studies
text, January 2017

Menon, Rajita; Ramanan, Vivek; Korolev, Kirill S.
arXiv
DOI: 10.48550/arxiv.1708.04577

Edaphic and host plant factors are linked to the composition of arbuscular mycorrhizal fungal communities in the root zone of endangered Ulmus chenmoui Cheng in China
journal, July 2019

Song, Juan; Chen, Long; Chen, Fengmao
Ecology and Evolution, Vol. 9, Issue 15
DOI: 10.1002/ece3.5446

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
journal, January 2015

Bikel, Shirley; Valdez-Lara, Alejandra; Cornejo-Granados, Fernanda
Computational and Structural Biotechnology Journal, Vol. 13
DOI: 10.1016/j.csbj.2015.06.001

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes
journal, August 2019

Tsao, Han-Fei; Scheikl, Ute; Herbold, Craig
Water Research, Vol. 159
DOI: 10.1016/j.watres.2019.04.028

Strategies to improve reference databases for soil microbiomes
journal, December 2016

Choi, Jinlyung; Yang, Fan; Stepanauskas, Ramunas
The ISME Journal, Vol. 11, Issue 4
DOI: 10.1038/ismej.2016.168

Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, July 2018

Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
Nature Biotechnology, Vol. 36, Issue 7
DOI: 10.1038/nbt0718-660a

Diversity, structure and convergent evolution of the global sponge microbiome
journal, June 2016

Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel
Nature Communications, Vol. 7, Issue 1
DOI: 10.1038/ncomms11870

Stability of peatland carbon to rising temperatures
journal, December 2016

Wilson, R. M.; Hopple, A. M.; Tfaily, M. M.
Nature Communications, Vol. 7, Article No. 13723
DOI: 10.1038/ncomms13723

Patterns of protist diversity associated with raw sewage in New York City
journal, July 2019

Maritz, Julia M.; Ten Eyck, Theresa A.; Elizabeth Alter, S.
The ISME Journal, Vol. 13, Issue 11
DOI: 10.1038/s41396-019-0467-z

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
journal, November 2015

Ziesemer, Kirsten A.; Mann, Allison E.; Sankaranarayanan, Krithivasan
Scientific Reports, Vol. 5, Issue 1
DOI: 10.1038/srep16498

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia
journal, December 2016

Mello, Bruno L.; Alessi, Anna M.; McQueen-Mason, Simon
Scientific Reports, Vol. 6, Issue 1
DOI: 10.1038/srep38781

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space
journal, March 2019

Helbert, William; Poulet, Laurent; Drouillard, Sophie
Proceedings of the National Academy of Sciences, Vol. 116, Issue 13
DOI: 10.1073/pnas.1815791116

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance
journal, October 2015

Kato, Hiromi; Mori, Hiroshi; Maruyama, Fumito
DNA Research, Vol. 22, Issue 6
DOI: 10.1093/dnares/dsv023

The sponge microbiome project
journal, August 2017

Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon
GigaScience, Vol. 6, Issue 10
DOI: 10.1093/gigascience/gix077

Genomes OnLine database (GOLD) v.7: updates and new features
journal, October 2018

Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
Nucleic Acids Research, Vol. 47, Issue D1
DOI: 10.1093/nar/gky977

Interactions between species introduce spurious associations in microbiome studies
journal, May 2017

Menon, Rajita; Ramanan, Vivek; Korolev, Kirill S.
PLOS Computational Biology
DOI: 10.1101/176677

Clonal reconstruction from time course genomic sequencing data
posted_content, November 2019

Ismail, Wazim Mohammed; Tang, Haixu
bioRxiv
DOI: 10.1101/832063

Impacts of indoor surface finishes on bacterial viability
journal, May 2019

Hu, Jinglin; Ben Maamar, Sarah; Glawe, Adam J.
Indoor Air, Vol. 29, Issue 4
DOI: 10.1111/ina.12558

The Power of Engaging Citizen Scientists for Scientific Progress
journal, March 2016

Garbarino, Jeanne; Mason, Christopher E.
Journal of Microbiology & Biology Education, Vol. 17, Issue 1
DOI: 10.1128/jmbe.v17i1.1052

First Release of the Bacterial Biobank of the Urban Environment (BBUE)
journal, October 2018

Antelo, Verónica; Salazar, Cecilia; Martínez, Arací
Microbiology Resource Announcements, Vol. 7, Issue 16
DOI: 10.1128/mra.01201-18

Extreme Dysbiosis of the Microbiome in Critical Illness
journal, August 2016

McDonald, Daniel; Ackermann, Gail; Khailova, Ludmila
mSphere, Vol. 1, Issue 4
DOI: 10.1128/msphere.00199-16

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics
journal, May 2018

Cardona, Cesar; Lax, Simon; Larsen, Peter
mSystems, Vol. 3, Issue 3
DOI: 10.1128/msystems.00052-18

Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions
journal, June 2019

Muller, Emilie E. L.
mSystems, Vol. 4, Issue 3
DOI: 10.1128/msystems.00080-19

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
journal, February 2019

Chen, Zigui; Hui, Pak Chun; Hui, Mamie
mSystems, Vol. 4, Issue 1
DOI: 10.1128/msystems.00271-18

The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont
journal, December 2019

Luter, Heidi M.; Whalan, Steve; Andreakis, Nikos
mSystems, Vol. 4, Issue 6
DOI: 10.1128/msystems.00743-19

A Robust Framework for Microbial Archaeology
journal, August 2017

Warinner, Christina; Herbig, Alexander; Mann, Allison
Annual Review of Genomics and Human Genetics, Vol. 18, Issue 1
DOI: 10.1146/annurev-genom-091416-035526

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
journal, January 2016

Leung, Elo; Huang, Amy; Cadag, Eithon
BMC Bioinformatics, Vol. 17, Issue 1
DOI: 10.1186/s12859-016-0887-y

Limitations of a metabolic network-based reverse ecology method for inferring host–pathogen interactions
journal, May 2017

Takemoto, Kazuhiro; Aie, Kazuki
BMC Bioinformatics, Vol. 18, Issue 1
DOI: 10.1186/s12859-017-1696-7

GLOSSary: the GLobal Ocean 16S subunit web accessible resource
journal, November 2018

Tangherlini, M.; Miralto, M.; Colantuono, C.
BMC Bioinformatics, Vol. 19, Issue S15
DOI: 10.1186/s12859-018-2423-8

Genetic influences on the human oral microbiome
journal, August 2017

Demmitt, Brittany A.; Corley, Robin P.; Huibregtse, Brooke M.
BMC Genomics, Vol. 18, Issue 1
DOI: 10.1186/s12864-017-4008-8

Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation
journal, July 2017

Oliveira, Jorge S.; Araújo, Wydemberg J.; Figueiredo, Ricardo M.
BMC Microbiology, Vol. 17, Issue 1
DOI: 10.1186/s12866-017-1077-4

The impact of skin care products on skin chemistry and microbiome dynamics
journal, June 2019

Bouslimani, Amina; da Silva, Ricardo; Kosciolek, Tomasz
BMC Biology, Vol. 17, Issue 1
DOI: 10.1186/s12915-019-0660-6

HOPS: automated detection and authentication of pathogen DNA in archaeological remains
journal, December 2019

Hübler, Ron; Key, Felix M.; Warinner, Christina
Genome Biology, Vol. 20, Issue 1
DOI: 10.1186/s13059-019-1903-0

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples
journal, August 2019

Casimiro-Soriguer, Carlos S.; Loucera, Carlos; Perez Florido, Javier
Biology Direct, Vol. 14, Issue 1
DOI: 10.1186/s13062-019-0246-9

Context and the human microbiome
journal, November 2015

McDonald, Daniel; Birmingham, Amanda; Knight, Rob
Microbiome, Vol. 3, Issue 1
DOI: 10.1186/s40168-015-0117-2

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota
journal, December 2018

Popovic, Ana; Bourdon, Celine; Wang, Pauline W.
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0612-3

Trait-based analysis of the human skin microbiome
journal, July 2019

Bewick, Sharon; Gurarie, Eliezer; Weissman, Jake L.
Microbiome, Vol. 7, Issue 1
DOI: 10.1186/s40168-019-0698-2

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond
journal, January 2016

Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru
Microbes and Environments, Vol. 31, Issue 3
DOI: 10.1264/jsme2.me16024

Comparing Two Common DNA Extraction Kits for the Characterization of Symbiotic Microbial Communities from Ascidian Tissue
journal, January 2018

Evans, James S.; López-Legentil, Susanna; Erwin, Patrick M.
Microbes and Environments, Vol. 33, Issue 4
DOI: 10.1264/jsme2.me18031

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
journal, January 2016

Ramiro-Garcia, Javier; Hermes, Gerben D. A.; Giatsis, Christos
F1000Research, Vol. 5
DOI: 10.12688/f1000research.9227.1

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples
journal, August 2017

Deck, John; Gaither, Michelle R.; Ewing, Rodney
PLOS Biology, Vol. 15, Issue 8
DOI: 10.1371/journal.pbio.2002925

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
journal, April 2016

Granger, Brian R.; Chang, Yi-Chien; Wang, Yan
PLOS Computational Biology, Vol. 12, Issue 4
DOI: 10.1371/journal.pcbi.1004875

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
journal, February 2017

Foster, Zachary S. L.; Sharpton, Thomas J.; Grünwald, Niklaus J.
PLOS Computational Biology, Vol. 13, Issue 2
DOI: 10.1371/journal.pcbi.1005404

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
journal, January 2016

Weiss, Sophie J.; Mansell, Thomas J.; Mortazavi, Pooneh
PLOS ONE, Vol. 11, Issue 1
DOI: 10.1371/journal.pone.0146916

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
text, January 2018

Louca, Stilianos; Doebeli, Michael; Parfrey, Laura W.
BioMed Central
DOI: 10.14288/1.0364063

Toward a global platform for linking soil biodiversity data
journal, July 2015

Ramirez, Kelly S.; Döring, Markus; Eisenhauer, Nico
Frontiers in Ecology and Evolution, Vol. 3
DOI: 10.3389/fevo.2015.00091

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons
journal, August 2016

Ferrera, Isabel; Giner, Caterina R.; Reñé, Albert
Frontiers in Marine Science, Vol. 3
DOI: 10.3389/fmars.2016.00147

DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017

Goodwin, Kelly D.; Thompson, Luke R.; Duarte, Bernardo
Frontiers in Marine Science, Vol. 4
DOI: 10.3389/fmars.2017.00107

Exploring the avian gut microbiota: current trends and future directions
journal, July 2015

Waite, David W.; Taylor, Michael W.
Frontiers in Microbiology, Vol. 6
DOI: 10.3389/fmicb.2015.00673

Back to the Future of Soil Metagenomics
journal, February 2016

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.00073

In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates
journal, April 2016

Saurav, Kumar; Bar-Shalom, Rinat; Haber, Markus
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.00416

Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model
journal, October 2016

Deines, Peter; Bosch, Thomas C. G.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01610

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium
journal, November 2016

Chase, Alexander B.; Arevalo, Philip; Polz, Martin F.
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01874

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys
journal, March 2017

Thijs, Sofie; Op De Beeck, Michiel; Beckers, Bram
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.00494

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities
journal, July 2017

Gravuer, Kelly; Eskelinen, Anu
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.01271

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution
journal, May 2018

Ingala, Melissa R.; Simmons, Nancy B.; Wultsch, Claudia
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.00803

Bacterial Associates of a Gregarious Riparian Beetle With Explosive Defensive Chemistry
journal, October 2018

McManus, Reilly; Ravenscraft, Alison; Moore, Wendy
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.02361

The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
journal, January 2019

Rocca, Jennifer D.; Simonin, Marie; Blaszczak, Joanna R.
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.03272

A Risky Business? Habitat and Social Behavior Impact Skin and Gut Microbiomes in Caribbean Cleaning Gobies
journal, April 2019

Xavier, Raquel; Mazzei, Renata; Pérez-Losada, Marcos
Frontiers in Microbiology, Vol. 10
DOI: 10.3389/fmicb.2019.00716

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks
journal, August 2019

Revillini, Daniel; Wilson, Gail W. T.; Miller, R. Michael
Frontiers in Plant Science, Vol. 10
DOI: 10.3389/fpls.2019.01018

A Bioinformatics Guide to Plant Microbiome Analysis
journal, October 2019

Lucaciu, Rares; Pelikan, Claus; Gerner, Samuel M.
Frontiers in Plant Science, Vol. 10
DOI: 10.3389/fpls.2019.01313

A Descriptive Review on the Prevalence of Gastrointestinal Disturbances and Their Multiple Associations in Autism Spectrum Disorder
journal, December 2019

Lefter, Radu; Ciobica, Alin; Timofte, Daniel
Medicina, Vol. 56, Issue 1
DOI: 10.3390/medicina56010011

Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight
journal, June 2019

Richardson, Elisabeth; Dacks, Joel B.
Microorganisms, Vol. 7, Issue 6
DOI: 10.3390/microorganisms7060178

Sampling Terrestrial Environments for Bacterial Polyketides
journal, April 2017

Hill, Patrick; Heberlig, Graham; Boddy, Christopher
Molecules, Vol. 22, Issue 5
DOI: 10.3390/molecules22050707

Characterizing the Composition of the Pediatric Gut Microbiome: A Systematic Review
journal, December 2019

Deering, Kane E.; Devine, Amanda; O’Sullivan, Therese A.
Nutrients, Vol. 12, Issue 1
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Outlier Detection in BLAST Hits
text, January 2017

Shah, Nidhi; Altschul, Stephen F.; Pop, Mihai
Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany
DOI: 10.4230/lipics.wabi.2017.23

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens
journal, January 2015

Luter, Heidi M.; Widder, Stefanie; Botté, Emmanuelle S.
PeerJ, Vol. 3
DOI: 10.7717/peerj.1435

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
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Similar Records in DOE PAGES and OSTI.GOV collections:

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

Journal Article Gilbert, Jack A. ; Meyer, Folker ; Jansson, Janet ; ... - Standards in Genomic Sciences

Understanding microbes (bacterial, archaeal, eukaryal and viral) in terms of who they are and what they do is the challenge of microbial ecology. This concept was explored and a conceptual framework and action plan sketched out at the Terabase Metagenomics Workshop held in Snowbird, Utah between 18th and 24th July 2010; it was at this meeting that concept of the Earth Microbiome Project was initiated [1]. The Earth Microbiome Project (EMP) presents a revolution in how we tackle this problem and defines both questions and a potential suite of tools to provide answers. The EMP will provide a quantum leapmore »« less
https://doi.org/10.4056/aigs.1443528

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Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

Journal Article Gilbert, Jack A. ; Meyer, Folker ; Antonopoulos, Dion ; ... - Standards in Genomic Sciences

Between July 18th and 24th 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled “Terabase Metagenomics” and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250more »« less
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Journal Article Ma, Bin ; Wang, Yiling ; Ye, Shudi ; ... - Microbiome

Microbial interactions shape the structure and function of microbial communities; microbial association networks in specic environments have been widely developed to explore these complex systems, but their wired pattern across microbiomes in various environments at the global scale remains unexplored. Here we have inferred an Earth microbial association network from a communal catalogue with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. Results: This non-random scale-free Earth microbial association network consisted of 8 taxonomy distinct modules linked with dierent environments, which featured environment specic microbial associations. Dierent topological features of subnetworks inferredmore »« less
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https://doi.org/10.1186/s40168-020-00857-2

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Droughts are common throughout the world. As the climate changes, droughts may become more frequent and intense. Still, scientists are uncertain about how drought will affect the natural world, particularly the bacteria, fungi, and other microbes that live in soils. These tiny life forms are crucial because they control the Earth’s flows of carbon and essential nutrients. Researchers at the University of California, Irvine, and Lawrence Berkeley National Laboratory teamed up to study how the microbiome, or collection of bacteria and fungi in the soil, deals with drought. Since 2007, the researchers have used shelters with retractable roofs to preventmore »« less
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The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We alsomore »« less
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Title: The Earth Microbiome project: successes and aspirations

Abstract

Citation Formats

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine journal, January 2014

Evidence for a persistent microbial seed bank throughout the global ocean journal, March 2013

Distinct microbial communities associated with buried soils in the Siberian tundra journal, December 2013

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010. journal, January 2010

Human and Environmental Impacts on River Sediment Microbial Communities journal, May 2014

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 journal, November 2011

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea journal, December 2011

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project journal, January 2010

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems journal, September 2011

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome journal, July 2012

QIIME allows analysis of high-throughput community sequencing data journal, April 2010

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States journal, October 2013

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program journal, November 2009

EMPeror: a tool for visualizing high-throughput microbial community data journal, November 2013

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples journal, July 2013

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments journal, March 2014

Microbes en masse: The sequencing machine journal, July 2012

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill journal, January 2014

Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes journal, November 2003

The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change journal, April 2021

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems text, January 2011

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program journal, November 2009

Microbes en masse: The sequencing machine journal, July 2012

Distinct microbial communities associated with buried soils in the Siberian tundra journal, December 2013

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill journal, January 2014

Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi journal, September 2020

Evidence for a persistent microbial seed bank throughout the global ocean journal, March 2013

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States journal, October 2013

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments journal, March 2014

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010. journal, January 2010

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project journal, January 2010

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 journal, November 2011

The gut microbiome of nonhuman primates: Lessons in ecology and evolution journal, June 2018

Composition and stability of the vervet monkey milk microbiome journal, May 2019

The gut microbiome in human neurological disease: A review: Gut Microbiome journal, March 2017

Edaphic and host plant factors are linked to the composition of arbuscular mycorrhizal fungal communities in the root zone of endangered Ulmus chenmoui Cheng in China journal, July 2019

Innovation Rather than Improvement: A Solvable High-Dimensional Model Highlights the Limitations of Scalar Fitness journal, January 2018

Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists journal, February 2020

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses journal, February 2018

Strategies to improve reference databases for soil microbiomes journal, December 2016

Cohesion: a method for quantifying the connectivity of microbial communities journal, July 2017

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies journal, July 2016

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea journal, August 2017

Stability of peatland carbon to rising temperatures journal, December 2016

An assessment of US microbiome research journal, January 2016

Microbial diversity knows no borders journal, January 2018

Microbial succession on decomposing root litter in a drought-prone Scots pine forest journal, May 2019

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades journal, May 2019

Vertical transmission of sponge microbiota is inconsistent and unfaithful journal, July 2019

Detecting macroecological patterns in bacterial communities across independent studies of global soils journal, November 2017

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data journal, January 2020

Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial journal, July 2018

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae journal, August 2016

Scaling laws predict global microbial diversity journal, May 2016

Caenorhabditis elegans responses to bacteria from its natural habitats journal, June 2016

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space journal, March 2019

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Biophysical processes supporting the diversity of microbial life in soil journal, August 2017

On the maverick Planctomycetes journal, July 2018

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Genomes OnLine database (GOLD) v.7: updates and new features journal, October 2018

DPSN: standardizing the short names of amplicon-sequencing primers to avoid ambiguity posted_content, January 2020

TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology posted_content, October 2018

An expectation-maximization-like algorithm enables accurate ecological modeling using longitudinal metagenome sequencing data posted_content, January 2018

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California posted_content, May 2018

Vertical transmission of sponge microbiota is inconsistent and unfaithful posted_content, January 2019

The Impact of Uremia and Intestinal Dysbiosis on Hepatic Drug Metabolism in a Rat Model of Progressive Chronic Kidney Disease posted_content, January 2019

Clonal reconstruction from time course genomic sequencing data posted_content, November 2019

Host genetics and geography influence microbiome composition in the sponge Ircinia campana journal, July 2019

Validation of a universal set of primers to study animal‐associated microeukaryotic communities journal, July 2019

Selection for novel metabolic capabilities in Salmonella enterica journal, March 2019

Impacts of indoor surface finishes on bacterial viability journal, May 2019

Puberty and the Evolution of Developmental Science journal, March 2019

Coral-the world's most diverse symbiotic ecosystem journal, October 2015

First Release of the Bacterial Biobank of the Urban Environment (BBUE) journal, October 2018

Extreme Dysbiosis of the Microbiome in Critical Illness journal, August 2016

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes journal, November 2017

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
journal, January 2014

Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

Distinct microbial communities associated with buried soils in the Siberian tundra
journal, December 2013

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
journal, January 2010

Human and Environmental Impacts on River Sediment Microbial Communities
journal, May 2014

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011
journal, November 2011

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
journal, December 2011

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
journal, September 2011

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
journal, July 2012

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
journal, November 2009

EMPeror: a tool for visualizing high-throughput microbial community data
journal, November 2013

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
journal, July 2013

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
journal, March 2014

Microbes en masse: The sequencing machine
journal, July 2012

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014

Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes
journal, November 2003

The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change
journal, April 2021

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
text, January 2011

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
journal, November 2009

Microbes en masse: The sequencing machine
journal, July 2012

Distinct microbial communities associated with buried soils in the Siberian tundra
journal, December 2013

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014

Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
journal, September 2020

Evidence for a persistent microbial seed bank throughout the global ocean
journal, March 2013

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
journal, March 2014

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
journal, January 2010

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011
journal, November 2011

The gut microbiome of nonhuman primates: Lessons in ecology and evolution
journal, June 2018

Composition and stability of the vervet monkey milk microbiome
journal, May 2019

The gut microbiome in human neurological disease: A review: Gut Microbiome
journal, March 2017

Edaphic and host plant factors are linked to the composition of arbuscular mycorrhizal fungal communities in the root zone of endangered Ulmus chenmoui Cheng in China
journal, July 2019

Innovation Rather than Improvement: A Solvable High-Dimensional Model Highlights the Limitations of Scalar Fitness
journal, January 2018

Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
journal, February 2020

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses
journal, February 2018

Strategies to improve reference databases for soil microbiomes
journal, December 2016

Cohesion: a method for quantifying the connectivity of microbial communities
journal, July 2017

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
journal, July 2016

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017

Stability of peatland carbon to rising temperatures
journal, December 2016

An assessment of US microbiome research
journal, January 2016

Microbial diversity knows no borders
journal, January 2018

Microbial succession on decomposing root litter in a drought-prone Scots pine forest
journal, May 2019

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
journal, May 2019

Vertical transmission of sponge microbiota is inconsistent and unfaithful
journal, July 2019

Detecting macroecological patterns in bacterial communities across independent studies of global soils
journal, November 2017

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data
journal, January 2020

Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial
journal, July 2018

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae
journal, August 2016

Scaling laws predict global microbial diversity
journal, May 2016

Caenorhabditis elegans responses to bacteria from its natural habitats
journal, June 2016

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space
journal, March 2019

Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis
journal, March 2019

Biophysical processes supporting the diversity of microbial life in soil
journal, August 2017

On the maverick Planctomycetes
journal, July 2018

The sponge microbiome project
journal, August 2017

Genomes OnLine database (GOLD) v.7: updates and new features
journal, October 2018

DPSN: standardizing the short names of amplicon-sequencing primers to avoid ambiguity
posted_content, January 2020

TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology
posted_content, October 2018

An expectation-maximization-like algorithm enables accurate ecological modeling using longitudinal metagenome sequencing data
posted_content, January 2018

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California
posted_content, May 2018

Vertical transmission of sponge microbiota is inconsistent and unfaithful
posted_content, January 2019

The Impact of Uremia and Intestinal Dysbiosis on Hepatic Drug Metabolism in a Rat Model of Progressive Chronic Kidney Disease
posted_content, January 2019

Clonal reconstruction from time course genomic sequencing data
posted_content, November 2019

Host genetics and geography influence microbiome composition in the sponge Ircinia campana
journal, July 2019

Validation of a universal set of primers to study animal‐associated microeukaryotic communities
journal, July 2019

Selection for novel metabolic capabilities in Salmonella enterica
journal, March 2019

Impacts of indoor surface finishes on bacterial viability
journal, May 2019

Puberty and the Evolution of Developmental Science
journal, March 2019

Coral-the world's most diverse symbiotic ecosystem
journal, October 2015

First Release of the Bacterial Biobank of the Urban Environment (BBUE)
journal, October 2018

Extreme Dysbiosis of the Microbiome in Critical Illness
journal, August 2016

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
journal, November 2017

The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont
journal, December 2019

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
journal, January 2016

MMinte: an application for predicting metabolic interactions among the microbial species in a community
journal, September 2016