The past, present and future of microbiome analyses

White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.; Baker, Erin S.; Jansson, Janet K.

doi:10.1038/nprot.2016.148

Title: The past, present and future of microbiome analyses

Journal Article · Thu Sep 29 00:00:00 EDT 2016 · Nature Protocols

DOI:https://doi.org/10.1038/nprot.2016.148· OSTI ID:1340873

White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.; Baker, Erin S.; Jansson, Janet K.

Microbes evolved on Earth approximately 3.5 billion years ago and eventually occupied every habitable environment in its biosphere. While microorganisms are responsible for key functions on Earth including carbon and nutrient cycling and determining the health and disease of its inhabitants (i.e. plants and animals), >99% of the estimated trillions of microbes have yet to be discovered.1 In addition, high microbial diversity has made it difficult to study specific functions carried out by complex microbial communities within "microbiomes", such as those inhabiting the soil and human gut.2,3 Fortunately, technological advances over the last few decades have greatly facilitated studies of complex microbiomes and their functions. Here we will specifically discuss advances related to nucleic acid sequencing and mass spectrometry analyses that have enabled exploration and understanding of complex microbiomes in a range of environments and our own bodies.4,5,6,7

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Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1340873

Report Number(s):: PNNL-SA-119986

Journal Information:: Nature Protocols, Vol. 11, Issue 11; ISSN 1754-2189

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

References (46)

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome Burnum, Kristin E.; Callister, Stephen J.; Nicora, Carrie D. The ISME Journal, Vol. 5, Issue 1 https://doi.org/10.1038/ismej.2010.97	journal	July 2010
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya mSystems, Vol. 1, Issue 3 https://doi.org/10.1128/mSystems.00045-16	journal	June 2016
Negative ion production with the electrospray ion source Yamashita, Masamichi; Fenn, John B. The Journal of Physical Chemistry, Vol. 88, Issue 20 https://doi.org/10.1021/j150664a046	journal	September 1984
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.59	journal	June 2012
Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel Gilbert, Jack A.; Meyer, Folker; Schriml, Lynn Standards in Genomic Sciences, Vol. 3, Issue 2 https://doi.org/10.4056/sigs.1202536	journal	October 2010
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw Mackelprang, Rachel; Waldrop, Mark P.; DeAngelis, Kristen M. Nature, Vol. 480, Issue 7377 https://doi.org/10.1038/nature10576	journal	November 2011
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms Sharon, Itai; Kertesz, Michael; Hug, Laura A. Genome Research, Vol. 25, Issue 4 https://doi.org/10.1101/gr.183012.114	journal	February 2015
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean Shi, Yanmei; Tyson, Gene W.; Eppley, John M. The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.189	journal	December 2010
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14238	journal	March 2015
Real-Time DNA Sequencing from Single Polymerase Molecules Eid, John; Fehr, Adrian; Gray, Jeremy Science, Vol. 323, Issue 5910, p. 133-138 https://doi.org/10.1126/science.1162986	journal	January 2009
A decade of metaproteomics: Where we stand and what the future holds: PROTEOMICS Wilmes, Paul; Heintz-Buschart, Anna; Bond, Philip L. PROTEOMICS, Vol. 15, Issue 20 https://doi.org/10.1002/pmic.201500183	journal	September 2015
Shotgun metaproteomics of the human distal gut microbiota Verberkmoes, Nathan C.; Russell, Alison L.; Shah, Manesh The ISME Journal, Vol. 3, Issue 2 https://doi.org/10.1038/ismej.2008.108	journal	October 2008
Environmental Genome Shotgun Sequencing of the Sargasso Sea Venter, J. C. Science, Vol. 304, Issue 5667 https://doi.org/10.1126/science.1093857	journal	April 2004
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates Zoetendal, Erwin G.; Raes, Jeroen; van den Bogert, Bartholomeus The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.212	journal	January 2012
The Orbitrap: a new mass spectrometer Hu, Qizhi; Noll, Robert J.; Li, Hongyan Journal of Mass Spectrometry, Vol. 40, Issue 4 https://doi.org/10.1002/jms.856	journal	January 2005
Enhancing bottom-up and top-down proteomic measurements with ion mobility separations Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M. PROTEOMICS, Vol. 15, Issue 16 https://doi.org/10.1002/pmic.201500048	journal	July 2015
A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes Willing, Ben P.; Dicksved, Johan; Halfvarson, Jonas Gastroenterology, Vol. 139, Issue 6 https://doi.org/10.1053/j.gastro.2010.08.049	journal	December 2010
A multi-omic future for microbiome studies Jansson, Janet K.; Baker, Erin S. Nature Microbiology, Vol. 1, Issue 5 https://doi.org/10.1038/nmicrobiol.2016.49	journal	April 2016
‘Omics’ of the mammalian gut – new insights into function Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet K. Current Opinion in Biotechnology, Vol. 23, Issue 3 https://doi.org/10.1016/j.copbio.2012.01.016	journal	June 2012
Community Proteomics of a Natural Microbial Biofilm Ram, R. J. Science, Vol. 308, Issue 5730 https://doi.org/10.1126/science. 1109070	journal	June 2005
The genome sequence of the colonial chordate, Botryllus schlosseri Voskoboynik, Ayelet; Neff, Norma F.; Sahoo, Debashis eLife, Vol. 2 https://doi.org/10.7554/eLife.00569	journal	July 2013
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations Levene, M. J. Science, Vol. 299, Issue 5607 https://doi.org/10.1126/science.1079700	journal	January 2003
Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Jacobs, Jon M. Molecular & Cellular Proteomics, Vol. 13, Issue 4, p. 1119-1127 https://doi.org/10.1074/mcp.M113.034595	journal	January 2014
Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens Aylward, Frank O.; Burnum-Johnson, Kristin E.; Tringe, Susannah G. Applied and Environmental Microbiology, Vol. 79, Issue 12 https://doi.org/10.1128/AEM.03833-12	journal	April 2013
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community Handley, Kim M.; VerBerkmoes, Nathan C.; Steefel, Carl I. The ISME Journal, Vol. 7, Issue 4 https://doi.org/10.1038/ismej.2012.148	journal	November 2012
Microbial community gene expression in ocean surface waters Frias-Lopez, J.; Shi, Y.; Tyson, G. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 10 https://doi.org/10.1073/pnas.0708897105	journal	March 2008
The Earth Microbiome project: successes and aspirations Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob BMC Biology, Vol. 12, Issue 1 https://doi.org/10.1186/s12915-014-0069-1	journal	August 2014
Accurate whole human genome sequencing using reversible terminator chemistry Bentley, David R.; Balasubramanian, Shankar; Swerdlow, Harold P. Nature, Vol. 456, Issue 7218 https://doi.org/10.1038/nature07517	journal	November 2008
DNA sequencing with chain-terminating inhibitors Sanger, F.; Nicklen, S.; Coulson, A. R. Proceedings of the National Academy of Sciences, Vol. 74, Issue 12 https://doi.org/10.1073/pnas.74.12.5463	journal	December 1977
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Fleischmann, R.; Adams, M.; White, O. Science, Vol. 269, Issue 5223 https://doi.org/10.1126/science.7542800	journal	July 1995
Performance comparison of benchtop high-throughput sequencing platforms Loman, Nicholas J.; Misra, Raju V.; Dallman, Timothy J. Nature Biotechnology, Vol. 30, Issue 5 https://doi.org/10.1038/nbt.2198	journal	April 2012
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
Diversity, stability and resilience of the human gut microbiota Lozupone, Catherine A.; Stombaugh, Jesse I.; Gordon, Jeffrey I. Nature, Vol. 489, Issue 7415 https://doi.org/10.1038/nature11550	journal	September 2012
Scaling laws predict global microbial diversity Locey, Kenneth J.; Lennon, Jay T. Proceedings of the National Academy of Sciences, Vol. 113, Issue 21 https://doi.org/10.1073/pnas.1521291113	journal	May 2016
DNA SEQUENCING:A Sequencing Method Based on Real-Time Pyrophosphate Ronaghi, M. Science, Vol. 281, Issue 5375 https://doi.org/10.1126/science.281.5375.363	journal	July 1998
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu Nature Biotechnology, Vol. 34, Issue 1 https://doi.org/10.1038/nbt.3416	journal	January 2016
A unified initiative to harness Earth's microbiomes Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L. Science, Vol. 350, Issue 6260 https://doi.org/10.1126/science.aac8480	journal	October 2015
The sequence of sequencers: The history of sequencing DNA Heather, James M.; Chain, Benjamin Genomics, Vol. 107, Issue 1 https://doi.org/10.1016/j.ygeno.2015.11.003	journal	January 2016
Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants Aylward, Frank O.; Khadempour, Lily; Tremmel, Daniel M. PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0134752	journal	August 2015
The methylomes of six bacteria Murray, Iain A.; Clark, Tyson A.; Morgan, Richard D. Nucleic Acids Research, Vol. 40, Issue 22 https://doi.org/10.1093/nar/gks891	journal	October 2012
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation: Metabolomics of leaf-cutter ant fungus gardens Huang, Eric L.; Aylward, Frank O.; Kim, Young-Mo Environmental Microbiology Reports, Vol. 6, Issue 4 https://doi.org/10.1111/1758-2229.12163	journal	April 2014
Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08055	journal	May 2009
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities Gilbert, Jack A.; Field, Dawn; Huang, Ying PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0003042	journal	August 2008
Assessing the performance of the Oxford Nanopore Technologies MinION Laver, T.; Harrison, J.; O’Neill, P. A. Biomolecular Detection and Quantification, Vol. 3 https://doi.org/10.1016/j.bdq.2015.02.001	journal	March 2015
The Complete Genome Sequence of Escherichia coli K-12 Blattner, F. R. Science, Vol. 277, Issue 5331 https://doi.org/10.1126/science.277.5331.1453	journal	September 1997
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio The ISME Journal, Vol. 8, Issue 7 https://doi.org/10.1038/ismej.2013.254	journal	January 2014

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