title: Demonstrating microbial co-occurrence pattern analyses within and between ecosystems.
abstract: Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities.
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University Ames, IA, USA.
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Williams
authors.affiliation: Mathematics and Computer Science, Argonne National Laboratory Argonne, IL, USA ; Microbiology and Microbial Genetics, Michigan State University East Lansing, MI, USA.
authors.forename: Adina
authors.initials: A
authors.lastname: Howe
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University Ames, IA, USA.
authors.forename: Kirsten S
authors.initials: KS
authors.lastname: Hofmockel
keywords: MGRAST; co-occurrence; community assembly; microbial communities; network theory
references.citation: BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S61
references.pmid: 20122237
references.citation: Nat Methods. 2012 Jun 10;9(8):811-4
references.pmid: 22688413
references.citation: ISME J. 2011 Sep;5(9):1414-25
references.pmid: 21430787
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Feb;69(2 Pt 2):026113
references.pmid: 14995526
references.citation: BMC Bioinformatics. 2003 Jan 13;4:2
references.pmid: 12525261
references.citation: ISME J. 2013 Aug;7(8):1493-506
references.pmid: 23575374
references.citation: Monogr Popul Biol. 1982;17:1-296
references.pmid: 7162524
references.citation: Appl Environ Microbiol. 2013 Nov;79(21):6617-25
references.pmid: 23974143
references.citation: Front Microbiol. 2013 Nov 27;4:342
references.pmid: 24348464
references.citation: Nature. 1998 Jun 4;393(6684):440-2
references.pmid: 9623998
references.citation: Nat Rev Microbiol. 2008 Sep;6(9):693-9
references.pmid: 18587409
references.citation: Bioinformatics. 2008 Jun 15;24(12):1461-2
references.pmid: 18441000
references.citation: Ecology. 2007 Jun;88(6):1345-53
references.pmid: 17601127
references.citation: Nat Rev Microbiol. 2012 Jul 16;10(8):538-50
references.pmid: 22796884
references.citation: Nat Methods. 2012 Apr 15;9(6):621-5
references.pmid: 22504588
references.citation: FEMS Microbiol Ecol. 2012 Sep;81(3):574-82
references.pmid: 22486161
references.citation: ISME J. 2012 Feb;6(2):330-42
references.pmid: 21881616
references.citation: Front Microbiol. 2012 Oct 11;3:347
references.pmid: 23087675
references.citation: PLoS One. 2013;8(2):e47879
references.pmid: 23408926
references.citation: PLoS Comput Biol. 2012;8(9):e1002687
references.pmid: 23028285
references.citation: Environ Microbiol. 2013 Sep;15(9):2517-31
references.pmid: 23647974
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15345-50
references.pmid: 20705897
references.citation: BMC Bioinformatics. 2008 Sep 19;9:386
references.pmid: 18803844
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7821-6
references.pmid: 12060727
references.citation: Annu Rev Microbiol. 2011;65:411-29
references.pmid: 21682646
references.citation: PLoS One. 2011;6(12):e28438
references.pmid: 22163302
references.citation: ISME J. 2012 Sep;6(9):1653-64
references.pmid: 22456445
references.citation: ISME J. 2011 Jul;5(7):1086-94
references.pmid: 21270841
references.citation: Trends Ecol Evol. 2005 Jun;20(6):345-53
references.pmid: 16701391
references.citation: Oecologia. 1990 Nov;85(1):74-79
references.pmid: 28310957
references.citation: Ecology. 2006 Jun;87(6):1399-410
references.pmid: 16869414
references.citation: Nat Rev Microbiol. 2010 Jul;8(7):523-9
references.pmid: 20531276
references.citation: Genome Res. 2010 Jul;20(7):947-59
references.pmid: 20458099
references.citation: ISME J. 2012 Feb;6(2):298-308
references.pmid: 21850055
references.citation: ISME J. 2013 Jun;7(6):1187-99
references.pmid: 23303371
references.citation: ISME J. 2012 Feb;6(2):343-51
references.pmid: 21900968
references.citation: Science. 2011 Dec 16;334(6062):1518-24
references.pmid: 22174245
references.citation: Nucleic Acids Res. 2010 Jul;38(12):3857-68
references.pmid: 20194113
references.citation: Front Microbiol. 2013 May 01;4:104
references.pmid: 23641242
references.citation: ISME J. 2013 Dec;7(12):2259-73
references.pmid: 23864126
references.citation: Science. 2009 Dec 18;326(5960):1694-7
references.pmid: 19892944
references.citation: Nature. 2009 May 14;459(7244):193-9
references.pmid: 19444205
references.citation: Front Microbiol. 2011 May 02;2:94
references.pmid: 21833332
references.citation: PLoS One. 2012;7(7):e40338
references.pmid: 22844402
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131