Computational methods for the analysis of tag sequences in metagenomics studies

Frontiers in Bioscience - Scholar

Volumn 4 S, Issue 4, 2012, Pages 1333-1343

  Chang, Qin ^a   Luan, Yihui ^a   Chen, Ting ^b,c   Fuhrman, Jed A ^b   Sun, Fengzhu ^b,c  

^a SHANDONG UNIVERSITY   (China)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

16S rRNA; Community comparison; Environment factors; Metagenomics; Operational taxonomic units (OTUs); Phylogeny; Review; Tag sequences

Indexed keywords

PROTEIN TAG; RNA 16S; RNA 18S;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; ENVIRONMENTAL FACTOR; GENETIC VARIABILITY; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOLECULAR PHYLOGENY; NONHUMAN; OPERATIONAL TAXONOMIC UNIT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ANIMAL; ENVIRONMENT; EXPRESSED SEQUENCE TAG; GENETICS; HUMAN; METAGENOME; METHODOLOGY; REVIEW;

OTUS;

ALGORITHMS; ANIMALS; ENVIRONMENT; EXPRESSED SEQUENCE TAGS; HUMANS; METAGENOME; METAGENOMICS; RNA, RIBOSOMAL, 16S;

EID: 84869419463     PISSN: 19450516     EISSN: 19450524     Source Type: Journal    
DOI: None     Document Type: Article

References (84)

1. J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy and R. M. Goodman: Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5(10), R245-249 (1998) (Pubitemid 29000111)
2. K. Chen and L. Pachter: Bioinformatics for wholegenome shotgun sequencing of microbial communities. PLoS Comput Biol 1(2), 106-112 (2005)
3. J. C. Wooley and Y. Ye: Metagenomics: Facts and Artifacts, and Computational Challenges. J Comput Sci Technol 25(1), 71-81 (2009)
4. D. A. Walsh, E. Bapteste, M. Kamekura and W. F. Doolittle: Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21(12), 2340-2351 (2004) (Pubitemid 39488904)
5. C. von Mering, P. Hugenholtz, J. Raes, S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward and P. Bork: Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126-1130 (2007) (Pubitemid 46328023)
6. E. Avaniss-Aghajani, K. Jones, D. Chapman and C. Brunk: A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17(1), 144-149 (1994) (Pubitemid 2114974)
7. W. T. Liu, T. L. Marsh, H. Cheng and L. J. Forney: Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11), 4516-4522 (1997) (Pubitemid 27485783)
8. G. Muyzer, E. C. de Waal and A. G. Uitterlinden: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3), 695-700 (1993) (Pubitemid 23072343)
9. M. Troussellier, H. Schafer, N. Batailler, L. Bernard, C. Courties, P. Lebaron, G. Muyzer, P. Servais and J. Vives-Rego: Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquatic Microbial Ecology 28(1), 13-24 (2002)
10. M. V. Brown and J. A. Fuhrman: Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquatic Microbial Ecology 41(1), 15-23 (2005) (Pubitemid 41784249)
11. M. M. Fisher and E. W. Triplett: Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65(10), 4630-4636 (1999)
12. J. A. Fuhrman, I. Hewson, M. S. Schwalbach, J. A. Steele, M. V. Brown and S. Naeem: Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A 103(35), 13104-13109 (2006) (Pubitemid 44338923)
13. J. A. Fuhrman, J. A. Steele, I. Hewson, M. S. Schwalbach, M. V. Brown, J. L. Green and J. H. Brown: A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A 105(22), 7774-7778 (2008) (Pubitemid 351872714)
14. J. B. H. Martiny, B. J. M. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman, J. L. Green, M. C. Horner-Devine, M. Kane, J. A. Krumins, C. R. Kuske, P. J. Morin, S. Naeem, L. Ovreas, A. L. Reysenbach, V. H. Smith and J. T. Staley: Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4(2), 102-112 (2006) (Pubitemid 43158153)
15. P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight and J. I. Gordon: A core gut microbiome in obese and lean twins. Nature 457(7228), 480-484 (2009)
16. P. J. Turnbaugh, R. E. Ley, M. A. Mahowald, V. Magrini, E. R. Mardis and J. I. Gordon: An obesityassociated gut microbiome with increased capacity for energy harvest. Nature 444(7122), 1027-1031 (2006) (Pubitemid 46018515)
17. Y. Sun, Y. Cai, V. Mai, W. Farmerie, F. Yu, J. Li and S. Goodison: Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data. Nucleic Acids Res 38(22), e205 (2010)
18. B. B. Oakley, T. L. Fiedler, J. M. Marrazzo and D. N. Fredricks: Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl Environ Microbiol 74(15), 4898-4909 (2008)
19. L. Dethlefsen, S. Huse, M. L. Sogin and D. A. Relman: The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6(11), e280 (2008)
20. C. Jernberg, S. Lofmark, C. Edlund and J. K. Jansson: Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1(1), 56-66 (2007) (Pubitemid 46717132)
21. S. R. Gill, M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turnbaugh, B. S. Samuel, J. I. Gordon, D. A. Relman, C. M. Fraser-Liggett and K. E. Nelson: Metagenomic analysis of the human distal gut microbiome. Science 312(5778), 1355-1359 (2006) (Pubitemid 43839542)
22. R. E. Ley, M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey, J. S. Bircher, M. L. Schlegel, T. A. Tucker, M. D. Schrenzel, R. Knight and J. I. Gordon: Evolution of mammals and their gut microbes. Science 320(5883), 1647-1651 (2008) (Pubitemid 351931256)
23. R. E. Ley, C. A. Lozupone, M. Hamady, R. Knight and J. I. Gordon: Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6(10), 776-788 (2008)
24. I. Nasidze, J. Li, D. Quinque, K. Tang and M. Stoneking: Global diversity in the human salivary microbiome. Genome Res 19(4), 636-643 (2009)
25. Z. Gao, C. H. Tseng, Z. Pei and M. J. Blaser: Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 104(8), 2927-2932 (2007) (Pubitemid 46327980)
26. E. A. Grice, H. H. Kong, G. Renaud, A. C. Young, G. G. Bouffard, R. W. Blakesley, T. G. Wolfsberg, M. L. Turner and J. A. Segre: A diversity profile of the human skin microbiota. Genome Res 18(7), 1043-1050 (2008) (Pubitemid 351931155)
27. E. M. Bik, P. B. Eckburg, S. R. Gill, K. E. Nelson, E. A. Purdom, F. Francois, G. Perez-Perez, M. J. Blaser and D. A. Relman: Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A 103(3), 732-737 (2006) (Pubitemid 43153094)
28. N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R. A. Edwards, B. Felts, S. Rayhawk, R. Knight, F. Rohwer and R. B. Jackson: Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73(21), 7059-7066 (2007) (Pubitemid 350076828)
29. D. B. Rusch, A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Remington, K. Beeson, B. Tran, H. Smith, H. Baden-Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews-Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y. H. Rogers, L. I. Falcon, V. Souza, G. Bonilla-Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gallardo, G. Tamayo-Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier and J. C. Venter: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3), e77 (2007)
30. M. L. Sogin, H. G. Morrison, J. A. Huber, D. Mark Welch, S. M. Huse, P. R. Neal, J. M. Arrieta and G. J. Herndl: Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103(32), 12115-12120 (2006) (Pubitemid 44215820)
31. S. G. Tringe and E. M. Rubin: Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6(11), 805-814 (2005)
32. S. G. Tringe, C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. W. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz and E. M. Rubin: Comparative metagenomics of microbial communities. Science 308(5721), 554-557 (2005) (Pubitemid 40570586)
33. G. W. Tyson, J. Chapman, P. Hugenholtz, E. E. Allen, R. J. Ram, P. M. Richardson, V. V. Solovyev, E. M. Rubin, D. S. Rokhsar and J. F. Banfield: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978), 37-43 (2004) (Pubitemid 38332350)
34. J. C. Venter, K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers and H. O. Smith: Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667), 66-74 (2004) (Pubitemid 38451457)
35. S. Yooseph, K. H. Nealson, D. B. Rusch, J. P. McCrow, C. L. Dupont, M. Kim, J. Johnson, R. Montgomery, S. Ferriera, K. Beeson, S. J. Williamson, A. Tovchigrechko, A. E. Allen, L. A. Zeigler, G. Sutton, E. Eisenstadt, Y. H. Rogers, R. Friedman, M. Frazier and J. C. Venter: Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468(7320), 60-66 (2010)
36. S. Yooseph, G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier and J. C. Venter: The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5(3), e16 (2007)
37. E. A. Dinsdale, R. A. Edwards, D. Hall, F. Angly, M. Breitbart, J. M. Brulc, M. Furlan, C. Desnues, M. Haynes, L. Li, L. McDaniel, M. A. Moran, K. E. Nelson, C. Nilsson, R. Olson, J. Paul, B. R. Brito, Y. Ruan, B. K. Swan, R. Stevens, D. L. Valentine, R. V. Thurber, L. Wegley, B. A. White and F. Rohwer: Functional metagenomic profiling of nine biomes. Nature 452(7187), 629-632 (2008) (Pubitemid 351483360)
38. N. R. Pace: A molecular view of microbial diversity and the biosphere. Science 276(5313), 734-740 (1997) (Pubitemid 27199842)
39. T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu and G. L. Andersen: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7), 5069-5072 (2006) (Pubitemid 44078840)
40. E. Pruesse, C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig, J. Peplies and F. O. Glockner: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35(21), 7188-7196 (2007)
41. A. E. Magurran: Measuring biological diversity. Blackwell Pub., Malden, Ma. (2004)
42. F. Meyer, D. Paarmann, M. D'Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening and R. A. Edwards: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008)
43. P. D. Schloss and J. Handelsman: Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71(3), 1501-1506 (2005) (Pubitemid 40396689)
44. P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, C. J. Robinson, J. W. Sahl, B. Stres, G. G. Thallinger, D. J. Van Horn and C. F. Weber: Introducing mothur: open-source, platform-independent, communitysupported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23), 7537-7541 (2009)
45. P. D. Schloss: The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6(7), e1000844 (2010)
46. J. R. White, S. Navlakha, N. Nagarajan, M. R. Ghodsi, C. Kingsford and M. Pop: Alignment and clustering of phylogenetic markers-implications for microbial diversity studies. BMC Bioinformatics 11, 152 (2010)
47. Y. Sun, Y. Cai, L. Liu, F. Yu, M. L. Farrell, W. McKendree and W. Farmerie: ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37(10), e76 (2009)
48. X. Hao, R. Jiang and T. Chen: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 27(5), 611-618 (2011)
49. S. M. Huse, D. M. Welch, H. G. Morrison and M. L. Sogin: Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12(7), 1889-1898 (2010)
50. P. D. Schloss and S. L. Westcott: Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis. Appl Environ Microbiol 77(10), 3219-3226 (2011)
51. Y. Sun, Y. Cai, S. M. Huse, R. Knight, W. G. Farmerie, X. Wang and V. Mai: A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief Bioinform, publshed online April 27 (2011)
52. Y. Ye: Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. BIBM, 153-157 (2010)
53. C. Quince, A. Lanzen, T. P. Curtis, R. J. Davenport, N. Hall, I. M. Head, L. F. Read and W. T. Sloan: Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6(9), 639-641 (2009)
54. C. Studholme, D. L. G. Hill and D. J. Hawkes: An overlap invariant entropy measure of 3D medical image alignment. Pattern Recognition 32(1), 71-86 (1999)
55. C. J. Van Rijsbergen: Information retrieval. Butterworths, London; Boston (1979)
56. W. Li, L. Jaroszewski and A. Godzik: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17(3), 282-283 (2001) (Pubitemid 32288218)
57. R. C. Edgar: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19), 2460-2461 (2010)
58. Y. Cai and Y. Sun: ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasi-linear computational time. Nucleic Acids Res Published online May 19 (2011)
59. P. Legendre and L. Legendre: Numerical ecology. Elsevier, Amsterdam ; New York (1998)
60. A. Chao, R. L. Chazdon, R. K. Colwell and T. J. Shen: A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters 8(2), 148-159 (2005) (Pubitemid 40218100)
61. J. Kuczynski, Z. Z. Liu, C. Lozupone, D. McDonald, N. Fierer and R. Knight: Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7(10), 813-819 (2010)
62. J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Pena, J. K. Goodrich, J. I. Gordon, G. A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C. A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J. R. Sevinsky, P. J. Tumbaugh, W. A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld and R. Knight: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5), 335-336 (2010)
63. P. D. Schloss and J. Handelsman: Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 72(10), 6773-6779 (2006) (Pubitemid 44582921)
64. P. D. Schloss: Evaluating different approaches that test whether microbial communities have the same structure. ISME J 2(3), 265-275 (2008) (Pubitemid 351334275)
65. A. P. Martin: Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68(8), 3673-3682 (2002) (Pubitemid 34836673)
66. P. D. Schloss and J. Handelsman: Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol 72(4), 2379-2384 (2006)
67. C. Lozupone and R. Knight: UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12), 8228-8235 (2005) (Pubitemid 41803949)
68. C. A. Lozupone, M. Hamady, S. T. Kelley and R. Knight: Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73(5), 1576-1585 (2007) (Pubitemid 46417883)
69. E. K. Costello, C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon and R. Knight: Bacterial community variation in human body habitats across space and time. Science 326(5960), 1694-1697 (2009)
70. R. E. Ley, F. Backhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight and J. I. Gordon: Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102(31), 11070-11075 (2005) (Pubitemid 41105994)
71. M. Hamady, C. Lozupone and R. Knight: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4(1), 17-27 (2010)
72. Q. Chang, Y. Luan and F. Sun: Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics 12(1), 118 (2011)
73. C. Lozupone, M. E. Lladser, D. Knights, J. Stombaugh and R. Knight: UniFrac: an effective distance metric for microbial community comparison. ISME J 5(2), 169-172 (2011)
74. S. Chaffron, H. Rehrauer, J. Pernthaler and C. von Mering: A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20(7), 947-959 (2010)
75. V. Batagelj and A. Mrvar: Pajek - Analysis and visualization of large networks. In: Graph Drawing Software. Ed M. Junger, P. Mutzel. (2003)
76. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13(11), 2498-2504 (2003) (Pubitemid 37428274)
77. Q. S. Ruan, D. Dutta, M. S. Schwalbach, J. A. Steele, J. A. Fuhrman and F. Z. Sun: Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22(20), 2532-2538 (2006) (Pubitemid 44560760)
78. L. C. Xia, J. A. Steele, J. Cram, Z. G. Cardon, S. L. Simmons, J. J. Vallino, J. A. Fuhrman and F. Sun: Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology (GIW2011) (2011)
79. S. F. Paver and A. D. Kent: Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes. Microbial Ecology 60(2), 406-418 (2010)
80. A. Shade, C. Y. Chiu and K. D. McMahon: Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment. Environ Microbiol 12(2), 455-466 (2010)
81. J. A. Steele, P. D. Countway, L. Xia, P. D. Vigil, J. M. Beman, D. Y. Kim, C. E. Chow, R. Sachdeva, A. C. Jones, M. S. Schwalbach, J. M. Rose, I. Hewson, A. Patel, F. Sun, D. A. Caron and J. A. Fuhrman: Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 5,1414-1425 (2011)
82. J. A. Fuhrman and J. A. Steele: Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquatic Microbial Ecology 53(1), 69-81 (2008)
83. J. A. Fuhrman: Microbial community structure and its functional implications. Nature 459(7244), 193-199 (2009)
84. J. A. Gilbert, D. Field, P. Swift, L. Newbold, A. Oliver, T. Smyth, P. J. Somerfield, S. Huse and I. Joint: The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11(12), 3132-3139 (2009)