Computational meta'omics for microbial community studies

Abstract

Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.

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     Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS (2009 ) SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 25: 1722–1730

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108. 108.

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109. 109.

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110. 110.
     Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment · 2012

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111. 111.

     Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI (2011 ) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332: 970–974

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112. 112.

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113. 113.

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114. 114.

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115. 115.

     Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL (2010 ) A catalog of reference genomes from the human microbiome. Science 328: 994–999

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116. 116.

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117. 117.

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118. 118.

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119. 119.

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120. 120.

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121. 121.

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122. 122.

     Patil KR, Roune L, McHardy AC (2012 ) The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences. PloS One 7: e38581

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123. 123.

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124. 124.

     Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT (2012 ) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci USA 109: 13272–13277

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125. 125.

     Peng Y, Leung HC, Yiu SM, Chin FY (2011 ) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27: i94–101

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126. 126.

     Peng Y, Leung HC, Yiu SM, Chin FY (2012 ) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420–1428

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127. 127.
     Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut · 2013

     No notice
128. 128.
     Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. · 2011

     Not checked
129. 129.

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130. 130.

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131. 131.

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132. 132.

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133. 133.

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134. 134.

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135. 135.
     MetaSim—A Sequencing Simulator for Genomics and Metagenomics · 2008

     No notice
136. 136.

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137. 137.

     Rosen GL, Reichenberger ER, Rosenfeld AM (2011 ) NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics 27: 127–129

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138. 138.

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139. 139.

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140. 140.

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141. 141.

     Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II (2011 ) The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe 10: 260–272

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142. 142.
     Metagenomic biomarker discovery and explanation · 2011

     No notice
143. 143.

     Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012 ) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9: 811–814

     Not in our library10.1038/nmeth.2066

144. 144.
     CAMERA: A Community Resource for Metagenomics · 2007

     No notice
145. 145.

     Shi Y, Tyson GW, DeLong EF (2009 ) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266–269

     Not in our library10.1038/nature08055

146. 146.

     Shi Y, Tyson GW, Eppley JM, DeLong EF (2011 ) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5: 999–1013

     Not in our library10.1038/ismej.2010.189

147. 147.

     Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011 ) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241–244

     Not in our library10.1038/nature10571

148. 148.

     Southward AJ, Langmead O, Hardman-Mountford NJ, Aiken J, Boalch GT, Dando PR, Genner MJ, Joint I, Kendall MA, Halliday NC, Harris RP, Leaper R, Mieszkowska N, Pingree RD, Richardson AJ, Sims DW, Smith T, Walne AW, Hawkins SJ (2005 ) Long-term oceanographic and ecological research in the Western English Channel. Adv Marine Biol 47: 1–105

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149. 149.

     Su CH, Hsu MT, Chiang S, Cheng JH, Weng FC, Wang D, Tsai HK (2011 ) MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering. Bioinformatics 27: 2298–2299

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150. 150.

     Tatusov RL, Koonin EV, Lipman DJ (1997 ) A genomic perspective on protein families. Science 278: 631–637

     Not in our library10.1126/science.278.5338.631

151. 151.
     TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences · 2004

     No notice
152. 152.

     The Human Microbiome Project Consortium. (2012a ) A framework for human microbiome research. Nature 486: 215–221

     Not in our library10.1038/nature11209

153. 153.

     The Human Microbiome Project Consortium. (2012b ) Structure, function and diversity of the healthy human microbiome. Nature 486: 207–214

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154. 154.

     Treangen TJ, Koren S, Astrovskaya I, Sommer D, Liu B, Pop M (2011a ) MetAMOS: a metagenomic assembly and analysis pipeline for AMOS. Genome Biol 12: 1–27

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155. 155.

     Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M (2011b ) Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics 33: 11.8.1–11.8.18

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156. 156.

     Tringe SG, Hugenholtz P (2008 ) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442–446

     Not in our library10.1016/j.mib.2008.09.011

157. 157.

     Turnbaugh PJ, Gordon JI (2008 ) An invitation to the marriage of metagenomics and metabolomics. Cell 134: 708–713

     Not in our library10.1016/j.cell.2008.08.025

158. 158.

     Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009a ) A core gut microbiome in obese and lean twins. Nature 457: 480–484

     Not in our library10.1038/nature07540

159. 159.

     Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI (2010 ) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci USA 107: 7503–7508

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160. 160.

     Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009b ) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14

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161. 161.

     Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004 ) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43

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162. 162.

     Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Equinda M, Lipuma L, Ling L, Gobourne A, No D (2013 ) Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun 81: 965–973

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163. 163.

     Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009 ) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3: 179–189

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164. 164.

     Wang Y, Leung HCM, Yiu S, Chin FYL (2012 ) MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species. Journal of Computational Biology 19: 241–249

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165. 165.

     Weber M, Teeling H, Huang S, Waldmann J, Kassabgy M, Fuchs BM, Klindworth A, Klockow C, Wichels A, Gerdts G (2010 ) Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J 5: 918–928

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166. 166.
     Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples · 2009

     No notice
167. 167.

     Wilmes P, Bond PL (2006 ) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92–97

     Not in our library10.1016/j.tim.2005.12.006

168. 168.
     One Bacterial Cell, One Complete Genome · 2010

     No notice
169. 169.
     Assembling the Marine Metagenome, One Cell at a Time · 2009

     No notice
170. 170.

     Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'Haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M (2009 ) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056–1060

     Not in our library10.1038/nature08656

171. 171.

     Wu M, Scott AJ (2012 ) Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28: 1033–1034

     Not in our library10.1093/bioinformatics/bts079

172. 172.

     Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R (2012 ) Human gut microbiome viewed across age and geography. Nature 486: 222–227

     Not in our library10.1038/nature11053

173. 173.

     Ye Y, Tang H (2009 ) An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol 7: 455–471

     Not in our library10.1142/s0219720009004151

174. 174.

     Zengler K, Palsson BO (2012 ) A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol 10: 366–372

     Not in our library10.1038/nrmicro2763

175. 175.

     Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ (2012 ) Decade-long bacterial community dynamics in cystic fibrosis airways. Pro Natl Acad Sci 109: 5809–5814

     Not in our library10.1073/pnas.1120577109

Cited by papers we hold 19

• Ecosystem-specific microbiota and microbiome databases in the era of big data · 2022
  Not checked
• A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease · 2022
  Not checked
• Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities · 2021
  No notice
• Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 · 2021
  No notice
• Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences · 2019
  No notice
• The Healthy Human Blood Microbiome: Fact or Fiction? · 2019
  No notice
• Advancing functional and translational microbiome research using meta-omics approaches · 2019
  No notice
• Gut Dysbiosis and Muscle Aging: Searching for Novel Targets against Sarcopenia · 2018
  No notice
• Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors · 2018
  No notice
• Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis · 2017
  No notice
• IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses · 2016
  No notice
• Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics · 2016
  No notice
• Fast and sensitive taxonomic classification for metagenomics with Kaiju · 2016
  No notice
• Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights · 2016
  No notice
• Review article: dietary fibre-microbiota interactions · 2015
  No notice
• The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics · 2015
  No notice
• Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible · 2014
  No notice
• Analysis of plant microbe interactions in the era of next generation sequencing technologies · 2014
  No notice
• Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota · 2013
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.