TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

McDaniel, E. A.; van Steenbrugge, J. J. M.; Noguera, D. R.; McMahon, K. D.; Raaijmakers, J. M.; Medema, M. H.; Oyserman, B. O.

doi:10.1038/s43705-022-00189-2

TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

Journal Article · Mon Nov 07 00:00:00 EST 2022 · ISME Communications

DOI:https://doi.org/10.1038/s43705-022-00189-2· OSTI ID:1922512

^[1]; van Steenbrugge, J. J. M. ^[2]; Noguera, D. R. ^[3]; McMahon, K. D. ^[3]; Raaijmakers, J. M. ^[4]; Medema, M. H. ^[4]; ^[2]

Univ. of Wisconsin, Madison, WI (United States); University of Wisconsin—Madison Department of Bacteriology
Wageningen Univ. (Netherlands); Netherlands Institute of Ecological Research, Wageningen (Netherlands)
Univ. of Wisconsin, Madison, WI (United States)
Netherlands Institute of Ecological Research, Wageningen (Netherlands); Leiden Univ. (Netherlands)

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018409

OSTI ID:: 1922512

Journal Information:: ISME Communications, Journal Name: ISME Communications Journal Issue: 1 Vol. 2; ISSN 2730-6151

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (88)

Gene regulation by phosphate in enteric bacteria Wanner, B. L. Journal of Cellular Biochemistry, Vol. 51, Issue 1 https://doi.org/10.1002/jcb.240510110	journal	January 1993
Time‐series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems Linz, Alexandra M.; Aylward, Frank O.; Bertilsson, Stefan Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11306	journal	January 2020
The microbiology of biological phosphorus removal in activated sludge systems Seviour, Robert J.; Mino, Takashi; Onuki, Motoharu FEMS Microbiology Reviews, Vol. 27, Issue 1 https://doi.org/10.1016/S0168-6445(03)00021-4	journal	April 2003
Enrichment, Phylogenetic Analysis and Detection of a Bacterium That Performs Enhanced Biological Phosphate Removal in Activated Sludge Hesselmann, Rolf P. X.; Werlen, Christoph; Hahn, Dittmar Systematic and Applied Microbiology, Vol. 22, Issue 3 https://doi.org/10.1016/S0723-2020(99)80055-1	journal	September 1999
Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity Wolfe, Benjamin E.; Button, Julie E.; Santarelli, Marcela Cell, Vol. 158, Issue 2 https://doi.org/10.1016/j.cell.2014.05.041	journal	July 2014
Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities Enke, Tim N.; Datta, Manoshi S.; Schwartzman, Julia Current Biology, Vol. 29, Issue 9 https://doi.org/10.1016/j.cub.2019.03.047	journal	May 2019
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae Journal of Molecular Biology, Vol. 428, Issue 4 https://doi.org/10.1016/j.jmb.2015.11.006	journal	February 2016
Road MAPs to engineer host microbiomes Oyserman, Ben O.; Medema, Marnix H.; Raaijmakers, Jos M. Current Opinion in Microbiology, Vol. 43 https://doi.org/10.1016/j.mib.2017.11.023	journal	June 2018
Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants Andersen, Martin H.; McIlroy, Simon J.; Nierychlo, Marta Systematic and Applied Microbiology, Vol. 42, Issue 1 https://doi.org/10.1016/j.syapm.2018.08.001	journal	January 2019
Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors Camejo, Pamela Y.; Owen, Brian R.; Martirano, Joseph Water Research, Vol. 102 https://doi.org/10.1016/j.watres.2016.06.033	journal	October 2016
Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess Gao, Han; Mao, Yanping; Zhao, Xiaotian Water Research, Vol. 155 https://doi.org/10.1016/j.watres.2019.02.020	journal	May 2019
“Candidatus Accumulibacter delftensis”: A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate Rubio-Rincón, F. J.; Weissbrodt, D. G.; Lopez-Vazquez, C. M. Water Research, Vol. 161 https://doi.org/10.1016/j.watres.2019.03.053	journal	September 2019
Prospects for multi-omics in the microbial ecology of water engineering McDaniel, Elizabeth A.; Wahl, Sebastian Aljoscha; Ishii, Shun'ichi Water Research, Vol. 205 https://doi.org/10.1016/j.watres.2021.117608	journal	October 2021
Quantification of Biologically and Chemically Bound Phosphorus in Activated Sludge from Full-Scale Plants with Biological P-Removal Petriglieri, Francesca; Petersen, Jette F.; Peces, Miriam Environmental Science & Technology, Vol. 56, Issue 8 https://doi.org/10.1021/acs.est.1c02642	journal	March 2022
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal Wilmes, Paul; Andersson, Anders F.; Lefsrud, Mark G. The ISME Journal, Vol. 2, Issue 8 https://doi.org/10.1038/ismej.2008.38	journal	May 2008
A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal Kristiansen, Rikke; Nguyen, Hien Thi Thu; Saunders, Aaron Marc The ISME Journal, Vol. 7, Issue 3 https://doi.org/10.1038/ismej.2012.136	journal	November 2012
Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal Flowers, Jason J.; He, Shaomei; Malfatti, Stephanie The ISME Journal, Vol. 7, Issue 12 https://doi.org/10.1038/ismej.2013.117	journal	July 2013
Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis Oyserman, Ben O.; Noguera, Daniel R.; del Rio, Tijana Glavina The ISME Journal, Vol. 10, Issue 4 https://doi.org/10.1038/ismej.2015.155	journal	November 2015
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge McIlroy, Simon Jon; Karst, Søren Michael; Nierychlo, Marta The ISME Journal, Vol. 10, Issue 9 https://doi.org/10.1038/ismej.2016.14	journal	February 2016
Engineering microbial consortia for controllable outputs Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun-Seob The ISME Journal, Vol. 10, Issue 9 https://doi.org/10.1038/ismej.2016.26	journal	March 2016
Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria Oyserman, Ben O.; Moya, Francisco; Lawson, Christopher E. The ISME Journal, Vol. 10, Issue 12 https://doi.org/10.1038/ismej.2016.67	journal	April 2016
Community structure and metabolism through reconstruction of microbial genomes from the environment Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip Nature, Vol. 428, Issue 6978 https://doi.org/10.1038/nature02340	journal	February 2004
The worldwide leaf economics spectrum Wright, Ian J.; Reich, Peter B.; Westoby, Mark Nature, Vol. 428, Issue 6985 https://doi.org/10.1038/nature02403	journal	April 2004
Algae acquire vitamin B12 through a symbiotic relationship with bacteria Croft, Martin T.; Lawrence, Andrew D.; Raux-Deery, Evelyne Nature, Vol. 438, Issue 7064 https://doi.org/10.1038/nature04056	journal	November 2005
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam Nature Biotechnology, Vol. 31, Issue 6 https://doi.org/10.1038/nbt.2579	journal	May 2013
Near-optimal probabilistic RNA-seq quantification Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll Nature Biotechnology, Vol. 34, Issue 5 https://doi.org/10.1038/nbt.3519	journal	April 2016
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities Martín, Héctor García; Ivanova, Natalia; Kunin, Victor Nature Biotechnology, Vol. 24, Issue 10 https://doi.org/10.1038/nbt1247	journal	September 2006
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Metabolic network analysis reveals microbial community interactions in anammox granules Lawson, Christopher E.; Wu, Sha; Bhattacharjee, Ananda S. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15416	journal	May 2017
Species-specific transcriptomic network inference of interspecies interactions McClure, Ryan S.; Overall, Christopher C.; Hill, Eric A. The ISME Journal, Vol. 12, Issue 8 https://doi.org/10.1038/s41396-018-0145-6	journal	May 2018
Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman–FISH Fernando, Eustace Y.; McIlroy, Simon Jon; Nierychlo, Marta The ISME Journal, Vol. 13, Issue 8 https://doi.org/10.1038/s41396-019-0399-7	journal	March 2019
Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change Malik, Ashish A.; Martiny, Jennifer B. H.; Brodie, Eoin L. The ISME Journal, Vol. 14, Issue 1 https://doi.org/10.1038/s41396-019-0510-0	journal	September 2019
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics Hao, Liping; Michaelsen, Thomas Yssing; Singleton, Caitlin Margaret The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-019-0571-0	journal	January 2020
“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems Petriglieri, Francesca; Singleton, Caitlin; Peces, Miriam The ISME Journal, Vol. 15, Issue 12 https://doi.org/10.1038/s41396-021-01029-2	journal	June 2021
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide Singleton, C. M.; Petriglieri, F.; Wasmund, K. The ISME Journal, Vol. 16, Issue 6 https://doi.org/10.1038/s41396-022-01212-z	journal	February 2022
Trait-based community assembly and succession of the infant gut microbiome Guittar, John; Shade, Ashley; Litchman, Elena Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08377-w	journal	February 2019
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing Singleton, Caitlin M.; Petriglieri, Francesca; Kristensen, Jannie M. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22203-2	journal	March 2021
The social network of microorganisms — how auxotrophies shape complex communities Zengler, Karsten; Zaramela, Livia S. Nature Reviews Microbiology, Vol. 16, Issue 6 https://doi.org/10.1038/s41579-018-0004-5	journal	March 2018
Common principles and best practices for engineering microbiomes Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland Nature Reviews Microbiology, Vol. 17, Issue 12 https://doi.org/10.1038/s41579-019-0255-9	journal	September 2019
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis Crits-Christoph, Alexander; Diamond, Spencer; Butterfield, Cristina N. Nature, Vol. 558, Issue 7710 https://doi.org/10.1038/s41586-018-0207-y	journal	June 2018
Genome-centric view of carbon processing in thawing permafrost Woodcroft, Ben J.; Singleton, Caitlin M.; Boyd, Joel A. Nature, Vol. 560, Issue 7716 https://doi.org/10.1038/s41586-018-0338-1	journal	July 2018
MetaTrans: an open-source pipeline for metatranscriptomics Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep26447	journal	May 2016
Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail Lavorel, S.; Garnier, E. Functional Ecology, Vol. 16, Issue 5 https://doi.org/10.1046/j.1365-2435.2002.00664.x	journal	October 2002
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis Akashi, Hiroshi; Gojobori, Takashi Proceedings of the National Academy of Sciences, Vol. 99, Issue 6 https://doi.org/10.1073/pnas.062526999	journal	March 2002
Microbial community transcriptional networks are conserved in three domains at ocean basin scales Aylward, Frank O.; Eppley, John M.; Smith, Jason M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 17 https://doi.org/10.1073/pnas.1502883112	journal	March 2015
On r- and K-Selection Pianka, Eric R. The American Naturalist, Vol. 104, Issue 940 https://doi.org/10.1086/282697	journal	November 1970
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts611	journal	October 2012
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Aramaki, Takuya; Blanc-Mathieu, Romain; Endo, Hisashi Bioinformatics, Vol. 36, Issue 7 https://doi.org/10.1093/bioinformatics/btz859	journal	November 2019
Restoring degraded microbiome function with self-assembled communities Gutierrez, Carlos Fernando; Sanabria, Janeth; Raaijmakers, Jos M. FEMS Microbiology Ecology, Vol. 96, Issue 12 https://doi.org/10.1093/femsec/fiaa225	journal	November 2020
Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge Kindaichi, Tomonori; Yamaoka, Shiro; Uehara, Ryohei FEMS Microbiology Ecology, Vol. 92, Issue 6 https://doi.org/10.1093/femsec/fiw078	journal	April 2016
The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants Nierychlo, Marta; Miłobędzka, Aleksandra; Petriglieri, Francesca FEMS Microbiology Ecology, Vol. 95, Issue 2 https://doi.org/10.1093/femsec/fiy228	journal	November 2018
KEGG as a reference resource for gene and protein annotation Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1070	journal	October 2015
Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Zhang, H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 4 https://doi.org/10.1099/ijs.0.02520-0	journal	July 2003
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community: B-vitamin mosaics Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M. Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14133	journal	May 2018
Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms Wang, Yubo; Gao, Han; Wells, George Environmental Microbiology, Vol. 23, Issue 6 https://doi.org/10.1111/1462-2920.15486	journal	May 2021
Radiation of nitrogen‐metabolizing enzymes across the tree of life tracks environmental transitions in Earth history Parsons, Chris; Stüeken, Eva E.; Rosen, Caleb J. Geobiology, Vol. 19, Issue 1 https://doi.org/10.1111/gbi.12419	journal	October 2020
Let the concept of trait be functional! Violle, Cyrille; Navas, Marie-Laure; Vile, Denis Oikos, Vol. 116, Issue 5 https://doi.org/10.1111/j.0030-1299.2007.15559.x	journal	May 2007
A trait-based approach for modelling microbial litter decomposition Allison, S. D. Ecology Letters, Vol. 15, Issue 9 https://doi.org/10.1111/j.1461-0248.2012.01807.x	journal	May 2012
Identity, abundance and ecophysiology of filamentous Chloroflexi species present in activated sludge treatment plants Kragelund, Caroline; Levantesi, Caterina; Borger, Arjan FEMS Microbiology Ecology, Vol. 59, Issue 3 https://doi.org/10.1111/j.1574-6941.2006.00251.x	journal	March 2007
Denitrification capabilities of two biological phosphorus removal sludges dominated by different â€˜ Candidatus Accumulibacterâ€™ clades Flowers, Jason J.; He, Shaomei; Yilmaz, Safak Environmental Microbiology Reports, Vol. 1, Issue 6 https://doi.org/10.1111/j.1758-2229.2009.00090.x	journal	December 2009
Comparative Metagenomics of Microbial Communities Tringe, S. G. Science, Vol. 308, Issue 5721 https://doi.org/10.1126/science.1107851	journal	April 2005
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla Wrighton, K. C.; Thomas, B. C.; Sharon, I. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1224041	journal	September 2012
"Candidatus Accumulibacter" Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes He, S.; Gall, D. L.; McMahon, K. D. Applied and Environmental Microbiology, Vol. 73, Issue 18 https://doi.org/10.1128/AEM.01207-07	journal	August 2007
Identification of Polyphosphate-Accumulating Organisms and Design of 16S rRNA-Directed Probes for Their Detection and Quantitation Crocetti, G. R.; Hugenholtz, P.; Bond, P. L. Applied and Environmental Microbiology, Vol. 66, Issue 3 https://doi.org/10.1128/AEM.66.3.1175-1182.2000	journal	March 2000
Identity and Ecophysiology of Uncultured Actinobacterial Polyphosphate-Accumulating Organisms in Full-Scale Enhanced Biological Phosphorus Removal Plants Kong, Yunhong; Nielsen, Jeppe Lund; Nielsen, Per Halkjær Applied and Environmental Microbiology, Vol. 71, Issue 7 https://doi.org/10.1128/AEM.71.7.4076-4085.2005	journal	July 2005
Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal McDaniel, Elizabeth A.; Wever, Renske; Oyserman, Ben O. Microbiology Resource Announcements, Vol. 10, Issue 18 https://doi.org/10.1128/MRA.00244-21	journal	May 2021
Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior Lozano, Gabriel L.; Bravo, Juan I.; Garavito Diago, Manuel F. mBio, Vol. 10, Issue 2 https://doi.org/10.1128/mBio.02846-18	journal	March 2019
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI Hamilton, Joshua J.; Garcia, Sarahi L.; Brown, Brittany S. mSystems, Vol. 2, Issue 4 https://doi.org/10.1128/mSystems.00091-17	journal	August 2017
Integrated Omic Analyses Provide Evidence that a “Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions Camejo, Pamela Y.; Oyserman, Ben O.; McMahon, Katherine D. mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/mSystems.00193-18	journal	January 2019
Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics McDaniel, Elizabeth A.; Moya-Flores, Francisco; Keene Beach, Natalie mSystems, Vol. 6, Issue 4 https://doi.org/10.1128/mSystems.00474-21	journal	August 2021
Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “ Candidatus Accumulibacter” Petriglieri, Francesca; Singleton, Caitlin M.; Kondrotaite, Zivile mSystems, Vol. 7, Issue 3 https://doi.org/10.1128/msystems.00016-22	journal	June 2022
SAMSA2: a standalone metatranscriptome analysis pipeline Westreich, Samuel T.; Treiber, Michelle L.; Mills, David A. BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2189-z	journal	May 2018
COMAN: a web server for comprehensive metatranscriptomics analysis Ni, Yueqiong; Li, Jun; Panagiotou, Gianni BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2964-z	journal	August 2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie E. L. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1116-8	journal	December 2016
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality Jiang, Yue; Xiong, Xuejian; Danska, Jayne Microbiome, Vol. 4, Issue 1 https://doi.org/10.1186/s40168-015-0146-x	journal	January 2016
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences Soneson, Charlotte; Love, Michael I.; Robinson, Mark D. F1000Research, Vol. 4 https://doi.org/10.12688/f1000research.7563.1	journal	January 2015
Design of synthetic bacterial communities for predictable plant phenotypes Herrera Paredes, Sur; Gao, Tianxiang; Law, Theresa F. PLOS Biology, Vol. 16, Issue 2 https://doi.org/10.1371/journal.pbio.2003962	journal	February 2018
BBMerge – Accurate paired shotgun read merging via overlap Bushnell, Brian; Rood, Jonathan; Singer, Esther PLOS ONE, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pone.0185056	journal	October 2017
Effects of Biodiversity on Ecosystem Functioning: a Consensus of Current Knowledge Hooper, D. U.; Chapin, F. S.; Ewel, J. J. Ecological Monographs, Vol. 75, Issue 1 https://doi.org/10.1890/04-0922	journal	February 2005
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00251	journal	May 2014
Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria Mann, Evelyne; Wetzels, Stefanie U.; Wagner, Martin Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00043	journal	January 2018
The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge Speirs, Lachlan B. M.; Rice, Daniel T. F.; Petrovski, Steve Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02015	journal	September 2019
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality Jiang, Yue; Xiong, Xuejian; Danska, Jayne figshare https://doi.org/10.6084/m9.figshare.c.3630188.v1	collection	January 2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie Figshare https://doi.org/10.6084/m9.figshare.c.3647516	collection	January 2016
Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren, A. Murat; Esen, Özcan C.; Quince, Christopher PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1319	journal	January 2015

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