Research graph
References from Experimental and computational approaches to unravel microbial community assembly. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1086/652373
10.1086/652373 · External reference
10.1126/science.1153213
10.1126/science.1153213 · External reference
10.1126/science.aat1168
10.1126/science.aat1168 · External reference
Stochastic community assembly: does it matter in microbial ecology?
10.1128/mmbr.00002-17 · 2017 · External reference
10.1038/nature24621
10.1038/nature24621 · External reference
10.1016/j.cub.2019.03.047
10.1016/j.cub.2019.03.047 · External reference
10.1038/s41467-019-08925-4
10.1038/s41467-019-08925-4 · External reference
Community coalescence: an eco-evolutionary perspective
10.1098/rstb.2019.0252 · 2020 · External reference
10.1038/ismej.2016.45
10.1038/ismej.2016.45 · External reference
General calibration of microbial growth in microplate readers
10.1038/srep38828 · 2016 · External reference
10.1038/s41396-018-0202-1
10.1038/s41396-018-0202-1 · External reference
Optimisation of the protocol for the LIVE/DEAD® BacLightTM bacterial viability kit for rapid determination of bacterial load
10.3389/fmicb.2019.00801 · 2019 · External reference
Context-dependent dynamics lead to the assembly of functionally distinct microbial communities
10.1038/s41467-020-15169-0 · 2020 · External reference
10.1371/journal.pgen.1004283
10.1371/journal.pgen.1004283 · External reference
The madness of microbiome: attempting to find consensus “Best Practice” for 16S microbiome studies
10.1128/aem.02627-17 · 2018 · External reference
Technicalities and glitches of terminal restriction fragment length polymorphism (T-RFLP)
10.1007/s12088-014-0461-0 · 2014 · External reference
10.1007/978-1-4939-6685-1_8
10.1007/978-1-4939-6685-1_8 · External reference
A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota
10.1371/journal.pgen.1004283 · 2014 · External reference
10.3390/pathogens3010109
10.3390/pathogens3010109 · External reference
10.1111/1462-2920.12308
10.1111/1462-2920.12308 · External reference
Botanical microbiomes on the cheap: inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi
10.1002/aps3.11334 · 2020 · External reference
Community fingerprinting in a sequencing world
10.1111/1574-6941.12308 · 2014 · External reference
10.1371/journal.pbio.1001330
10.1371/journal.pbio.1001330 · External reference
Deciphering links between bacterial interactions and spatial organization in multispecies biofilms
10.1038/s41396-019-0494-9 · 2019 · External reference
10.1111/1462-2920.13594
10.1111/1462-2920.13594 · External reference
Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment
10.1038/ncomms5643 · 2014 · External reference
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
10.7554/elife.37090 · 2018 · External reference
Dynamics in the microbial cytome—single cell analytics in natural systems
10.1016/j.copbio.2014.01.011 · 2014 · External reference
10.1038/s41592-018-0185-x
10.1038/s41592-018-0185-x · External reference
Neutral and selective dynamics in a synthetic microbial community
2018 · External reference
10.1038/s41579-019-0158-9
10.1038/s41579-019-0158-9 · External reference
10.1016/j.mib.2016.03.015
10.1016/j.mib.2016.03.015 · External reference
Fitness and productivity increase with ecotypic diversity among Escherichia coli strains that coevolved in a simple, constant environment
2020 · External reference
Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm
10.1038/s41396-018-0112-2 · 2018 · External reference
10.1038/s41396-018-0165-2
10.1038/s41396-018-0165-2 · External reference
10.1016/j.syapm.2012.03.004
10.1016/j.syapm.2012.03.004 · External reference
10.1126/science.aay0240
10.1126/science.aay0240 · External reference
Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly
10.1038/s41598-019-41542-1 · 2019 · External reference
10.1021/acs.est.8b06044
10.1021/acs.est.8b06044 · External reference
The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil
10.1038/sj.ismej.2007.27 · 2007 · External reference
Relating the metatranscriptome and metagenome of the human gut
10.1073/pnas.1319284111 · 2014 · External reference
10.1111/1755-0998.12239
10.1111/1755-0998.12239 · External reference
10.1111/1462-2920.13861
10.1111/1462-2920.13861 · External reference
Modernized tools for streamlined genetic manipulation and comparative study of wild and diverse proteobacterial lineages
10.1128/mbio.01877-18 · 2018 · External reference
Magic pools: parallel assessment of transposon delivery vectors in bacteria
2018 · External reference
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
10.1128/mbio.00306-15 · 2015 · External reference
Targeted genome editing of bacteria within microbial communities
2020 · External reference
10.1111/j.1462-2920.2004.00687.x
10.1111/j.1462-2920.2004.00687.x · External reference
Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester
10.1128/aem.01955-16 · 2017 · External reference
10.1111/j.1574-6941.2011.01284.x
10.1111/j.1574-6941.2011.01284.x · External reference
Metaproteomics: sample preparation and methodological considerations
10.1007/978-3-030-12298-0_8 · 2019 · External reference
10.1038/s41396-020-0683-6
10.1038/s41396-020-0683-6 · External reference
10.1016/j.numecd.2009.04.018
10.1016/j.numecd.2009.04.018 · External reference
Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics
10.1128/mbio.00484-12 · 2013 · External reference
10.1016/j.csbj.2014.11.009
10.1016/j.csbj.2014.11.009 · External reference
10.1038/ismej.2007.30
10.1038/ismej.2007.30 · External reference
10.1371/journal.pone.0227434
10.1371/journal.pone.0227434 · External reference
10.1038/s41559-019-0994-z
10.1038/s41559-019-0994-z · External reference
10.1038/s41592-018-0176-y
10.1038/s41592-018-0176-y · External reference
10.1038/nbt.3935
10.1038/nbt.3935 · External reference
10.1038/s41587-020-0548-6
10.1038/s41587-020-0548-6 · External reference
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
10.1038/s41467-019-10927-1 · 2019 · External reference
MMinte: an application for predicting metabolic interactions among the microbial species in a community
10.1186/s12859-016-1230-3 · 2016 · External reference
MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota
10.1128/msystems.00606-19 · 2020 · External reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
10.1111/mec.13536
10.1111/mec.13536 · External reference
10.1111/j.1600-0706.2011.20301.x
10.1111/j.1600-0706.2011.20301.x · External reference
Disentangling the importance of ecological niches from stochastic processes across scales
10.1098/rstb.2011.0063 · 2011 · External reference
10.1890/0012-9658(2006)87[1387:ntateo]2.0.co;2
10.1890/0012-9658(2006)87[1387:ntateo]2.0.co;2 · External reference
Difficulty in inferring microbial community structure based on co-occurrence network approaches
10.1186/s12859-019-2915-1 · 2019 · External reference
Strengthening insights in microbial ecological networks from theory to applications
2019 · External reference
10.1093/femsre/fuy030
10.1093/femsre/fuy030 · External reference
Web-gLV: a web based platform for Lotka-Volterra based modeling and simulation of microbial populations
10.3389/fmicb.2019.00288 · 2019 · External reference
10.1016/j.mib.2018.07.004
10.1016/j.mib.2018.07.004 · External reference
Community structure follows simple assembly rules in microbial microcosms
10.1038/s41559-017-0109 · 2017 · External reference
Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions
10.7554/elife.25051 · 2017 · External reference
10.1098/rsif.2019.0423
10.1098/rsif.2019.0423 · External reference
An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data
10.1038/s41467-019-09785-8 · 2019 · External reference
10.1101/2020.03.09.984278
10.1101/2020.03.09.984278 · External reference
Metabolic capabilities of Escherichia coli II. Optimal growth patterns
10.1006/jtbi.1993.1203 · 1993 · External reference
10.1038/nbt.1614
10.1038/nbt.1614 · External reference
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
10.1038/msb4100162 · 2007 · External reference
Review and perspective on mathematical modeling of microbial ecosystems
10.1042/bst20170265 · 2018 · External reference
Perspectives and challenges in microbial communities metabolic modeling
10.3389/fgene.2017.00088 · 2017 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
Minimizing the number of optimizations for efficient community dynamic flux balance analysis
10.1371/journal.pcbi.1007786 · 2020 · External reference
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
10.1093/bioinformatics/btv036 · 2015 · External reference
10.1073/pnas.1421834112
10.1073/pnas.1421834112 · External reference
The power of metabolism for predicting microbial community dynamics
10.1128/msystems.00146-19 · 2019 · External reference
10.1038/s41467-018-07946-9
10.1038/s41467-018-07946-9 · External reference
10.1093/nar/gky537
10.1093/nar/gky537 · External reference
10.1093/bioinformatics/btq183
10.1093/bioinformatics/btq183 · External reference
10.1038/nrmicro.2016.62
10.1038/nrmicro.2016.62 · External reference
A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia
10.1128/jb.00865-16 · 2017 · External reference
10.1371/journal.pcbi.1005544
10.1371/journal.pcbi.1005544 · External reference
10.1038/s41598-020-60130-2
10.1038/s41598-020-60130-2 · External reference
10.1038/s41396-019-0522-9
10.1038/s41396-019-0522-9 · External reference
Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau
10.7717/peerj.6746 · 2019 · External reference
10.1186/s40168-020-00827-8
10.1186/s40168-020-00827-8 · External reference
A conceptual framework for the phylogenetically constrained assembly of microbial communities
10.1186/s40168-019-0754-y · 2019 · External reference
The scales of the zebrafish: host-microbiota interactions from proteins to populations
10.1016/j.mib.2017.05.011 · 2017 · External reference
10.1073/pnas.1917265117
10.1073/pnas.1917265117 · External reference
Deciphering microbial interactions in synthetic human gut microbiome communities
10.15252/msb.20178157 · 2018 · External reference
10.1016/j.tim.2016.02.019
10.1016/j.tim.2016.02.019 · External reference
Environmental selection, dispersal, and organism interactions shape community assembly in high-throughput enrichment culturing
10.1128/aem.01253-17 · 2017 · External reference
10.1126/sciadv.aay8676
10.1126/sciadv.aay8676 · External reference
10.1073/pnas.1900102116
10.1073/pnas.1900102116 · External reference
10.1016/j.coisb.2017.09.002
10.1016/j.coisb.2017.09.002 · External reference
Using cultivated microbial communities to dissect microbiome assembly: challenges, limitations, and the path ahead
10.1128/msystems.00161-17 · 2018 · External reference
10.1128/9781555816827.ch1
10.1128/9781555816827.ch1 · External reference
10.1038/ncomms9493
10.1038/ncomms9493 · External reference
Deciphering composition and function of the root microbiome of a legume plant
10.1186/s40168-016-0220-z · 2017 · External reference
10.1038/nature16192
10.1038/nature16192 · External reference
10.1038/s41587-019-0104-4
10.1038/s41587-019-0104-4 · External reference
Introducing THOR, a model microbiome for genetic dissection of community behavior
10.1128/mbio.02846-18 · 2019 · External reference
10.1101/2020.02.19.956078
10.1101/2020.02.19.956078 · External reference
Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly
10.7554/elife.36521 · 2018 · External reference
Deciphering links between bacterial interactions and spatial organization in multispecies biofilms
10.1038/s41396-019-0494-9 · 2019 · External reference
10.1038/s41564-018-0242-3
10.1038/s41564-018-0242-3 · External reference
10.1038/s41396-019-0498-5
10.1038/s41396-019-0498-5 · External reference
10.1038/s41559-020-1272-9
10.1038/s41559-020-1272-9 · External reference
10.1111/1574-6976.12072
10.1111/1574-6976.12072 · External reference
10.1016/j.chom.2019.01.018
10.1016/j.chom.2019.01.018 · External reference
10.1016/j.cels.2019.06.008
10.1016/j.cels.2019.06.008 · External reference
10.1038/s41467-020-16200-0
10.1038/s41467-020-16200-0 · External reference
10.1016/j.mib.2017.11.018
10.1016/j.mib.2017.11.018 · External reference
10.1371/journal.pone.0155080
10.1371/journal.pone.0155080 · External reference
Artificial microbial arenas: materials for observing and manipulating microbial consortia
10.1002/adma.201900284 · 2019 · External reference
10.1021/acs.accounts.6b00503
10.1021/acs.accounts.6b00503 · External reference
Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes
2019 · External reference
