The impact of skin care products on skin chemistry and microbiome dynamics
Amina Bouslimani Ricardo da Silva Tomasz Kosciolek Stefan Janssen Chris Callewaert Amnon Amir Kathleen Dorrestein Alexey V. Melnik Livia S. Zaramela Ji-Nu Kim Gregory Humphrey Tara Schwartz Karenina Sanders Caitriona Brennan Tal Luzzatto-Knaan Gail Ackermann Daniel McDonald Karsten Zengler Rob Knight Pieter C. Dorrestein
Rob Knight
Knight Rob
ORCID: 0000-0002-0975-9019
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt.3893
Current understanding of the human microbiome. 10.1038/nm.4517
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. 10.1080/19490976.2021.1961203
Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. 10.1038/s41396-021-00935-9
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 10.1101/2020.11.13.370387
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. 10.1101/2020.08.17.238444
Methods for phylogenetic analysis of microbiome data. 10.1038/s41564-018-0156-0
Publisher Correction: Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-018-0114-x
Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-017-0072-8
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. 10.1371/journal.pcbi.1009056
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. 10.1101/gr.275777.121
Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. 10.1101/2021.07.16.452756
Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 10.1038/s41396-021-01016-7
Structure-based protein function prediction using graph convolutional networks. 10.1038/s41467-021-23303-9
Challenges in benchmarking metagenomic profilers. 10.1038/s41592-021-01141-3
Taxonomic signatures of cause-specific mortality risk in human gut microbiome. 10.1038/s41467-021-22962-y
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. 10.1111/biom.13481
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition. 10.1128/msystems.01329-20
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 10.1038/nbt.1823
The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. 10.4056/aigs.1443528
Origins of the genetic code: The escaped triplet theory 10.1146/annurev.biochem.74.082803.133119
Defining the human microbiome 10.1111/j.1753-4887.2012.00493.x
Dietary prebiotics and bioactive milk fractions improve NREM sleep, enhance REM sleep rebound and attenuate the stress-induced decrease in diurnal temperature and gut microbial alpha diversity 10.3389/fnbeh.2016.00240
Meta-analyses of human gut microbes associated with obesity and IBD 10.1016/j.febslet.2014.09.039
Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations 10.1128/mBio.01526-14
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment 10.1145/1646468.1646481
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill 10.1038/ismej.2013.254
Meeting report for the 1st skin microbiota workshop, boulder, co October 15-16 2012 10.1186/1944-3277-9-13
Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk 10.1017/S0007114516004165
Host remodeling of the gut microbiome and metabolic changes during pregnancy 10.1016/j.cell.2012.07.008
A distinct immunogenic region of glutamic acid decarboxylase 65 is naturally processed and presented by human islet cells to cytotoxic CD8 T cells 10.1111/cei.12436
Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities 10.1128/AEM.01996-06
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation 10.1073/pnas.0902366106
A population of Pax7-expressing muscle progenitor cells show differential responses to muscle injury dependent on developmental stage and injury extent 10.3389/fnagi.2015.00161
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch 10.1016/j.jmb.2013.02.023
Authors' reply to Mawer and Wilcox and Mullish and Williams 10.1136/bmj.h6132
The bacterial microbiota in the oral mucosa of rural Amerindians 10.1099/mic.0.043174-0
Selection, history and chemistry: The three faces of the genetic code 10.1016/S0968-0004(99)01392-4
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species 10.1007/s00442-015-3507-z
Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems 10.1890/10-0426.1
Specification of sensory neurons occurs through diverse developmental programs functioning in the brain and spinal cord 10.1002/dvdy.24184
Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses 10.1186/s40168-016-0153-6
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges 10.1101/gr.085464.108
Tfap2 transcription factors in zebrafish neural crest development and ectodermal evolution 10.1002/jez.b.21189
Direct sequencing of the human microbiome readily reveals community differences 10.1186/gb-2010-11-5-210
Human gut microbiome viewed across age and geography 10.1038/nature11053
Sources of bacteria in outdoor air across cities in the midwestern United States 10.1128/AEM.05498-11
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity 10.3389/fmicb.2014.00298
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice 10.1053/j.gastro.2013.01.047
Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment 10.1111/1462-2920.12539
How delivery mode and feeding can shape the bacterial community in the infant gut 10.1503/cmaj.130147
Moving pictures of the human microbiome 10.1186/gb-2011-12-5-r50
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010 10.4056/sigs.1333437
The impact of the gut microbiota on human health: An integrative view 10.1016/j.cell.2012.01.035
Forensic identification using skin bacterial communities 10.1073/pnas.1000162107
Which is more important for classifying microbial communities: Who's there or what they can do? 10.1038/ismej.2014.157
Comparison of fecal collection methods for microbiota studies in Bangladesh 10.1128/AEM.00361-17
Using the gut microbiota as a novel tool for examining colobine primate GI health 10.1016/j.gecco.2016.06.004
Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113
The ecology of the phyllosphere: Geographic and phylogenetic variability in the distribution of bacteria on tree leaves 10.1111/j.1462-2920.2010.02258.x
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins 10.1073/pnas.1000071108
Metabolie syndrome and altered gut microbiota in mice lacking toll-like receptor 5 10.1126/science.1179721
A Microbiome Foundation for the Study of Crohn's Disease 10.1016/j.chom.2017.02.012
Comparison of collection methods for fecal samples for discovery metabolomics in epidemiologic studies 10.1158/1055-9965.EPI-16-0409
Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories 10.1261/rna.2183806
Bacterial phylogeny structures soil resistomes across habitats 10.1038/nature13377
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences 10.1038/ismej.2011.208
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes 10.1111/1462-2920.13684
Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice 10.1016/j.chom.2012.07.004
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers 10.1093/nar/gkn491
Evolution of mammals and their gut microbes 10.1126/science.1155725
Vertebrate genome evolution: A slow shuffle or a big bang? 10.1002/(SICI)1521-1878(199908)21:8<697::AID-BIES9>3.0.CO;2-X
Biogeography and habitat modelling of high-alpine bacteria 10.1038/ncomms1055
Vertebrate hosts as Islands: Dynamics of selection, immigration, loss, persistence, and potential function of bacteria on salamander skin 10.3389/fmicb.2016.00333
MIxS-BE: A MIxS extension defining a minimum information standard for sequence data from the built environment 10.1038/ismej.2013.176
Finding specific RNA motifs: Function in a zeptomole world? 10.1261/rna.2138803
Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis 10.1016/j.biocon.2015.04.007
Convergence of gut microbiomes in myrmecophagous mammals 10.1111/mec.12501
Changes through time: Integrating microorganisms into the study of succession 10.1016/j.resmic.2010.06.002
Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples 10.1128/AEM.04137-13
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns 10.1038/nmeth.1499
The molecular basis of nuclear genetic code change in ciliates 10.1016/S0960-9822(01)00028-8
Using QIIME to analyze 16s rRNA gene sequences from microbial communities 10.1002/9780471729259.mc01e05s27
Culturing: Looking it up in our gut 10.1038/nmicrobiol.2016.169
Human oral, gut, and plaque microbiota in patients with atherosclerosis 10.1073/pnas.1011383107
Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions 10.3389/fmicb.2011.00153
Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks 10.1038/nmicrobiol.2016.177
Xenobiotics and the human gut microbiome: Metatranscriptomics reveal the active players 10.1016/j.cmet.2013.02.013
Experimental and analytical tools for studying the human microbiome 10.1038/nrg3129
Cohabiting family members share microbiota with one another and with their dogs 10.7554/eLife.00458
The gut microbiota in human energy homeostasis and obesity 10.1016/j.tem.2015.07.002
EMPeror: A tool for visualizing high-throughput microbial community data 10.1186/2047-217X-2-16
Is the genetic code really a frozen accident? New evidence from in vitro selection 10.1111/j.1749-6632.1999.tb08915.x
PyCogent: A toolkit for making sense from sequence 10.1186/gb-2007-8-8-r171
Microbes do not follow the elevational diversity patterns of plants and animals 10.1890/10-1170.1
QIIME allows analysis of high-throughput community sequencing data 10.1038/nmeth.f.303
UniFrac: A new phylogenetic method for comparing microbial communities 10.1128/AEM.71.12.8228-8235.2005
Soil bacterial and fungal communities across a pH gradient in an arable soil 10.1038/ismej.2010.58
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity 10.1111/mec.12846
Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505
Faecal transplants 10.1136/bmj.h5149
TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata 10.1093/bioinformatics/btr517
From molecules to dynamic biological communities 10.1007/s10539-013-9364-4
Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species 10.1007/s00248-017-1041-8
Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separation 10.1016/j.surg.2016.10.033
Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1 10.1371/journal.pone.0050636
The human microbiome: Eliminating the biomedical/environmental dichotomy in microbial ecology 10.1111/j.1462-2920.2006.01222_3.x
Gut microbes and the brain: Paradigm shift in neuroscience 10.1523/JNEUROSCI.3299-14.2014
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat 10.1016/j.chom.2009.08.003
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish 10.1016/j.chom.2012.08.003
A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins 10.1074/mcp.M800384-MCP200
Context and the human microbiome 10.1186/s40168-015-0117-2
Seasonal variation of postmortem microbial communities 10.1007/s12024-015-9667-7
Diversity of rickettsiales in the microbiome of the lone star tick, amblyomma americanum 10.1128/AEM.02987-13
The under-recognized dominance of Verrucomicrobia in soil bacterial communities 10.1016/j.soilbio.2011.03.012
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 10.1371/journal.pbio.1001920
Diversity, distribution and sources of bacteria in residential kitchens 10.1111/1462-2920.12036
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor 10.1126/science.1229000
Composition of human skin microbiota affects attractiveness to malaria mosquitoes 10.1371/journal.pone.0028991
Finding the Missing Links among Metabolites, Microbes, and the Host 10.1016/j.immuni.2014.05.015
Do proteins predate DNA? 10.1126/science.286.5440.690
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing 10.1038/nmeth.2276
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex 10.1038/nmeth.1184
PyNAST: A flexible tool for aligning sequences to a template alignment 10.1093/bioinformatics/btp636
Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits 10.1021/acssynbio.5b00133
Bacterial colonization and succession in a newly opened hospital 10.1126/scitranslmed.aah6500
High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity 10.1053/j.gastro.2009.08.042
The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease 10.1016/j.surg.2016.05.005
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing 10.1053/j.gastro.2011.02.011
Alterations in the gut microbiota associated with HIV-1 infection 10.1016/j.chom.2013.08.006
Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness 10.1097/MCC.0000000000000321
Diversity, structure and convergent evolution of the global sponge microbiome 10.1038/ncomms11870
New insight into the diversity of life's building blocks: Evenness, not variance 10.1089/ast.2011.2280
Bacteria from diverse habitats colonize and compete in the mouse gut 10.1016/j.cell.2014.09.008
Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs) 10.1371/journal.pone.0054703
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives 10.1093/nar/gkq066
Mosquito microbiome dynamics, a background for prevalence and seasonality of West Nile virus 10.3389/fmicb.2017.00526
Evolutionary rates vary among rRNA structural elements 10.1093/nar/gkm101
Simple, recurring RNA binding sites for L-arginine 10.1261/rna.1979410
Rewiring the keyboard: Evolvability of the genetic code 10.1038/35047500
Widespread colonization of the lung by Tropheryma whipplei in HIV infection 10.1164/rccm.201211-2145OC
Artificial Selection: Finding Function amongst Randomized Sequences 10.1002/9783527619504.ch47
Effects of field conditions on fecal microbiota 10.1016/j.mimet.2016.09.017
Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127
An Elegan(t) Screen for Drug-Microbe Interactions 10.1016/j.chom.2017.04.014
The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome 10.1186/2047-217X-1-7
Variation in the microbiota of Ixodes ticks with regard to geography, species, and sex 10.1128/AEM.01562-15
Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas) 10.1038/ismej.2015.168
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection 10.1186/s40168-015-0070-0
Using QIIME to analyze 16S rrna gene sequences from microbial communities 10.1002/0471250953.bi1007s36
Sharing and archiving nucleic acid structure mapping data 10.1261/rna.2753211
Advancing analytical algorithms and pipelines for billions of microbial sequences 10.1016/j.copbio.2011.11.028
Obesity alters gut microbial ecology 10.1073/pnas.0504978102
Why microbiome treatments could pay off soon 10.1038/scientificamerican0315-S5
Pathological rate matrices: From primates to pathogens 10.1186/1471-2105-9-550
Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats 10.1371/journal.pone.0125889
Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes 10.1111/j.1462-2920.2010.02277.x
Advancing the microbiome research community 10.1016/j.cell.2014.09.022
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences 10.7717/peerj.545
Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States 10.1126/science.1243768
Interleukin-1β (IL-1β) promotes susceptibility of toll-like receptor 5 (TLR5) deficient mice to colitis 10.1136/gut.2011.240556
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis 10.1093/bib/bbr009
Characterizing microbial communities through space and time 10.1016/j.copbio.2011.11.017
Collecting fecal samples for microbiome analyses in epidemiology studies 10.1158/1055-9965.EPI-15-0951
Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle 10.1152/ajpregu.00387.2012
DNA extraction for streamlined metagenomics of diverse environmental samples 10.2144/000114559
Fecal microbiome in epidemiologic studies-response 10.1158/1055-9965.EPI-16-0161
Bacterial communities of disease vectors sampled across time, space, and species 10.1038/ismej.2009.111
The hospital microbiome project: Meeting report for the 1st hospital microbiome project workshop on sampling design and building science measurements, chicago, usa, june 7th-8th 2012 10.4056/sigs.3717348
Short-term temporal variability in airborne bacterial and fungal populations 10.1128/AEM.01467-07
Linking long-term dietary patterns with gut microbial enterotypes 10.1126/science.1208344
Evidence for a persistent microbial seed bank throughout the global ocean 10.1073/pnas.1217767110
Metagenomic covariation along densely sampled environmental gradients in the Red Sea 10.1038/ismej.2016.99
How biologists conceptualize genes: An empirical study 10.1016/j.shpsc.2004.09.005
Worlds within worlds: Evolution of the vertebrate gut microbiota 10.1038/nrmicro1978
Ribosomal RNA, the lens into life 10.1261/rna.050799.115
Sequencing our way towards understanding global eukaryotic biodiversity 10.1016/j.tree.2011.11.010
Stress response, gut microbial diversity and sexual signals correlate with social interactions 10.1098/rsbl.2016.0352
Size, constant sequences, and optimal selection 10.1261/rna.2161305
Rethinking enterotypes 10.1016/j.chom.2014.09.013
tRNA creation by hairpin duplication 10.1007/s00239-004-0315-1
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease 10.1016/j.cell.2016.11.018
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample 10.1073/pnas.1000080107
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision 10.1038/ismej.2015.235
Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (plethodon cinereus) 10.1038/ismej.2013.200
Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water 10.1016/j.watres.2014.11.003
RNA-amino acid binding: A stereochemical era for the genetic code 10.1007/s00239-009-9270-1
Short pyrosequencing reads suffice for accurate microbial community analysis 10.1093/nar/gkm541
Heritable components of the human fecal microbiome are associated with visceral fat 10.1186/s13059-016-1052-7
Genetic Determinants of the Gut Microbiome in UK Twins 10.1016/j.chom.2016.04.017
Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) 10.1186/1471-2180-13-114
Succession of microbial consortia in the developing infant gut microbiome 10.1073/pnas.1000081107
Dynamics of the human gut microbiome in inflammatory bowel disease 10.1038/nmicrobiol.2017.4
The founding charter of the Genomic Observatories Network 10.1186/2047-217X-3-2
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses 10.1038/ismej.2008.127
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans 10.1126/science.1198719
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples 10.1111/j.1574-6968.2010.01965.x
RNA structure prediction from evolutionary patterns of nucleotide composition 10.1093/nar/gkn987
Genetic and environmental control of host-gut microbiota interactions 10.1101/gr.194118.115
Analysis of membrane proteins from human chronic myelogenous leukemia cells: Comparison of extraction methods for multidimensional LC-MS/MS 10.1021/pr050313z
Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code 10.1007/s00239-004-0314-2
Comparison of methods for estimating the nucleotide substitution matrix 10.1186/1471-2105-9-511
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal 10.1261/rna.881308
Tools for the microbiome: Nano and beyond 10.1021/acsnano.5b07826
Database-Driven Grid Computing and Distributed Web Applications: A Comparison 10.1002/9780470191637.ch11
Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data 10.1016/J.ENG.2017.01.020
Estimate of the abundance of cardiomyopathic mutations in the β-myosin gene 10.1016/j.ijcard.2008.12.199
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA 10.1261/rna.2220210
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation 10.1016/j.tim.2011.07.006
Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis 10.1111/j.1365-294X.2012.05552.x
Keemei: Cloud-based validation of tabular bioinformatics file formats in Google Sheets 10.1186/s13742-016-0133-6
Vertebrate decomposition is accelerated by soil microbes 10.1128/AEM.00957-14
Satellite remote sensing data can be used to model marine microbial metabolite turnover 10.1038/ismej.2014.107
Diversity, stability and resilience of the human gut microbiota 10.1038/nature11550
Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau 10.1111/j.1462-2920.2012.02799.x
Bacterial communities associated with the lichen symbiosis 10.1128/AEM.02257-10
Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood 10.1101/gr.140608.112
Guilt by association: The arginine case revisited 10.1017/S1355838200000145
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest 10.1038/ismej.2014.36
Global patterns in bacterial diversity 10.1073/pnas.0611525104
Fast find: A novel computational approach to analyzing combinatorial motifs 10.1186/1471-2105-7-1
Predictive modeling of gingivitis severity and susceptibility via oral microbiota 10.1038/ismej.2014.32
Conceptualizing a Genomics Software Institute (GSI) 10.4056/sigs.2485911
Tracking down the sources of experimental contamination in microbiome studies 10.1186/s13059-014-0564-2
Replenishing our defensive microbes 10.1002/bies.201300018
Insights from Characterizing Extinct Human Gut Microbiomes 10.1371/journal.pone.0051146
The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome 10.1371/journal.pbio.1001377
Unlocking the potential of metagenomics through replicated experimental design 10.1038/nbt.2235
Tiny microbes, enormous impacts: What matters in gut microbiome studies? 10.1186/s13059-016-1086-x
ConStrains identifies microbial strains in metagenomic datasets 10.1038/nbt.3319
Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646
Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome 10.1002/mds.26942
PH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils 10.1016/j.soilbio.2014.03.014
Fat and vitamin intakes during pregnancy have stronger relations with a proinflammatory maternal microbiota than does carbohydrate intake 10.1186/s40168-016-0200-3
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents 10.1038/ismej.2012.81
Microbiology of death 10.1016/j.cub.2016.03.042
A meta-analysis of changes in bacterial and archaeal communities with time 10.1038/ismej.2013.54
PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers 10.1093/bioinformatics/btr087
SnapShot: The Human Microbiome 10.1016/j.cell.2014.07.019
Microbial Skin Inhabitants: Friends Forever 10.1016/j.cell.2016.04.035
The microbiome explored: Recent insights and future challenges 10.1038/nrmicro2973
Supervised classification of microbiota mitigates mislabeling errors 10.1038/ismej.2010.148
Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics 10.1021/ac035229m
Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease 10.1109/BigData.2016.7840731
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms 10.1038/ismej.2012.8
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate 10.1007/s00248-017-0938-6
Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei 10.1128/AEM.00447-09
The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study 10.1097/PSY.0000000000000512
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys 10.1038/ismej.2011.186
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences 10.1038/ismej.2011.187
The Earth Microbiome project: Successes and aspirations 10.1186/s12915-014-0069-1
Microbial biogeography of public restroom surfaces 10.1371/journal.pone.0028132
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer 10.1038/nm.4039
Mathematical approaches for describing microbial populations: Practice and theory for extrapolation of rich environments 10.1002/9781118409855.ch4
Meeting report of the RNA ontology consortium January 8-9, 2011 10.4056/sigs.1724282
Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life 10.3945/ajcn.115.115451
Prevalence and genetic diversity of Blastocystis in family units living in the United States 10.1016/j.meegid.2016.08.018
Ancient human oral plaque preserves a wealth of biological data 10.1038/ng.2930
Examining the global distribution of dominant archaeal populations in soil 10.1038/ismej.2010.171
A lightweight, scalable grid computing framework for parallel bioinformatics applications 10.1109/HPCS.2005.7
Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness 10.1371/journal.pone.0096375
Activating and inhibiting connections in biological network dynamics 10.1186/1745-6150-3-49
Microbiota at multiple body sites during pregnancy in a rural tanzanian population and effects of Moringa-supplemented probiotic yogurt 10.1128/AEM.00780-15
Temporal variability is a personalized feature of the human microbiome 10.1186/s13059-014-0531-y
Can Your Microbiome Tell You What to Eat? 10.1016/j.cmet.2015.11.009
Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon 10.1371/journal.pone.0073140
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics 10.1186/1471-2148-8-327
Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments 10.1038/ismej.2010.167
MotifCluster: An interactive online tool for clustering and visualizing sequences using shared motifs 10.1186/gb-2008-9-8-r128
Longitudinal analysis of microbial interaction between humans and the indoor environment 10.1126/science.1254529
The influence of sex, handedness, and washing on the diversity of hand surface bacteria 10.1073/pnas.0807920105
Human genetics shape the gut microbiome 10.1016/j.cell.2014.09.053
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity 10.1128/mBio.01371-14
Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape 10.1371/journal.pone.0173811
A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system 10.7554/eLife.01104.001
Gut microbiota from twins discordant for obesity modulate metabolism in mice 10.1126/science.1241214
Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil 10.1016/j.soilbio.2010.02.003
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags 10.1186/1471-2180-10-206
The 'rare biosphere': A reality check 10.1038/nmeth0909-636
Variable responses of human and non-human primate gut microbiomes to a Western diet 10.1186/s40168-015-0120-7
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences 10.1038/nbt.2676
Global patterns in the biogeography of bacterial taxa 10.1111/j.1462-2920.2010.02315.x
RNASTAR: An RNA structural alignment repository that provides insight into the evolution of natural and artificial RNAs 10.1261/rna.032052.111
Spatial and temporal variability of the human microbiota 10.1111/j.1469-0691.2012.03861.x
Cross-biome comparison of microbial association networks 10.3389/fmicb.2015.01200
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice 10.1016/j.cmet.2012.12.007
Mass spectrometry based molecular 3D-cartography of plant metabolites 10.3389/fpls.2017.00429
Comparison of Collection Methods for Fecal Samples in Microbiome Studies 10.1093/aje/kww177
Translating the human microbiome 10.1038/nbt.2543
Specialized metabolites from the microbiome in health and disease 10.1016/j.cmet.2014.10.016
The treatment-naive microbiome in new-onset Crohn's disease 10.1016/j.chom.2014.02.005
Molecular cartography of the human skin surface in 3D 10.1073/pnas.1424409112
Reports of the death of the gene are greatly exaggerated 10.1007/s10539-006-9039-5
Antibiotic discovery is a walk in the park 10.1073/pnas.1618221114
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota 10.1038/ismej.2015.64
Natural and artificial RNAs occupy the same restricted region of sequence space 10.1261/rna.1923210
Stable tRNA-based phylogenies using only 76 nucleotides 10.1261/rna.726010
The microbiome quality control project: Baseline study design and future directions 10.1186/s13059-015-0841-8
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis 10.1371/journal.ppat.0040020
Normalization and microbial differential abundance strategies depend upon data characteristics 10.1186/s40168-017-0237-y
Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere 10.1371/journal.pone.0073079
TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational Grids 10.1002/0471756504.ch26
Anal gas evacuation and colonic microbiota in patients with flatulence: Effect of diet 10.1136/gutjnl-2012-303013
Unique strain of Rickettsia parkeri associated with the hard tick Dermacentor parumapertus Neumann in the western United States 10.1128/AEM.03463-16
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease 10.1371/journal.pone.0080702
Bringing the Dynamic Microbiome to Life with Animations 10.1016/j.chom.2016.12.009
The Human Microbiome Project 10.1038/nature06244
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota 10.1073/pnas.1306070110
Multilevel research strategies and biological systems 10.1086/677889
Microbiota and host nutrition across plant and animal kingdoms 10.1016/j.chom.2015.04.009
What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat clostridium difficile infection? 10.1016/j.cgh.2013.10.009
Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns 10.1099/mic.0.2007/011833-0
Co-habiting amphibian species harbor unique skin bacterial communities in wild populations 10.1038/ismej.2011.129
Our microbial selves: What ecology can teach us 10.1038/embor.2011.137
Postprandial remodeling of the gut microbiota in Burmese pythons 10.1038/ismej.2010.71
Parallel evolution of the genetic code in arthropod mitochondrial genomes 10.1371/journal.pbio.0040127
Origin of microbial biomineralization and magnetotaxis during the Archean 10.1073/pnas.1614654114
UCHIME improves sensitivity and speed of chimera detection 10.1093/bioinformatics/btr381
Parallel mapping of antibiotic resistance alleles in Escherichia coli 10.1371/journal.pone.0146916
Individual diet has sex-dependent effects on vertebrate gut microbiota 10.1038/ncomms5500
Conducting a microbiome study 10.1016/j.cell.2014.06.037
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake 10.1101/gr.107987.110
Boulder ALignment editor (ALE): A web-based RNA alignment tool 10.1093/bioinformatics/btr258
Insights and inferences about integron evolution from genomic data 10.1186/1471-2164-9-261
CodonExplorer: An interactive online database for the analysis of codon usage and sequence composition 10.1007/978-1-59745-251-9_10
Bioinformatics Assessment of β-Myosin Mutations Reveals Myosin's High Sensitivity to Mutations 10.1016/j.tcm.2008.04.001
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea 10.1038/ismej.2011.139
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites 10.1016/j.jaci.2012.03.010
Responses of gut microbiota to diet composition and weight loss in lean and obese mice 10.1038/oby.2011.111
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil 10.1128/AEM.00358-07
The RNA structure alignment ontology 10.1261/rna.1601409
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch) 10.1111/ele.12301
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project 10.4056/sigs.1433550
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota 10.1016/j.chom.2015.08.005
The genomic standards consortium: Bringing standards to life for microbial ecology 10.1038/ismej.2011.39
The long-term stability of the human gut microbiota 10.1126/science.1237439
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins 10.1126/scitranslmed.3002701
Carcass mass has little influence on the structure of gravesoil microbial communities 10.1007/s00414-015-1206-2
Supervised classification of human microbiota 10.1111/j.1574-6976.2010.00251.x
A core gut microbiome in obese and lean twins 10.1038/nature07540
Defining seasonal marine microbial community dynamics 10.1038/ismej.2011.107
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons 10.1101/gr.112730.110
Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks 10.1016/j.mimet.2015.03.021
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions 10.1038/nmeth0910-668b
Euphorbia plant latex is inhabited by diverse microbial communities 10.3732/ajb.1500223
Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data 10.1038/ismej.2009.97
Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy 10.7554/eLife.11405.001
An ancient origin of magnetotactic bacteria 10.1073/pnas.1707301114
Global biogeography of highly diverse protistan communities in soil 10.1038/ismej.2012.147
Evolution of Symbiotic Bacteria in the Distal Human Intestine 10.1371/journal.pbio.0050156
Advancing our understanding of the human microbiome using QIIME 10.1016/B978-0-12-407863-5.00019-8
Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae 10.7554/eLife.24214
BayesFold: Rational 2° folds that combine thermodynamic, covariation; and chemical data for aligned RNA sequences 10.1261/rna.5168504
The amphibian skin-associated microbiome across species, space and life history stages 10.1111/mec.12510
Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer 10.1038/ismej.2012.26
Meta-analyses of studies of the human microbiota 10.1101/gr.151803.112
Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice 10.1073/pnas.1600324113
Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids 10.1093/nar/gki886
Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings 10.1016/j.antiviral.2013.12.004
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data 10.3233/AO-2011-0082
Microbiota restoration: Natural and supplemented recovery of human microbial communities 10.1038/nrmicro2473
Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids 10.1016/j.febslet.2005.05.038
Multiple pattern matching: A Markov chain approach 10.1007/s00285-007-0109-3
Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities 10.1371/journal.pone.0047879
Microbiome Tools for Forensic Science 10.1016/j.tibtech.2017.03.006
Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli 10.1002/bit.26217
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys 10.1038/ismej.2011.82
Lake microbial communities are resilient after a whole-ecosystem disturbance 10.1038/ismej.2012.56
Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) 10.1002/ajp.22555
Bacterial community structures are unique and resilient in full-scale bioenergy systems 10.1073/pnas.1015676108
Structural basis for diversity in the SAM clan of riboswitches 10.1073/pnas.1312918111
Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow Nests 10.1007/s00248-013-0338-5
Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850
The Ecology of Microbial Communities Associated with Macrocystis pyrifera 10.1371/journal.pone.0067480
Does protein structure influence trypsin miscleavage? 10.1109/MEMB.2005.1436461
HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats 10.1371/journal.pone.0105684
Toward effective probiotics for autism and other neurodevelopmental disorders 10.1016/j.cell.2013.11.035
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns 10.1073/pnas.1002601107
Species divergence and the measurement of microbial diversity 10.1111/j.1574-6976.2008.00111.x
Microbial endocrinology: The interplay between the microbiota and the endocrine system 10.1093/femsre/fuu010
Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn 10.1073/pnas.1012458107
Bayesian community-wide culture-independent microbial source tracking 10.1038/nmeth.1650
MICROBIOME. A unified initiative to harness Earth's microbiomes. 10.1126/science.aac8480
How mitochondria redefine the code 10.1007/s002390010220
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 10.1371/journal.pcbi.1002863
Walls talk: Microbial biogeography of homes spanning urbanization 10.1126/sciadv.1501061
CodonExplorer: An online tool for analyzing codon usage and sequence composition, scaling from genes to genomes 10.1093/bioinformatics/btp141
Biphasic assembly of the murine intestinal microbiota during early development 10.1038/ismej.2013.15
SitePainter: A tool for exploring biogeographical patterns 10.1093/bioinformatics/btr685
Bacterial community variation in human body habitats across space and time 10.1126/science.1177486
Human immunodeficiency virus nef signature sequences are associated with pulmonary hypertension 10.1089/aid.2011.0021
The unifrac significance test is sensitive to tree topology 10.1186/s12859-015-0640-y
Host-associated and free-living phage communities differ profoundly in phylogenetic composition 10.1371/journal.pone.0016900
Human-associated microbial signatures: Examining their predictive value 10.1016/j.chom.2011.09.003
Key challenges in proteomics and proteoinformatics 10.1109/MEMB.2005.1436456
The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice 10.1126/scitranslmed.3000322
Toward a predictive understanding of earth’s microbiomes to address 21st century challenges 10.1128/mBio.00714-16
A preliminary survey of lichen associated eukaryotes using pyrosequencing 10.1017/S0024282911000648
The convergence of carbohydrate active gene repertoires in human gut microbes 10.1073/pnas.0807339105
Analysis of the gut microbiota in the old order amish and its relation to the metabolic syndrome 10.1371/journal.pone.0043052
The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 10.4056/sigs.2134923
Using the nucleotide substitution rate matrix to detect horizontal gene transfer 10.1186/1471-2105-7-476
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat 10.1038/ismej.2012.79
Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity 10.1098/rspb.2016.1553
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale 10.1128/AEM.00335-09
Precision medicine in alcoholic and nonalcoholic fatty liver disease via modulating the gut microbiota 10.1152/ajpgi.00245.2016
The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework 10.3390/ijms10114723
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts 10.1101/gr.138198.112
The intestinal metabolome: An intersection between microbiota and host 10.1053/j.gastro.2014.03.001
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins 10.1073/pnas.1002355107
Genomic standards consortium projects 10.4056/sigs.5559680
UniFrac: An effective distance metric for microbial community comparison 10.1038/ismej.2010.133
Let researchers try new paths 10.1038/538451a
Host-bacterial coevolution and the search for new drug targets 10.1016/j.cbpa.2008.01.015
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients 10.1038/ismej.2011.159
Technology and techniques for microbial ecology via DNA sequencing 10.1513/AnnalsATS.201306-160MG
The Western English Channel contains a persistent microbial seed bank 10.1038/ismej.2011.162
DivergentSet, a tool for picking non-redundant sequences from large sequence collections 10.1074/mcp.T600022-MCP200
The Genomic Standards Consortium 10.1371/journal.pbio.1001088
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context 10.1186/1471-2105-7-371
Life through a microbial lens 10.1007/s11016-009-9288-4
Why microbiome treatments could pay off soon 10.1038/518S5a
The Microbiome and Human Biology. 10.1146/annurev-genom-083115-022438
Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort". 10.1128/msystems.00023-17
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. 10.1186/s40168-017-0269-3
Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. 10.1128/msystems.00195-16
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. 10.1158/1940-6207.capr-17-0010
Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-Oxide. 10.1165/rcmb.2017-0086oc
Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes". 10.1128/msphere.00296-17
Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9
Oral probiotic versus placebo and the maternal microbiome during pregnancy: A randomized controlled trial 10.1016/j.ajog.2019.11.064
Using microbiome tools for estimating the postmortem interval 10.1016/B978-0-12-815379-6.00012-X
Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. 10.1128/mbio.02901-19
Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue 10.1111/1556-4029.13949
Fructose stimulated de novo lipogenesis is promoted by inflammation 10.1038/s42255-020-0261-2
The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences 10.1016/j.chom.2020.06.022
The emergence of microbiome centres 10.1038/s41564-019-0644-x
Expanding the scope and scale of microbiome research 10.1186/s13059-019-1804-2
Are microbiome studies ready for hypothesis-driven research? 10.1016/j.mib.2018.07.002
Molecular and microbial microenvironments in chronically diseased lungs associated with cystic fibrosis 10.1128/mSystems.00375-19
Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice 10.1113/JP277336
Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026
Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India 10.1128/mSphere.00731-20
Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes 10.1038/s41396-018-0175-0
Major shifts in gut microbiota during development and its relationship to growth in ostriches 10.1111/mec.15087
Voices in methods development 10.1038/s41592-019-0585-6
Engineering the microbiome for animal health and conservation 10.1177/1535370219830075
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces 10.1186/s40168-019-0666-x
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity 10.1186/s13059-019-1831-z
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020
The microbiome and its potential for pharmacology 10.1007/164_2019_317
Age- And sex-dependent patterns of gut microbial diversity in human adults 10.1128/mSystems.00261-19
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice 10.1016/j.cell.2019.05.004
Reply to Sun et al., “Identifying composition novelty in microbiome studies: Improvement of prediction accuracy” 10.1128/mBio.01234-19
Effects of the microalgae Chlamydomonas on gastrointestinal health 10.1016/j.jff.2019.103738
Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media 10.1093/gigascience/giaa156
Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study 10.3389/fpsyt.2021.648475
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics 10.1038/s41587-020-0660-7
Comparison of oral collection methods for studies of microbiota 10.1158/1055-9965.EPI-18-0312
Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00901-19
Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome 10.1371/journal.pone.0229001
Redbiom: A rapid sample discovery and feature characterization system 10.1128/mSystems.00215-19
Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort 10.1128/mBio.01751-18
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks 10.1371/journal.pcbi.1007007
Reply to Moossavi and Azad, “quantifying and interpreting the association between early-life gut microbiota composition and childhood obesity” 10.1128/MBIO.00047-19
Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus 10.1038/s41396-018-0214-x
Quantifying and understanding well-to-well contamination in microbiome research 10.1128/mSystems.00186-19
Preserving microbial diversity. 10.1126/science.aau8816
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. 10.4049/jimmunol.1800614
GABA-modulating bacteria of the human gut microbiota 10.1038/s41564-018-0307-3
Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude 10.1145/3311790.3399614
Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing 10.1021/acs.est.0c07952
Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice 10.3389/fpsyt.2020.00518
Publisher Correction: The gut-liver axis and the intersection with the microbiome. 10.1038/s41575-018-0031-8
Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis 10.1016/j.eurpsy.2018.05.011
The microbiome and human cancer 10.1126/science.abc4552
Best practices for analysing microbiomes 10.1038/s41579-018-0029-9
Consent insufficient for data release−Response 10.1126/science.aax7509
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans 10.1016/j.cell.2020.09.009
Microbial biogeography and ecology of the mouth and implications for periodontal diseases 10.1111/prd.12268
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota 10.1038/s41467-018-05284-4
Erratum to: The sponge microbiome project. 10.1093/gigascience/giy145
Guiding longitudinal sampling in IBD cohorts 10.1136/gutjnl-2017-315352
A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease 10.1038/s41467-019-09455-9
Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3
High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county 10.1128/MSYSTEMS.00045-21
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians 10.1016/j.cgh.2018.09.017
Coordinating and assisting research at the SARS-CoV-2/ microbiome nexus 10.1128/MSYSTEMS.00999-20
Expanding magnetic organelle biogenesis in the domain Bacteria 10.1186/s40168-020-00931-9
Toward unrestricted use of public genomic data 10.1126/science.aaw1280
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection 10.1186/s40168-021-01026-9
Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates 10.1128/mBio.02524-19
Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease 10.1073/pnas.2017129117
Ground beef microbiome changes with antimicrobial decontamination interventions and product storage 10.1371/journal.pone.0217947
Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a “Two Hit” Stressor Model 10.3389/fphys.2020.524833
Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) 10.1177/0022034519881978
SARS-CoV-2 Screening among Symptom-Free Healthcare Workers 10.1017/ice.2021.81
Links between gut microbiome composition and fatty liver disease in a large population sample 10.1080/19490976.2021.1888673
Docent: Transforming personal intuitions to scientific hypotheses through content learning and process training 10.1145/3231644.3231646
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity 10.1093/ibd/izaa262
Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4
Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome 10.1038/s41598-019-49823-5
Evaluating metagenomic prediction of the metaproteome in a 4.5-year study of a patient with Crohn’s disease 10.1128/MSYSTEMS.00337-18
SHOGUN: A modular, accurate and scalable framework for microbiome quantification 10.1093/bioinformatics/btaa277
CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection 10.1073/pnas.2003656117
Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets 10.1128/MSYSTEMS.01216-20
Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study 10.1111/cts.12785
Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment 10.1093/sleep/zsz113
IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024
Reduced independence in daily living is associated with the gut microbiome in people with HIV and HCV 10.1128/mSystems.00528-20
Host variables confound gut microbiota studies of human disease 10.1038/s41586-020-2881-9
High-Resolution longitudinal dynamics of the cystic fibrosis sputum microbiome and metabolome through antibiotic therapy 10.1128/mSystems.00292-20
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing 10.1038/s41592-020-01041-y
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes 10.1186/s40168-020-00857-2
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities 10.1016/j.cels.2019.09.004
Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria 10.1128/mSystems.00083-18
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6
Disease-modifying therapies alter gut microbial composition in MS 10.1212/NXI.0000000000000517
Current Concepts, Opportunities, and Challenges of Gut Microbiome-Based Personalized Medicine in Nonalcoholic Fatty Liver Disease 10.1016/j.cmet.2020.11.010
Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi 10.1002/ajp.22989
Large-scale replicated field study of maize rhizosphere identifies heritable microbes 10.1073/pnas.1800918115
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3
Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models. 10.1038/s41591-018-0219-z
Three-dimensional culture of oral progenitor cells: Effects on small extracellular vesicles production and proliferative function 10.1111/jop.12981
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017 10.1186/s40168-018-0596-z
Human skin, oral, and gut microbiomes predict chronological age 10.1128/mSystems.00630-19
Identifying and predicting novelty in microbiome studies 10.1128/mBio.02099-18
Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry 10.1053/j.gastro.2020.09.038
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media 10.1038/s41597-019-0331-z
High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity 10.1128/mSystems.00166-18
Species-level functional profiling of metagenomes and metatranscriptomes 10.1038/s41592-018-0176-y
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases 10.1038/s41586-019-1237-9
Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes 10.1056/NEJMoa2003697
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 10.1038/s41467-020-16366-7
Is there convergence of gut microbes in blood-feeding vertebrates? 10.1098/rstb.2018.0249
The genetic basis for adaptation of modeldesigned syntrophic co-cultures 10.1371/journal.pcbi.1006213
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information 10.1101/gr.260380.119
Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes 10.1128/AEM.00369-19
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7
Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0
Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study 10.1002/ijc.33473
Microbe-metabolite associations linked to the rebounding murine gut microbiome postcolonization with vancomycin-resistant enterococcus faecium 10.1128/mSystems.00452-20
A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children 10.1128/mSystems.00293-19
Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the ApcMin/+ mouse model 10.1002/ijc.33477
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9
Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8
Role of the microbiome in human development 10.1136/gutjnl-2018-317503
Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9
The gut microbiome, aging, and longevity: A systematic review 10.3390/nu12123759
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media 10.1038/s41597-019-0051-4
Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome 10.3389/fphys.2021.663950
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations 10.1016/j.tim.2018.11.003
A distinct microbiome signature in posttreatment lyme disease patients 10.1128/mBio.02310-20
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1186/s40168-020-00960-4
Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis 10.1177/1352458520924594
Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w
Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9
Farm-like indoor microbiota in non-farm homes protects children from asthma development 10.1038/s41591-019-0469-4
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120
Creating a 3D microbial and chemical snapshot of a human habitat. 10.1038/s41598-018-21541-4
Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. 10.1371/journal.pntd.0006344
Microbiome and metagenome analyses of a closed habitat during human occupation 10.1128/mSystems.00367-20
Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations 10.1371/journal.pone.0224757
Temporal, environmental, and biological drivers of the mucosal microbiome in a Wild Marine Fish, Scomber japonicus 10.1128/MSPHERE.00401-20
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2
Altered Gut Microbiota and Host Metabolite Profiles in Women with Human Immunodeficiency Virus 10.1093/cid/ciz1117
Multiple-disease detection and classification across cohorts via microbiome search 10.1128/mSystems.00150-20
Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. 10.1186/s13059-020-01970-z
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection 10.1084/jem.20192276
Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003
Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary 10.2144/btn-2018-0192
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States 10.1016/j.cell.2021.03.052
Regional variation limits applications of healthy gut microbiome reference ranges and disease models 10.1038/s41591-018-0164-x
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus 10.1186/s12866-018-1341-2
Learning representations of microbe–metabolite interactions 10.1038/s41592-019-0616-3
Establishing microbial composition measurement standards with reference frames 10.1038/s41467-019-10656-5
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny 10.1186/s13059-019-1807-z
American Gut: An open platform for citizen science microbiome research 10.1128/MSYSTEMS.00031-18
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 10.2144/BTN-2020-0153
Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/s41586-018-0304-y
Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing 10.1016/j.envint.2020.105604
Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations 10.1053/j.gastro.2019.11.305
Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/MSYSTEMS.00269-18
Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014
Challenges in the construction of knowledge bases for human microbiome-disease associations 10.1186/s40168-019-0742-2
Evaluating organism-wide changes in the metabolome and microbiome following a single dose of antibiotic 10.1128/MSYSTEMS.00340-20
Links between environment, diet, and the hunter-gatherer microbiome 10.1080/19490976.2018.1494103
Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9
The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment 10.3389/fmicb.2020.02015
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4
Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1
A novel sparse compositional technique reveals microbial perturbations 10.1128/MSYSTEMS.00016-19
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study 10.1038/s41598-020-59016-0
Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load 10.1128/MSYSTEMS.01182-20
Associations of the fecal microbial proteome composition and proneness to diet-induced obesity 10.1074/mcp.RA119.001623
Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8
Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics 10.1093/gbe/evy133
Early-life gut dysbiosis linked to juvenile mortality in ostriches 10.1186/s40168-020-00925-7
Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures 10.1016/j.cell.2020.07.040
Species abundance information improves sequence taxonomy classification accuracy 10.1038/s41467-019-12669-6
Organ-level protein networks as a reference for the host effects of the microbiome 10.1101/gr.256875.119
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893) 10.1038/nbt0718-660d
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota 10.1038/s41597-020-00656-2
Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1128/mSystems.00635-19
Animal Models for Microbiome Research and Drug Discovery 10.1016/j.ddmod.2019.09.001
FXR Regulates Intestinal Cancer Stem Cell Proliferation 10.1016/j.cell.2019.01.036
The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months 10.1093/ajcn/nqaa011
Intermittent hypoxia and hypercapnia reproducibly change the gut microbiome and metabolome across rodent model systems 10.1128/mSystems.00058-19
Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 10.1186/s40168-020-00951-5
Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals 10.1161/JAHA.120.016641
Longitudinal survey of microbiome associated with particulate matter in a megacity 10.1186/s13059-020-01964-x
Early-career scientists shaping the world 10.1128/mSystems.00196-19
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z
The gut-liver axis and the intersection with the microbiome 10.1038/s41575-018-0011-z
A gut bacterial amyloid promotes a-synuclein aggregation and motor impairment in mice 10.7554/eLife.53111
Leveling up citizen science 10.1038/s41587-020-0694-x
Evaluating the information content of shallow shotgun metagenomics 10.1128/mSystems.00069-18
Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study 10.1016/j.envres.2021.111084
Depression in individuals coinfected with HIV and HCV is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00465-20
Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota 10.1038/s41396-020-00855-0
Microbial ecology of atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota 10.1128/AEM.00411-20
Handwashing and detergent treatment greatly reduce SARS-CoV-2 viral load on halloween candy handled by COVID-19 patients 10.1128/mSystems.01074-20
Author Correction: Farm-like indoor microbiota in non-farm homes protects children from asthma development. 10.1038/s41591-019-0546-8
The Effects of Captivity on the Mammalian Gut Microbiome. 10.1093/icb/icx090
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0218-196a
Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. 10.1080/2162402x.2017.1361593
Genetic influences on the human oral microbiome. 10.1186/s12864-017-4008-8
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 10.1126/science.aan4834
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. 10.1073/pnas.1711235114
Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection. 10.1021/acs.analchem.7b02423
The sponge microbiome project. 10.1093/gigascience/gix077
Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants. 10.1093/icb/icx088
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. 10.1038/nbt.3981
Impacts of the Human Gut Microbiome on Therapeutics. 10.1146/annurev-pharmtox-042017-031849
Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. 10.1128/msystems.00093-17
Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. 10.1038/nature24485
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. 10.1128/mbio.01343-17
Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. 10.1371/journal.pone.0184336
A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. 10.1016/j.chom.2017.10.001
Evaluating the impact of domestication and captivity on the horse gut microbiome. 10.1038/s41598-017-15375-9
Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/nature25028
Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes. 10.1128/msystems.00092-17
Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. 10.1111/1365-2656.12781
Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). 10.1128/mbio.01836-17
Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. 10.1128/msystems.00188-17
Expanding our Understanding of the Role of the Microbiome in Health and Disease. 10.1016/j.arcmed.2018.02.002
Bacterial density rather than diversity correlates with hatching success across different avian species. 10.1093/femsec/fiy022
Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. 10.1073/pnas.1712337115
Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. 10.3390/genes9020104
Improving saliva shotgun metagenomics by chemical host DNA depletion. 10.1186/s40168-018-0426-3
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. 10.1128/msystems.00218-17
Bacterial community changes in an industrial algae production system. 10.1016/j.algal.2017.09.010
Earth Microbiome Project and Global Systems Biology. 10.1128/msystems.00217-17
Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. 10.1093/femsec/fiy063
Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space. 10.1089/bfm.2018.29072.rjk
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. 10.1128/msystems.00021-18
Gut microbiota utilize immunoglobulin A for mucosal colonization. 10.1126/science.aaq0926
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. 10.1186/s40168-018-0470-z
Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. 10.1016/j.cels.2018.04.010
Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. 10.1128/msystems.00020-18
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. 10.3389/fmicb.2018.02559
Microbiota as in farm homes protect children from asthma 10.1183/13993003.congress-2018.oa337
Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19) 10.1093/cdn/nzz040.or01-08-19
Neighborhoods to Nucleotides—Advances and Gaps for an Obesity Disparities Systems Epidemiology Model 10.1007/s40471-019-00221-5
Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054
Visualizing 'omic feature rankings and log-ratios using Qurro. 10.1093/nargab/lqaa023
A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. 10.1016/j.cmet.2020.06.005
Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. 10.1158/1055-9965.epi-20-0824
Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos. 10.1093/ajcn/nqab001
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 10.21203/
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 10.1101/2021.02.06.21251159
The early evolution of the genetic code. 10.1016/s0092-8674(00)80866-1
Measuring adaptation within the genetic code. 10.1016/s0968-0004(99)01531-5
Early fixation of an optimal genetic code. 10.1093/oxfordjournals.molbev.a026331
An amphioxus Krox gene: insights into vertebrate hindbrain evolution. 10.1007/s004270000092
Identification of conserved C2H2 zinc-finger gene families in the Bilateria. 10.1186/gb-2001-2-5-research0016
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. 10.1186/gb-2001-2-4-research0010
Analyzing partially randomized nucleic acid pools: straight dope on doping. 10.1093/nar/gng030
Do universal codon-usage patterns minimize the effects of mutation and translation error? 10.1186/gb-2005-6-11-r91
Information, probability, and the abundance of the simplest RNA active sites. 10.2741/3137
Systems biology: Understanding function from genes to networks 10.2174/157016409788680974
The mind-body-microbial continuum. 10.31887/dcns.2011.13.1/agonzalez
Analytic Strategies for Understanding Host-Associated Microbial Communities: Faster and cheaper DNA sequencing technologies combined with open-access analytic software packages are opening new vistas 10.1128/microbe.6.389.1
Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 10.1186/2049-2618-2-16
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0718-660a
A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. 10.7554/elife.01104
Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. 10.7554/elife.11405
Chris Callewaert
Callewaert Chris
ORCID: 0000-0001-7697-9188
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18
Best practices for analysing microbiomes 10.1038/s41579-018-0029-9
Dupilumab-mediated IL-4R alpha blockade decreases Staphylococcus aureus colonization and increases microbial diversity in patients with Atopic Dermatitis (AD) 10.1016/j.jid.2018.06.036
Impacts of the Human Gut Microbiome on Therapeutics 10.1146/annurev-pharmtox-042017-031849
The Microbiome and Human Biology 10.1146/annurev-genom-083115-022438
Towards a bacterial treatment for armpit malodour 10.1111/exd.13259
The effect of feed water dissolved organic carbon concentration and composition on organic micropollutant removal and microbial diversity in soil columns simulating river bank filtration 10.1016/j.chemosphere.2015.09.017
A laboratory-scale column study comparing organic micropollutant removal and microbial diversity for two soil types 10.1016/j.scitotenv.2015.07.056
Bacterial Exchange in Household Washing Machines 10.3389/fmicb.2015.01381
Novel biocompatible nanocapsules for slow release of fragrances on the human skin 10.1016/j.nbt.2014.09.001
Artificial sweat composition to grow and sustain a mixed human axillary microbiome 10.1016/j.mimet.2014.05.005
Deodorants and antiperspirants affect the axillary bacterial community 10.1007/s00403-014-1487-1
Microbial Odor Profile of Polyester and Cotton Clothes after a Fitness Session 10.1128/AEM.01422-14
Characterization of Staphylococcus and Corynebacterium Clusters in the Human Axillary Region 10.1371/journal.pone.0070538
The resource footprint of biobased products: a key issue in the sustainable development of biorefineries 10.1002/bbb.304
IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024
Biological and Chemical Processes that Lead to Textile Malodour Development 10.3390/microorganisms8111709
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6
A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children 10.1128/msystems.00293-19
Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4
Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091
Zeb2 drives invasive and microbiota-dependent colon carcinoma 10.1038/s43018-020-0070-2
Publisher Correction: Zeb2 drives invasive and microbiota-dependent colon carcinoma 10.1038/s43018-020-0097-4
Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin 10.3389/fmicb.2020.577474
Dietary emulsifiers alter composition and activity of the human gut microbiota in vitro, irrespective of chemical or natural emulsifier origin 10.1101/2020.06.28.174946
Skin Microbiome and its Interplay with the Environment 10.1007/s40257-020-00551-x
102 Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Patients With Atopic Dermatitis 10.1016/j.jid.2019.07.106
Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions 10.3390/microorganisms9020353
The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship 10.3390/microorganisms9061192
Tomasz Kosciolek
Kosciolek Tomasz
ORCID: 0000-0002-9915-7387
De novo structure prediction of globular proteins aided by sequence variation-derived contacts 10.1371/journal.pone.0092197
Protein binding site analysis by means of structural interaction fingerprint patterns 10.1016/j.bmcl.2011.09.027
MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins 10.1093/bioinformatics/btu791
Impact of template choice on homology model efficiency in virtual screening 10.1021/ci500001f
Opportunities and limitations in applying coevolution-derived contacts to protein 10.1515/bams-2014-0013
Best practices for analysing microbiomes 10.1038/s41579-018-0029-9
IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024
Structure-Based Protein Function Prediction using Graph Convolutional Networks 10.1101/786236
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4
Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1
Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder 10.1016/j.jpsychires.2018.01.013
Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6
Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9
Docent: Transforming personal intuitions to scientific hypotheses through content learning and process training 10.1145/3231644.3231646
Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis 10.1016/j.eurpsy.2018.05.011
Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using de Novo Fragment-Based Protein Structure Predictions 10.1038/s41598-017-07156-1
Accurate contact predictions using covariation techniques and machine learning 10.1002/prot.24863
The microbiome and its potential for pharmacology 10.1007/164_2019_317
Gut instinct: Creating scientific theories with online learners 10.1145/3025453.3025769
Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026
Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004
Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100
Design and synthesis of novel cannabinoid ligands based on a 1,2,3-triazole scaffold 10.2174/157018013804725134
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18
Ricardo da Silva
da Silva Ricardo
ORCID: 0000-0001-6378-0479
Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter 10.1007/s13361-018-2069-9
Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3
A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles 10.1371/journal.pone.0207051
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18
Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737
Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns 10.1039/c7cc08411k
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089
Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication 10.1021/acs.jnatprod.8b00292
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381
Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054
High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols 10.1021/acsjnatprod.6b00722
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung 10.1016/j.chom.2017.10.001
Application of MALDI Mass Spectrometry in Natural Products Analysis 10.1055/s-0042-104800
From Sample to Multi-Omics Conclusions in under 48 Hours 10.1128/mSystems.00038-16
Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113
A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry 10.1016/j.aca.2015.01.002
Illuminating the dark matter in metabolomics 10.1073/pnas.1516878112
Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing 10.1039/c3np70086k
ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics 10.1093/bioinformatics/btu019
Queen signals in a stingless bee: suppression of worker ovary activation and spatial distribution of active compounds 10.1038/srep07449
Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis 10.1128/MSYSTEMS.00375-19
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/J.FOODCHEM.2019.125290
In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation 10.1016/J.FOODCHEM.2019.05.099
Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation 10.1021/ACS.JNATPROD.8B00916
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/S12915-019-0660-6
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L 10.3389/FPLS.2019.00846
Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin 10.1021/ACS.ANALCHEM.8B05854
Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9
Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim 10.1021/acsinfecdis.9b00513
Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9
Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292
Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6
Time-Scale Shifting of Volatile Semiochemical Levels in Wild Type Lychnophora ericoides (Brazilian arnica) and Pollinator Records 10.1055/a-1320-4556
Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells 10.1038/s41419-020-03275-2
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020
Convergent evolution of pain-inducing defensive venom components in spitting cobras 10.1126/science.abb9303
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/msystems.00601-21
CHAPTER 10. Perspectives for the Future 10.1039/9781788010399-00264
CHAPTER 3. Metabolomics 10.1039/9781788010399-00057
Mass Spectrometry in Chemical Biology 10.1039/9781788010399
Stefan Janssen
Janssen Stefan
ORCID: 0000-0003-0955-0589
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease 10.1016/j.cell.2016.11.018
The RNA shapes studio 10.1093/bioinformatics/btu649
Ambivalent covariance models 10.1186/s12859-015-0569-1
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples 10.1128/mSystems.00218-17
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information 10.1128/mSystems.00021-18
Creating a 3D microbial and chemical snapshot of a human habitat 10.1038/s41598-018-21541-4
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software 10.1038/nmeth.4458
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18
Shape based indexing for faster search of RNA family databases 10.1186/1471-2105-9-131
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction 10.1186/1471-2105-12-429
Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis 10.1093/bioinformatics/btt022
Faster computation of exact RNA shape probabilities 10.1093/bioinformatics/btq014
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs 10.1007/978-3-642-15294-8_5
Bellman's GAP: a declarative language for dynamic programming 10.1145/2003476.2003484
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti 10.1186/1471-2164-11-245
Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9
Assessing taxonomic metagenome profilers with OPAL 10.1101/372680
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2
Assessing taxonomic metagenome profilers with OPAL 10.1186/s13059-019-1646-y
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4
Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID 10.1038/s41467-019-13570-y
Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1
An intact gut microbiome protects genetically predisposed mice against leukemia 10.1182/blood.2019004381
Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets 10.1128/mSystems.01216-20
Results from a pilot study on the oral microbiome in children and adolescents with chronic nonbacterial osteomyelitis 10.1007/s00393-021-01035-x