Paperbase

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Garg, Neha Wang, Mingxun Hyde, Embriette da Silva, Ricardo R. Melnik, Alexey V. Protsyuk, Ivan Bouslimani, Amina Lim, Yan Wei Wong, Richard Humphrey, Greg Ackermann, Gail Spivey, Timothy Brouha, Sharon S. Bandeira, Nuno Lin, Grace Y. Rohwer, Forest Conrad, Douglas J. Alexandrov, Theodore Knight, Rob Dorrestein, Pieter C.

Cell Host and Microbe, 2017

https://doi.org/10.1016/j.chom.2017.10.001

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

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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

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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

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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

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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

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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

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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

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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

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Gut microbiomes of Malawian twin pairs discordant for kwashiorkor 10.1126/science.1229000

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Finding the Missing Links among Metabolites, Microbes, and the Host 10.1016/j.immuni.2014.05.015

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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

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Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs) 10.1371/journal.pone.0054703

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Mosquito microbiome dynamics, a background for prevalence and seasonality of West Nile virus 10.3389/fmicb.2017.00526

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Rewiring the keyboard: Evolvability of the genetic code 10.1038/35047500

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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

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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

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Advancing the microbiome research community 10.1016/j.cell.2014.09.022

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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

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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

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Meta-analyses of studies of the human microbiota 10.1101/gr.151803.112

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Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities 10.1371/journal.pone.0047879

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The Ecology of Microbial Communities Associated with Macrocystis pyrifera 10.1371/journal.pone.0067480

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HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats 10.1371/journal.pone.0105684

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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

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Oral probiotic versus placebo and the maternal microbiome during pregnancy: A randomized controlled trial 10.1016/j.ajog.2019.11.064

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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 Apc^Min^/+ 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

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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/rs.3.rs-56028/v1

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

Neha Garg

Garg Neha

ORCID: 0000-0002-2760-7123

https://www.garglab-microbiomegt.com/

Creating a 3D microbial and chemical snapshot of a human habitat 10.1038/s41598-018-21541-4

Dereplication of peptidic natural products through database search of mass spectra 10.1038/nchembio.2219

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae 10.7554/eLife.24214

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules 10.1128/mSystems.00058-17

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment 10.1128/mSystems.00016-17

Natural products as mediators of disease 10.1039/c6np00063k

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung 10.1016/j.chom.2017.10.001

Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis 10.1021/acschembio.6b01031

Characterization of the Stereochemical Configuration of Lanthionines Formed by the Lanthipeptide Synthetase GeoM 10.1002/bip.22876

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats 10.1021/acs.analchem.6b03456

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome 10.1038/ismej.2015.207

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen 10.1128/mSystems.00139-16

Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins 10.1021/acs.orglett.5b02113

Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures 10.1016/j.ijms.2014.06.005

Chemical Rescue and Inhibition Studies to Determine the Role of Arg301 in Phosphite Dehydrogenase 10.1371/journal.pone.0087134

Mass spectrometry of natural products: current, emerging and future technologies 10.1039/c4np00044g

Mode of action and structure-activity relationship studies of geobacillin I 10.1038/ja.2013.112

Specialized Metabolites from the Microbiome in Health and Disease 10.1016/j.cmet.2014.10.016

Substrate Specificity of the Lanthipeptide Peptidase ElxP and the Oxidoreductase ElxO 10.1021/cb5002526

The Intestinal Metabolome: An Intersection Between Microbiota and Host 10.1053/j.gastro.2014.03.001

In vitro activity of the nisin dehydratase NisB 10.1073/pnas.1222488110

Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase 10.1186/1472-6750-12-75

Lantibiotics from Geobacillus thermodenitrificans 10.1073/pnas.1116815109

Production of Lantipeptides in Escherichia coli 10.1021/ja109044r

Mass Spectrometry-Based Integration and Expansion of the Chemical Diversity Harbored Within a Marine Sponge. 10.1007/s13361-019-02207-5

The chemical topology of a bacterial swarm. 10.1074/jbc.H118.003178

Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates. 10.1016/bs.mie.2018.01.028

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis 10.1128/msystems.00375-19

Feature-based molecular networking in the GNPS analysis environment. 10.1038/s41592-020-0933-6

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors. 10.3390/md18020124

Global chemical effects of the microbiome include new bile-acid conjugations. 10.1038/s41586-020-2047-9

Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim. 10.1021/acsinfecdis.9b00513

Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids. 10.1021/acschembio.0c00375

A community resource for paired genomic and metabolomic data mining. 10.1038/s41589-020-00724-z

Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures. 10.1128/msystems.01387-20

LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome. 10.1016/j.cell.2021.04.001

Forest Rohwer

Rohwer Forest

ORCID: 0000-0003-1548-5429

The birth of viromics: an interview with Forest Rohwer 10.2217/fmb-2018-0223

Forest Rohwer at the 2010 DOE JGI User Meeting 10.4016/17298.01

SYBR Green or Gold Staining v1 10.17504/protocols.io.c7sznd

Global Phage Diversity 10.1016/s0092-8674(03)00276-9

Coral Microbiology 10.5670/oceanog.2007.60

Real-time microbial ecology 10.1111/j.1462-2920.2006.01222_9.x

The Human Virome 10.1007/978-1-4419-7089-3_4

Crystal Structure of a Metagenomic Thioredoxin 10.2210/pdb3vfi/pdb

Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. 10.1128/msystems.01074-20

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes. 10.1128/msystems.00648-20

Virulence as a Side Effect of Interspecies Interaction in Vibrio Coral Pathogens. 10.1128/mbio.00201-20

A multiomic analysis of in situ coral-turf algal interactions. 10.1073/pnas.1915455117

Phage and bacteria diversification through a prophage acquisition ratchet 10.1101/2020.04.08.028340

Multi-omics study of keystone species in the cystic fibrosis lung microbiome 10.21203/rs.3.rs-18792/v1

Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents. 10.1002/ece3.6138

Evidence for a biological source of widespread, reproducible nighttime oxygen spikes in tropical reef ecosystems has implications for coral health 10.1101/2020.03.08.982645

Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. 10.1186/s12864-020-6523-2

Gp4 is a nuclease required for morphogenesis of T4-like bacteriophages. 10.1016/j.virol.2020.01.008

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. 10.1080/19490976.2019.1701353

A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes 10.1101/865204

Biophysical and physiological processes causing oxygen loss from coral reefs. 10.7554/elife.49114

Impact of bacteria motility in the encounter rates with bacteriophage in mucus. 10.1038/s41598-019-52794-2

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. 10.1128/msystems.00375-19

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs 10.1101/676148

Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information. 10.1128/mbio.00431-19

Diel population and functional synchrony of microbial communities on coral reefs. 10.1038/s41467-019-09419-z

Biophysical and physiological causes of coral reef microbialization 10.1101/495481

Erratum for Schooley et al., "Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection". 10.1128/aac.02221-18

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. 10.1186/s40168-018-0573-6

Gradients in Primary Production Predict Trophic Strategies of Mixotrophic Corals across Spatial Scales. 10.1016/j.cub.2018.08.057

Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism. 10.1098/rspb.2018.1307

Relevance of coral geometry in the outcomes of the coral-algal benthic war 10.1101/327031

Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers". 10.1128/mbio.02207-17

A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction. 10.1016/j.cub.2017.10.051

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers. 10.1128/mbio.01874-17

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

Meta-mass shift chemical profiling of metabolomes from coral reefs. 10.1073/pnas.1710248114

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Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters. 10.1073/pnas.1508355112

Closing the gaps on the viral photosystem-I psaDCAB gene organization. 10.1111/1462-2920.13036

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Metabolic cascades in marine microbial communities. 10.1073/pnas.1504310112

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. 10.1038/ismej.2014.266

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. 10.1038/ismej.2014.234

Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures. 10.1016/j.ijms.2014.06.005

Diversity of viral photosystem-I psaA genes. 10.1038/ismej.2014.244

Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples. 10.3791/52117

Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology. 10.3791/52131

Stochastic tracking of infection in a CF lung. 10.1371/journal.pone.0111245

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Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. 10.1073/pnas.1403319111

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The origins of ambient biological sound from coral reef ecosystems in the Line Islands archipelago. 10.1121/1.4865922

Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. 10.1128/mbio.00956-13

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. 10.1002/prot.24489

Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. 10.1038/ismej.2013.229

Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. 10.1128/jcm.02204-13

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. 10.1073/pnas.1319470110

Innate and acquired bacteriophage-mediated immunity. 10.4161/bact.25857

Influence of coral and algal exudates on microbially mediated reef metabolism. 10.7717/peerj.108

Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates. 10.7717/peerj.107

Visualization of oxygen distribution patterns caused by coral and algae. 10.7717/peerj.106

Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data. 10.1371/journal.pone.0064285

Bacteriophage adhering to mucus provide a non-host-derived immunity. 10.1073/pnas.1305923110

Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. 10.1371/journal.pone.0058404

Structure and function of a cyanophage-encoded peptide deformylase. 10.1038/ismej.2013.4

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. 10.1038/ismej.2012.161

Janzen-Connell effects in a broadcast-spawning Caribbean coral: distance-dependent survival of larvae and settlers. 10.1890/12-0985.1

Environmental distribution of coral-associated relatives of apicomplexan parasites. 10.1038/ismej.2012.129

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Cystic fibrosis therapy: a community ecology perspective. 10.1165/rcmb.2012-0059ps

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Oxygen minimum zones harbour novel viral communities with low diversity. 10.1111/j.1462-2920.2012.02891.x

Assessing coral reefs on a Pacific-wide scale using the microbialization score. 10.1371/journal.pone.0043233

Unseen players shape benthic competition on coral reefs. 10.1016/j.tim.2012.08.004

Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. 10.1016/j.jcf.2012.07.009

Going viral: next-generation sequencing applied to phage populations in the human gut. 10.1038/nrmicro2853

The Microbial Olympics. 10.1038/nrmicro2837

Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. 10.1016/j.cub.2012.04.047

Grinder: a versatile amplicon and shotgun sequence simulator. 10.1093/nar/gks251

Black reefs: iron-induced phase shifts on coral reefs 10.1038/ismej.2011.148

Metagenomics and future perspectives in virus discovery. 10.1016/j.coviro.2011.12.004

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. 10.1038/ismej.2011.169

Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. 10.1371/journal.pone.0027973

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae. 10.1098/rspb.2011.2155

New abundant microbial groups in aquatic hypersaline environments. 10.1038/srep00135

Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. 10.1165/rcmb.2011-0253oc

Black reefs: iron-induced phase shifts on coral reefs. 10.1038/ismej.2011.114

Spatial distribution of microbial communities in the cystic fibrosis lung. 10.1038/ismej.2011.104

Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. 10.1371/journal.pone.0020579

Comparative metagenomics of microbial traits within oceanic viral communities. 10.1038/ismej.2011.2

Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. 10.1111/j.1462-2920.2010.02419.x

Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. 10.1111/j.1462-2920.2010.02304.x

Viruses in the faecal microbiota of monozygotic twins and their mothers. 10.1038/nature09199

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. 10.1186/1471-2105-11-341

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. 10.1073/pnas.1000089107

The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem. 10.1371/journal.pone.0010950

Viral and microbial community dynamics in four aquatic environments. 10.1038/ismej.2010.1

Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. 10.1111/j.1462-2920.2010.02163.x

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. 10.1371/journal.pcbi.1000593

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. 10.1186/1471-2164-10-570

Hyperspectral and physiological analyses of coral-algal interactions. 10.1371/journal.pone.0008043

Roles of viruses in the environment. 10.1111/j.1462-2920.2009.02101.x

Explaining microbial population genomics through phage predation. 10.1038/nrmicro2235

Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. 10.1371/journal.pone.0007370

Photosystem I gene cassettes are present in marine virus genomes. 10.1038/nature08284

Genomic analysis of multiple Roseophage SIO1 strains. 10.1111/j.1462-2920.2009.02021.x

Viruses manipulate the marine environment. 10.1038/nature08060

Metagenomic analysis of stressed coral holobionts. 10.1111/j.1462-2920.2009.01935.x

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Laboratory procedures to generate viral metagenomes. 10.1038/nprot.2009.10

Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. 10.1073/pnas.0808985105

Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. 10.1371/journal.pone.0003263

Dissecting microbial employment. 10.1038/nbt0908-997

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. 10.1111/j.1462-2920.2008.01725.x

Viral communities associated with healthy and bleaching corals. 10.1111/j.1462-2920.2008.01652.x

Viral diversity and dynamics in an infant gut. 10.1016/j.resmic.2008.04.006

The airborne metagenome in an indoor urban environment. 10.1371/journal.pone.0001862

Functional metagenomic profiling of nine biomes. 10.1038/nature06810

Biodiversity and biogeography of phages in modern stromatolites and thrombolites. 10.1038/nature06735

Microbial ecology of four coral atolls in the Northern Line Islands. 10.1371/journal.pone.0001584

Baselines and degradation of coral reefs in the Northern Line Islands. 10.1371/journal.pone.0001548

Phylogenetic classification of short environmental DNA fragments. 10.1093/nar/gkn038

A bacterial metapopulation adapts locally to phage predation despite global dispersal. 10.1101/gr.6835308

Metagenomic analysis of the microbial community associated with the coral Porites astreoides. 10.1111/j.1462-2920.2007.01383.x

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. 10.1128/aem.00358-07

Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. 10.1128/aem.00461-07

Power law rank-abundance models for marine phage communities. 10.1111/j.1574-6968.2007.00790.x

Phage metagenomics. 10.1016/s0076-6879(06)21020-6

The marine viromes of four oceanic regions. 10.1371/journal.pbio.0040368

Rapid estimation of microbial numbers in water using bulk fluorescence. 10.1111/j.1462-2920.2006.01062.x

Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California. 10.1111/j.1574-6968.2006.00345.x

Finding novel genes in bacterial communities isolated from the environment. 10.1093/bioinformatics/btl247

Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. 10.1111/j.1461-0248.2006.00937.x

Using pyrosequencing to shed light on deep mine microbial ecology. 10.1186/1471-2164-7-57

An application of statistics to comparative metagenomics. 10.1186/1471-2105-7-162

FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. 10.1186/1471-2105-7-57

RNA viral community in human feces: prevalence of plant pathogenic viruses. 10.1371/journal.pbio.0040003

Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. 10.2144/000112019

Here a virus, there a virus, everywhere the same virus? 10.1016/j.tim.2005.04.003

Complete genome sequence of phiHSIC, a pseudotemperate marine phage of Listonella pelagia. 10.1128/aem.71.6.3311-3320.2005

Viral metagenomics. 10.1038/nrmicro1163

A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains. 10.1128/jb.187.9.2992-3001.2005

Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. 10.1371/journal.pbio.0030144

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. 10.1186/1471-2105-6-41

2004 ASM Conference on the New Phage Biology: the 'Phage Summit'. 10.1111/j.1365-2958.2005.04509.x

Microbial communities associated with skeletal tumors on Porites compressa. 10.1016/j.femsle.2005.01.004

Widespread association of a Rickettsiales-like bacterium with reef-building corals. 10.1111/j.1462-2920.2004.00647.x

Movement of viruses between biomes. 10.1128/aem.70.10.5842-5846.2004

Transfer of photosynthesis genes to and from Prochlorococcus viruses. 10.1073/pnas.0401526101

Global distribution of nearly identical phage-encoded DNA sequences. 10.1016/j.femsle.2004.05.042

Diversity and population structure of a near-shore marine-sediment viral community. 10.1098/rspb.2003.2628

Phage community dynamics in hot springs. 10.1128/aem.70.3.1633-1640.2004

Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C. 10.1128/jb.185.21.6434-6447.2003

Multispecies microbial mutualisms on coral reefs: the host as a habitat. 10.1086/378684

Metagenomic analyses of an uncultured viral community from human feces. 10.1128/jb.185.20.6220-6223.2003

Use of fluorescently labeled phage in the detection and identification of bacterial species. 10.1366/00037020360696008

IL-2 activation of a PI3K-dependent STAT3 serine phosphorylation pathway in primary human T cells. 10.1016/s0898-6568(03)00003-2

Marine phage genomics. 10.1016/s1096-4959(02)00168-9

Genomic analysis of uncultured marine viral communities. 10.1073/pnas.202488399

The Phage Proteomic Tree: a genome-based taxonomy for phage. 10.1128/jb.184.16.4529-4535.2002

Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. 10.1128/aem.68.7.3628-3633.2002

FastGroup: a program to dereplicate libraries of 16S rDNA sequences. 10.1186/1471-2105-2-9

Production of shotgun libraries using random amplification. 10.2144/01311rr02

Detection of DNA damage in prokaryotes by terminal deoxyribonucleotide transferase-mediated dUTP nick end labeling. 10.1128/aem.66.3.1001-1006.2000

Characterization of an IL-2 dependent human T-cell leukemia-virus type-I (HTLV-I) infected cell-line - a system for studying HTLV-I mediated transformation. 10.3892/ijo.5.5.1163

Ricardo da Silva

da Silva Ricardo

ORCID: 0000-0001-6378-0479

http://ccbl.fcfrp.usp.br

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

REDES MOLECULARES: UMA ANÁLISE SOBRE ANOTAÇÕES E DESCOBERTA DE NOVOS ATIVOS 10.21577/0100-4042.20170777

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