Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
出版年份 2022 全文链接
标题
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
作者
关键词
-
出版物
Nature Microbiology
Volume 7, Issue 12, Pages 2128-2150
出版商
Springer Science and Business Media LLC
发表日期
2022-11-29
DOI
10.1038/s41564-022-01266-x
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- Critical Assessment of Metagenome Interpretation: the second round of challenges
- (2022) Fernando Meyer et al. NATURE METHODS
- Nitrogen use efficiency, rhizosphere bacterial community, and root metabolome reprogramming due to maize seed treatment with microbial biostimulants
- (2022) Paola Ganugi et al. PHYSIOLOGIA PLANTARUM
- Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
- (2022) Qiyun Zhu et al. mSystems
- Effect of host breeds on gut microbiome and serum metabolome in meat rabbits
- (2021) Xiaoxing Ye et al. BMC Veterinary Research
- High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
- (2021) Søren M. Karst et al. NATURE METHODS
- Metabolomic shifts associated with heat stress in coral holobionts
- (2021) Amanda Williams et al. Science Advances
- A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
- (2021) Justin P Shaffer et al. BIOTECHNIQUES
- Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
- (2021) Anna Paola Carrieri et al. Scientific Reports
- Functional profiling of COVID-19 respiratory tract microbiomes
- (2021) Niina Haiminen et al. Scientific Reports
- EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
- (2021) Kalen Cantrell et al. mSystems
- Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
- (2021) Ling Xu et al. Nature Communications
- Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
- (2021) Robin Schmid et al. Nature Communications
- Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality
- (2021) Erika P. Santoro et al. Science Advances
- Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome
- (2021) Celeste Allaband et al. mSystems
- NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products
- (2021) Hyun Woo Kim et al. JOURNAL OF NATURAL PRODUCTS
- Biosynthesis, evolution and ecology of microbial terpenoids
- (2021) Mariana Avalos et al. NATURAL PRODUCT REPORTS
- A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations
- (2021) Efrat Muller et al. Microbiome
- Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors
- (2020) Ipsita Mohanty et al. Marine Drugs
- Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa
- (2020) Elle M. Barnes et al. Frontiers in Microbiology
- Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance
- (2020) Ming-Yuan Xue et al. Microbiome
- Integrated Metagenomic and Metabolomic Analyses of the Effect of Astragalus Polysaccharides on Alleviating High-Fat Diet–Induced Metabolic Disorders
- (2020) Ying Hong et al. Frontiers in Pharmacology
- Feature-based molecular networking in the GNPS analysis environment
- (2020) Louis-Félix Nothias et al. NATURE METHODS
- Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants
- (2020) Mahaveer P. Sharma et al. Frontiers in Microbiology
- Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
- (2020) Kai Dührkop et al. NATURE BIOTECHNOLOGY
- Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale
- (2020) Edward E. Seabolt et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- A Novel Sparse Compositional Technique Reveals Microbial Perturbations
- (2019) Cameron Martino et al. mSystems
- SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
- (2019) Kai Dührkop et al. NATURE METHODS
- Novel insights from uncultivated genomes of the global human gut microbiome
- (2019) Stephen Nayfach et al. NATURE
- The Integrative Human Microbiome Project
- (2019) NATURE
- Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
- (2019) Jason Lloyd-Price et al. NATURE
- antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
- (2019) Kai Blin et al. NUCLEIC ACIDS RESEARCH
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- (2019) Evan Bolyen et al. NATURE BIOTECHNOLOGY
- Establishing microbial composition measurement standards with reference frames
- (2019) James T. Morton et al. Nature Communications
- A Review of the Microbial Production of Bioactive Natural Products and Biologics
- (2019) Janette V. Pham et al. Frontiers in Microbiology
- Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
- (2019) Jeremiah J. Minich et al. mSystems
- Toward understanding the origin and evolution of cellular organisms
- (2019) Minoru Kanehisa PROTEIN SCIENCE
- Learning representations of microbe–metabolite interactions
- (2019) James T. Morton et al. NATURE METHODS
- Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences
- (2019) Vincent Libis et al. Nature Communications
- Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)
- (2019) Travis C. Glenn et al. PeerJ
- The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
- (2019) Jeffrey A. van Santen et al. ACS Central Science
- Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
- (2019) Qiyun Zhu et al. Nature Communications
- Best practices for analysing microbiomes
- (2018) Rob Knight et al. NATURE REVIEWS MICROBIOLOGY
- Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
- (2018) Nicholas A. Bokulich et al. Microbiome
- Towards predicting the environmental metabolome from metagenomics with a mechanistic model
- (2018) Daniel R. Garza et al. Nature Microbiology
- Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
- (2018) Melanie Schirmer et al. Nature Microbiology
- Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
- (2018) Stefan Janssen et al. mSystems
- KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples
- (2018) Jeremiah J. Minich et al. mSystems
- Function and functional redundancy in microbial systems
- (2018) Stilianos Louca et al. Nature Ecology & Evolution
- Structure and function of the global topsoil microbiome
- (2018) Mohammad Bahram et al. NATURE
- Qiita: rapid, web-enabled microbiome meta-analysis
- (2018) Antonio Gonzalez et al. NATURE METHODS
- Dereplication of microbial metabolites through database search of mass spectra
- (2018) Hosein Mohimani et al. Nature Communications
- Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets
- (2018) Michael Hoggard et al. Frontiers in Microbiology
- Species-level functional profiling of metagenomes and metatranscriptomes
- (2018) Eric A. Franzosa et al. NATURE METHODS
- The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
- (2018) Rolf Henrik Nilsson et al. NUCLEIC ACIDS RESEARCH
- High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity
- (2018) Jeremiah J. Minich et al. mSystems
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Strains, functions and dynamics in the expanded Human Microbiome Project
- (2017) Jason Lloyd-Price et al. NATURE
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality
- (2017) Gregory C. A. Amos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Disentangling metabolic functions of bacteria in the honey bee gut
- (2017) Lucie Kešnerová et al. PLOS BIOLOGY
- Atropos: specific, sensitive, and speedy trimming of sequencing reads
- (2017) John P. Didion et al. PeerJ
- Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment
- (2017) Katy J. Califf et al. mSystems
- Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
- (2017) Amnon Amir et al. mSystems
- Global chemical analysis of biology by mass spectrometry
- (2017) Alexander A. Aksenov et al. Nature Reviews Chemistry
- A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture
- (2016) Terrence H. Bell et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- “Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
- (2016) Marco Fondi et al. Genome Biology and Evolution
- The evolution of genome mining in microbes – a review
- (2016) Nadine Ziemert et al. NATURAL PRODUCT REPORTS
- Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
- (2016) Mingxun Wang et al. NATURE BIOTECHNOLOGY
- Dereplication of peptidic natural products through database search of mass spectra
- (2016) Hosein Mohimani et al. Nature Chemical Biology
- Decoupling function and taxonomy in the global ocean microbiome
- (2016) S. Louca et al. SCIENCE
- Antibiotics, birth mode, and diet shape microbiome maturation during early life
- (2016) Nicholas A. Bokulich et al. Science Translational Medicine
- Fragmentation trees reloaded
- (2016) Sebastian Böcker et al. Journal of Cheminformatics
- VSEARCH: a versatile open source tool for metagenomics
- (2016) Torbjørn Rognes et al. PeerJ
- Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view
- (2016) Silvia Turroni et al. Scientific Reports
- Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
- (2015) A Apprill et al. AQUATIC MICROBIAL ECOLOGY
- Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
- (2015) Alma E. Parada et al. ENVIRONMENTAL MICROBIOLOGY
- Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
- (2015) Jenni Hultman et al. NATURE
- Searching molecular structure databases with tandem mass spectra using CSI:FingerID
- (2015) Kai Dührkop et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structure and function of the global ocean microbiome
- (2015) S. Sunagawa et al. SCIENCE
- Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys
- (2015) William Walters et al. mSystems
- Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
- (2015) Shirley Bikel et al. Computational and Structural Biotechnology Journal
- Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients
- (2014) Colleen R Kelly et al. AMERICAN JOURNAL OF GASTROENTEROLOGY
- Integrated metagenomic and metaproteomic analyses of marine biofilm communities
- (2014) Dagmar H. Leary et al. BIOFOULING
- geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
- (2014) Matthew W. Pennell et al. BIOINFORMATICS
- Arsenic Exposure Perturbs the Gut Microbiome and Its Metabolic Profile in Mice: An Integrated Metagenomics and Metabolomics Analysis
- (2014) Kun Lu et al. ENVIRONMENTAL HEALTH PERSPECTIVES
- The gut microbiota, bacterial metabolites and colorectal cancer
- (2014) Petra Louis et al. NATURE REVIEWS MICROBIOLOGY
- Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities
- (2013) Nicholas A. Bokulich et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Specialized microbial metabolites: functions and origins
- (2013) Julian Davies JOURNAL OF ANTIBIOTICS
- The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
- (2013) Pelin Yilmaz et al. NUCLEIC ACIDS RESEARCH
- EMPeror: a tool for visualizing high-throughput microbial community data
- (2013) Yoshiki Vázquez-Baeza et al. GigaScience
- The role of planktonicFlavobacteriain processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
- (2012) Timothy J. Williams et al. ENVIRONMENTAL MICROBIOLOGY
- Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
- (2012) J Gregory Caporaso et al. ISME Journal
- Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities
- (2012) Yan Wei Lim et al. Journal of Cystic Fibrosis
- A cross-platform toolkit for mass spectrometry and proteomics
- (2012) Matthew C Chambers et al. NATURE BIOTECHNOLOGY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
- (2012) Christine Vogel et al. NATURE REVIEWS GENETICS
- Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
- (2012) Anna Klindworth et al. NUCLEIC ACIDS RESEARCH
- Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches
- (2012) José C. Carvalho et al. OIKOS
- Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
- (2012) Alison R. Erickson et al. PLoS One
- Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
- (2012) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use
- (2012) M. Kleiner et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.
- (2011) Leland Wilkinson BIOMETRICS
- Removing Noise From Pyrosequenced Amplicons
- (2011) Christopher Quince et al. BMC BIOINFORMATICS
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
- (2011) Pelin Yilmaz et al. NATURE BIOTECHNOLOGY
- MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
- (2010) Tomáš Pluskal et al. BMC BIOINFORMATICS
- Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
- (2010) THORSTEN STOECK et al. MOLECULAR ECOLOGY
- Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
- (2010) J. G. Caporaso et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global patterns in belowground communities
- (2009) Noah Fierer et al. ECOLOGY LETTERS
- Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- (2009) M. Hamady et al. GENOME RESEARCH
- Bacterial competition: surviving and thriving in the microbial jungle
- (2009) Michael E. Hibbing et al. NATURE REVIEWS MICROBIOLOGY
- A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes
- (2009) Linda A. Amaral-Zettler et al. PLoS One
- SIRIUS: decomposing isotope patterns for metabolite identification†
- (2008) Sebastian Böcker et al. BIOINFORMATICS
- Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs
- (2008) Hege Vestheim et al. Frontiers in Zoology
- Functional metagenomic profiling of nine biomes
- (2008) Elizabeth A. Dinsdale et al. NATURE
- Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
- (2008) Micah Hamady et al. NATURE METHODS
- A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement
- (2008) Mário Almeida-Neto et al. OIKOS
- Resistance, resilience, and redundancy in microbial communities
- (2008) S. D. Allison et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started