The need for an integrated multi‐OMICs approach in microbiome science in the food system

Plant‐microbiome interactions under a changing world: responses, consequences, and perspective

(2022) Pankaj Trivedi et al.   NEW PHYTOLOGIST

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

(2022) Rocío Olmo et al.   Frontiers in Microbiology

High‐resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities

(2021) Yen Ning Chai et al.   PLANT CELL AND ENVIRONMENT

Analysing endometrial microbiome: methodological considerations and recommendations for good practice

(2021) Nerea M Molina et al.   HUMAN REPRODUCTION

Enabling sustainable agriculture through understanding and enhancement of microbiomes

(2021) Pankaj Trivedi et al.   NEW PHYTOLOGIST

Integrative Metagenomics–Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu

(2021) Chi Zhao et al.   Frontiers in Microbiology

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

(2021) Zhiqiang Pang et al.   Frontiers in Plant Science

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline

(2021) Nuria Planell et al.   Frontiers in Genetics

Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

(2021) Eric Banan-Mwine Daliri et al.   Biomolecules

Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

(2021) Guodong Rao et al.   Foods

Metabolic profile of main organic acids and its regulatory mechanism in solid-state fermentation of Chinese cereal vinegar

(2021) Yanfang Wu et al.   FOOD RESEARCH INTERNATIONAL

Specific modulation of the root immune system by a community of commensal bacteria

(2021) Paulo J. P. L. Teixeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

(2021) Irene Franciosa et al.   FOOD RESEARCH INTERNATIONAL

Transcriptomic analysis reveals the metabolic mechanism of patulin by Saccharomyces cerevisiae during fermentation

(2021) Chao Yang et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots

(2021) Muhammad Syamsu Rizaludin et al.   Metabolites

Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity

(2021) Ilario Ferrocino et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metagenomic analysis reveals the linkages between bacteria and the functional enzymes responsible for potential ammonia and biogenic amine production in alfalfa silage

(2021) Rongrong Li et al.   JOURNAL OF APPLIED MICROBIOLOGY

Multi ‘omic data integration: A review of concepts, considerations, and approaches

(2021) Tasha M. Santiago-Rodriguez et al.   SEMINARS IN PERINATOLOGY

Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community

(2021) Jaderson Silveira Leite Armanhi et al.   Frontiers in Microbiology

The Microbiome in Autoimmune Liver Diseases: Metagenomic and Metabolomic Changes

(2021) Yanping Zheng et al.   Frontiers in Physiology

Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease

(2021) Salma Sultan et al.   Frontiers in Physiology

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

(2020) Shane Thomas O’Donnell et al.   Frontiers in Microbiology

Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product

(2020) Chang-Cheng Zhao et al.   FOOD RESEARCH INTERNATIONAL

Healthy soils for healthy plants for healthy humans

(2020) Heribert Hirt   EMBO REPORTS

The microbiota of dairy milk: A review

(2020) Eugenio Parente et al.   INTERNATIONAL DAIRY JOURNAL

Development of Microbiome Biobanks – Challenges and Opportunities

(2020) M.J. Ryan et al.   TRENDS IN MICROBIOLOGY

Longitudinal metatranscriptomic analysis of a meat spoilage microbiome detects abundant continued fermentation and environmental stress responses during shelf life and beyond.

(2020) Jenni Hultman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

(2020) Rafael Soares Correa de Souza et al.   Frontiers in Plant Science

Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation

(2020) Xiaoning Huang et al.   Microorganisms

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes

(2020) Jonas Coelho Kasmanas et al.   NUCLEIC ACIDS RESEARCH

Predictive interactome modeling for precision microbiome engineering

(2020) Aimee K Kessell et al.   Current Opinion in Chemical Engineering

Identification of biogenic amine-producing microbes during fermentation of ganjang, a Korean traditional soy sauce, through metagenomic and metatranscriptomic analyses

(2020) Kyung Hyun Kim et al.   FOOD CONTROL

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

(2019) Stéphane Compant et al.   Journal of Advanced Research

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

(2019) Marko Verce et al.   Frontiers in Microbiology

Unveiling the mechanisms for the plant volatile organic compound linalool to control gray mold on strawberry fruits

(2019) Yanqun Xu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Inferring Interaction Networks From Multi-Omics Data

(2019) Johann S. Hawe et al.   Frontiers in Genetics

Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake

(2019) Samantha J. Noel et al.   Animals

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

(2019) Farhana R. Pinu et al.   Metabolites

Causes and consequences of a conserved bacterial root microbiome response to drought stress

(2019) Ling Xu et al.   CURRENT OPINION IN MICROBIOLOGY

Unified feature association networks through integration of transcriptomic and proteomic data

(2019) Ryan S. McClure et al.   PLoS Computational Biology

Does Soil Contribute to the Human Gut Microbiome?

(2019) Winfried E.H. Blum et al.   Microorganisms

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae

(2019) Jing Yuan et al.   Cell Metabolism

Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses

(2019) Byung Hee Chun et al.   FOOD MICROBIOLOGY

Alternate antimicrobial resistance genes in multidrug resistant Salmonella spp. isolated from retail meats in Vietnam using RNA‐sequencing analysis

(2019) Minh N. Nghiem et al.   JOURNAL OF FOOD SAFETY

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

(2019) Omri M. Finkel et al.   PLOS BIOLOGY

Gut Microbiota Modulation on Intestinal Mucosal Adaptive Immunity

(2019) Li Wang et al.   Journal of Immunology Research

Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

(2019) Duo Jiang et al.   Frontiers in Genetics

The soil microbiome — from metagenomics to metaphenomics

(2018) Janet K Jansson et al.   CURRENT OPINION IN MICROBIOLOGY

Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism

(2018) Preeti Pathak et al.   HEPATOLOGY

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

(2018) Erica M Forsberg et al.   Nature Protocols

Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD

(2018) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

(2018) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are microbiome studies ready for hypothesis-driven research?

(2018) Anupriya Tripathi et al.   CURRENT OPINION IN MICROBIOLOGY

In vitro elucidation of suppression effects of composts to soil-borne pathogen Phytophthora nicotianae on pepper plants using 16S amplicon sequencing and metaproteomics

(2018) Margarita Ros et al.   RENEWABLE AGRICULTURE AND FOOD SYSTEMS

Insights Into Culturomics of the Rumen Microbiome

(2018) Tamar Zehavi et al.   Frontiers in Microbiology

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

(2017) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Let the Core Microbiota Be Functional

(2017) Philippe Lemanceau et al.   TRENDS IN PLANT SCIENCE

Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils

(2017) Ruth Gómez Expósito et al.   Frontiers in Microbiology

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

(2017) Chijioke O. Elekwachi et al.   Frontiers in Microbiology

A parts list for fungal cellulosomes revealed by comparative genomics

(2017) Charles H. Haitjema et al.   Nature Microbiology

A web application for sample size and power calculation in case-control microbiome studies

(2016) Federico Mattiello et al.   BIOINFORMATICS

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach

(2016) Federica Del Chierico et al.   HEPATOLOGY

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis

(2016) Eugenio Parente et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Network analysis of transcriptomics expands regulatory landscapes inSynechococcussp. PCC 7002

(2016) Ryan S. McClure et al.   NUCLEIC ACIDS RESEARCH

Staling of Chinese steamed bread: Quantification and control

(2016) Fan Zhu   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

(2016) Francesca De Filippis et al.   Scientific Reports

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis

(2015) Zeneng Wang et al.   CELL

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

(2015) Weili Xiong et al.   PROTEOMICS

Role of the normal gut microbiota

(2015) Sai Manasa Jandhyala   WORLD JOURNAL OF GASTROENTEROLOGY

Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

(2015) Eric Dugat-Bony et al.   PLoS One

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

(2014) Stéphane Chaillou et al.   ISME Journal

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine

(2014) Joanita Sulaiman et al.   Frontiers in Microbiology

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders

(2014) N Tennoune et al.   Translational Psychiatry

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Proteogenomics for environmental microbiology

(2013) Jean Armengaud et al.   PROTEOMICS

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Metabolite profiles and the risk of developing diabetes

(2011) Thomas J Wang et al.   NATURE MEDICINE

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One