Microbiome and -omics application in food industry

Interactions between Salmonella Enteritidis and food processing facility isolate Bacillus paramycoides B5 in dual-species biofilms

(2022) Jing-Guo Xu et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome

(2022) Gabriele Andrea Lugli et al.   ENVIRONMENTAL MICROBIOLOGY

The diversity and function of sourdough starter microbiomes

(2021) Elizabeth A Landis et al.   eLife

Automated design of synthetic microbial communities

(2021) Behzad D. Karkaria et al.   Nature Communications

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

(2021) Chi Zhao et al.   Frontiers in Microbiology

Influence of taxonomic and functional content of microbial communities on the quality of fermented cocoa pulp-bean mass

(2021) Jatziri Mota-Gutierrez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2021) Francesco Beghini et al.   eLife

A global metagenomic map of urban microbiomes and antimicrobial resistance

(2021) David Danko et al.   CELL

Characterization of the aromatic profile of purple passion fruit (Passiflora edulis Sims) during ripening by HS-SPME-GC/MS and RNA sequencing

(2021) Changbao Li et al.   FOOD CHEMISTRY

Construction of a synthetic microbial community for the biosynthesis of volatile sulfur compound by multi-module division of labor

(2021) Rubing Du et al.   FOOD CHEMISTRY

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

(2021) Irene Franciosa et al.   FOOD RESEARCH INTERNATIONAL

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

Calling for a systems approach in microbiome research and innovation

(2021) Annelein Meisner et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Enhancing the proportion of gluconic acid with a microbial community reconstruction method to improve the taste quality of Kombucha

(2021) Ruyi Li et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

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

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

Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese

(2021) Lang Sun et al.   mSystems

Use of an Ecosystem-Based Approach to Shed Light on the Heterogeneity of the Contamination Pattern of Listeria monocytogenes on Conveyor Belt Surfaces in a Swine Slaughterhouse in the Province of Quebec, Canada

(2021) Fanie Shedleur-Bourguignon et al.   Pathogens

Toward a Global Ecology of Fermented Foods

(2021) Robert R. Dunn et al.   CURRENT ANTHROPOLOGY

Counteracting the effect of reducing nitrate/nitrite levels on dry fermented sausage aroma by Debaryomyces Hansenii inoculation

(2020) Laura Perea-Sanz et al.   MEAT SCIENCE

Exploring the Ambiguous Status of Coagulase-Negative Staphylococci in the Biosafety of Fermented Meats: The Case of Antibacterial Activity Versus Biogenic Amine Formation

(2020) David Van der Veken et al.   Microorganisms

Ecology of lactobacilli present in Italian cheeses produced from raw milk

(2020) Christian Milani et al.   APPLIED AND ENVIRONMENTAL 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

Effect of synthetic microbial community on nutraceutical and sensory qualities of kombucha

(2020) Shuai Wang et al.   INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

(2020) Jinshui Zheng et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

(2020) Edoardo Pasolli et al.   Nature Communications

In vitro antifungal effects of spices on ochratoxin A production and related gene expression in Penicillium nordicum on a dry-cured fermented sausage medium

(2020) Micaela Álvarez et al.   FOOD CONTROL

Microbiological characterization of Gioddu, an Italian fermented milk

(2020) Antonietta Maoloni et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Evaluation of MALDI–TOF MS as a tool for detection of Listeria spp. directly from selective enrichment broth from food and stool samples

(2020) Thais Martins Campos Araújo et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Is there any still undisclosed biodiversity in Ciauscolo salami? A new glance into the microbiota of an artisan production as revealed by high-throughput sequencing

(2020) Luca Belleggia et al.   MEAT SCIENCE

Development of Microbiome Biobanks – Challenges and Opportunities

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

Microbiome definition re-visited: old concepts and new challenges

(2020) Gabriele Berg et al.   Microbiome

The sources and transmission routes of microbial populations throughout a meat processing facility

(2020) Benjamin Zwirzitz et al.   npj Biofilms and Microbiomes

Editorial: Exploring the need to include microbiomes into EFSA's scientific assessments

(2020) Caroline Merten et al.   EFSA Journal

Spatiotemporal Distribution of the Environmental Microbiota in Food Processing Plants as Impacted by Cleaning and Sanitizing Procedures: The Case of Slaughterhouses and Gaseous Ozone

(2020) Cristian Botta et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interspecies assertiveness of Lactobacillus curvatus and Lactobacillus sakei in sausage fermentations

(2020) Dorothee Janßen et al.   INTERNATIONAL JOURNAL OF FOOD 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

Highly multiplexed spatial mapping of microbial communities

(2020) Hao Shi et al.   NATURE

Microbiome Research: Open Communication Today, Microbiome Applications in the Future

(2020) Bettina Schelkle et al.   Microorganisms

Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter

(2020) Yang Yang et al.   FOOD RESEARCH INTERNATIONAL

Metatranscriptome-based investigation of flavor-producing core microbiota in different fermentation stages of dajiang, a traditional fermented soybean paste of Northeast China

(2020) Feiyu An et al.   FOOD CHEMISTRY

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

(2020) Eiseul Kim et al.   FOOD MICROBIOLOGY

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

(2019) Marko Verce et al.   Frontiers in Microbiology

Colonization of the human gut by bovine bacteria present in Parmesan cheese

(2019) Christian Milani et al.   Nature Communications

Is it useful to use several “omics” for obtaining valuable results?

(2019) Magdalena Zapalska-Sozoniuk et al.   MOLECULAR BIOLOGY REPORTS

Culture-enriched human gut microbiomes reveal core and accessory resistance genes

(2019) Frédéric Raymond et al.   Microbiome

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

(2019) Vincent Somerville et al.   BMC 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

Enzymatic biocontrol of spoilage fungi from salami

(2019) Karine Cence et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

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

(2019) Farhana R. Pinu et al.   Metabolites

Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database

(2019) Eugenio Parente et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities

(2019) Xiaoqing Tan et al.   Microbiome

Assessment of antibiotic resistance in staphylococci involved in fermented meat product processing

(2019) Constanza Maria Lopez et al.   Current Opinion in Food Science

Rapid Detection of Microbial Mass Spectra VITEK-MS for Campylobacter jejuni and Listeria monocytogenes

(2019) Tu Bowen et al.   Food Analytical Methods

Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures

(2019) Haiyang Chen et al.   WATER RESEARCH

Efficacy of the Combined Protective Cultures of Penicillium chrysogenum and Debaryomyces hansenii for the Control of Ochratoxin A Hazard in Dry-Cured Ham

(2019) Eva Cebrián et al.   Toxins

Advancing functional and translational microbiome research using meta-omics approaches

(2019) Xu Zhang et al.   Microbiome

Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation

(2019) Kyung Hyun Kim et al.   FOOD MICROBIOLOGY

Potential of yeasts isolated from dry-cured ham to control ochratoxin A production in meat models

(2018) Belén Peromingo et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Characterization of airborne viromes in cheese production plants

(2018) Stefano Colombo et al.   JOURNAL OF APPLIED MICROBIOLOGY

Recent Past, Present, and Future of the Food Microbiome

(2018) Francesca De Filippis et al.   Annual Review of Food Science and Technology

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

(2018) Aaron M. Walsh et al.   Microbiome

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

(2018) A. S. Bertuzzi et al.   mSystems

A vegetable fermentation facility hosts distinct microbiomes reflecting the production environment

(2018) Jonah E. Einson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mesophilic Sporeformers Identified in Whey Powder by Using Shotgun Metagenomic Sequencing

(2018) Aoife J. McHugh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Are microbiome studies ready for hypothesis-driven research?

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

To target or not to target? Definitions and nomenclature for targeted versus non-targeted analytical food authentication

(2018) Nicolai Zederkopff Ballin et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions

(2018) Francesca De Filippis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Inner Workings: Mapping the microbiome location helps elucidate its role

(2018) Marcus Woo   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

(2017) Conor J. Doyle et al.   ENVIRONMENTAL MICROBIOLOGY

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment

(2017) Heidy M.W. den Besten et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Next generation microbiological risk assessment meta-omics: The next need for integration

(2017) Luca Cocolin et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

The gut mycobiome of the Human Microbiome Project healthy cohort

(2017) Andrea K. Nash et al.   Microbiome

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

(2016) Valentina Alessandria et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

(2016) Giuseppina Stellato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant

(2016) Maria Calasso et al.   FOOD MICROBIOLOGY

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

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Francesca De Filippis et al.   Scientific Reports

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

(2015) Vasileios Pothakos et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Understanding the bacterial communities of hard cheese with blowing defect

(2015) Daniela Bassi et al.   FOOD MICROBIOLOGY

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity

(2014) Benjamin E. Wolfe et al.   CELL

Traditional cheeses: Rich and diverse microbiota with associated benefits

(2014) Marie-Christine Montel et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

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

(2014) Joanita Sulaiman et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

(2013) Stéphane Chaillou et al.   PLoS One

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE