Strain-level multiomics analysis reveals significant variation in cheeses from different regions

Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3

(2021) Orestis Nousias et al.   Marine Genomics

Metabolic footprinting revealed key biochemical changes in a brown fermented milk product using Streptococcus thermophilus

(2020) DanYang Li et al.   JOURNAL OF DAIRY SCIENCE

Phage-based forensic tool for spatial visualization of bacterial contaminants in cheese

(2020) Sarah Kozak et al.   JOURNAL OF DAIRY SCIENCE

Environmental Life Cycle Assessment of goat cheese production in Brazil: a path towards sustainability

(2020) Caroline Ferreira Soares Cabral et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Characteristic physicochemical indexes and flavor compounds in Xinjiang Kazak cheese during ripening

(2020) Zhenli Xu et al.   Food Bioscience

Lactic acid bacteria isolated from traditional Italian dairy products: activity against Listeria monocytogenes and modelling of microbial competition in soft cheese

(2020) Felice Panebianco et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

The Interrelationship Between Microbiota and Peptides During Ripening as a Driver for Parmigiano Reggiano Cheese Quality

(2020) Benedetta Bottari et al.   Frontiers in Microbiology

An in-vitro assessment of antifungal and antibacterial activity of cow, camel, ewe, and goat milk kefir and probiotic yogurt

(2020) Maryam Azizkhani et al.   Journal of Food Measurement and Characterization

Microbiota and Metabolite Profiling Combined With Integrative Analysis for Differentiating Cheeses of Varying Ripening Ages

(2020) Roya Afshari et al.   Frontiers in Microbiology

Dynamic changes in bacterial microbiota succession and flavour development during milk fermentation of Kazak artisanal cheese

(2020) Xiaochun Zheng et al.   INTERNATIONAL DAIRY JOURNAL

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

(2019) Edoardo Pasolli et al.   CELL

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Isotopic dilution assay development of nisin A in cream cheese, mascarpone, processed cheese and ripened cheese by LC-MS/MS method

(2019) Chee Wei Lim et al.   FOOD CHEMISTRY

Overview on GHG emissions of raw milk production and a comparison of milk and cheese carbon footprints of two different systems from northern Spain

(2019) Amanda Laca et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

PacBio sequencing reveals bacterial community diversity in cheeses collected from different regions

(2019) Chengcong Yang et al.   JOURNAL OF DAIRY SCIENCE

Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation

(2019) So-Ra Han et al.   MICROBIAL PATHOGENESIS

Lactobacillus demonstrate thiol-independent metabolism of methylglyoxal: Implications toward browning prevention in Parmesan cheese

(2018) N.N. Gandhi et al.   JOURNAL OF DAIRY SCIENCE

Symposium review: Interaction of starter cultures and nonstarter lactic acid bacteria in the cheese environment 1

(2018) J. Blaya et al.   JOURNAL OF DAIRY SCIENCE

Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis

(2018) Burcin Karabey et al.   JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE

Drivers that establish and assembly the lactic acid bacteria biota in cheeses

(2018) Marco Gobbetti et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Population Dynamics of Lactobacillus helveticus in Swiss Gruyère-Type Cheese Manufactured With Natural Whey Cultures

(2018) Aline Moser et al.   Frontiers in Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Molecular techniques reveal more secrets of fermented foods

(2018) Aly Farag El Sheikha et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

MetaSort untangles metagenome assembly by reducing microbial community complexity

(2017) Peifeng Ji et al.   Nature Communications

Extensive horizontal gene transfer in cheese-associated bacteria

(2017) Kevin S Bonham et al.   eLife

Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

(2017) Daniel M. Linares et al.   Frontiers in Microbiology

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

(2016) Eleonora Sattin et al.   Frontiers in Microbiology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS