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Microorganisms
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Microbial Ecology of Dairy Products: From Diversity to Functions 2.0
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Microbial Ecology of Dairy Products: From Diversity to Functions 2.0

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 15 July 2024 | Viewed by 3754

Special Issue Editors

Dr. Pascal Bonnarme

E-Mail Website
Guest Editor
AgroParisTech INRA, Ctr Biotechnol Agroind, INRA, UMR Genie & Microbiol Proc Alimentaires 782, F-78850 Thiverval Grignon, France
Interests: fermented products; food microbial community design; microbial metabolism; aromatic compounds production
Special Issues, Collections and Topics in MDPI journals
Dr. Christophe Chassard

E-Mail Website
Guest Editor
INRA Aurillac, l'Unité de Recherche Fromagères (URF), Centre de recherche Auvergne-Rhônes-Alpes, 20 rue Côte de Reyne, 15000 Aurillac, France
Interests: cheese; food microbiota; functionnality of microbes; microbial ecosystems; health impact
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue “Microbial Ecology of Dairy Products: From Diversity to Functions”.

Microbial ecology of dairy products is an important and growing area of research in food microbiology. There is a need to understand microbial interactions, microbe–matrix interactions, and the origins and diversity of food microbes, as well as their functionality at different scales (e.g., lab, dairy product models, dairy artisanal and industrial products). The emergence of advanced technologies, including next-generation sequencing approaches and related omics approaches, offer new perspectives for research to deeply investigate the food microbiome. Any research related to dairy fermentation, from the production to the biopreservation of dairy products, will be considered in this topic. This includes the phenotypic and genomic characterization of dairy microbes and communities, the development of microbial solutions (starters and other technological microbes) and investigations of complex microbial ecosystems from origin and diversity to function. We want to share knowledge about dairy food technology and safety, targeting most of the large portfolio of dairy products (e.g., milk, raw milk, any foods made from fermented milk, cheese).

Dr. Pascal Bonnarme
Dr. Christophe Chassard
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

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Research

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22 pages, 2359 KiB  
Article
Taxonomy, Sequence Variance and Functional Profiling of the Microbial Community of Long-Ripened Cheddar Cheese Using Shotgun Metagenomics
by Hassan Mahmoud Mohamed, Zoha Barzideh, Myra Siddiqi and Gisèle LaPointe
Microorganisms 2023, 11(8), 2052; https://doi.org/10.3390/microorganisms11082052 - 10 Aug 2023
Viewed by 1241
Abstract
Shotgun metagenomic sequencing was used to investigate the diversity of the microbial community of Cheddar cheese ripened over 32 months. The changes in taxa abundance were compared from assembly-based, non-assembly-based, and mOTUs2 sequencing pipelines to delineate the community profile for each age group. [...] Read more.
Shotgun metagenomic sequencing was used to investigate the diversity of the microbial community of Cheddar cheese ripened over 32 months. The changes in taxa abundance were compared from assembly-based, non-assembly-based, and mOTUs2 sequencing pipelines to delineate the community profile for each age group. Metagenomic assembled genomes (MAGs) passing the quality threshold were obtained for 11 species from 58 samples. Although Lactococcus cremoris and Lacticaseibacillus paracasei were dominant across the shotgun samples, other species were identified using MG-RAST. NMDS analysis of the beta diversity of the microbial community revealed the similarity of the cheeses in older age groups (7 months to 32 months). As expected, the abundance of Lactococcus cremoris consistently decreased over ripening, while the proportion of permeable cells increased. Over the ripening period, the relative abundance of viable Lacticaseibacillus paracasei progressively increased, but at a variable rate among trials. Reads attributed to Siphoviridae and Ascomycota remained below 1% relative abundance. The functional profiles of PMA-treated cheeses differed from those of non-PMA-treated cheeses. Starter rotation was reflected in the single nucleotide variant profiles of Lactococcus cremoris (SNVs of this species using mOTUs2), while the incoming milk was the leading factor in discriminating Lacticaseibacillus paracasei/casei SNV profiles. The relative abundance estimates from Kraken2, non-assembly-based (MG-RAST) and marker gene clusters (mOTUs2) were consistent across age groups for the two dominant taxa. Metagenomics enabled sequence variant analysis below the bacterial species level and functional profiling that may affect the metabolic interactions between subpopulations in cheese during ripening, which could help explain the overall flavour development of cheese. Future work will integrate microbial variants with volatile profiles to associate the development of compounds related to cheese flavour at each ripening stage. Full article
(This article belongs to the Special Issue Microbial Ecology of Dairy Products: From Diversity to Functions 2.0)
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Review

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33 pages, 788 KiB  
Review
In Vivo Functional Properties of Dairy Bacteria
by Giuseppe Aprea, Ilaria Del Matto, Patrizia Tucci, Lucio Marino, Silvia Scattolini and Franca Rossi
Microorganisms 2023, 11(7), 1787; https://doi.org/10.3390/microorganisms11071787 - 11 Jul 2023
Cited by 4 | Viewed by 2254
Abstract
This literature review aimed to collect investigations on the in vivo evidence for bacteria associated with fermented dairy foods to behave as probiotics with beneficial effects in the prevention and treatment of various diseases. All main bacterial groups commonly present in high numbers [...] Read more.
This literature review aimed to collect investigations on the in vivo evidence for bacteria associated with fermented dairy foods to behave as probiotics with beneficial effects in the prevention and treatment of various diseases. All main bacterial groups commonly present in high numbers in fermented milks or cheeses were taken into account, namely starter lactic acid bacteria (SLAB) Lactobacillus delbrueckii subsp. bulgaricus and lactis, L. helveticus, Lactococcus lactis, Streptococcus thermophilus, non-starter LAB (NSLAB) Lacticaseibacillus spp., Lactiplantibacillus plantarum, dairy propionibacteria, and other less frequently encountered species. Only studies regarding strains of proven dairy origin were considered. Studies in animal models and clinical studies showed that dairy bacteria ameliorate symptoms of inflammatory bowel disease (IBD), mucositis, metabolic syndrome, aging and oxidative stress, cancer, bone diseases, atopic dermatitis, allergies, infections and damage caused by pollutants, mild stress, and depression. Immunomodulation and changes in the intestinal microbiota were the mechanisms most often involved in the observed effects. The results of the studies considered indicated that milk and dairy products are a rich source of beneficial bacteria that should be further exploited to the advantage of human and animal health. Full article
(This article belongs to the Special Issue Microbial Ecology of Dairy Products: From Diversity to Functions 2.0)
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