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Article ; Online: Secrets of the cheese microbiome.

Ercolini, Danilo

Nature food

2020 Volume 1, Issue 8, Page(s) 466–467

Language	English
Publishing date	2020-08-13
Publishing country	England
Document type	Journal Article
ISSN	2662-1355
ISSN (online)	2662-1355
DOI	10.1038/s43016-020-0131-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exciting strain-level resolution studies of the food microbiome.

Ercolini, Danilo

Microbial biotechnology

2017 Volume 10, Issue 1, Page(s) 54–56

MeSH term(s)	Bacteria/classification ; Bacteria/isolation & purification ; Food Microbiology/methods ; Food Quality ; Food Safety ; Fungi/classification ; Fungi/isolation & purification ; Microbiological Techniques/methods ; Microbiological Techniques/trends ; Microbiota ; Viruses/classification ; Viruses/isolation & purification
Language	English
Publishing date	2017-01-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7907
ISSN (online)	1751-7915
ISSN	1751-7907
DOI	10.1111/1751-7915.12593
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Article ; Online: Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment.

Valentino, Vincenzo / De Filippis, Francesca / Sequino, Giuseppina / Ercolini, Danilo

Applied and environmental microbiology

2023 Volume 89, Issue 8, Page(s) e0076523

Abstract: Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, ... ...

Abstract	Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate
MeSH term(s)	Humans ; Ice Cream ; Virulence ; Bacteria/genetics ; Food Handling ; Biofilms ; Anti-Infective Agents ; Food Microbiology
Chemical Substances	Anti-Infective Agents
Language	English
Publishing date	2023-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.00765-23
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Article ; Online: Outlook on next-generation probiotics from the human gut.

De Filippis, Francesca / Esposito, Alessia / Ercolini, Danilo

Cellular and molecular life sciences : CMLS

2022 Volume 79, Issue 2, Page(s) 76

Abstract: Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored ... ...

Abstract	Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.
MeSH term(s)	Akkermansia/metabolism ; Bacteria/classification ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Clostridiales/metabolism ; Dysbiosis/microbiology ; Faecalibacterium prausnitzii/metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; Prevotella/metabolism ; Probiotics/pharmacology
Language	English
Publishing date	2022-01-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-021-04080-6
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Article ; Online: Fermented foods, their microbiome and its potential in boosting human health.

Valentino, Vincenzo / Magliulo, Raffaele / Farsi, Dominic / Cotter, Paul D / O'Sullivan, Orla / Ercolini, Danilo / De Filippis, Francesca

Microbial biotechnology

2024 Volume 17, Issue 2, Page(s) e14428

Abstract: Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some ... ...

Abstract	Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.
MeSH term(s)	Humans ; Microbiota ; Gastrointestinal Microbiome ; Probiotics ; Fermented Foods ; Fermentation
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7915
ISSN (online)	1751-7915
ISSN	1751-7915
DOI	10.1111/1751-7915.14428
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Article ; Online: Relationships between diet and gut microbiome in an Italian and Dutch cohort: does the dietary protein to fiber ratio play a role?

Tagliamonte, Silvia / Puhlmann, Marie-Luise / De Filippis, Francesca / Guerville, Mathilde / Ercolini, Danilo / Vitaglione, Paola

European journal of nutrition

2023 Volume 63, Issue 3, Page(s) 741–750

Abstract: Purpose: To investigate the relationships between the habitual diet, the protein to fiber ratio (P/F), and the gut microbiome in one Italian and one Dutch cohort of healthy subjects consuming an omnivore diet.: Methods: The Italian cohort included 19 ...

Abstract	Purpose: To investigate the relationships between the habitual diet, the protein to fiber ratio (P/F), and the gut microbiome in one Italian and one Dutch cohort of healthy subjects consuming an omnivore diet. Methods: The Italian cohort included 19 males (M_IT, BMI 25.2 ± 0.72 kg/m Results: M_IT consumed higher levels of proteins than F_NL and F_IT, whereas dietary fiber intake did not differ among groups. Data showed that consumption of plant protein to animal protein (PP/AP) and PP to total proteins ratio can determine a differentiation of F_NL more than the absolute amount of dietary fiber. Conversely, the protein to fiber (P/F) and AP to total proteins better characterized M_IT. M_IT harbored the highest abundance of proteolytic microorganisms and the lowest microbial gene richness. Conversely, F_NL had more fiber-degrading microorganisms like Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Roseburia sp., Coprococcus eutactus and Parabacteroides along with the highest number of genes encoding carbohydrate-active enzymes and gene richness. It was predicted that by each unit decrease in the P/F a 3% increase in gene richness occurred. Conclusion: Study findings suggested that dietary P/F, rather than the absolute amount of dietary fiber, could contribute to the shaping of the microbiome towards a more proteolytic or fiber-degrading gut ecosystem. Clinicaltrials: gov Identifier NCT04205045-01-10-2018, retrospectively registered. Dutch Trial Register NTR7531-05-10-2018.
MeSH term(s)	Male ; Female ; Animals ; Humans ; Young Adult ; Adult ; Gastrointestinal Microbiome ; Diet ; Carbohydrates ; Dietary Fiber/metabolism ; Feces/chemistry ; Dietary Proteins ; Microbiota ; Italy
Chemical Substances	Carbohydrates ; Dietary Fiber ; Dietary Proteins
Language	English
Publishing date	2023-12-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1466536-0
ISSN	1436-6215 ; 1436-6207
ISSN (online)	1436-6215
ISSN	1436-6207
DOI	10.1007/s00394-023-03308-4
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Article ; Online: Psychobiotics, gut microbiota and fermented foods can help preserving mental health.

Casertano, Melania / Fogliano, Vincenzo / Ercolini, Danilo

Food research international (Ottawa, Ont.)

2021 Volume 152, Page(s) 110892

Abstract: Psychobiotics include a novel class of probiotic microorganisms that convey benefit upon the host's mental health via the dynamic microbiota-gut-brain crosstalk. Research is bolstering the concept that gut bacteria are involved in the transmission of ... ...

Abstract	Psychobiotics include a novel class of probiotic microorganisms that convey benefit upon the host's mental health via the dynamic microbiota-gut-brain crosstalk. Research is bolstering the concept that gut bacteria are involved in the transmission of information between the gut and the brain, engaging neural, immune, and endocrine pathways. Factors such as diet, stress and aging can shape the microbiota composition in a process that may also influence the onset and development of mental diseases. This review aims to provide an outline of the link between the microbiota and brain function focusing on preclinical and clinical evidence of the potential application of psychobiotics in the context of the cognitive process and performance. The occurrence of metabolic precursors of neurotransmitters in foods that can be converted by the gut microbiota and play a role in the gut-brain axis is discussed. The understanding of the molecular mechanisms by which communication occurs is still at its infancy; however clinical studies have shown that dietary interventions based on psychobiotics might be a novel nutritional approach targeting gut microbiota for managing cognitive performance and preventing memory decline across the lifespan.
MeSH term(s)	Brain ; Fermented Foods ; Gastrointestinal Microbiome ; Mental Health ; Probiotics
Language	English
Publishing date	2021-12-22
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1111695-x
ISSN	1873-7145 ; 0963-9969
ISSN (online)	1873-7145
ISSN	0963-9969
DOI	10.1016/j.foodres.2021.110892
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Article ; Online: High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.

Ercolini, Danilo

Applied and environmental microbiology

2013 Volume 79, Issue 10, Page(s) 3148–3155

Abstract: Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in ... ...

Abstract	Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.
MeSH term(s)	Bacteria/genetics ; Bacteria/growth & development ; Biota ; Ecosystem ; Fermentation ; Food Contamination/analysis ; Food Microbiology ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Microbiota ; RNA, Bacterial/analysis ; Sequence Analysis, RNA
Chemical Substances	RNA, Bacterial
Language	English
Publishing date	2013-03-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.00256-13
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Article ; Online: Relationships between diet and gut microbiome in an Italian and Dutch cohort

Tagliamonte, Silvia / Puhlmann, Marie Luise / De Filippis, Francesca / Guerville, Mathilde / Ercolini, Danilo / Vitaglione, Paola

European Journal of Nutrition

does the dietary protein to fiber ratio play a role?

2024 Volume 63, Issue 3

Abstract	Purpose: To investigate the relationships between the habitual diet, the protein to fiber ratio (P/F), and the gut microbiome in one Italian and one Dutch cohort of healthy subjects consuming an omnivore diet. Methods: The Italian cohort included 19 males (M_IT, BMI 25.2 ± 0.72 kg/m2, age 25.4 ± 0.96 years) and 20 females (F_IT, BMI 23.9 ± 0.81 kg/m2, age 23.8 ± 0.54 years); the Dutch cohort included 30 females (F_NL, BMI: 23.9 ± 0.81 kg/m2, age: 23.8 ± 0.54 years). Individual diets were recorded through Food Frequency Questionnaires and analyzed to assess the nutrient composition. Gut microbiome was assessed in fecal samples. Results: M_IT consumed higher levels of proteins than F_NL and F_IT, whereas dietary fiber intake did not differ among groups. Data showed that consumption of plant protein to animal protein (PP/AP) and PP to total proteins ratio can determine a differentiation of F_NL more than the absolute amount of dietary fiber. Conversely, the protein to fiber (P/F) and AP to total proteins better characterized M_IT. M_IT harbored the highest abundance of proteolytic microorganisms and the lowest microbial gene richness. Conversely, F_NL had more fiber-degrading microorganisms like Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, Roseburia sp., Coprococcus eutactus and Parabacteroides along with the highest number of genes encoding carbohydrate-active enzymes and gene richness. It was predicted that by each unit decrease in the P/F a 3% increase in gene richness occurred. Conclusion: Study findings suggested that dietary P/F, rather than the absolute amount of dietary fiber, could contribute to the shaping of the microbiome towards a more proteolytic or fiber-degrading gut ecosystem. ClinicalTrials.gov Identifier NCT04205045—01-10-2018, retrospectively registered. Dutch Trial Register NTR7531—05-10-2018.
Keywords	Dietary fiber ; Gene richness ; Gut microbiome ; Nutrient ratios ; Proteins
Subject code	590
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	1466536-0
ISSN	1436-6215 ; 1436-6207
ISSN (online)	1436-6215
ISSN	1436-6207
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Outlook on next-generation probiotics from the human gut

De Filippis, Francesca / Esposito, Alessia / Ercolini, Danilo

Cellular and molecular life sciences. 2022 Feb., v. 79, no. 2

2022

Abstract	Probiotics currently available on the market generally belong to a narrow range of microbial species. However, recent studies about the importance of the gut microbial commensals on human health highlighted that the gut microbiome is an unexplored reservoir of potentially beneficial microbes. For this reason, academic and industrial research is focused on identifying and testing novel microbial strains of gut origin for the development of next-generation probiotics. Although several of these are promising for the prevention and treatment of many chronic diseases, studies on human subjects are still scarce and approval from regulatory agencies is, therefore, rare. In addition, some issues need to be overcome before implementing their wide application on the market, such as the best methods for cultivation and storage of these oxygen-sensitive taxa. This review summarizes the most recent evidence related to NGPs and provides an outlook to the main issues that still limit their wide employment.
Keywords	digestive system ; employment ; human health ; humans ; intestinal microorganisms ; markets ; probiotics
Language	English
Dates of publication	2022-02
Size	p. 76.
Publishing place	Springer International Publishing
Document type	Article
Note	Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-021-04080-6
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