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Microorganisms
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Microbiomes for the Sustainable Production of Safe and Secure Foods
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Microbiomes for the Sustainable Production of Safe and Secure Foods

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

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 45218

Special Issue Editors

Prof. Dr. Marco Candela

E-Mail Website
Guest Editor
Alma Mater Studiorum Università di Bologna, Bologna, Italy
Interests: earth microbiomes, animal microbiome, plant microbiome, microbiome-human coevolution, microbiome biotechnology, metagenomics
Dr. Elena Biagi

E-Mail Website
Co-Guest Editor
Alma Mater Studiorum Università di Bologna, Bologna, Italy
Interests: gut microbiome in heath and disease; gut microbiome and longevity; microbiome and phenotypic plasticity; microbiome biotechnology; metagenomics

Special Issue Information

Dear Colleagues,

Food systems play a Janus-faced role in the growth and development of the planet: while they provide human societies with food, they also exert strong pressures on natural resources. The related costs of these pressures on the environment are growing exponentially. Climate change is occurring faster than expected, and natural resources are being degraded more severely than previously thought. By 2050, the planet will be inhabited by 9.7 billion people, and this implies an unprecedented challenge for mankind. Food systems need to boost the production of safe and nutritious food while drastically reducing their footprint on natural resources. Microbiomes are central to human, plant, animal, and ultimately, planet health, and their exploitation has been indicated as one of the possible strategies to achieve sustainable production of safe and secure food for future generations. Indeed, microbiomes potentially represent an untapped resource of probiotic functions for all the actors involved in the food system, improving productivity, quality, safety, and sustainability of the whole food production chain. In particular, animal and plant microbiomes can be of strategic importance to improve food productivity and quality thanks to their positive impact on host physiology, energy homeostasis, and feed efficiency. On the other hand, environmental microbiomes can be crucial to achieving a sustainable intensification of food systems by enhancing the ecosystem capacity to buffer the food system pressures on the environment. However, to reach the ambitious goal of a microbiome-optimized and sustainable food system, more knowledge on food system microbiomes still needs to be produced. Only with a better understanding of their dynamics, circulation, and ecological services, we will be able to model (and mold) their optimal configuration for sustainable food production.

Prof. Dr. Marco Candela
Dr. Elena Biagi
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.

Keywords

  • microbiomes
  • food systems
  • food security
  • food production
  • food quality

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Published Papers (9 papers)

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Research

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17 pages, 2747 KiB  
Article
Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages
by Giorgia Palladino, Simone Rampelli, Daniel Scicchitano, Margherita Musella, Grazia Marina Quero, Fiorella Prada, Arianna Mancuso, Anne Mette Seyfarth, Silvia Turroni, Marco Candela and Elena Biagi
Microorganisms 2021, 9(2), 455; https://doi.org/10.3390/microorganisms9020455 - 22 Feb 2021
Cited by 16 | Viewed by 4402
Abstract
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of [...] Read more.
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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43 pages, 3954 KiB  
Article
Yeast Biodiversity in Fermented Doughs and Raw Cereal Matrices and the Study of Technological Traits of Selected Strains Isolated in Spain
by Rosana Chiva, Lorena Celador-Lera, José Antonio Uña, Ana Jiménez-López, María Espinosa-Alcantud, Enrique Mateos-Horganero, Soledad Vega, María Ángeles Santos, Encarna Velázquez and Mercedes Tamame
Microorganisms 2021, 9(1), 47; https://doi.org/10.3390/microorganisms9010047 - 26 Dec 2020
Cited by 16 | Viewed by 5033
Abstract
Bakers use pure microorganisms and/or traditional sourdoughs as the leavening agent for making bread. The performance of each starter and the substances produced by the microorganisms greatly affect the dough rheology and features of breads. Modern sourdoughs inoculated with selected lactic acid bacteria [...] Read more.
Bakers use pure microorganisms and/or traditional sourdoughs as the leavening agent for making bread. The performance of each starter and the substances produced by the microorganisms greatly affect the dough rheology and features of breads. Modern sourdoughs inoculated with selected lactic acid bacteria and yeasts are microbiologically stable, safer than traditional sourdoughs, and easy to use. However, the commercial repertoire of baker’s yeasts is still limited. Therefore, there is a demand for new strains of yeast species, capable of conferring distinctive traits to breads made from a variety of agri-food matrices, in the design of innovative starters. In this context, we report the first comprehensive study on yeasts isolated from a wide range of fermented doughs, cereal flours, and grains of Spain. Nine yeast species were identified from 433 isolates, which were distributed among separate clades. Moreover, phenotypic traits of potential technological relevance were identified in selected yeast strains. Mother doughs (MDs) showed the greatest yeast biodiversity, whereas commercial Saccharomyces starters or related and wild strains often dominated the bakery doughs. A metataxonomic analysis of wheat and tritordeum MDs revealed a greater richness of yeast species and percentage variations related to the consistency, flour type, and fermentation time of MDs. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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15 pages, 4220 KiB  
Article
Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes
by Idoia Goiri, Xabier Díaz de Otálora, Roberto Ruiz, Jagoba Rey, Raquel Atxaerandio, Jose Luis Lavín, David San Martin, Mikel Orive, Bruno Iñarra, Jaime Zufia, Jabi Urkiza and Aser García-Rodríguez
Microorganisms 2020, 8(12), 1961; https://doi.org/10.3390/microorganisms8121961 - 10 Dec 2020
Cited by 7 | Viewed by 3008
Abstract
Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, [...] Read more.
Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, 50, and 100 g SCG/kg). Ruminal samples were collected on day 50. DNA was extracted and subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA genes. Bioinformatic analyses were performed using QIIME (v.1.9.0). SCG increased dose-dependently bacterial diversity and altered bacterial structure. Further, 60, 78, and 449 operational taxonomic unit (OUT) were different between control and 30, 50 and 100 g/kg SCG groups, respectively. Higher differences were observed between the control and 100 g/kg SCG group, where OTU of the genera Treponema, CF231, Butyrivibrio, BF331, Anaeroplasma, Blautia, Fibrobacter, and Clostridium were enriched with SCG. Correlations between volatile fatty acids (VFA) and bacterial taxa were sparser in the SCG groups and had little overlap. Certain bacterial taxa presented different signs of the correlation with VFA in SCG and control groups, but Butyrivibrio and Blautia consistently correlated with branched-chain VFA in all groups. SCG induced shifts in the ruminal bacterial community and altered the correlation networks among bacterial taxa and ruminal VFA. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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16 pages, 845 KiB  
Article
Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
by Claudia Sala, Hanne Mordhorst, Josephine Grützke, Annika Brinkmann, Thomas N. Petersen, Casper Poulsen, Paul D. Cotter, Fiona Crispie, Richard J. Ellis, Gastone Castellani, Clara Amid, Mikhayil Hakhverdyan, Soizick Le Guyader, Gerardo Manfreda, Joël Mossong, Andreas Nitsche, Catherine Ragimbeau, Julien Schaeffer, Joergen Schlundt, Moon Y. F. Tay, Frank M. Aarestrup, Rene S. Hendriksen, Sünje Johanna Pamp and Alessandra De Cesareadd Show full author list remove Hide full author list
Microorganisms 2020, 8(12), 1861; https://doi.org/10.3390/microorganisms8121861 - 25 Nov 2020
Cited by 7 | Viewed by 4576
Abstract
An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant [...] Read more.
An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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21 pages, 6514 KiB  
Article
Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome
by Elena Biagi, Carlo Mengucci, Monica Barone, Gianfranco Picone, Alex Lucchi, Pietro Celi, Gilberto Litta, Marco Candela, Gerardo Manfreda, Patrizia Brigidi, Francesco Capozzi and Alessandra De Cesare
Microorganisms 2020, 8(8), 1134; https://doi.org/10.3390/microorganisms8081134 - 27 Jul 2020
Cited by 14 | Viewed by 3850
Abstract
The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota—host relationship can improve chickens’ immunological status and metabolic fitness. Here, we present the results [...] Read more.
The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota—host relationship can improve chickens’ immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3–V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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Review

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23 pages, 404 KiB  
Review
Timely Control of Gastrointestinal Eubiosis: A Strategic Pillar of Pig Health
by Paolo Trevisi, Diana Luise, Federico Correa and Paolo Bosi
Microorganisms 2021, 9(2), 313; https://doi.org/10.3390/microorganisms9020313 - 3 Feb 2021
Cited by 19 | Viewed by 4193
Abstract
The pig gastrointestinal tract (GIT) is an open ecosystem in which microorganisms and their host are mutually involved and continually adapt to different factors and problems which may or may not be host dependent or due to the production system. The aim of [...] Read more.
The pig gastrointestinal tract (GIT) is an open ecosystem in which microorganisms and their host are mutually involved and continually adapt to different factors and problems which may or may not be host dependent or due to the production system. The aim of the present review is to highlight the factors affecting the GIT microbial balance in young pigs, focusing on the pre- and post-weaning phases, to define a road map for improving pig health and the production efficiency of the food chain. Birth and weaning body weight, physiological maturation, colostrum and milk (composition and intake), genetic background, environmental stressors and management practices, antibiotic use and diet composition are considered. Overall, there is a lack of knowledge regarding the effect that some factors, including weaning age, the use of creep feed, the composition of the colostrum and milk and the use of antibiotics, may have on the gut microbiome of piglets. Furthermore, the information on the gut microbiome of piglets is mainly based on the taxonomy description, while there is a lack of knowledge regarding the functional modification of the microbiota, essential for the exploitation of microbiota potential for modulating pig physiology. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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20 pages, 951 KiB  
Review
Autochthonous Probiotics in Meat Products: Selection, Identification, and Their Use as Starter Culture
by Paulo E. S. Munekata, Mirian Pateiro, Wangang Zhang, Rubén Domínguez, Lujuan Xing, Elena Movilla Fierro and José M. Lorenzo
Microorganisms 2020, 8(11), 1833; https://doi.org/10.3390/microorganisms8111833 - 21 Nov 2020
Cited by 18 | Viewed by 4246
Abstract
The increasing demand for functional food is pushing the food industry to innovate the conventional and well-known foods. Producing functional foods, especially with probiotics in meat products, is an intricate and multistage task that involves: the selection of microorganisms with probiotic potential, the [...] Read more.
The increasing demand for functional food is pushing the food industry to innovate the conventional and well-known foods. Producing functional foods, especially with probiotics in meat products, is an intricate and multistage task that involves: the selection of microorganisms with probiotic potential, the identification at strain level, and the evaluation of probiotic strains in the processing of meat products. The resistance to digestion, followed by the successful colonization in the small intestine and the safety are the main criteria used to select and identify (at strain level) a probiotic, as reported in recent studies about the autochthonous microbiota of meat products. Further insertion (as starter culture) in a meat system for fermentation is the simplest approach to obtain a probiotic meat product. Among the innumerous microorganisms naturally found in meat products, lactic acid bacteria (LAB) play a central role by fitting in both probiotic and meat products processing criteria. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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15 pages, 730 KiB  
Review
Scientific Prospects for Cannabis-Microbiome Research to Ensure Quality and Safety of Products
by Vladimir Vujanovic, Darren R. Korber, Silva Vujanovic, Josko Vujanovic and Suha Jabaji
Microorganisms 2020, 8(2), 290; https://doi.org/10.3390/microorganisms8020290 - 20 Feb 2020
Cited by 31 | Viewed by 11800
Abstract
Cannabis legalization has occurred in several countries worldwide. Along with steadily growing research in Cannabis healthcare science, there is an increasing interest for scientific-based knowledge in plant microbiology and food science, with work connecting the plant microbiome and plant health to product quality [...] Read more.
Cannabis legalization has occurred in several countries worldwide. Along with steadily growing research in Cannabis healthcare science, there is an increasing interest for scientific-based knowledge in plant microbiology and food science, with work connecting the plant microbiome and plant health to product quality across the value chain of cannabis. This review paper provides an overview of the state of knowledge and challenges in Cannabis science, and thereby identifies critical risk management and safety issues in order to capitalize on innovations while ensuring product quality control. It highlights scientific gap areas to steer future research, with an emphasis on plant-microbiome sciences committed to using cutting-edge technologies for more efficient Cannabis production and high-quality products intended for recreational, pharmaceutical, and medicinal use. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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Other

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10 pages, 258 KiB  
Perspective
Microbiome Research: Open Communication Today, Microbiome Applications in the Future
by Bettina Schelkle and Quentin Galland
Microorganisms 2020, 8(12), 1960; https://doi.org/10.3390/microorganisms8121960 - 10 Dec 2020
Cited by 3 | Viewed by 3152
Abstract
Microbiome research has recently gained centre-stage in both basic science and translational applications, yet researchers often feel that public communication about its potential overpromises. This manuscript aims to share a perspective on how scientists can engage in more open, ethical and transparent communication [...] Read more.
Microbiome research has recently gained centre-stage in both basic science and translational applications, yet researchers often feel that public communication about its potential overpromises. This manuscript aims to share a perspective on how scientists can engage in more open, ethical and transparent communication using an ongoing research project on food systems microbiomes as a case study. Concrete examples of strategically planned communication efforts are outlined, which aim to inspire and empower other researchers. Finally, we conclude with a discussion on the benefits of open and transparent communication from early-on in innovation pathways, mainly increasing trust in scientific processes and thus paving the way to achieving societal milestones such as the UN Sustainable Development Goals and the EU Green Deal. Full article
(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)
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