Y. T. Mekonnen,  F. Savini, F. Giacometti, V. Indio,  A. Seguino, A. Serraino, M. Candela,  and A. De Cesare. (2024)

While the demand for poultry meat is growing exponentially, poultry production is facing huge challenges, primary represented by increase of raw material costs and effects of global warming. The latter is quickly changing the microbiomes circulating within and around the poultry food system, raising concerns on occurrence of known and emerging pathogens in both the chickens and derived meat. In this systematic review aimed to compile the available body of knowledge about microbiome-related nutritional interventions contributing to improve the chicken health and having an impact on the reduction of colonization by foodborne pathogens in the gut.

Scicchitano D, Leuzzi D, Babbi G, Palladino G, Turroni S, Laczny CC, Wilmes P, Correa F, Leekitcharoenphon P, Savojardo C, Luise D, Martelli P, Trevisi P, Aarestrup FM, Candela M, Rampelli S. (2024)

Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment. In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them.

 

Palladino, G., Caroselli, E., Tavella, T., D’Amico, F., Prada, F., Mancuso, A., … & Biagi, E. (2022)

 In this paper, using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA).

 

Trapella, G., Cinti, N., Parma, L., De Marco, A., Dell’Acqua, A. N., Turroni, S., … & Palladino, G. (2023).

 This study explores the connections between microbiome variations at the clam-sediment interface and the nutritional status of clams collected at four Italian production sites along the Emilia Romagna coast, with different mortality incidence, higher in the Northern sites and lower in the Southern sites.

 

Scicchitano, D., Babbi, G., Palladino, G., Turroni, S., Mekonnen, Y. T., Laczny, C., … & Rampelli, S. (2024).

Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households  in three different farms in Italy during a complete rearing cycle.

 

Trapella, G., Scicchitano, D., Foresto, L., Dell’acqua, A. N., Radaelli, E., Turroni, S., … & Candela, M..

In this paper, we explore the impact of different anthropogenic stressors, namely, mussel farming, methane extraction platforms, and summer mass tourism, on the epipelagic microbiomes of the North-Western Adriatic Sea.

 

Palladino, G., Rampelli, S., Scicchitano, D., Nanetti, E., Iuffrida, L., Wathsala, R. H. G. R., … & Candela, M. (2023).

Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. However, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. In this paper we explore the potential and application in this area.

Carmen Escudero-Martinez and Davide Bulgarelli

Can microbiota be selectively chosen and employed to enhance plant growth, and to what extent does this influence occur? In this paper, CIRCLES partners conduct experiments to explore this question and demonstrate practical applications

 

R. A. Terrazas, S. Robertson-Albertyn, A. M. Corral, C. Escudero-Martinez, R. Kapadia, K. Balbirnie-Cumming, J. Morris, P. E. Hedley, M. Barret , G. Torres-Cortes, E. Paterson, E. M. Baggs , J. Abbott, D. Bulgarelli

How significant is the link between the rhizosphere microbiota and the overall health of a plant? In this paper, CIRCLES partners delve into this relationship, using cereal barley as an illustrative example.

Senga Robertson-Albertyn, James C. Abbott, Federico Concas, Lynn H. Brown, Jamie N. Orr, Timothy S. George, Davide

In this paper CIRCLES partner investigate on 41 bacteria isolated from the rhizosphere of cultivated barley. The rhizosphere microbiota is the microbial communities thriving at the root-soil interface and represent an untapped resource of plant probiotic functions

Krista Peltoniemi, Sannakajsa Velmala, Hannu Fritze, Tuula Jyske, Saija Rasi, Taina Pennanen

Does a correlation exist between the loss of microbiome diversity resulting from deforestation and the depletion of soil carbon in arable lands? Can the population of microbiomes, particularly fungi, be restored to nourish the soil? In this paper, CIRCLES researches provide answers to these questions and explains how bark from the Finnish forestry industry can be utilized as a soil nutrient

 

Nanetti, E., Palladino, G., Scicchitano, D., Trapella, G., Cinti, N., Fabbrini, M., Cozzi, A., Accetta, G., Tassini, C., Iannaccone, L., Candela, M., Rampelli, S. (2023) Composition and biodiversity of soil and root-associated microbiome in Vitis vinifera cultivar Lambrusco distinguish the microbial terroir of the Lambrusco DOC protected designation of origin area on a local scale.

Can microbiomes at the soil-plant interface be a determinant factor of the terroir properties in grapevine production? CIRCLES partners have investigated  the variation in microbial communities associated with the roots of Vitis vinifera cultivar Lambrusco, as well as with surrounding bulk soils, in different vineyards across the “Consorzio Tutela Lambrusco DOC” protected designation of origin area (PDO, Emilia Romagna, Italy). The results provide deeper insight into the microbial terroir of PDO areas.

Fabbrini, M., Candela, M., Turroni, S., Brigidi, P., & Rampelli, S. (2022). Exploring clade differentiation of the Faecalibacterium prausnitzii complex

CIRCLES partners have investigated on the most prevalent and abundant polyphyletic health-promoting components of the human gut microbiome to better understand its biology in the human gut.

Palladino, G., Rampelli, S., Camp, C.G., Scicchitano, D., Trapella, G., Nanetti, E., Angelini, V., Cleo, D., Turroni, S., Corinaldesi, C., Candela, M. (2022). Plasticity of the Anemonia viridis microbiota in response to different levels of combined anthropogenic and environmental stresses. Frontiers in Marine Science, 1871

How costal-habitat forming species respond to local and global stressors adapting to anthropogenic pressures? CIRCLES partners have investigated the response of the anemone microbiota to the combined anthropogenic and environmental stressors that typically characterize the touristic hotspots of the Mediterranean coastal sites. The results provide novel insight into the responses of the A. viridis microbiota to the increasing levels of anthropogenic and environmental pressures.

Alegria Terrazas, R., Robertson-Albertyn, S., Corral, A. M., Escudero-Martinez, C., Kapadia, R., Balbirnie-Cumming, K., … & Bulgarelli, D. (2022). Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies. Msystems, e00934-22.(https://journals.asm.org/doi/10.1128/msystems.00934-22)

How can microbes help plants grow better? CIRCLES partners have investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley. Their findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.

Schelkle and Galand (2020) Microbiome Research: Open Communication Today, Microbiome Applications in the Future. Microorganisms Journal. 8 (12). (https://doi.org/10.3390/microorganisms8121960)

CIRCLES partners have published an article that aims to share a perspective on how scientists can engage in more open, ethical and transparent communication, using the ongoing CIRCLES research project on food systems microbiomes as a case study. This publication was featured in the “Microbiomes for the Sustainable Production of Safe and Secure Foods” Special Issue.

Musella, et al. (2020) Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment. Science of the Total Environment. 137209 (https://doi.org/10.1016/j.scitotenv.2020.137209).

CIRCLES partners have published an exciting article on the microbiota and environment of mussels in the Adriatic sea. They specifically analysed microbiota composition of the digestive glands of mussels, and how this affects their health and productivity as well as the surrounding environmental quality.

Schelkle (2019) The role of microbes in producing our food. AgroFOOD Industry Hi Tech. (1722-6996 AIHTEI).

CIRCLES project partner Bettina Schelkle was invited to write a column on ‘The Role of Microbes in Producing our Food’, where she explains about the ubiquitous presence of microbes in our environment, and how they can be used in food innovation and sustainability.

Caradonia, et al. (2019) Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants. Phytobiomes Journal. 2471-2906 (https://doi.org/10.1094/PBIOMES-06-19-0028-R).

Researchers from Italy, Brazil and the United Kingdom have published an article for CIRCLES with the aim to contribute to the creation of future-proof sustainable crops. This joint research paper reveals the influence that nitrogen fertilizers have on the microbiota of tomatoes, especially on the root-soil interface.

Palladino, et al. (2021) Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages. Microorganisms 9 (https://doi.org/10.3390/microorganisms9020455)

Aiming at assessing the consequences of aquaculture on the surrounding environment, CIRCLES partners have collaborated to study the impact of the presence of fish cages on the microbiome of wild animals in the Mediterranean, using a common gastropod as model organism.

Palladino, et al. (2021) Seasonal Changes in Microbial Communities Associated With the Jewel Anemone Corynactis viridis. Frontiers in Marine Science. (https://doi.org/10.3389/fmars.2021.627585)

In this recently published scientific article, CIRCLES researchers explore the bacterial community structure, and its seasonal variations of anemones.