1
|
Rossi A, Marroni F, Renoldi N, Di Filippo G, Gover E, Marino M, Innocente N. An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking. J Dairy Sci 2024; 107:4288-4297. [PMID: 38462069 DOI: 10.3168/jds.2024-24463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
The use of natural milk culture (NMC) represents a key factor in Protected Designation of Origin (PDO) Montasio cheese, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMC is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMC collected from 10 PDO Montasio cheese dairies was investigated by employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMC, and a subdominant population made of other streptococci and Ligilactobacillus salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMC. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staphylococcus aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMC and clarify their role in the creation of the characteristics of PDO Montasio cheese.
Collapse
Affiliation(s)
- Anna Rossi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Niccolò Renoldi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Giulia Di Filippo
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Elisabetta Gover
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Marilena Marino
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy.
| | - Nadia Innocente
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| |
Collapse
|
2
|
Zhang Y, Yu P, Tao F. Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage. Molecules 2024; 29:2745. [PMID: 38930811 PMCID: PMC11206652 DOI: 10.3390/molecules29122745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.
Collapse
Affiliation(s)
- Yinan Zhang
- Key Laboratory of Milk and Dairy Products Detection and Monitoring Technology for State Market Regulation, Shanghai Institute of Quality Inspection and Technical Research, Shanghai 200233, China
| | - Peng Yu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China;
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
3
|
Nissen L, Casciano F, Chiarello E, Di Nunzio M, Bordoni A, Gianotti A. Sourdough process and spirulina-enrichment can mitigate the limitations of colon fermentation performances of gluten-free breads in non-celiac gut model. Food Chem 2024; 436:137633. [PMID: 37839115 DOI: 10.1016/j.foodchem.2023.137633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023]
Abstract
In this work, the impact of gluten free (GF) breads enriched with spirulina on the ecology of the colon microbiota of non-celiac volunteers was investigated. Simulation of digestion of GF breads was conducted with an in vitro gut model. Microbiomics and metabolomics analyses were done during colon fermentations to study the modulation of the microbiota. From the results, a general increase in Proteobacteria and no reduction of detrimental microbial metabolites were observed in any conditions. Notwithstanding, algae enriched sourdough breads showed potential functionalities, as the improvement of some health-related ecological indicators, like i) microbiota eubiosis; ii) production of bioactive volatile organic fatty acids; iii) production of bioactives terpenes. Our results indicate that a sourdough fermentation and algae enrichment can mitigate the negative effect of GF breads on gut microbiota of non-celiac consumers.
Collapse
Affiliation(s)
- Lorenzo Nissen
- DiSTAL - Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CIRI - Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CRBA, Centre for Applied Biomedical Research, Alma Mater Studiorum - University of Bologna, Policlinico di Sant'Orsola, Bologna 40100, Italy.
| | - Flavia Casciano
- DiSTAL - Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CRBA, Centre for Applied Biomedical Research, Alma Mater Studiorum - University of Bologna, Policlinico di Sant'Orsola, Bologna 40100, Italy.
| | - Elena Chiarello
- DiSTAL - Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy.
| | - Mattia Di Nunzio
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, via Celoria 2, 20133 Milan, Italy.
| | - Alessandra Bordoni
- DiSTAL - Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CIRI - Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy.
| | - Andrea Gianotti
- DiSTAL - Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CIRI - Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum - University of Bologna, P.za G. Goidanich, 60, 47521 Cesena, Italy; CRBA, Centre for Applied Biomedical Research, Alma Mater Studiorum - University of Bologna, Policlinico di Sant'Orsola, Bologna 40100, Italy.
| |
Collapse
|
4
|
Fusco V, Chieffi D, Fanelli F, Montemurro M, Rizzello CG, Franz CMAP. The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential. Front Microbiol 2023; 14:1289937. [PMID: 38169702 PMCID: PMC10758620 DOI: 10.3389/fmicb.2023.1289937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.
Collapse
Affiliation(s)
- Vincenzina Fusco
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Daniele Chieffi
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Marco Montemurro
- National Research Council, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | | | | |
Collapse
|
5
|
Levante A, Bertani G, Marrella M, Mucchetti G, Bernini V, Lazzi C, Neviani E. The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process. Front Microbiol 2023; 14:1196879. [PMID: 37649628 PMCID: PMC10462780 DOI: 10.3389/fmicb.2023.1196879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/30/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem. Methods In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps. Results and discussion All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.
Collapse
Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | | | | | | | | |
Collapse
|
6
|
Pozzi A, Nazzicari N, Capoferri R, Radovic S, Bongioni G. Assessment of residual plant DNA in bulk milk for Grana Padano PDO production by a metabarcoding approach. PLoS One 2023; 18:e0289108. [PMID: 37490502 PMCID: PMC10368264 DOI: 10.1371/journal.pone.0289108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.
Collapse
Affiliation(s)
- Anna Pozzi
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | - Nelson Nazzicari
- CREA-Council for Agricultural Research and Analysis of Agricultural Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza, Lodi, Italy
| | - Rossana Capoferri
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | | | - Graziella Bongioni
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| |
Collapse
|
7
|
Busetta G, Garofalo G, Barbera M, Di Trana A, Claps S, Lovallo C, Franciosi E, Gaglio R, Settanni L. Metagenomic, microbiological, chemical and sensory profiling of Caciocavallo Podolico Lucano cheese. Food Res Int 2023; 169:112926. [PMID: 37254352 DOI: 10.1016/j.foodres.2023.112926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 06/01/2023]
Abstract
In this study, Caciocavallo Podolico Lucano (CPL) cheese was deeply characterized for its bacterial community, chemical composition and sensory aspects. The entire cheese making process (from milk collection to ripened cheese) was performed by strictly applying the traditional protocol for CPL production in four dairy factories (A-D) representative of the production area. The vat made of wood represents the main transformation tool for CPL cheese production and the biofilms hosted onto the internal surfaces of all vats analyzed in this study were dominated by lactic acid bacteria. Total mesophilic microorganisms present in bulk milk (4.7-5.0 log CFU/ml) increased consistently after contact with the wooden vat surfaces (5.4-6.4 log CFU/ml). The application of Illumina sequencing technology identified barely 18 taxonomic groups among processed samples; streptococci and lactobacilli constituted the major groups of the wooden vat biofilms [94.74-99.70 % of relative abundance (RA)], while lactobacilli dominated almost entirely (94.19-100 % of total RA) the bacterial community of ripened cheeses. Except coagulase positive staphylococci, undesirable bacteria were undetectable. Among chemical parameters, significant variations were registered for unsaturated, monounsaturated, polyunsaturated fatty acids and antioxidant properties (significantly lower for CPL cheeses produced in factory B). The cheeses from factories A, C and D were characterized by a higher lactic acid and persistence smell attributes than factory B. This work indicated that the strict application of CPL cheese making protocol harmonized the main microbiological, physicochemical and sensory parameters of the final cheeses produced in the four factories investigated.
Collapse
Affiliation(s)
- Gabriele Busetta
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Giuliana Garofalo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Marcella Barbera
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Adriana Di Trana
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali (SAFE), University of Basilicata, Viale dell'Ateneo Lucano, 10, Potenza 85100, Italy
| | - Salvatore Claps
- CREA Research, Centre for Animal Production and Aquaculture, S.S. 7 Via Appia, Bella Muro, PZ 85051, Italy
| | - Carmela Lovallo
- CREA Research, Centre for Animal Production and Aquaculture, S.S. 7 Via Appia, Bella Muro, PZ 85051, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy.
| | - Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| |
Collapse
|
8
|
Savary O, Coton E, Maillard MB, Gaucheron F, Le Meur C, Frisvad J, Thierry A, Jany JL, Coton M. Functional diversity of Bisifusarium domesticum and the newly described Nectriaceae cheese-associated species. Food Res Int 2023; 168:112691. [PMID: 37120186 DOI: 10.1016/j.foodres.2023.112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023]
Abstract
Bisifusarium domesticum is among the main molds used during cheese-making for its "anticollanti" property that prevents the sticky smear defect of some cheeses. Previously, numerous cheese rinds were sampled to create a working collection and not only did we isolate B. domesticum but we observed a completely unexpected diversity of "Fusarium-like" fungi belonging to the Nectriaceae family. Four novel cheese-associated species belonging to two genera were described: Bisifusarium allantoides, Bisifusarium penicilloides, Longinectria lagenoides, and Longinectria verticilliformis. In this study, we thus aimed at determining their potential functional impact during cheese-making by evaluating their lipolytic and proteolytic activities as well as their capacity to produce volatile (HS-Trap GC-MS) and non-volatile secondary metabolites (HPLC & LC-Q-TOF). While all isolates were proteolytic and lipolytic, higher activities were observed at 12 °C for several B. domesticum, B. penicilloides and L. lagenoides isolates, which is in agreement with typical cheese ripening conditions. Using volatilomics, we identified multiple cheese-related compounds, especially ketones and alcohols. B. domesticum and B. penicilloides isolates showed higher aromatic potential although compounds of interest were also produced by B. allantoides and L. lagenoides. These species were also lipid producers. Finally, an untargeted extrolite analysis suggested a safety status of these strains as no known mycotoxins were produced and revealed the production of potential novel secondary metabolites. Biopreservation tests performed with B. domesticum suggested that it may be an interesting candidate for biopreservation applications in the cheese industry in the future.
Collapse
|
9
|
Rüstemoğlu M, Erkan ME, Cengiz G, Hajyzadeh M. Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential. Heliyon 2023; 9:e13334. [PMID: 36846685 PMCID: PMC9950837 DOI: 10.1016/j.heliyon.2023.e13334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Food safety has been a major concern for consumers. Origin of food products matter for consumers such that the quality, reputation, or other special characteristics can be attributed essentially to that origin. While a geographical indication informs consumers for the origin of the product, it develops a competitive advantage for the markets. To detect distinguishing features of dairy products, the microbial composition of its microbiota is one of the emerging areas of interest. Utilizing novel approaches such as Next Generation Sequencing (NGS) technology to decipher the genetic code of 16s rRNA genes to characterize the bacterial population is widely applied. The bacterial microbiota of the herby cheese samples which were collected from Şırnak province in the South Eastern region of Turkey was examined by an NGS approach for purpose of finding geographical indication possibilities. In brief, Firmicutes is the dominant phyla where Lactobacillaceae and Streptococcaceae are abundant families across the analyzed herby cheese microbiota. The most prominent species is Companilactobacillus ginsenosidimutans detected as the dominant member of the bacterial consortia in 16 herby cheese samples. Another remarkable finding reported here is the Weissella jogaejeotgali which was detected in 15 cheese samples. Albeit the abundance of Levilactobacillus koreensis is low at the microbiome level it was identified in four herby cheese samples. As expected, lactic acid bacteria such as Lactobacillus delbrueckii, Lactococcus raffinolactis and Tetragenococcus halophilus were also identified. On the other hand, bacterial diversity and microbial composition among cheese samples are not significantly affected by mixing different herbs on the manufacturing of herby cheeses. To the best of our knowledge, C. ginsenosidimutans, W. jogaejeotgali and L. koreensis are identified and reported for the first time in a dairy product and the bacterial richness and evenness of herby cheese are higher than those of most other cheeses. These findings make the cheeses in the geography where the samples were produced more valuable and provide opportunities for them to receive geographical indications. Thus, it will create added value while marketing the products.
Collapse
Affiliation(s)
- Mustafa Rüstemoğlu
- Şırnak University, Faculty of Agriculture, Plant Protection Department 73300 İdil, Şırnak, Turkey,Corresponding author.
| | - Mehmet Emin Erkan
- Dicle University, Faculty of Veterinary Medicine, Department of Food Hygiene and Technology, 21280 Diyarbakir, Turkey
| | - Gazal Cengiz
- Şırnak University, Faculty of Health Sciences, Department of Health Management, Şırnak, Turkey
| | - Mortaza Hajyzadeh
- Şırnak University, Faculty of Agriculture, Field Crops Department 73300 İdil, Şırnak, Turkey
| |
Collapse
|
10
|
Beneficial metabolic transformations and prebiotic potential of hemp bran and its alcalase hydrolysate, after colonic fermentation in a gut model. Sci Rep 2023; 13:1552. [PMID: 36707683 PMCID: PMC9883387 DOI: 10.1038/s41598-023-27726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
Hemp seed bran (HB) is an industrial food byproduct that is generally discarded. Knowledge on the functional capabilities of HB is limited and it is not known the impact of HB on human colon microbiota, where vegetable fibers are metabolized. In this work, we investigated in depth the prebiotic potential of HB and HB protein extract hydrolyzed by alcalase (HBPA) in comparison to fructooligosaccharides (FOS) after human distal colonic fermentation using MICODE (multi-unit in vitro colon gut model). During the 24 h of fermentation, metabolomics (SPME GC/MS) and microbiomics (MiSeq and qPCR) analyses were performed. The results indicated that HBPA on a colonic fermentation had a higher prebiotic index than HB (p < 0.05), and slightly lower to that of FOS (p > 0.05). This feature was described and explained as HBPA colonic fermentation produces beneficial organic fatty acids (e.g. Pentanoic and Hexanoic acids); reduces detrimental phenol derivates (e.g. p-Cresol); produces bioactives VOCs (e.g. Acetophenone or 4-Terpineol); increases beneficial bacteria (e.g. 1.76 fold and 2.07 fold more of Bifidobacterium bifidum and Bacteroides fragilis, respectively) and limits opportunistic bacteria (e.g. 3.04 fold and 2.07 fold less of Bilophila wadsworthia and Desulfovibrio, respectively). Our study evidenced the prebiotic role of HB and HBPA, and within the principles of OneHealth it valorizes a byproduct from the queen plant of sustainable crops as a food supplement.
Collapse
|
11
|
Calabrese FM, Russo N, Celano G, Pino A, Lopreiato V, Litrenta F, Di Bella G, Liotta L, De Angelis M, Caggia C, Randazzo CL. Effect of olive by-products feed supplementation on physicochemical and microbiological profile of Provola cheese. Front Microbiol 2023; 14:1112328. [PMID: 36726372 PMCID: PMC9885796 DOI: 10.3389/fmicb.2023.1112328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction With the purpose to evaluate the effects of dietary olive cake, a source of bioactive phenolic compounds, as feed supplementation of lactating dairy cows on fatty acid composition, volatile organic compounds, and microbiological profiles of Provola cheese, we performed a two-arm study where control and experimental administered cows derived dairy have been compared. Methods Our panel of analyses include metabolomics, physicochemical detected variables, culture dependent and independent analyses, and a stringent statistical approach aimful at disclosing only statistically significant results. Results and discussion Looking at the physicochemical variable's profiles, a higher content of unsaturated fatty acids, polyunsaturated fatty acid, and conjugated linoleic acids as well of proteins were observed in experimental cheese samples, indicating the beneficial effect of dietary supplementation. Furthermore, based on volatilome composition, a clear cluster separation between control and experimental cheeses was obtained, mainly related to terpenes degradation, able of influencing their aroma and taste. Microbiological results showed a decrease of some spoilage related microbial groups in experimental cheeses, probably due to the inhibitory effect exerted by polyphenols compounds, that contrarily did not affect the core taxa of all cheese samples. This paper confirmed the promising utilization of olive by-product in farming practices to obtain more sustainable and safe dairy food products with lower environmental impact, mainly in Sicily and Mediterranean area, where waste disposal poses serious environmental and economic problems.
Collapse
Affiliation(s)
| | - Nunziatina Russo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy,ProBioEtna SRL, Spin-off of University of Catania, Catania, Italy
| | - Giuseppe Celano
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy,ProBioEtna SRL, Spin-off of University of Catania, Catania, Italy
| | - Vincenzo Lopreiato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Federica Litrenta
- Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Giuseppa Di Bella
- Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy,ProBioEtna SRL, Spin-off of University of Catania, Catania, Italy
| | - Cinzia L. Randazzo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy,ProBioEtna SRL, Spin-off of University of Catania, Catania, Italy,*Correspondence: Cinzia L. Randazzo,
| |
Collapse
|
12
|
Decadt H, Weckx S, De Vuyst L. The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production. Front Microbiol 2023; 14:1128394. [PMID: 36876114 PMCID: PMC9978159 DOI: 10.3389/fmicb.2023.1128394] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.
Collapse
Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
13
|
The Impact of Different Inoculation Schemes on the Microbiota, Physicochemical and Sensory Characteristics of Greek Kopanisti Cheese throughout Production and Ripening. Microorganisms 2022; 11:microorganisms11010066. [PMID: 36677358 PMCID: PMC9863000 DOI: 10.3390/microorganisms11010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Kopanisti is a Greek PDO cheese, which is traditionally produced by the addition of an amount of over-mature Kopanisti, called Mana Kopanisti, to initiate cheese ripening. The aim of this study was the production of four types of Kopanisti cheese (A-D) using pasteurized cow milk, and a combination of the following starters/adjuncts in order to test their ability to be used in Kopanisti cheese production: A: Lactococcus lactis subsp. lactis and Lacticaseibacillus paracasei, B: L. lactis and Lc. paracasei/Mana Kopanisti, C: L. lactis and Lc. paracasei/Ligilactobacillus acidipiscis and Loigolactobacillus rennini, D: Lig. acidipiscis and Loig. rennini. Throughout production and ripening, classical microbiological, metataxonomics and physicochemical analyses were employed, while the final products (Day 35) were subjected to sensory analysis as well. Most interestingly, beta-diversity analysis of the metataxonomics data revealed the clusters constructed among the Kopanisti types based on the different inoculation schemes. On day 35, Kopanisti A-C types clustered together due to their similar 16S microbiota, while Kopanisti D was highly differentiated. On the contrary, ITS data clustered Kopanisti B and C together, while Kopanisti A and D were grouped seperately. Finally, based on the sensory evaluation, Kopanisti C appeared to have the most suitable bacteria cocktail for the Kopanisti cheese production. Therefore, not only were the conventional starters used, but also the Lig. acidipiscis and Loig. rennini strains could be used in a standardized Kopanisti cheese production that could lead to final products of high quality and safety.
Collapse
|
14
|
Fusco V, Chieffi D, De Angelis M. Invited review: Fresh pasta filata cheeses: Composition, role, and evolution of the microbiota in their quality and safety. J Dairy Sci 2022; 105:9347-9366. [DOI: 10.3168/jds.2022-22254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
|
15
|
Isolation, identification, and antimicrobial activity of lactic acid bacteria associated with two traditional Colombian types of cheese: Quesillo and double-cream cheese. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
16
|
Sharafi H, Moradi M, Amiri S. Application of Cheese Whey Containing Postbiotics of Lactobacillus acidophilus LA5 and Bifidobacterium animalis BB12 as a Preserving Liquid in High-Moisture Mozzarella. Foods 2022; 11:3387. [PMID: 36359999 PMCID: PMC9655881 DOI: 10.3390/foods11213387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 09/06/2023] Open
Abstract
High-moisture mozzarella cheese (HMMC) is a highly perishable cheese with a short shelf life. In this study, the effects of UF cheese whey containing postbiotics from Lactobacillus acidophilus LA-5 (P-LA-5), Bifidobacterium animalis BB-12 (P-BB-12), and their combination on the microbial (i.e., psychrophiles, mesophiles, lactic acid bacteria, and mold-yeast population) and sensory properties of HMMC were investigated. Postbiotics were prepared in a cheese whey model medium as a novel growth media and used as a preserving liquid in HMMC. The results demonstrate that postbiotics reduced the growth of all microorganisms (1.5-2 log CFU/g reduction) and P-LA5 and P-BB12 had the highest antibacterial performance on mesophiles and psychrophiles, respectively. Mold and yeast had the highest susceptibility to the postbiotics. Postbiotics showed a significant effect on maintaining the microbial quality of HMMC during storage, proposing postbiotics as a new preserving liquid for HMMC.
Collapse
Affiliation(s)
- Houshmand Sharafi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University,
Urmia 1177, Iran
| | - Mehran Moradi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University,
Urmia 1177, Iran
| | - Saber Amiri
- Department of Food Science and Technology, Faculty of Agriculture, Urmia University, Urmia 1177, Iran
| |
Collapse
|
17
|
Nissen L, Aniballi C, Casciano F, Elmi A, Ventrella D, Zannoni A, Gianotti A, Bacci ML. Maternal amoxicillin affects piglets colon microbiota: microbial ecology and metabolomics in a gut model. Appl Microbiol Biotechnol 2022; 106:7595-7614. [PMID: 36239764 PMCID: PMC9666337 DOI: 10.1007/s00253-022-12223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022]
Abstract
Abstract The first weeks of life represent a crucial stage for microbial colonization of the piglets’ gastrointestinal tract. Newborns’ microbiota is unstable and easily subject to changes under stimuli or insults. Nonetheless, the administration of antibiotics to the sow is still considered as common practice in intensive farming for pathological conditions in the postpartum. Therefore, transfer of antibiotic residues through milk may occurs, affecting the piglets’ colon microbiota. In this study, we aimed to extend the knowledge on antibiotic transfer through milk, employing an in vitro dedicated piglet colon model (MICODE—Multi Unit In vitro Colon Model). The authors’ focus was set on the shifts of the piglets’ microbiota composition microbiomics (16S r-DNA MiSeq and qPCR—quantitative polymerase chain reaction) and on the production of microbial metabolites (SPME GC/MS—solid phase micro-extraction gas chromatography/mass spectrometry) in response to milk with different concentrations of amoxicillin. The results showed an effective influence of amoxicillin in piglets’ microbiota and metabolites production; however, without altering the overall biodiversity. The scenario is that of a limitation of pathogens and opportunistic taxa, e.g., Staphylococcaceae and Enterobacteriaceae, but also a limitation of commensal dominant Lactobacillaceae, a reduction in commensal Ruminococcaceae and a depletion in beneficial Bifidobactericeae. Lastly, an incremental growth of resistant species, such as Enterococcaceae or Clostridiaceae, was observed. To the authors’ knowledge, this study is the first evaluating the impact of antibiotic residues towards the piglets’ colon microbiota in an in vitro model, opening the way to include such approach in a pipeline of experiments where a reduced number of animals for testing is employed. Key points • Piglet colon model to study antibiotic transfer through milk. • MICODE resulted a robust and versatile in vitro gut model. • Towards the “3Rs” Principles to replace, reduce and refine the use of animals used for scientific purposes (Directive 2010/63/UE). Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12223-3.
Collapse
Affiliation(s)
- Lorenzo Nissen
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum University of Bologna: Universita Di Bologna, P.za Goidanich 60, 47521, Cesena, Italy.,Interdepartmental Centre of Agri-Food Industrial Research (CIRI-AGRO), Alma Mater Studiorum University of Bologna: Universita Di Bologna, Via Q. Bucci 336, 47521, Cesena, Italy
| | - Camilla Aniballi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna: Universita Di Bologna, via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy
| | - Flavia Casciano
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum University of Bologna: Universita Di Bologna, P.za Goidanich 60, 47521, Cesena, Italy
| | - Alberto Elmi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna: Universita Di Bologna, via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy
| | - Domenico Ventrella
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna: Universita Di Bologna, via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy.
| | - Augusta Zannoni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna: Universita Di Bologna, via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy.,Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV), Alma Mater Studiorum University of Bologna: Universita Di Bologna, 40126, Bologna, Italy
| | - Andrea Gianotti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum University of Bologna: Universita Di Bologna, P.za Goidanich 60, 47521, Cesena, Italy.,Interdepartmental Centre of Agri-Food Industrial Research (CIRI-AGRO), Alma Mater Studiorum University of Bologna: Universita Di Bologna, Via Q. Bucci 336, 47521, Cesena, Italy
| | - Maria Laura Bacci
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna: Universita Di Bologna, via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy.,Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV), Alma Mater Studiorum University of Bologna: Universita Di Bologna, 40126, Bologna, Italy
| |
Collapse
|
18
|
Marques CS, Arruda TR, Silva RRA, Ferreira ALV, Oliveira WLDA, Rocha F, Mendes LA, de Oliveira TV, Vanetti MCD, Soares NDFF. Exposure to cellulose acetate films incorporated with garlic essential oil does not lead to homologous resistance in Listeria innocua ATCC 33090. Food Res Int 2022; 160:111676. [DOI: 10.1016/j.foodres.2022.111676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022]
|
19
|
Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
Collapse
Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
20
|
K-Clique Multiomics Framework: A Novel Protocol to Decipher the Role of Gut Microbiota Communities in Nutritional Intervention Trials. Metabolites 2022; 12:metabo12080736. [PMID: 36005608 PMCID: PMC9412844 DOI: 10.3390/metabo12080736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The availability of omics data providing information from different layers of complex biological processes that link nutrition to human health would benefit from the development of integrated approaches combining holistically individual omics data, including those associated with the microbiota that impacts the metabolisation and bioavailability of food components. Microbiota must be considered as a set of populations of interconnected consortia, with compensatory capacities to adapt to different nutritional intake. To study the consortium nature of the microbiome, we must rely on specially designed data analysis tools. The purpose of this work is to propose the construction of a general correlation network-based explorative tool, suitable for nutritional clinical trials, by integrating omics data from faecal microbial taxa, stool metabolome (1H NMR spectra) and GC-MS for stool volatilome. The presented approach exploits a descriptive paradigm necessary for a true multiomics integration of data, which is a powerful tool to investigate the complex physiological effects of nutritional interventions.
Collapse
|
21
|
Li H, Xi B, Yang X, Wang H, He X, Li W, Gao Y. Evaluation of change in quality indices and volatile flavor components in raw milk during refrigerated storage. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
22
|
Azhdari S, Moradi M. Application of antimicrobial coating based on carboxymethyl cellulose and natamycin in active packaging of cheese. Int J Biol Macromol 2022; 209:2042-2049. [PMID: 35504417 DOI: 10.1016/j.ijbiomac.2022.04.185] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
Abstract
The effects of carboxymethyl cellulose (CMC)-natamycin (N; 0.05 and 0.5%) coating on the quality of high-moisture mozzarella cheese (HMMC) were examined. The cheeses were immersed in the coating solutions and then kept at 7 °C for 8 days and microbial specifications (i.e., total mesophilic count, total psychrophilic count, lactic acid bacteria, and yeast-mold), pH, weight loss, and sensory properties were examined. The results of the agar spot diffusion assay represented inhibitory effects of CMC-N coating solution on Aspergillus flavus, A. fumigatus, A. niger, Penicillium citrinum, and Candida albicans. In HMMC, the natamycin-free CMC coating caused a significant decrease (p < 0.05) in all microbial groups, while the addition of natamycin to the coating only reduced the count of mold and yeast. As a result, the coating with natamycin at 0.05 and 0.5% represented a 0.6 and 0.9 log cycle reduction in yeast-mold populations, respectively. Based on the total mesophilic count, the control samples reached the 7 log CFU/g on day 4, indicating a 4-day shelf life of HMMC, while in HMMC coated with and without natamycin this limit was achieved on the 8th day of storage, which indicates that the coatings have doubled the HMMC shelf life.
Collapse
Affiliation(s)
- Sajad Azhdari
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University, 1177 Urmia, Iran
| | - Mehran Moradi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University, 1177 Urmia, Iran.
| |
Collapse
|
23
|
Nicosia FD, Puglisi I, Pino A, Caggia C, Randazzo CL. Plant Milk-Clotting Enzymes for Cheesemaking. Foods 2022; 11:foods11060871. [PMID: 35327293 PMCID: PMC8949083 DOI: 10.3390/foods11060871] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
The reduced availability and the increasing prices of calf rennet, coupled to the growing global demand of cheese has led, worldwide, to explore alternative clotting enzymes, capable to replace traditional rennet, during the cheesemaking. In addition, religious factors and others related to the vegetarianism of some consumers, have led to alternative rennet substitutes. Nowadays, several plant-derived milk-clotting enzymes are available for cheesemaking technology. Many efforts have also been made to compare their effects on rheological and sensory properties of cheese to those arising from animal rennet. However, vegetable clotting enzymes are still partially suitable for cheesemaking, due to excessive proteolytic activity, which contribute to bitter flavor development. This review provides a literature overview of the most used vegetable clotting enzymes in cheese technology, classified according to their protease class. Finally, clotting and proteolytic activities are discussed in relation to their application on the different cheesemaking products.
Collapse
Affiliation(s)
- Fabrizio Domenico Nicosia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (F.D.N.); (I.P.); (A.P.); (C.C.)
| | - Ivana Puglisi
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (F.D.N.); (I.P.); (A.P.); (C.C.)
| | - Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (F.D.N.); (I.P.); (A.P.); (C.C.)
- ProBioEtna, Spin-off of University of Catania, 95123 Catania, Italy
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (F.D.N.); (I.P.); (A.P.); (C.C.)
- ProBioEtna, Spin-off of University of Catania, 95123 Catania, Italy
| | - Cinzia Lucia Randazzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (F.D.N.); (I.P.); (A.P.); (C.C.)
- ProBioEtna, Spin-off of University of Catania, 95123 Catania, Italy
- Correspondence:
| |
Collapse
|
24
|
Effect of Packaging and Portioning on the Dynamics of Water–Fat Serum Release from Fresh Pasta Filata Soft Cheese. Foods 2022; 11:foods11030296. [PMID: 35159448 PMCID: PMC8834549 DOI: 10.3390/foods11030296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
The aim of the present study was to analyze the impact of cheese fragmentation and packaging on the dynamics of water–fat serum released from pasta filata cheese made from cow’s milk and its mixture with sheep’s milk. The addition of sheep’s milk reduced the amount of leachate from the vacuum-packed cheeses and did not cause as much loss of gloss as in the case of cow’s milk cheeses. This was also reflected in the microscopic images of the cheese samples. Consumers showed less acceptance of cow’s milk pasta filata cheeses than cheeses made with a mixture of cow’s and sheep’s milk (they had the same fat content, acidity, hardness, and oiling-off, but better stretching). The data describing water–fat serum release from pasta filata cheese within 24 h of unpacking was modeled with the use of the feed-forward artificial neural networks, whose architecture is based on Multi-Layer Perceptron with a single hidden layer. The model inputs comprised four independent variables, including one quantitative (i.e., time) and the other qualitative ones, which had the following states: type of raw material (cow’s milk, cow-sheep’s milk), way of sample portioning (whole, quarters, slices), packing method (vacuum packed and packed in brine).
Collapse
|
25
|
Isolation and Identification of Lactic Acid Bacteria from Natural Whey Cultures of Buffalo and Cow Milk. Foods 2022; 11:foods11020233. [PMID: 35053966 PMCID: PMC8774387 DOI: 10.3390/foods11020233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/24/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
In southern Italy, some artisanal farms produce mozzarella and caciocavallo cheeses by using natural whey starter (NWS), whose microbial diversity is responsible for the characteristic flavor and texture of the final product. We studied the microbial community of NWS cultures of cow’s milk (NWSc) for the production of caciocavallo and buffalo’s milk (NWSb) for the production of mozzarella, both from artisanal farms. Bacterial identification at species and strain level was based on an integrative strategy, combining culture-dependent (sequencing of the 16S rDNA, species/subspecies-specific Polymerase Chain Reaction (PCR) and clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and culture-independent (next-generation sequencing analysis, NGS) approaches. Results obtained with both approaches showed the occurrence of five species of lactic acid bacteria in NWSb (Lactococcus lactis subsp. lactis, Lactobacillus fermentum, Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus) and five species in NWSc (Lc. lactis subsp. lactis, Enterococcus faecium, and S. thermophilus, Lb. helveticus, and Lb. delbrueckii), with the last two found only by the NGS analysis. Moreover, RAPD profiles, performed on Lc. lactis subsp. lactis different isolates from both NWSs, showed nine strains in NWSb and seven strains in NWSc, showing a microbial diversity also at strain level. Characterization of the microbiota of natural whey starters aims to collect new starter bacteria to use for tracing microbial community during the production of artisanal cheeses, in order to preserve their quality and authenticity, and to select new Lactic Acid Bacteria (LAB) strains for the production of functional foods.
Collapse
|
26
|
Gonçalves FC, de Oliveira VM, Martins FT, Lião LM, Ferri PH, Queiroz Júnior LHK. Predicting chemical shelf life of mozzarella cheese submitted to irregular refrigeration practices by Nuclear Magnetic Resonance spectroscopy and statistical analysis. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
Esquivel-Hernández DA, García-Pérez JS, López-Pacheco IY, Iqbal HMN, Parra-Saldívar R. Resource recovery of lignocellulosic biomass waste into lactic acid - Trends to sustain cleaner production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113925. [PMID: 34731961 DOI: 10.1016/j.jenvman.2021.113925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/16/2021] [Accepted: 10/07/2021] [Indexed: 02/08/2023]
Abstract
Biomass waste generation concerns regulatory authorities to develop novel methods to sustain biotransformation processes. Particularly, lactic acid (LA) is a bulk commodity chemical used in diverse industries and holds a growing global market demand. Recently, lignocellulosic waste biomass is preferred for LA bio-production because of its non-edible and inexpensive nature. However, the information about new pretreatment methods for lignocellulosic feedstock, and novel strains capable to produce LA through fermentation is limited. Therefore, this review highlights the advancement of pretreatments methods of lignocellulosic biomass and biotransformation. Herein, we first briefly explored the main sources of lignocellulosic waste biomass, then we explored their latest advances in pretreatment processes particularly supercritical fluid extraction, and microwave-assisted extraction. Approaches for bioconversion were also analyzed, such as consolidated bioprocessing (CBP), simultaneous saccharification and fermentation (SSF), separate hydrolysis fermentation (SHF), among other alternatives. Also, new trends and approaches were documented, such as metagenomics to find novel strains of microorganisms and the use of recombinant strategies for the creation of new strains. Finally, we developed a holistic and sustainable perspective based on novel microbial ecology tools such as next-gen sequencing, bioinformatics, and metagenomics. All these shed light on the needs to culture powerful microbial isolates, co-cultures, and mixed consortia to improve fermentation processes with the aim of optimizing cultures and feedstock pretreatments.
Collapse
Affiliation(s)
- Diego A Esquivel-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico; Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - J Saúl García-Pérez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | - Itzel Y López-Pacheco
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
| | | |
Collapse
|
28
|
Torrijos R, Nazareth TM, Calpe J, Quiles JM, Mañes J, Meca G. Antifungal activity of natamycin and development of an edible film based on hydroxyethylcellulose to avoid Penicillium spp. growth on low-moisture mozzarella cheese. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
29
|
Dimov SG, Gyurova A, Zagorchev L, Dimitrov T, Georgieva-Miteva D, Peykov S. NGS-Based Metagenomic Study of Four Traditional Bulgarian Green Cheeses from Tcherni Vit. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
30
|
Buffalo Milk as a Source of Probiotic Functional Products. Microorganisms 2021; 9:microorganisms9112303. [PMID: 34835429 PMCID: PMC8620832 DOI: 10.3390/microorganisms9112303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
In the past two decades, consumption of food has been accruing due to its health claims which include gastrointestinal health, improved immunity, and well-being. Currently, the dairy industry is the sector where probiotics are most widely used, especially in fermented milk, cheese, yoghurt, butter, and dairy beverages. Although, it is still necessary to face many challenges regarding their stability and functionality in food. Considering the increasing demand for healthy products, it is necessary to develop strategies that aim to increase the consumption of functional foods in order to meet probiotic usefulness criteria and the consumer market. This review aimed to promote the utilization of buffalo milk considering its probiotic effects as a functional food and natural remedy to various ailments, emphasizing the potential of innovation and the importance of milk-based products as health promoters. The intake of probiotics plays an important role in modulating the health of the host, as a result of a balanced intestinal microbiota, reducing the risk of development of various diseases such as cancer, colitis, lactose intolerance, heart diseases, and obesity, among other disorders. However, further studies should be carried out to deepen the knowledge on the relationship between raw buffalo milk, its dairy products microbiota and consumer’s health beneficial effects, as well as to implement a strategy to increase the variety and availability of its products as a functional food in the market.
Collapse
|
31
|
Abreu ACDS, Carazzolle MF, Crippa BL, Barboza GR, Mores Rall VL, de Oliveira Rocha L, Silva NCC. Bacterial diversity in organic and conventional Minas Frescal cheese production using targeted 16S rRNA sequencing. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
32
|
Biodiversity and succession of lactic microbiota involved in Brazilian buffalo mozzarella cheese production. Braz J Microbiol 2021; 53:303-316. [PMID: 34661886 DOI: 10.1007/s42770-021-00629-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022] Open
Abstract
The biodiversity and succession of lactic acid bacteria (LAB) involved in the production and storage of Brazilian buffalo mozzarella cheese were evaluated. The isolates were characterized by Gram staining and catalase test, by the ability to grow at different conditions: temperatures, pH, concentrations of NaCl, and production of CO2 from glucose. The biodiversity and succession of 152 LAB isolated during cheese production were evaluated by 16S rRNA gene sequencing, Random Amplified Polymorphic DNA (RAPD-PCR), and Restriction Fragment Length Polymorphism (RFLP-PCR) techniques. Most of the strains grow well at 30 °C and are tolerant to 6.5% of NaCl, and in general, the best pH for growing was 9.6. Leuconostoc mesenteroides, Lacticaseibacillus casei, Limosilactobacillus fermentum, and Enterococcus sp. were prevalent and present in almost all steps of production. The LAB strains are typically found in the traditional Italian cheese, except the Leuconostoc citreum species. Sixty clusters were obtained by RAPD-PCR with 85% of similarity (114 isolates) while most of the LAB was clustered with 100% of similarity by the RFLP-PCR technique. The applied techniques enabled a valuable elucidation of the LAB biodiversity and succession, contributing to a better understanding of the specific microbial cultures with a technological aptitude of this cheese.
Collapse
|
33
|
Liu X, Wu Y, Guan R, Jia G, Ma Y, Zhang Y. Advances in research on calf rennet substitutes and their effects on cheese quality. Food Res Int 2021; 149:110704. [PMID: 34600696 DOI: 10.1016/j.foodres.2021.110704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022]
Abstract
Milk coagulation is an important step in cheese production, and milk-clotting enzymes (MCEs) play a major role in this process. Calf rennet is the most widely used MCE in the cheese industry. The use of calf rennet substitutes is becoming necessary due to the limited availability of calf rennet and the increase in cheese consumption. The objective of this review is to summarize the latest findings on calf rennet substitutes (animal MCEs, plant-derived MCEs, recombinant MCEs and microbial MCEs) and their application in cheese production. Special emphasis has been placed on aspects of the effects of these substitutes on hydrolysis, functional peptides, cheese variety and cheese yield. The advantages and disadvantages of different calf rennet substitutes are discussed, in which microbial MCEs have the advantages of less expensive production, greater biochemical diversity, easier genetic modification, etc. In particular, some of these MCEs have suitable characteristics for cheese production and are considered to be the most potential calf rennet substitutes. Moreover, challenges and future perspectives are presented to provide inspiration for the development of excellent calf rennet substitutes.
Collapse
Affiliation(s)
- Xiaofeng Liu
- College of Food Science and Technology, Zhejiang University of Technology, Zhejiang, Hangzhou 310014, China; Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yuanfeng Wu
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Rongfa Guan
- College of Food Science and Technology, Zhejiang University of Technology, Zhejiang, Hangzhou 310014, China
| | - Guochao Jia
- School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Henan, Zhengzhou 450044, China
| | - YuChen Ma
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yao Zhang
- Zhejiang Provincial Key Lab for Chem and Bio Processing Technology of Farm Produces, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China.
| |
Collapse
|
34
|
Gérard A, El-Hajjaji S, Burteau S, Fall PA, Pirard B, Taminiau B, Daube G, Sindic M. Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria monocytogenes. Food Microbiol 2021; 100:103861. [PMID: 34416961 DOI: 10.1016/j.fm.2021.103861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/05/2021] [Accepted: 06/13/2021] [Indexed: 12/29/2022]
Abstract
High throughput sequencing could become a powerful tool in food safety. This study was the first to investigate artisanal cheeses from Belgium (31 batches) using metagenetics, in relation to Listeria monocytogenes growth data acquired during a previous project. Five cheese types were considered, namely unripened acid-curd cheeses, smear- and mold-ripened soft cheeses, and Gouda-type and Saint-Paulin-type cheeses. Each batch was analyzed in triplicate the first and the last days of storage at 8 °C. Globally, 2697 OTUs belonging to 277 genera and to 15 phyla were identified. Lactococcus was dominant in all types, but Streptococcus was co-dominant in smear-ripened soft cheeses and Saint-Paulin-type cheeses. The dominant population was not always associated with added starter cultures. Bacterial richness and diversity were significantly higher in both types of soft cheeses than in other categories, including particular genera like Prevotella, Faecalibacterium and Hafnia-Obesumbacterium in mold-ripened cheeses and Brevibacterium, Brachybacterium, Microbacterium, Bacteroides, Corynebacterium, Marinilactibacillus, Fusobacterium, Halomonas and Psychrobacter in smear-ripened soft cheeses. A strong correlation was observed between no growth of L. monocytogenes in a smear-ripened cheese and the presence of an unknown Fusobacterium (relative abundance around 10%). This in silico correlation should be confirmed by further experiments in vitro and in situ.
Collapse
Affiliation(s)
- Amaury Gérard
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium.
| | - Soundous El-Hajjaji
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Sophie Burteau
- Genalyse Partner sa, rue Hayeneux, 62, 4040, Herstal, Belgium
| | | | - Barbara Pirard
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Bernard Taminiau
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Georges Daube
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Marianne Sindic
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| |
Collapse
|
35
|
Zago M, Rossetti L, Bardelli T, Carminati D, Nazzicari N, Giraffa G. Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences. Foods 2021; 10:1826. [PMID: 34441603 PMCID: PMC8392751 DOI: 10.3390/foods10081826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.
Collapse
Affiliation(s)
- Miriam Zago
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Lia Rossetti
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Tommaso Bardelli
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 26900 Lodi, Italy;
| | - Domenico Carminati
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Giorgio Giraffa
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| |
Collapse
|
36
|
Wang L, Zhong K, Luo A, Chen J, Shen Y, Wang X, He Q, Gao H. Dynamic changes of volatile compounds and bacterial diversity during fourth to seventh rounds of Chinese soy sauce aroma liquor. Food Sci Nutr 2021; 9:3500-3511. [PMID: 34262710 PMCID: PMC8269578 DOI: 10.1002/fsn3.2291] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022] Open
Abstract
Chinese soy sauce aroma liquor (CSSL) is a famous Baijiu. Multiple rounds of fermentation, the characteristic of CSSL processing, contributes to the differences in the quality of the liquor of different rounds. In this study, the grains on cooled, stacked, and fermented stages of 4th to 7th rounds were taken, of which the environmental factors, bacterial diversity, and volatile compounds were comprehensively analyzed. Lactobacillaceae, Bacillaceae, Thermoactinomycetaceae, and Enterobacteriaceae were the top four families, of which Lactobacillaceae dominated the fermented stage of each round. Principal component analysis (PCA) and principal coordinate analysis (PCoA) supported the popular view that the liquors of 3rd to 5th rounds possess the best quality. Lactobacillaceae is an extremely critical bacterium for CSSL fermentation. This study provides comprehensive understanding regarding the dynamic changes in fermented grains during the 4th to 7th rounds, which could help to improve the processing technology of CSSL.
Collapse
Affiliation(s)
- Lingchang Wang
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
| | - Kai Zhong
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
| | - Aimin Luo
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business UniversityBeijingChina
| | - Jian Chen
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
| | - Yi Shen
- Sichuan Langjiu Group Co., LtdLuzhouChina
| | - Xi Wang
- Sichuan Langjiu Group Co., LtdLuzhouChina
| | - Qiang He
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
| | - Hong Gao
- College of Biomass Science and Engineering and Healthy Food Evaluation Research CenterSichuan UniversityChengduChina
- Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan ProvinceSichuan UniversityChengduChina
| |
Collapse
|
37
|
Combined effect of ultrasound and basic electrolyzed water on the microbiological and oxidative profile of low-sodium mortadellas. Int J Food Microbiol 2021; 353:109310. [PMID: 34174509 DOI: 10.1016/j.ijfoodmicro.2021.109310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/08/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022]
Abstract
Ultrasound (US) and basic electrolyzed water (BEW) are considered emerging technologies; however, few studies have addressed the combination of both technologies in emulsified meat products. This study aimed to evaluate the individual and combined effect of US (25 kHz; 175 W; 20 min) and BEW (pH 10.99; -92.33 mV) on the microbiological and oxidative profile of low-sodium mortadellas (30% of NaCl reduction) stored for 90 days at 5 °C. The use of BEW alone increased the pH and reduced the redox potential of mortadellas, while the US did not affect these parameters. The combined application of US and BEW reduced the lactic acid bacteria counts by up to 0.36 log CFU/g. In addition, BEW stimulated the growth of lipolytic bacteria. The treatments subjected to US application alone showed a lower growth rate of lipolytic bacteria, lower lipid and protein oxidation, and higher ΔE* values. Therefore, the application of US and BEW may be a promising strategy to improve the microbiological and oxidative quality of mortadella during storage.
Collapse
|
38
|
Saleem IM, Gulzar N, Nadeem M, Sameen A, Rafiq S, Rehman S. Influence of hen egg white lysozyme N‐acetylmuramide glycan hydrolase on the antimicrobial activity and textural characteristics of high‐moisture mozzarella cheese. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Iqra Muqadas Saleem
- Department of Dairy Technology University of Veterinary and Animal Sciences Lahore Pakistan
| | - Nabila Gulzar
- Department of Dairy Technology University of Veterinary and Animal Sciences Lahore Pakistan
| | - Muhammad Nadeem
- Department of Dairy Technology University of Veterinary and Animal Sciences Lahore Pakistan
| | - Aysha Sameen
- National Institute of Food Science & TechnologyUniversity of Agriculture Faisalabad Pakistan
| | - Saima Rafiq
- Department of Food Science and Technology University of Poonch Rawalakot Pakistan
| | - Sadia Rehman
- Department of Dairy Technology University of Veterinary and Animal Sciences Lahore Pakistan
| |
Collapse
|
39
|
Michailidou S, Pavlou E, Pasentsis K, Rhoades J, Likotrafiti E, Argiriou A. Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding. Food Microbiol 2021; 99:103836. [PMID: 34119120 DOI: 10.1016/j.fm.2021.103836] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/14/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.
Collapse
Affiliation(s)
- Sofia Michailidou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece.
| | - Eleftherios Pavlou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Konstantinos Pasentsis
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Jonathan Rhoades
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece; Department of Food Science and Nutrition, University of the Aegean, Myrina, 81400, Lemnos, Greece
| |
Collapse
|
40
|
A Food-Grade Resin with LDH–Salicylate to Extend Mozzarella Cheese Shelf Life. Processes (Basel) 2021. [DOI: 10.3390/pr9050884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mozzarella cheese can be considered by far the world’s most popular Italian dairy product. Extending the shelf life of mozzarella cheese is an important issue in the dairy industry due to the high risk of contamination by several bacteria species, including spoilage pseudomonads. In this work, active packaging was prepared by coating traditional polyethylene terephthalate (PET) containers of “ovoline” mozzarella cheese with a food-grade resin mixed with a layered double hydroxide (LDH) in which salicylate anion was intercalatedby ionic exchange.. This antimicrobial molecule is listed in EC-Directive 10/2011/EC of 14 January 2011. Morphological arrangement of the molecule into the LDH layers was evaluated by X-ray diffraction (XRD) and controlled release followed by UV spectroscopy. Then, active trays were used to pack the mozzarella cheeses stored for 20 days at 4 °C and under thermal abuse (15 °C). Samples from both conditions showed coliform reduction (by ca. 2 log CFU/g) throughout the storage period. Depending on temperature, total mesophilic aerobic bacteria, Pseudomonas spp., yeasts, and mold loads were reduced in the first 3 days; at 4 °C. Slower acidification and lower proteolysis were also found in treated samples in comparison to control ones. The fitting of the Gompertz function to coliforms and spoilage pseudomonads highlighted an increase in the shelf life of mozzarella cheese of ca. 2 days at 4 °C. These results suggest that salicylate–LDH-coated PET may be applied to extend the shelf-life of mozzarella cheese and also counteract its spoilage if accidental interruptions to refrigeration occur.
Collapse
|
41
|
Impact of DNA extraction methods on 16S rRNA-based profiling of bacterial communities in cheese. J Microbiol Methods 2021; 184:106210. [PMID: 33774112 DOI: 10.1016/j.mimet.2021.106210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 11/21/2022]
Abstract
Numerous factors associated with sample preparation, DNA extraction, primer choice, sequencing platform and data analysis can affect the accuracy of 16S rRNA sequencing results. The DNA extraction method is considered critical for the success of sequencing as it can be the source of considerable variations in the analysis of the microbiome. In this study, the impact of various DNA extraction methods on the results of analysis of bacterial communities in cheese was evaluated. DNA was isolated from Mozzarella as a model cheese using optimized bead-based homogenization followed by different extraction procedures. Five commercial kits and two open-formula DNA extraction protocols were evaluated for amplicon sequencing of a 16S rRNA fragment of ~1460 bp. In addition, model cheese samples artificially contaminated by defined concentrations of Listeria monocytogenes and Escherichia coli, as representatives of Gram positive and Gram negative bacteria, were analysed. Six out of seven DNA extraction procedures were found to be able to provide amplifiable bacterial DNA suitable for 16S rRNA sequence analysis, but individual extraction procedures led to variable results. In particular, lysis supported with bead-beating led to a higher proportion of G+ bacteria in relative abundance profiles, probably because of the more efficient cell wall disruption. Artificially added bacterial species were reliably detected with a quantitative response. The results demonstrated a risk in comparing the data on bacterial communities in cheese when different DNA extraction protocols are used and highlighted the need to choose a standardized approach when comparison across multiple sequencing runs is required.
Collapse
|
42
|
Nam JH, Cho YS, Rackerby B, Goddik L, Park SH. Shifts of microbiota during cheese production: impact on production and quality. Appl Microbiol Biotechnol 2021; 105:2307-2318. [PMID: 33661344 DOI: 10.1007/s00253-021-11201-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023]
Abstract
The high-throughput DNA sequencing (HTS) method is used to identify microbes in cheese and their potential functional properties. The technique can be applied to the microbiota of the cheese processing environment, raw milk, curd, whey, and starter cultures, and be used to improve the quality, safety, and other physicochemical properties of the final product. The HTS method is also utilized to study the microbiota shift of different types of cheeses during processing, as the composition and functional properties of the microbiome provide unique characteristics to different cheeses. Although there are several reviews that focused on microbiota of various types of cheeses, this review focuses on evaluating the microbiota shift of different types of cheese production and highlights key bacteria in each step of the processing as well as microbiota of various types of cheeses. KEY POINTS: • High-throughput sequencing can be applied to identify microbiota in cheese. • Microbiota in cheese is changed during making process and aging. • Starter culture plays an important role to establish microbiota in cheese.
Collapse
Affiliation(s)
- Jun Haeng Nam
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Yong Sun Cho
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
- Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Bryna Rackerby
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Lisbeth Goddik
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA.
| |
Collapse
|
43
|
Nissen L, Casciano F, Chiarello E, Di Nunzio M, Bordoni A, Gianotti A. Colonic In Vitro Model Assessment of the Prebiotic Potential of Bread Fortified with Polyphenols Rich Olive Fiber. Nutrients 2021; 13:nu13030787. [PMID: 33673592 PMCID: PMC7997273 DOI: 10.3390/nu13030787] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
The use of olive pomace could represent an innovative and low-cost strategy to formulate healthier and value-added foods, and bakery products are good candidates for enrichment. In this work, we explored the prebiotic potential of bread enriched with Polyphenol Rich Fiber (PRF), a defatted olive pomace byproduct previously studied in the European Project H2020 EcoProlive. To this aim, after in vitro digestion, the PRF-enriched bread, its standard control, and fructo-oligosaccharides (FOS) underwent distal colonic fermentation using the in vitro colon model MICODE (multi-unit colon gut model). Sampling was done prior, over and after 24 h of fermentation, then metabolomic analysis by Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (SPME GCMS), 16S-rDNA genomic sequencing of colonic microbiota by MiSeq, and absolute quantification of main bacterial species by qPCR were performed. The results indicated that PRF-enriched bread generated positive effects on the host gut model: (i) surge in eubiosis; (ii) increased abundance of beneficial bacterial groups, such as Bifidobacteriaceae and Lactobacillales; (iii) production of certain bioactive metabolites, such as low organic fatty acids; (iv) reduction in detrimental compounds, such as skatole. Our study not only evidenced the prebiotic role of PRF-enriched bread, thereby paving the road for further use of olive by-products, but also highlighted the potential of the in vitro gut model MICODE in the critical evaluation of functionality of food prototypes as modulators of the gut microbiota.
Collapse
Affiliation(s)
- Lorenzo Nissen
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- Correspondence: ; Tel.: +39-0547-338-146
| | - Flavia Casciano
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Elena Chiarello
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Mattia Di Nunzio
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Alessandra Bordoni
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Andrea Gianotti
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| |
Collapse
|
44
|
Zotta T, Ricciardi A, Condelli N, Parente E. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci Nutr 2021; 62:3898-3912. [PMID: 33455430 DOI: 10.1080/10408398.2020.1870927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.
Collapse
Affiliation(s)
- Teresa Zotta
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Annamaria Ricciardi
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Nicola Condelli
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| |
Collapse
|
45
|
Yap M, Feehily C, Walsh CJ, Fenelon M, Murphy EF, McAuliffe FM, van Sinderen D, O'Toole PW, O'Sullivan O, Cotter PD. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome. Sci Rep 2020; 10:21665. [PMID: 33303873 PMCID: PMC7728742 DOI: 10.1038/s41598-020-78773-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
Collapse
Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mark Fenelon
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Fionnuala M McAuliffe
- APC Microbiome Ireland, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
| |
Collapse
|
46
|
Costantino G, Calasso M, Minervini F, De Angelis M. Use of Exopolysaccharide-Synthesizing Lactic Acid Bacteria and Fat Replacers for Manufacturing Reduced-Fat Burrata Cheese: Microbiological Aspects and Sensory Evaluation. Microorganisms 2020; 8:microorganisms8101618. [PMID: 33096692 PMCID: PMC7588969 DOI: 10.3390/microorganisms8101618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/17/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022] Open
Abstract
This study aimed to set-up a biotechnological protocol for manufacturing a reduced-fat Burrata cheese using semi-skimmed milk and reduced-fat cream, in different combinations with exopolysaccharides-synthesizing bacterial starters (Streptococcus thermophilus, E1, or Lactococcus lactis subsp. lactis and Lc. lactis subsp. cremoris, E2) and carrageenan or xanthan. Eight variants of reduced-fat cheese (fat concentration 34–51% lower than traditional full-fat Burrata cheese, used as the control) were obtained using: (i) semi-skimmed milk and reduced-fat cream alone (RC) or in combination with (ii) xanthan (RCX), (iii) carrageenan (RCC), (iv) starter E1 (RCE1), (v) starter E2 (RCE2), (vi) both starters (RCE1-2), (vii) E1 and xanthan (RCXE1), or E1 and carrageenan (RCCE1). Post-acidification occurred for the RCC, RCX, and RCE2 Burrata cheeses, due to the higher number of mesophilic cocci found in these cheeses after 16 days of storage. Overall, mesophilic and thermophilic cocci, although showing cheese variant-depending dynamics, were dominant microbial groups, flanked by Pseudomonas sp. during storage. Lactobacilli, increasing during storage, represented another dominant microbial group. The panel test gave highest scores to RCE1-2 and RCXE1 cheeses, even after 16 days of storage. The 16S-targeted metagenomic analysis revealed that a core microbiota (S. thermophilus, Streptococcus lutetiensis, Lc. lactis, Lactococcus sp., Leuconostoc lactis, Lactobacillus delbrueckii, and Pseudomonas sp.), characterized the Burrata cheeses. A consumer test, based on 105 people, showed that more than 50% of consumers did not distinguish the traditional full-fat from the RCXE1 reduced-fat Burrata cheese.
Collapse
|
47
|
Hu D, Xu Y, Yu D, Xia W, Jiang Q. The impacts of salt with Chinese liquor on the inhibition of microbial spoilage and quality attributes of grass carp (
Ctenopharyngodon idellus
) fillets stored at 4°C. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dan Hu
- State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan University Wuxi China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province Wuxi China
| | - Yanshun Xu
- State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan University Wuxi China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province Wuxi China
| | - Dawei Yu
- State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan University Wuxi China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province Wuxi China
| | - Wenshui Xia
- State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan University Wuxi China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province Wuxi China
| | - Qixing Jiang
- State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan University Wuxi China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province Wuxi China
| |
Collapse
|
48
|
Biolcati F, Ferrocino I, Bottero MT, Dalmasso A. Short communication: High-throughput sequencing approach to investigate Italian artisanal cheese production. J Dairy Sci 2020; 103:10015-10021. [PMID: 32952028 DOI: 10.3168/jds.2020-18208] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
In this study, high-throughput sequencing (HTS) was used to investigate the microbiota of Robiola di Roccaverano production, an artisanal Protected Designation of Origin soft cheese made with raw goat milk by addition of a natural milk starter (NMS), from the Piedmont region of Italy. Different steps of production of Robiola di Roccaverano cheese at one artisanal dairy were monitored. Matched samples of milk, NMS, curd, and 5-d and 15-d matured cheeses were collected at different periods of the year. The DNA sequences obtained by HTS belonged to 5 phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Tenericutes. In milk, Proteobacteria and Firmicutes were mainly found, and several operational taxonomic units (OTU) belonging to contaminant bacteria such as Pseudomonas, Serratia, and Staphylococcus were observed. However, in NMS, curd, and 5- and 15-d cheeses, Firmicutes were principally observed where OTU of Lactococcus lactis were predominant, followed by Leuconostoc mesenteroides OTU. The results of the analysis showed high bacterial diversity in milk samples compared with NMS, curd, and 5- and 15-d cheeses, suggesting strong action of NMS in driving the characteristics of the final products.
Collapse
Affiliation(s)
- Federica Biolcati
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy; Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università di Torino, 10095 Grugliasco, Italy.
| | - Ilario Ferrocino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università di Torino, 10095 Grugliasco, Italy
| | - Maria Teresa Bottero
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy
| | - Alessandra Dalmasso
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy
| |
Collapse
|
49
|
Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis. Food Microbiol 2020; 93:103613. [PMID: 32912585 DOI: 10.1016/j.fm.2020.103613] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.
Collapse
|
50
|
Gaglio R, Cirlincione F, Di Miceli G, Franciosi E, Di Gerlando R, Francesca N, Settanni L, Moschetti G. Microbial dynamics in durum wheat kernels during aging. Int J Food Microbiol 2020; 324:108631. [DOI: 10.1016/j.ijfoodmicro.2020.108631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/11/2020] [Indexed: 12/18/2022]
|