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Stachelska MA, Ekielski A, Karpiński P, Żelaziński T, Kruszewski B. New Genetic Determinants for qPCR Identification and the Enumeration of Selected Lactic Acid Bacteria in Raw-Milk Cheese. Molecules 2024; 29:1533. [PMID: 38611811 PMCID: PMC11013805 DOI: 10.3390/molecules29071533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Lactic acid bacteria (LAB) play an important role in the ripening of cheeses and contribute to the development of the desired profile of aroma and flavor compounds. Therefore, it is very important to monitor the dynamics of bacterial proliferation in order to obtain an accurate and reliable number of their cells at each stage of cheese ripening. This work aimed to identify and conduct a quantitative assessment of the selected species of autochthonous lactic acid bacteria from raw cow's milk cheese by the development of primers and probe pairs based on the uniqueness of the genetic determinants with which the target microorganisms can be identified. For that purpose, we applied real-time quantitative PCR (qPCR) protocols to quantify Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactococcus lactis subsp. cremoris cells in cheese directly after production and over three-month and six-month ripening periods. While L. lactis subsp. cremoris shows good acidification ability and the ability to produce antimicrobial compounds, L. delbrueckii subsp. bulgaricus has good proteolytic ability and produces exo-polysaccharides, and S. thermophilus takes part in the formation of the diacetyl flavor compound by metabolizing citrate to develop aroma, they all play an important role in the cheese ripening. The proposed qPCR protocols are very sensitive and reliable methods for a precise enumeration of L. delbrueckii subsp. bulgaricus, S. thermophilus, and L. lactis subsp. cremoris in cheese samples.
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Affiliation(s)
- Milena Alicja Stachelska
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Adam Ekielski
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Piotr Karpiński
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Tomasz Żelaziński
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Bartosz Kruszewski
- Department of Food Technology and Assessment, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159 C, 02-776 Warsaw, Poland
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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:S0022-0302(24)00535-6. [PMID: 38462069 DOI: 10.3168/jds.2024-24463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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 PDO Montasio cheeses, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMCs is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMCs collected from 10 PDO Montasio cheese dairies was investigated 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 NMCs, and a subdominant population made of other streptococci and L. salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMCs. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staph. 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 NMCs and clarify their role in the creation of the characteristics of PDO Montasio cheese.
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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
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3
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Galli BD. Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin. J Sci Food Agric 2024. [PMID: 38380878 DOI: 10.1002/jsfa.13403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 02/22/2024]
Abstract
Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Bruno Domingues Galli
- Faculty of Agriculture, Environmental and Food Sciences, Free University of Bolzano-Bozen, Bolzano, Italy
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Cardin M, Cardazzo B, Coton M, Carraro L, Lucchini R, Novelli E, Coton E, Mounier J. Ecological diversity and associated volatilome of typical mountain Caciotta cheese from Italy. Int J Food Microbiol 2024; 411:110523. [PMID: 38134579 DOI: 10.1016/j.ijfoodmicro.2023.110523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/24/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Traditional products are particularly appreciated by consumers and among these products, cheese is a major contributor to the Italian mountainous area economics. In this study, shotgun metagenomics and volatilomics were used to understand the biotic and abiotic factors contributing to mountain Caciotta cheese typicity and diversity. Results showed that the origin of cheese played a significant role; however, curd cooking temperature, pH, salt concentration and water activity also had an impact. Viral communities exhibited higher biodiversity and discriminated cheese origins in terms of production farms. Among the most dominant bacteria, Streptococcus thermophilus showed higher intraspecific diversity and closer relationship to production farm when compared to Lactobacillus delbrueckii. However, despite a few cases in which the starter culture was phylogenetically separated from the most dominant strains sequenced in the cheese, starter cultures and dominant cheese strains clustered together suggesting substantial starter colonization in mountain Caciotta cheese. The Caciotta cheese volatilome contained prominent levels of alcohols and ketones, accompanied by lower proportions of terpenes. Volatile profile not only demonstrated a noticeable association with production farm but also significant differences in the relative abundances of enzymes connected to flavor development. Moreover, correlations of different non-homologous isofunctional enzymes highlighted specific contributions to the typical flavor of mountain Caciotta cheese. Overall, this study provides a deeper understanding of the factors shaping typical mountain Caciotta cheese, and the potential of metagenomics for characterizing and potentially authenticating food products.
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Affiliation(s)
- Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy; Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy.
| | - Monika Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Rosaria Lucchini
- Italian Health Authority and Research Organization for Animal Health and Food Safety (Istituto zooprofilattico sperimentale delle Venezie), Viale Università 10, 35020 Legnaro, PD, Italy
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Emmanuel Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Jérôme Mounier
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Innocente N, Renoldi N, Moret E, Maifreni M, Marino M. Volatilome of brine-related microorganisms in a curd-based medium. J Dairy Sci 2023; 106:8404-8414. [PMID: 37641243 DOI: 10.3168/jds.2022-23051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/16/2023] [Indexed: 08/31/2023]
Abstract
The possible contribution of brine-derived microflora to the sensory attributes of cheese is still a rather unexplored field. In this study, 365 bacteria and 105 yeast strains isolated from 11 cheese brines were qualitatively tested for proteolytic and lipolytic activities, and positive strains were identified by sequencing. Among bacteria, Staphylococcus equorum was the most frequent, followed by Macrococcus caseolyticus and Corynebacterium flavescens. As for yeasts, Debaryomyces hansenii, Clavispora lusitaniae, and Torulaspora delbrueckii were most frequently identified. A total of 38% of bacteria and 59% of yeasts showed at least 1 of the metabolic activities tested, with lipolytic activity being the most widespread (81% of bacteria and 95% of yeasts). Subsequently 15 strains of bacteria and 10 yeasts were inoculated in a curd-based medium and assessed via headspace-solid phase microextraction coupled with gas chromatography-mass spectrometry to determine their volatilome. After a 30-d incubation at 12°C, most strains showed a viability increase of about 2 log cfu/mL, suggesting good adaptability to the cheese environment. A total of 26 compounds were detected in the headspace, carbonyl compounds and alcohols being the major contributors to the volatile profile of the curd-based medium. Multivariate analysis was carried out to elucidate the overall differences in volatiles produced by selected strains. Principal component analysis and hierarchical clustering analysis demonstrated that the brine-related microorganisms were separated into 3 different groups, suggesting their different abilities to produce volatile compounds. Some of the selected strains have been shown to have interesting aromatic potential and to possibly contribute to the sensory properties of cheese.
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Affiliation(s)
- Nadia Innocente
- 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
| | - Erica Moret
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Michela Maifreni
- 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
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Yang F, Zhang L, Zhang Y, Zeng Y, Li Y, Zeng P. Culture-dependent and culture-independent approaches to reveal the aflatoxin B1-producing fungi in Pixian Doubanjiang, a typical condiment in Chinese cuisine. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Johnson MA, Vinatzer BA, Li S. Reference-Free Plant Disease Detection Using Machine Learning and Long-Read Metagenomic Sequencing. Appl Environ Microbiol 2023; 89:e0026023. [PMID: 37184398 PMCID: PMC10304783 DOI: 10.1128/aem.00260-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
Surveillance for early disease detection is crucial to reduce the threat of plant diseases to food security. Metagenomic sequencing and taxonomic classification have recently been used to detect and identify plant pathogens. However, for an emerging pathogen, its genome may not be similar enough to any public genome to permit reference-based tools to identify infected samples. Also, in the case of point-of care diagnosis in the field, database access may be limited. Therefore, here we explore reference-free detection of plant pathogens using metagenomic sequencing and machine learning (ML). We used long-read metagenomes from healthy and infected plants as our model system and constructed k-mer frequency tables to test eight different ML models. The accuracy in classifying individual reads as coming from a healthy or infected metagenome were compared. Of all models, random forest (RF) had the best combination of short run-time and high accuracy (over 0.90) using tomato metagenomes. We further evaluated the RF model with a different tomato sample infected with the same pathogen or a different pathogen and a grapevine sample infected with a grapevine pathogen and achieved similar performances. ML models can thus learn features to successfully perform reference-free detection of plant diseases whereby a model trained with one pathogen-host system can also be used to detect different pathogens on different hosts. Potential and challenges of applying ML to metagenomics in plant disease detection are discussed. IMPORTANCE Climate change may lead to the emergence of novel plant diseases caused by yet unknown pathogens. Surveillance for emerging plant diseases is crucial to reduce their threat to food security. However, conventional genomic based methods require knowledge of existing plant pathogens and cannot be applied to detecting newly emerged pathogens. In this work, we explored reference-free, meta-genomic sequencing-based disease detection using machine learning. By sequencing the genomes of all microbial species extracted from an infected plant sample, we were able to train machine learning models to accurately classify individual sequencing reads as coming from a healthy or an infected plant sample. This method has the potential to be integrated into a generic pipeline for a meta-genomic based plant disease surveillance approach but also has limitations that still need to be overcome.
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Affiliation(s)
- Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia, USA
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
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Bettera L, Dreier M, Schmidt RS, Gatti M, Berthoud H, Bachmann HP. Selective enrichment of the raw milk microbiota in cheese production: Concept of a natural adjunct milk culture. Front Microbiol 2023; 14:1154508. [PMID: 37180227 PMCID: PMC10169670 DOI: 10.3389/fmicb.2023.1154508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/30/2023] [Indexed: 05/16/2023] Open
Abstract
In cheese production, microorganisms are usually added at the beginning of the process as primary starters to drive curd acidification, while secondary microorganisms, with other pro-technological features important for cheese ripening, are added as selected cultures. This research aimed to investigate the possibilities of influencing and selecting the raw milk microbiota using artisanal traditional methods, providing a simple method to produce a natural supplementary culture. We investigated the production of an enriched raw milk whey culture (eRWC), a natural adjunct microbial culture produced from mixing an enriched raw milk (eRM) with a natural whey culture (NWC). The raw milk was enriched by spontaneous fermentation for 21 d at 10°C. Three milk enrichment protocols were tested: heat treatment before incubation, heat treatment plus salt addition, and no treatment. The eRMs were then co-fermented with NWC (ratio of 1:10) at 38°C for 6 h (young eRWC) and 22 h (old eRWC). Microbial diversity during cultures' preparation was evaluated through the determination of colony forming units on selective growth media, and next-generation sequencing (16S rRNA gene amplicon sequencing). The enrichment step increased the streptococci and lactobacilli but reduced microbial richness and diversity of the eRMs. Although the lactic acid bacteria viable count was not significantly different between the eRWCs, they harbored higher microbial richness and diversity than NWC. Natural adjunct cultures were then tested in cheese making trials, following the microbial development, and assessing the chemical quality of the 120 d ripened cheeses. The use of eRWCs slowed the curd acidification in the first hours of cheese making but the pH 24 h after production settled to equal values for all the cheeses. Although the use of diverse eRWCs contributed to having a richer and more diverse microbiota in the early stages of cheese making, their effect decreased over time during ripening, showing an inferior effect to the raw milk microbiota. Even if more research is needed, the optimization of such a tool could be an alternative to the practice of isolating, geno-pheno-typing, and formulating mixed-defined-strain adjunct cultures that require knowledge and facilities not always available for artisanal cheese makers.
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Affiliation(s)
- Luca Bettera
- Department of Food and Drug, University of Parma, Parma, Italy
- Agroscope, Bern, Switzerland
| | | | | | - Monica Gatti
- Department of Food and Drug, University of Parma, Parma, Italy
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Yang J, Chung M, Park Y. Association of Fermented Products with Risk of Cancer Recurrence and Mortality among Breast Cancer Survivors: A Prospective Cohort Study. Nutr Cancer 2023; 75:1189-1199. [PMID: 36908185 DOI: 10.1080/01635581.2023.2186259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
We hypothesized that the intake of fermented soy and dairy products, but not fermented vegetable products, was associated with reduced cancer recurrence and mortality in breast cancer survivors. Women (n = 606) who underwent dietary survey using a 24-h recall within 3 years of breast cancer surgery were recruited, and were followed up for a mean of 89 mo,. Cox proportional hazards regression analysis showed that the risk of cancer recurrence was inversely associated with the intake of fermented soy products (Hazard ratios (HRs):0.976, 95% confidence intervals (CI):0.95-0.99) and fermented dairy products (HRs:0.992, 95% CI:0.98-0.99). Furthermore, the risk of cancer recurrence was inversely associated with the intake of fermented soy products in hormone receptor-positive (HRs:0.296, 95% CI:0.11-0.79), estrogen receptor-positive (HRs:0.971, 95% CI:0.94-0.99), and progesterone receptor-positive (HRs:0.972, 95% CI:0.94-0.99) patients. Mortality was inversely associated with the intake of fermented soy products (HRs:0.967, 95% CI:0.93-0.99). Disease-free survival (P = 0.001) and overall survival (P = 0.004) were positively associated with intake of fermented soy products. Intake of fermented vegetable products had no significant effect on cancer recurrence or mortality. This study suggests that the intake of fermented soy and dairy could be beneficial in preventing cancer recurrence.
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Affiliation(s)
- Jubin Yang
- Department of Food and Nutrition, Hanyang University, Seoul, Republic of Korea
| | - Minsung Chung
- Department of Surgery, Hanyang University Hospital, Seoul, Republic of Korea
| | - Yongsoon Park
- Department of Food and Nutrition, Hanyang University, Seoul, Republic of Korea
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Bisson G, Maifreni M, Innocente N, Marino M. Application of pre-adaptation strategies to improve the growth of probiotic lactobacilli under food-relevant stressful conditions. Food Funct 2023; 14:2128-2137. [PMID: 36745384 DOI: 10.1039/d2fo03215e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
While formulating a probiotic food, it is mandatory to make sure that the viability of probiotics is adequate at the point of consumption, which can be strongly compromised by stressful conditions due to low pH and high osmolarity. In this study, three probiotic lactobacilli were subjected to different pre-adaptation conditions, and the turbidimetric growth kinetics in challenging conditions (pH 4.0-6.5, NaCl 1-7%, sucrose 0.1-0.7 M) were evaluated. Different effects were observed for Lactobacillus acidophilus, Lacticaseibacillus casei, and Lactiplantibacillus plantarum. Indeed, pre-exposition to sub-optimal conditions in terms of pH and % NaCl significantly improved the ability of L. acidophilus and L. casei to overcome the osmotic stress due to salt or sucrose, and similar effects were observed for acidic stress. L. plantarum showed to be more tolerant to the challenging conditions applied in this study. Anyway, the pre-adaptation at conditions SUB_1 (pH 4.5 and NaCl 4%) and SUB_2 (pH 5 and NaCl 2%) speeded-up its growth kinetics by reducing the length of the lag phase under sucrose stress and enhancing the maximum growth rate at the highest pH tested. Moreover, an improvement in biomass amount was observed under sucrose stress. The whole data evidenced that the application of the appropriate pre-adaptation condition could contribute to making probiotics more robust towards challenging conditions due to food matrix, processing, and storage as well as gastrointestinal transit. Further studies will be necessary to gain insight into the proteomics and metabolomics responsible for increased tolerance to stressful conditions.
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Affiliation(s)
- Giulia Bisson
- Department of Agricultural, Food, Animal and Environmental Sciences, University of Udine, via Sondrio 2/A, 33100 Udine, Italy.
| | - Michela Maifreni
- Department of Agricultural, Food, Animal and Environmental Sciences, University of Udine, via Sondrio 2/A, 33100 Udine, Italy.
| | - Nadia Innocente
- Department of Agricultural, Food, Animal and Environmental Sciences, University of Udine, via Sondrio 2/A, 33100 Udine, Italy.
| | - Marilena Marino
- Department of Agricultural, Food, Animal and Environmental Sciences, University of Udine, via Sondrio 2/A, 33100 Udine, Italy.
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11
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Bettera L, Levante A, Bancalari E, Bottari B, Gatti M. Lactic acid bacteria in cow raw milk for cheese production: Which and how many? Front Microbiol 2023; 13:1092224. [PMID: 36713157 PMCID: PMC9878191 DOI: 10.3389/fmicb.2022.1092224] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: "which and how many LAB are present in cow raw milk used for cheese production?," this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the "history" of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.
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Jeilu O, Gessesse A, Simachew A, Johansson E, Alexandersson E. Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing. Front Microbiol 2022; 13:999876. [PMID: 36569062 PMCID: PMC9772273 DOI: 10.3389/fmicb.2022.999876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Soda lakes are unique poly-extreme environments with high alkalinity and salinity that support diverse microbial communities despite their extreme nature. In this study, prokaryotic and eukaryotic microbial diversity in samples of the three soda lakes, Lake Abijata, Lake Chitu and Lake Shala in the East African Rift Valley, were determined using amplicon sequencing. Culture-independent analysis showed higher diversity of prokaryotic and eukaryotic microbial communities in all three soda lakes than previously reported. A total of 3,603 prokaryotic and 898 eukaryotic operational taxonomic units (OTUs) were found through culture-independent amplicon sequencing, whereas only 134 bacterial OTUs, which correspond to 3%, were obtained by enrichment cultures. This shows that only a fraction of the microorganisms from these habitats can be cultured under laboratory conditions. Of the three soda lakes, samples from Lake Chitu showed the highest prokaryotic diversity, while samples from Lake Shala showed the lowest diversity. Pseudomonadota (Halomonas), Bacillota (Bacillus, Clostridia), Bacteroidota (Bacteroides), Euryarchaeota (Thermoplasmata, Thermococci, Methanomicrobia, Halobacter), and Nanoarchaeota (Woesearchaeia) were the most common prokaryotic microbes in the three soda lakes. A high diversity of eukaryotic organisms were identified, primarily represented by Ascomycota and Basidiomycota. Compared to the other two lakes, a higher number of eukaryotic OTUs were found in Lake Abijata. The present study showed that these unique habitats harbour diverse microbial genetic resources with possible use in biotechnological applications, which should be further investigated by functional metagenomics.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
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13
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Cardinali F, Foligni R, Ferrocino I, Harasym J, Orkusz A, Milanović V, Franciosa I, Garofalo C, Mannozzi C, Mozzon M, Cocolin L, Aquilanti L, Osimani A. Microbiological, morpho-textural, and volatile characterization of Portuguese Queijo de Nisa PDO cheese. Food Res Int 2022; 162:112011. [DOI: 10.1016/j.foodres.2022.112011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
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14
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Guo R, Ju N, Wang Y, Gou M, Li P, Luo Y. Metagenomic reveals succession in the bacterial community and predicts changes in raw milk during refrigeration. J Food Saf 2022. [DOI: 10.1111/jfs.13028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Rong Guo
- College of Food and Wine Ningxia University Yinchuan P.R. China
| | - Ning Ju
- College of Food and Wine Ningxia University Yinchuan P.R. China
| | - Yuanyuan Wang
- College of Food and Wine Ningxia University Yinchuan P.R. China
| | - Meng Gou
- College of Food and Wine Ningxia University Yinchuan P.R. China
| | - Puyu Li
- College of Food and Wine Ningxia University Yinchuan P.R. China
| | - Yulong Luo
- College of Food and Wine Ningxia University Yinchuan P.R. China
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15
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Saeed M, Shoaib A, Kandimalla R, Javed S, Almatroudi A, Gupta R, Aqil F. Microbe-based therapies for colorectal cancer: Advantages and limitations. Semin Cancer Biol 2022; 86:652-665. [PMID: 34020027 DOI: 10.1016/j.semcancer.2021.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 01/27/2023]
Abstract
Cancer is one of the leading global causes of death in both men and women. Colorectal cancer (CRC) alone accounts for ∼10 % of total new global cases and poses an over 4% lifetime risk of developing cancer. Recent advancements in the field of biotechnology and microbiology concocted novel microbe-based therapies to treat various cancers, including CRC. Microbes have been explored for human use since centuries, especially for the treatment of various ailments. The utility of microbes in cancer therapeutics is widely explored, and various bacteria, fungi, and viruses are currently in use for the development of cancer therapeutics. The human gut hosts about 100 trillion microbes that release their metabolites in active, inactive, or dead conditions. Microbial secondary metabolites, proteins, immunotoxins, and enzymes are used to target cancer cells to induce cell cycle arrest, apoptosis, and death. Various approaches, such as dietary interventions, the use of prebiotics and probiotics, and fecal microbiota transplantation have been used to modulate the gut microbiota in order to prevent or treat CRC pathogenesis. The present review highlights the role of the gut microbiota in CRC precipitation, the potential mechanisms and use of microorganisms as CRC biomarkers, and strategies to modulate microbiota for the prevention and treatment of CRC.
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Affiliation(s)
- Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
| | - Ambreen Shoaib
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Raghuram Kandimalla
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Shamama Javed
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia
| | - Ramesh Gupta
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Farrukh Aqil
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, University of Louisville, Louisville, KY 40202, USA.
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16
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Ferreira LR, de Almeida TT, Andretta M, Perin LM, Camargo AC, de Carvalho AF, Nero LA. Further culture-independent characterization of the lactic microbiota of Serro artisanal cheese. Braz J Microbiol 2022; 53:1593-1598. [PMID: 35689157 DOI: 10.1007/s42770-022-00778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
This study aimed to provide a further characterization of the lactic microbiota present in Minas artisanal cheese (MAC) from the Serro region by using culture-independent methods, as a complementary analysis of a previous study. The total DNA extracted from MAC samples (n = 55) was subjected to repetitive extragenic palindromic-PCR (rep-PCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Rep-PCR analysis showed that core microbiota of Serro MAC was closely related, independent of the production town, farm size, or time of production. The sequencing of PCR-DGGE bands identified the prevalence of Lactococcus lactis in all samples, and Streptococcus salivarius was also identified. Thus, we conclude that when more accurate methods are unavailable, rep-PCR can be used as a culture-independent method to demonstrate if the microbiota is closely related or not among the samples. PCR-DGGE results also matched to the main findings of high-throughput sequencing, previously presented, confirming its confidence to detect the main microbial groups present in the raw milk cheeses.
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Affiliation(s)
- Letícia Rocha Ferreira
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil.,Departamento de Tecnologia de Alimentos, Inovaleite - Laboratório de Ciência E Tecnologia Do Leite E Derivados, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Thaiza Teixeira de Almeida
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil.,Departamento de Tecnologia de Alimentos, Inovaleite - Laboratório de Ciência E Tecnologia Do Leite E Derivados, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Milimani Andretta
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Luana Martins Perin
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Anderson Carlos Camargo
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil.,Departamento de Tecnologia de Alimentos, Inovaleite - Laboratório de Ciência E Tecnologia Do Leite E Derivados, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Antônio Fernandes de Carvalho
- Departamento de Tecnologia de Alimentos, Inovaleite - Laboratório de Ciência E Tecnologia Do Leite E Derivados, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil
| | - Luís Augusto Nero
- Departamento de Veterinária, InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Campus Universitário, Centro, Viçosa MG, 36570 900, Brazil.
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17
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Cardinali F, Foligni R, Ferrocino I, Harasym J, Orkusz A, Franciosa I, Milanović V, Garofalo C, Mannozzi C, Mozzon M, Cocolin L, Osimani A, Aquilanti L. Microbial diversity, morpho-textural characterization, and volatilome profile of the Portuguese thistle-curdled cheese Queijo da Beira Baixa PDO. Food Res Int 2022; 157:111481. [DOI: 10.1016/j.foodres.2022.111481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/04/2022]
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18
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Young Kim S, Ban G, Won Hong Y, Ji Jang M, Ae Kim S. Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing. Food Res Int 2022; 152:110896. [DOI: 10.1016/j.foodres.2021.110896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/19/2022]
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19
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Uzoukwu EU, Phandanouvong-Lozano V, Usman H, Sfeir C, Niepa THR. Droplet-based microsystems as novel assessment tools for oral microbial dynamics. Biotechnol Adv 2022; 55:107903. [PMID: 34990774 DOI: 10.1016/j.biotechadv.2021.107903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
The human microbiome comprises thousands of microbial species that live in and on the body and play critical roles in human health and disease. Recent findings on the interplay among members of the oral microbiome, defined by a personalized set of microorganisms, have elucidated the role of bacteria and yeasts in oral health and diseases including dental caries, halitosis, and periodontal infections. However, the majority of these studies rely on traditional culturing methods which are limited in their ability of replicating the oral microenvironment, and therefore fail to evaluate key microbial interactions in microbiome dynamics. Novel culturing methods have emerged to address this shortcoming. Here, we reviewed the potential of droplet-based microfluidics as an alternative approach for culturing microorganisms and assessing the oral microbiome dynamics. We discussed the state of the art and recent progress in the field of oral microbiology. Although at its infancy, droplet-based microtechnology presents an interesting potential for elucidating oral microbial dynamics and pathophysiology. We highlight how new findings provided by current microfluidic-based methodologies could advance the investigation of the oral microbiome. We anticipate that our work involving the droplet-based microfluidic technique with a semipermeable membrane will lay the foundations for future microbial dynamics studies and further expand the knowledge of the oral microbiome and its implication in oral health.
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Affiliation(s)
| | | | - Huda Usman
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA
| | - Charles Sfeir
- Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Periodontics and Preventive Dentistry, University of Pittsburgh, PA, USA; Department of Oral Biology, University of Pittsburgh, PA, USA; The Center for Craniofacial Regeneration, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA
| | - Tagbo H R Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, PA, USA; Department of Mechanical Engineering and Materials Science, University of Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA.
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20
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Affiliation(s)
- Svetoslav G Dimov
- Department of Genetics Faculty of Biology Sofia University “St. Kliment Ohridski” 8, Dragan Tzankov blvd. Sofia 1164 Bulgaria
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21
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Wu Y, Li Y, Gesudu Q, Zhang J, Sun Z, Halatu H, Menghe B, Liu W. Bacterial composition and function during fermentation of Mongolia koumiss. Food Sci Nutr 2021; 9:4146-4155. [PMID: 34401066 PMCID: PMC8358363 DOI: 10.1002/fsn3.2377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 05/16/2021] [Indexed: 11/22/2022] Open
Abstract
Koumiss is a fermented mare's milk beverage that has attracted increasing attention due to its nutritional richness and important economic value. Bacteria in koumiss play a major role in pH decreasing and reducing spoilage through bacterial inhibition. The dynamic changes in nutritional content were determined firstly during fermentation, and then the metagenomics sequencing technology was applied to profile koumiss core microbiota at the species level. We also clarified the function and effect of the bacteria on the nutritional content of the final product. We also investigated active microbial function by comparing the metagenomics of representative samples collected at different time points during the fermentation process. This study dynamically revealed the bacterial composition and function of traditional koumiss during its making process. Twenty-three major functional categories related to amino acid and fat synthesis, metabolism, and so on were identified. Functional category L (represented replication-, recombination-, and repair-related functions) was one of the most important categories with the highest relative abundance in all of the 23 major functional categories. CoG category having a significant correlation with Lactococcus piscium was the most abundant. The change in metabolic activity of bacteria at different fermentation time points showed that the metabolic activity was more active in the first 24 hr and then began to stabilize. LAB play the major role in the koumiss pH decreasing and quality improvement. The functional genes of related metabolic activity of lactic acid bacteria were more active in the first 24 hr of koumiss fermentation and then began to stabilize.
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Affiliation(s)
- Yue Wu
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Yu Li
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Qimu Gesudu
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Juntao Zhang
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Haobisi Halatu
- Inner Mongolia International Mongolian HospitalHohhotChina
| | - Bilege Menghe
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and EngineeringMinistry of Education of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Key Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural Affairs of ChinaInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotChina
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22
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Zampieri A, Babbucci M, Carraro L, Milan M, Fasolato L, Cardazzo B. Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum. Foods 2021; 10:1271. [PMID: 34204939 PMCID: PMC8228196 DOI: 10.3390/foods10061271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023] Open
Abstract
Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.
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Affiliation(s)
| | | | | | | | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, Italy; (A.Z.); (M.B.); (L.C.); (M.M.); (B.C.)
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23
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Azuddin NF, Mohd MH, Rosely NFN, Mansor A, Zakaria L. Molecular Phylogeny of Endophytic Fungi from Rattan ( Calamus castaneus Griff.) Spines and Their Antagonistic Activities against Plant Pathogenic Fungi. J Fungi (Basel) 2021; 7:301. [PMID: 33920922 PMCID: PMC8071255 DOI: 10.3390/jof7040301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/30/2022] Open
Abstract
Calamus castaneus is a common rattan palm species in the tropical forests of Peninsular Malaysia and is noticeable by the yellow-based spines that cover the stems. This study aimed to determine the prevalence of fungal endophytes within C. castaneus spines and whether they inhibit the growth of fungal pathogens. Twenty-one genera with 40 species of fungal endophytes were isolated and identified from rattan palm spines. Based on molecular identification, the most common isolates recovered from the spines were Colletotrichum (n = 19) and Diaporthe spp. (n = 18), followed by Phyllosticta spp., Xylaria sp., Trichoderma spp., Helminthosporium spp., Penicillium spp., Fusarium spp., Neopestalotiopsis spp., Arthrinium sp., Cyphellophora sp., Cladosporium spp., Curvularia sp., Bionectria sp., and Acremonium spp. Non-sporulating fungi were also identified, namely Nemania primolutea, Pidoplitchkoviella terricola, Muyocopron laterale, Acrocalymma fici, Acrocalymma medicaginis, and Endomelanconiopsis endophytica. The isolation of these endophytes showed that the spines harbor endophytic fungi. Most of the fungal endophytes inhibited the growth of several plant pathogenic fungi, with 68% of the interactions resulting in mutual inhibition, producing a clear inhibition zone of <2 mm. Our findings demonstrate the potential of the fungal endophytes from C. castaneus spines as biocontrol agents.
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Affiliation(s)
| | | | | | | | - Latiffah Zakaria
- School of Biological Sciences, Universiti Sains Malaysia, Penang USM 11800, Malaysia; (N.F.A.); (M.H.M.); (N.F.N.R.); (A.M.)
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24
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Dapkevicius MLE, Sgardioli B, Câmara SPA, Poeta P, Malcata FX. Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles. Foods 2021; 10:821. [PMID: 33920106 DOI: 10.3390/foods10040821] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.
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25
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Zhadyra S, Han X, Anapiyayev BB, Tao F, Xu P. Bacterial diversity analysis in Kazakh fermented milks Shubat and Ayran by combining culture-dependent and culture-independent methods. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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ZHOU X, GUAN Q, QIN Y, QIN Z, DU B, LIN D. Dynamic changes in physic-chemical properties and bacterial community during natural fermentation of tomatoes. Food Sci Technol 2021. [DOI: 10.1590/fst.63520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xiaoli ZHOU
- Guiyang University, China; Guiyang University, China
| | | | | | | | - Bin DU
- Guiyang University, China; Guiyang University, China
| | - Dong LIN
- Guiyang University, China; Guiyang University, China
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27
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Kim E, Cho EJ, Yang SM, Kim MJ, Kim HY. Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing. Food Microbiol 2020; 94:103641. [PMID: 33279067 DOI: 10.1016/j.fm.2020.103641] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 12/22/2022]
Abstract
Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Eun-Ji Cho
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Balzan S, Carraro L, Merlanti R, Lucatello L, Capolongo F, Fontana F, Novelli E, Larini I, Vitulo N, Cardazzo B. Microbial metabarcoding highlights different bacterial and fungal populations in honey samples from local beekeepers and market in north-eastern Italy. Int J Food Microbiol 2020; 334:108806. [PMID: 32805512 DOI: 10.1016/j.ijfoodmicro.2020.108806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023]
Abstract
Due to its chemical properties, honey does not foster the growth of microorganisms, however it may contain a rich microbial community, including viable, stressed, and not viable microbes. In order to characterize honey microbiota focusing on the difference between products from beekeepers and large retail in the present study a culture-independent approach based on DNA metabarcoding was applied. Honey samples were collected from Local Beekeepers (LB) and Market sales (M) during four years with the aim to investigate the microbiological quality in the honey market. Extraction and amplification of DNA from honey samples showed reduced efficiency with increasing age of honey, with the loss of 50-80% of samples four years old (2014). For this reason, only samples of similar age were compared and the analysis of microbial communities focused on year 2017, for a total of 75 samples. Differences in alpha and beta-diversity were evidenced comparing microbial communities between LB and M samples. In particular, contaminant bacteria dominated the microbiota in M samples while LB samples were enriched in Lactic Acid Bacteria (LAB) that cannot be isolated with culture-dependent approaches.
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Affiliation(s)
- Stefania Balzan
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Lisa Carraro
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Roberta Merlanti
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Lorena Lucatello
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Francesca Capolongo
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy.
| | - Federico Fontana
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Enrico Novelli
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Ilaria Larini
- Dept. of Biotechnology, University of Verona, Cà Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Nicola Vitulo
- Dept. of Biotechnology, University of Verona, Cà Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Barbara Cardazzo
- Dept. of Comparative Biomedicine and Food Science, University of Padua, Viale Università 16, 35020 Legnaro, PD, Italy
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Tagliazucchi D, Baldaccini A, Martini S, Bianchi A, Pizzamiglio V, Solieri L. Cultivable non-starter lactobacilli from ripened Parmigiano Reggiano cheeses with different salt content and their potential to release anti-hypertensive peptides. Int J Food Microbiol 2020; 330:108688. [PMID: 32497940 DOI: 10.1016/j.ijfoodmicro.2020.108688] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/15/2020] [Accepted: 05/24/2020] [Indexed: 01/19/2023]
Abstract
The impact of salt and fat intake on human health drives the consumer's attention towards dairy food with reduced salt and fat contents. How changes in salt and fat content modulate dairy LAB population and the associated proteolytic activities have been poorly studied. Here, non-starter LAB populations from 12 Parmigiano Reggiano (PR) cheeses (12-month ripened), clustered in low salt and fat content (LL-PR) and high salt and fat content (HH-PR) groups, were investigated and identified at specie-level with molecular assays. Lactobacillus rhamnosus was dominant in HH-PR samples, whereas Lactobacillus paracasei in LL-PR samples. (GTG)5 rep-PCR analysis discriminated 11 and 12 biotypes for L. rhamnosus and L. paracasei isolates, respectively. Screening for proteolytic activity identified L. rhamnosus strains more proteolytic than L. paracasei, and, within L. rhamnosus species, HH-PR strains were generally more proteolytic than LL-PR strains. Two L. rhamnosus representatives, namely strain 0503 from LL-PR and strain 2006 from HH-PR, were functionally characterized in cow milk fermentation assay. HH-PR strain 2006 overcame LL-PR strain 0503 in acidification performance, leading to a fermented milk with higher angiotensin I-converting enzyme inhibitory and antioxidant activities. L. rhamnosus 2006 was more prone to release VPP, while L. rhamnosus 0503 released higher amount of IPP. This study provides evidences that salt/fat content affects NSLAB cultivable fraction and the associated proteolytic ability resulting in a complex occurrence of bioactive peptides featuring health-promoting properties.
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Affiliation(s)
- Davide Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Andrea Baldaccini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Serena Martini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Aldo Bianchi
- Consorzio del Formaggio Parmigiano Reggiano, via J.F. Kennedy 18, 42124 Reggio Emilia, Italy
| | - Valentina Pizzamiglio
- Consorzio del Formaggio Parmigiano Reggiano, via J.F. Kennedy 18, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy.
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31
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Lu Y, Tan X, Lv Y, Yang G, Chi Y, He Q. Physicochemical properties and microbial community dynamics during Chinese horse bean-chili-paste fermentation, revealed by culture-dependent and culture-independent approaches. Food Microbiol 2020; 85:103309. [PMID: 31500715 DOI: 10.1016/j.fm.2019.103309] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
The production of Chinese horse bean-chili-paste (CHCP) involves three fermentation phases: chili-to-moromi fermentation (CF) phase, horse bean-to-meju fermentation (HF) phase and moromi-meju mixed fermentation (MF) phase. To understand the microbial dynamics among these three phases and the potential roles of viable microbes for fermentation, microbial community dynamics was investigated by using culture-dependent and culture-independent methods. Furthermore, the capacities of enzyme-producing of the isolates were determined. During the CF phase, reducing sugar content increased from 3.1% to 3.49%, while pH declined from 4.85 to 4.5. The protein content in the HF phase and MF phase reduced sharply from 22.23% to 10.29% and 4.39%-1.19%, respectively. Bacillus sp., Staphylococcus sp., Oceanobacillus sp., Candida sp., Zygosaccharomyces sp. and Aspergillus sp. dominated the CF phase, while Bacillus sp., Candida sp. and Zygosaccharomyces sp. were the dominant microorganisms in both the HF and MF phases. B. amyloliquefaciens, B. methylotrophicus, B. subtilis, B. licheniformis and A. oryzae possessed strong capacities of producing enzymes, i.e. α-amylase, cellulase and xylanase, acid protease and leucine aminopeptidase, and could make a great contribution to CHCP fermentation.
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Affiliation(s)
- Yunhao Lu
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Xinyi Tan
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Yuanping Lv
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China
| | - Guohua Yang
- Sichuan Dandan Pixian-douban Co., Ltd., Chengdu, 610065, PR China
| | - Yuanlong Chi
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
| | - Qiang He
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, PR China.
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Nissen L, di Carlo E, Gianotti A. Prebiotic potential of hemp blended drinks fermented by probiotics. Food Res Int 2020; 131:109029. [PMID: 32247454 DOI: 10.1016/j.foodres.2020.109029] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
Plant-based drinks as substitute for milk consumption are raising striking interest in the food industry. Soy and rice drinks are the most studied and successful milk substitutes. An untapped source is hemp seed, which is a powerhouse of nutrients bearing bioactive compounds, but the production of derived drink is limited. The present work is about introducing new formulations of commercial hemp seed-derived drink to be fermented with probiotics (Lactobacillus fermentum, Lb. plantarum and Bifidobacterium bifidum). In this work for the first time the prebiotic activity of different hemp seed drinks was assessed by cultural and quantitative PCR methods. In addition, to better describe the prebiotic potential, VOCs alkenes and volatile organic acids were characterized by a metabolomic approach via GC-MS SPME. Obtained results showed that the hemp seed drinks had strong prebiotic activity, ability to support probiotics growth and to increase the content of some bioactive compounds. These outputs are in part due to the presence of different terpenes that inhibit the growth of enteropathogens and to high levels of acetate, propionate and butyrate produced during fermentation that support the growth of probiotics. Although the health potential of hemp seed is well known, derived drinks are hitherto scarcely transformed and distributed, thus this work could provide some basics to produce prebiotic and probiotic fermented hemp seed drinks.
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Affiliation(s)
- Lorenzo Nissen
- Alma Mater Studiorum - University of Bologna, DISTAL (Dept. of Agricultural and Food Sciences), V.le Fanin 44, 40127 Bologna, Italy.
| | - Emanuele di Carlo
- Alma Mater Studiorum - University of Bologna, DISTAL (Dept. of Agricultural and Food Sciences), V.le Fanin 44, 40127 Bologna, Italy.
| | - Andrea Gianotti
- Alma Mater Studiorum - University of Bologna, DISTAL (Dept. of Agricultural and Food Sciences), V.le Fanin 44, 40127 Bologna, Italy.
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33
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Kamilari E, Tomazou M, Antoniades A, Tsaltas D. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? Int J Food Sci 2019; 2019:5837301. [PMID: 31886165 PMCID: PMC6925717 DOI: 10.1155/2019/5837301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
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Affiliation(s)
- Elena Kamilari
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
| | | | | | - Dimitrios Tsaltas
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
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34
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Eugster E, Fuchsmann P, Schlichtherle-cerny H, Bütikofer U, Irmler S. Formation of alanine, α-aminobutyrate, acetate, and 2-butanol during cheese ripening by Pediococcus acidilactici FAM18098. Int Dairy J 2019; 96:21-8. [DOI: 10.1016/j.idairyj.2019.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Affiliation(s)
- Aly Farag El Sheikha
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
- McMaster University, Department of Biology, Hamilton, Ontario, Canada
- Minufiya University, Faculty of Agriculture, Department of Food Science and Technology, Shibin El Kom, Minufiya Government, Egypt
| | - Dian-Ming Hu
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
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37
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Pagliano G, Ventorino V, Panico A, Romano I, Robertiello A, Pirozzi F, Pepe O. The effect of bacterial and archaeal populations on anaerobic process fed with mozzarella cheese whey and buttermilk. J Environ Manage 2018; 217:110-122. [PMID: 29597107 DOI: 10.1016/j.jenvman.2018.03.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
Dairy wastes can be conveniently processed and valorized in a biorefinery value chain since they are abundant, zero-cost and all year round available. For a comprehensive knowledge of the microbial species involved in producing biofuels and valuable intermediates from dairy wastes, the changes in bacterial and archaeal population were evaluated when H2, CH4 and chemical intermediates were produced. Batch anaerobic tests were conducted with a mixture of mozzarella cheese whey and buttermilk as organic substrate, inoculated with 1% and 3% w/v industrial animal manure pellets. The archaeal methanogens concentration increased in the test inoculated at 3% (w/v) when H2 and CH4 production occurred, being 1 log higher than that achieved in the test inoculated at 1% (w/v). Many archaeal species, mostly involved in the production of CH4, were identified by sequencing denaturing gradient gel electrophoresis (DGGE) bands. Methanoculleus, Methanocorpusculum and Methanobrevibacter genera were dominant archaea involved in the anaerobic process for bioenergy production from mozzarella cheese whey and buttermilk mixture.
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Affiliation(s)
- Giorgia Pagliano
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | | | - Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - Alessandro Robertiello
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - Francesco Pirozzi
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy.
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Stachelska MA. Quantitative assessment of Lactococcus lactis subsp. cremoris present in artisanal raw cow’s milk cheese. ACTA VET BRNO 2018; 87:189-95. [DOI: 10.2754/avb201887020189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis subsp. cremoris belongs to lactic acid bacteria that play a crucial role in cheese production and it is known to be beneficial to human health. The aim of the study was to establish a rapid and accurate quantitative real-time polymerase chain reaction (qPCR) method to detect and enumerate L. lactis subsp. cremoris in artisanal raw cow’s milk cheese. Artisanal raw cow’s milk cheese samples were used to check for presence and number of L. lactis subsp. cremoris strains. The method applies a set of target-specific PCR (polymerase chain reaction) primers and a fluorogenic probe, and amplifies a part of the LACR_RS01280 gene that encodes the aminoacetone oxidase family flavin adenine dinucleotide (FAD) binding enzyme. All 5 L. lactis subsp. cremoris strains examined were found to be qPCR positive. There was no signal recorded for 8 strains which belong to closely related species. The limit of detection amounted to ten copies per reaction and the assay indicated a linear dynamic range of seven logs. This method may be applied in detection and enumeration of L. lactis subsp. cremoris in cheese during its ripening. Moreover, it may be applied to examine the distribution of L. lactis subsp. cremoris during the cheese production and ripening.
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Jayawardena RS, Purahong W, Zhang W, Wubet T, Li X, Liu M, Zhao W, Hyde KD, Liu J, Yan J. Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0398-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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40
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Dai W, Yu W, Xuan L, Tao Z, Xiong J. Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression. Appl Microbiol Biotechnol 2018. [PMID: 29516148 DOI: 10.1007/s00253-018-8891-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is now recognized that some gut diseases attribute to polymicrobial pathogens infections. Thus, traditional isolation of single pathogen from disease subjects could bias the identification of causal agents. To fill this gap, using Illumina sequencing of the bacterial 16S rRNA gene, we explored the dynamics of gut bacterial communities over a shrimp disease progression. The results showed significant differences in the gut bacterial communities between healthy and diseased shrimp. Potential pathogens were inferred by a local pathogens database, of which two OTUs (affiliated with Vibrio tubiashii and Vibrio harveyi) exhibited significantly higher abundances in diseased shrimp as compared to healthy subjects. The two OTUs cumulatively contributed 64.5% dissimilarity in the gut microbiotas between shrimp health status. Notably, the random Forest model depicted that profiles of the two OTUs contributed 78.5% predicted accuracy of shrimp health status. Removal of the two OTUs from co-occurrence networks led to network fragmentation, suggesting their gatekeeper features. For these evidences, the two OTUs were inferred as candidate pathogens. Three virulence genes (bca, tlpA, and fdeC) that were coded by the two candidate pathogens were inferred by a virulence factor database, which were enriched significantly (P < 0.05 in the three cases, as validated by qPCR) in diseased shrimp as compared to healthy ones. The two candidate pathogens were repressed by Flavobacteriaceae, Garvieae, and Photobacrerium species in healthy shrimp, while these interactions shifted into synergy in disease cohorts. Collectively, our findings offer a frame to identify potential polymicrobial pathogen infections from an ecological perspective.
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Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Weina Yu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Lixia Xuan
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhen Tao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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41
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Bokulich NA, Bamforth CW, Mills DA. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. Journal of the American Society of Brewing Chemists 2018. [DOI: 10.1094/asbcj-2012-0709-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology and Department of Food Science and Technology
| | | | - David A. Mills
- Department of Viticulture and Enology and Department of Food Science and Technology, University of California, Davis 95616
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42
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Marino M, Innocente N, Maifreni M, Mounier J, Cobo-Díaz JF, Coton E, Carraro L, Cardazzo B. Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing. Front Microbiol 2017; 8:2119. [PMID: 29163411 PMCID: PMC5675859 DOI: 10.3389/fmicb.2017.02119] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/18/2017] [Indexed: 11/13/2022] Open
Abstract
This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values. Acidity values showed a great variability too, probably in relation to the brine use prior to sampling. Despite their high salt content, brine microbial loads ranged from 2.11 to 6.51 log CFU/mL for the total mesophilic count. Microbial community profiling assessed by 16S rRNA gene sequencing showed that these ecosystems were dominated by Firmicutes and Proteobacteria, followed by Actinobacteria and Bacteroidetes. Cheese type and brine salinity seem to be the main parameters accountable for brine microbial diversity. On the contrary, brine pH, acidity and protein concentration, correlated to cheese brine age, did not have any selective effect on the microbiota composition. Nine major genera were present in all analyzed brines, indicating that they might compose the core microbiome of cheese brines. Staphylococcus aureus was occasionally detected in brines using selective culture media. Interestingly, bacterial genera associated with a functional and technological use were frequently detected. Indeed Bifidobacteriaceae, which might be valuable probiotic candidates, and specific microbial genera such as Tetragenococcus, Corynebacterium and non-pathogenic Staphylococcus, which can contribute to sensorial properties of ripened cheeses, were widespread within brines.
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Affiliation(s)
- Marilena Marino
- Dipartimento di Scienze Agroalimentari Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Nadia Innocente
- Dipartimento di Scienze Agroalimentari Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Michela Maifreni
- Dipartimento di Scienze Agroalimentari Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Institut Brestois Santé Agro Matière (IBSAM), École Supérieure d'Ingénieurs en Agroalimentaire de Bretagne Atlantique (ESIAB), Université de Brest, Plouzané, France
| | - José F Cobo-Díaz
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Institut Brestois Santé Agro Matière (IBSAM), École Supérieure d'Ingénieurs en Agroalimentaire de Bretagne Atlantique (ESIAB), Université de Brest, Plouzané, France
| | - Emmanuel Coton
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Institut Brestois Santé Agro Matière (IBSAM), École Supérieure d'Ingénieurs en Agroalimentaire de Bretagne Atlantique (ESIAB), Université de Brest, Plouzané, France
| | - Lisa Carraro
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Padova, Italy
| | - Barbara Cardazzo
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Padova, Italy
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Londoño-zapata AF, Durango-zuleta MM, Sepúlveda-valencia JU, Moreno Herrera CX. Characterization of lactic acid bacterial communities associated with a traditional Colombian cheese: Double cream cheese. Lebensm Wiss Technol 2017; 82:39-48. [DOI: 10.1016/j.lwt.2017.03.058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ramezani M, Hosseini S, Ferrocino I, Amoozegar M, Cocolin L. Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese. Food Microbiol 2017; 66:64-71. [DOI: 10.1016/j.fm.2017.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/28/2016] [Accepted: 03/20/2017] [Indexed: 11/21/2022]
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45
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Wang B, Liu W, Liu X, Franks AE, Teng Y, Luo Y. Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods. Sci Total Environ 2017; 590-591:297-303. [PMID: 28274604 DOI: 10.1016/j.scitotenv.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Microcosms for enrichment of DDT degrading microorganisms were monitored using culture-dependent and -independent methods. Culture dependent methods isolated several strains with DDT degradation potential, Pseudomonas species being the most frequent. One isolate, Streptomyces sp. strain D3, had a degradation rate of 77% with 20mgL-1 of DDT after 7days incubation, D3 also had degradation rates of 75% and 30% for PCB77 (3,3',4,4'-tetrachloro biphenyl) and PCNB (pentachloronitrobenzene) respectively. Culture-independent high-throughput sequencing identified a different subset of the microbial community within the enrichment microcosms to the culture dependent method. Pseudomonas, the most frequently isolated strain, only represented the 12th most abundant operational taxonomic unit in the sequencing dataset (relative abundance 0.9%). The most frequently observed bacterial genus in the culture-independent analysis did not correspond with those recovered by culture-dependent methods. These results suggested that deep sequencing followed by a targeted isolation approach might provide an advantageous route to bioremediation studies.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaoyan Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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Sánchez-Gamboa C, Hicks-Pérez L, Gutiérrez-Méndez N, Heredia N, García S, Nevárez-Moorillón GV. Seasonal influence on the microbial profile of Chihuahua cheese manufactured from raw milk. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cristina Sánchez-Gamboa
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Liliana Hicks-Pérez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Néstor Gutiérrez-Méndez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Norma Heredia
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Santos García
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Guadalupe V Nevárez-Moorillón
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
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Chen F, Zhu L, Qiu H. Isolation and Probiotic Potential of Lactobacillus Salivarius and Pediococcus Pentosaceus in Specific Pathogen Free Chickens. Rev Bras Cienc Avic 2017. [DOI: 10.1590/1806-9061-2016-0413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- F Chen
- Qingdao Agricultural University, China
| | - L Zhu
- Qingdao Agricultural University, China
| | - H Qiu
- Qingdao Agricultural University, China
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Andreani NA, Carraro L, Fasolato L, Balzan S, Lucchini R, Novelli E, Cardazzo B. Characterisation of the Thermostable Protease AprX in Strains of Pseudomonas Fluorescens and Impact on the Shelf-life of Dairy Products: Preliminary Results. Ital J Food Saf 2016; 5:6175. [PMID: 28217561 PMCID: PMC5225826 DOI: 10.4081/ijfs.2016.6175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 01/13/2023] Open
Abstract
Bacterial proteases are involved in food spoilage and shelf-life reduction. Among the bacterial proteases, a predominant role in spoilage of dairy products seems to be played by the thermostable metallo-protease AprX, which is produced by various strains of Pseudomonas fluorescens. Differences in AprX enzyme activity among different strains were highlighted, but the most proteolytic strains were not identified. In this study, the presence of the aprX gene was evaluated in 69 strains isolated from food matrices and 18 reference strains belonging to the P. fluorescens group, which had been previously typed by the multi locus sequence typing method. Subsequently, a subset of reference strains was inoculated in ultra-high temperature milk, and the expression of the aprX gene was evaluated at 22 and 6°C. On the same milk samples, the proteolytic activity was then evaluated through Azocasein and trinitrobenzenesulfonic acid solution assays. Finally, to assess the applicability of the former assay directly on dairy products the proteolityc activity was tested on industrial ricotta samples using the Azocasein assay. These results demonstrate the spread of aprX gene in most strains tested and the applicability of Azocasein assay to monitor the proteolytic activity in dairy products.
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Affiliation(s)
- Nadia Andrea Andreani
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
| | - Stefania Balzan
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
| | - Rosaria Lucchini
- Institute for Experimental Veterinary Medicine of Venezie , Legnaro (PD), Italy
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padua , Legnaro (PD), Italy
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Bakhtiary F, Sayevand HR, Remely M, Hippe B, Hosseini H, Haslberger AG. Evaluation of Bacterial Contamination Sources in Meat Production Line. J FOOD QUALITY 2016. [DOI: 10.1111/jfq.12243] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Farzaneh Bakhtiary
- Department of Nutritional Sciences; University of Vienna; Vienna Austria
| | | | - Marlene Remely
- Department of Nutritional Sciences; University of Vienna; Vienna Austria
| | - Berit Hippe
- Department of Nutritional Sciences; University of Vienna; Vienna Austria
| | - Hedayat Hosseini
- Food Science and Technology Department, Shahid Beheshti University of Medical Sciences; Tehran Iran
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Delorme C, Legravet N, Jamet E, Hoarau C, Alexandre B, El-Sharoud WM, Darwish MS, Renault P. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme. Int J Food Microbiol 2016; 242:70-81. [PMID: 27894009 DOI: 10.1016/j.ijfoodmicro.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/27/2023]
Abstract
We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.
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Affiliation(s)
- Christine Delorme
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nicolas Legravet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuel Jamet
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Caroline Hoarau
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Bolotin Alexandre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Walid M El-Sharoud
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Mohamed S Darwish
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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