Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

Kamilari, Eleni; Anagnostopoulos, Dimitrios A.; Papademas, Photis; Efthymiou, Marina; Tretiak, Svitlana; Tsaltas, Dimitrios

doi:10.3390/fermentation6040100

Cited by 13 publications

(7 citation statements)

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“…The identified species were A. baumannii, A. johnsonii, A. soli and A. ursingii. Acinetobacter is a psychrotrophic contaminant that has been found to contaminate raw goat milk [61], and its psychrotrophic isolates from raw milk can be highly lipolytic [50]. Moraxella osloensis, which is a zoonotic pathogen that has been detected in goat milk [30], was also detected in five of the samples in very low concentrations.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the species Enhydrobacter aerosaccus, which belongs to the phylum Proteobacteria but not to a specific family (characterized as Incertae sedis) was identified in all the samples (0.01-2.48%). Enhydrobacter aerosaccus is an aquatic Gram-negative facultative anaerobic and gas-vacuolated rod [67] that has been commonly found in sheep and goat milk [61].…”

Section: Discussionmentioning

confidence: 99%

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Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

et al. 2021

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Background: The identification of bacterial species in fermented PDO (protected designation of origin) cheese is important since they contribute significantly to the final organoleptic properties, the ripening process, the shelf life, the safety and the overall quality of cheese. Methods: Ten commercial PDO feta cheeses from two geographic regions of Greece, Epirus and Thessaly, were analyzed by 16S metagenomic analysis. Results: The biodiversity of all the tested feta cheese samples consisted of five phyla, 17 families, 38 genera and 59 bacterial species. The dominant phylum identified was Firmicutes (49% of the species), followed by Proteobacteria (39% of the species), Bacteroidetes (7% of the species), Actinobacteria (4% of the species) and Tenericutes (1% of the species). Streptococcaceae and Lactobacillaceae were the most abundant families, in which starter cultures of lactic acid bacteria (LAB) belonged, but also 21 nonstarter lactic acid bacteria (NSLAB) were identified. Both geographical areas showed a distinctive microbiota fingerprint, which was ultimately overlapped by the application of starter cultures. In the rare biosphere of the feta cheese, Zobellella taiwanensis and Vibrio diazotrophicus, two Gram-negative bacteria which were not previously reported in dairy samples, were identified. Conclusions: The application of high-throughput DNA sequencing may provide a detailed microbial profile of commercial feta cheese produced with pasteurized milk.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

et al. 2021

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“…Raw fastq sequences were quality filtered, and Qiime 2 version 2020.2 was used to calculate the diversity indexes Shannon, Simpson, and Chao1, regarding alpha diversity; unweighted [ 24 ] and weighted [ 25 ] uniFrac distances, regarding beta diversity; and observed OTU diversity metrics [ 26 ], as previously described [ 27 ]. Samples were rarefied at 15,637 for bacteria and 19,145 for fungi.…”

Section: Methodsmentioning

confidence: 99%

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Kamilari

Tsaltas

Stanton

et al. 2022

Foods

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The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses—namely Greek and Cypriot—using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.

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“…Raw fastq sequences were quality filtered, and the diversity indexes Shannon, Simpson, and Chao1 regarding alpha diversity and Bray Curtis dissimilarity regarding beta diversity, were performed using Qiime 2 version 2020.2 ( Bolyen et al, 2019 ), as previously described ( Kamilari et al, 2020a ). Before diversity analyses, samples were rarefied ( Supplementary Table 9 ).…”

Section: Methodsmentioning

confidence: 99%

Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs

Kamilari

Mina

Karallis³

et al. 2021

Front. Microbiol.

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Wine production in Cyprus has strong cultural ties with the island’s tradition, influencing local and foreign consumers’ preferences and contributing significantly to Cyprus’ economy. A key contributor to wine quality and sensorial characteristics development is the microbiota that colonizes grapes and performs alcoholic fermentation. Still, the microbial patterns of wines produced in different geographic regions (terroir) in Cyprus remain unknown. The present study investigated the microbial diversity of five terroirs in Cyprus, two from the PGI Lemesos region [Kyperounta (PDO Pitsilia) and Koilani (PDO Krasochoria)], and three from the PGI Pafos region [Kathikas (PDO Laona Akamas), Panayia, and Statos (PDO Panayia)], of two grape varieties, Xynisteri and Maratheftiko, using high-throughput amplicon sequencing. Through a longitudinal analysis, we examined the evolution of the bacterial and fungal diversity during spontaneous alcoholic fermentation. Both varieties were characterized by a progressive reduction in their fungal alpha diversity (Shannon index) throughout the process of fermentation. Additionally, the study revealed a distinct separation among different terroirs in total fungal community composition (beta-diversity) for the variety Xynisteri. Also, Kyperounta terroir had a distinct total fungal beta-diversity from the other terroirs for Maratheftiko. Similarly, a significant distinction was demonstrated in total bacterial diversity between the PGI Lemesos region and the PGI Pafos terroirs for grape juice of the variety Xynisteri. Pre-fermentation, the fungal diversity for Xynisteri and Maratheftiko was dominated by the genera Hanseniaspora, Aureobasidium, Erysiphe, Aspergillus, Stemphylium, Penicillium, Alternaria, Cladosporium, and Mycosphaerella. During and post-fermentation, the species Hanseniaspora nectarophila, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Aureobasidium pullulans, became the predominant in most must samples. Regarding the bacterial diversity, Lactobacillus and Streptococcus were the predominant genera for both grape varieties in all stages of fermentation. During fermentation, an increase was observed in the relative abundance of some bacteria, such as Acetobacter, Gluconobacter, and Oenococcus oeni. Finally, the study revealed microbial biomarkers with statistically significant higher relative representation, associated with each geographic region and each grape variety, during the different stages of fermentation. The present study’s findings provide an additional linkage between the grape microbial community and the wine terroir.

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Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

Cited by 13 publications

References 50 publications

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs

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