High-throughput sequencing of microbial communities in Poro cheese, an artisanal Mexican cheese

Aldrete-Tapia, Jesús Alejandro; Escobar-Ramírez, Meyli Claudia; Tamplin, Mark L.; Hernández‐Iturriaga, Montserrat

doi:10.1016/j.fm.2014.05.022

Cited by 115 publications

(88 citation statements)

References 31 publications

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“…Firmicutes (86.7%), Proteobacteria (12.9%), Actinobacteria (0.3%) and Bacteroidetes (0.1%), which is in agreement with the findings of other works on artisanal cheese (Aldrete-Tapia et al, 2014;Alegría et al, 2012;Fuka et al, 2013;Quigley et al, 2012). A total of 337 OTUs were obtained and 54 bacterial genera were identified.…”

Section: Identification Of Core Bacterial Community Members and Abundsupporting

confidence: 88%

“…they represented 0.01-1% of the total sequences. Lactobacilli and leuconostocs are part of the LAB in artisanal cheeses (e. g. Aldrete-Tapia et al, 2014;Quigley et al, 2012), contributing to their flavor and texture (Peláez and Requena, 2005). Pantoea has been found as part of the enterobacteri-al microbiota of raw milk (Lafarge et al, 2004) and artisanal cheeses .…”

Section: Identification Of Core Bacterial Community Members and Abundmentioning

confidence: 99%

“…Halotolerant bacteria may be transferred to the cheeses by the salt (Ishikawa et al, 2007). Bacteroidetes that take part in the microbiota of some artisanal Pico cheese-makers (Elizabethkingia in A, Flavobacterium in C and Chryseobacterium in B and C) are also present in other cheeses and may have a negative impact on product quality (Aldrete-Tapia et al, 2014;Collins et al, 2003;Montel et al, 2014). Exiguobacterium was part of the dominant microbiota in cheese-maker A (1.042%).…”

Section: Comparison Between Cheese-makers and Ripening Timesmentioning

confidence: 99%

“…These methods have been recently used in other dairy products, demonstrating the feasibility of generating deeply sequenced metagenomes for microbial identification and to study the dynamics of microbial communities (review by Bokulich and Mills, 2012;Ercolini, 2013). Recent studies in microbial diversity in cheeses (De Filippis et al, 2014;Ercolini et al, 2012;Masoud et al, 2011) and more specifically artisanal cheeses (Aldrete-Tapia et al, 2014;Alegría et al, 2012;Fuka et al, 2013;Quigley et al, 2012) have validated the application of this methodology in community screening to unravel the microbial structure and to detect determinants of safety and quality in cheese (Lusk et al, 2012;Montel et al, 2014;O'Sullivan et al, 2013). Pyrosequencing was chose for its sensitivity, which provided great sequence coverage and allowed to obtain a complete picture of the diverse microbial communities involved at the different fermentation times.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Riquelme

Câmara

Dapkevicius

et al. 2015

International Journal of Food Microbiology

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This work presents the first study on the bacterial communities in Pico cheese, a traditional cheese of the Azores (Portugal), made from raw cow's milk. Pyrosequencing of tagged amplicons of the V3-V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.Pyrosequencing revealed a high bacterial diversity in Pico cheese. Four phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) and 54 genera were identified. The predominant genus was Lactococcus (77% of the sequences). Sequences belonging to major cheese-borne pathogens were not found. Staphylococcus accounted for 0.5% of the sequences. Significant differences in bacterial community composition were observed between cheese-maker B and the other two units that participated in the study. However, OTU analysis identified a set of taxa (Lactococcus, Streptococcus, Acinetobacter, Enterococcus, Lactobacillus, Staphylococcus, Rothia, Pantoea and unclassified genera belonging to the Enterobacteriaceae family) that would represent the core components of artisanal Pico cheese microbiota. A diverse bacterial community was present at early maturation, with an increase in the number of phylotypes up to 2 weeks, followed by a decrease at the end of ripening. The most remarkable trend in abundance patterns throughout ripening was an increase in the number of sequences belonging to the Lactobacillus genus, with a concomitant decrease in Acinetobacter, and Stenotrophomonas. Microbial rank abundance curves showed that Pico cheese's bacterial communities are characterized by a few dominant taxa and many low-abundance, highly diverse taxa that integrate the socalled "rare biosphere".2

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Section: Identification Of Core Bacterial Community Members and Abundsupporting

confidence: 88%

Section: Identification Of Core Bacterial Community Members and Abundmentioning

confidence: 99%

Section: Comparison Between Cheese-makers and Ripening Timesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Riquelme

Câmara

Dapkevicius

et al. 2015

International Journal of Food Microbiology

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“…NGS has been applied extensively to a variety of environments, including the sea (11) and soil (12) as well as the gut (13). More recently, NGS of bacterial 16S rRNA amplicons has been used to characterize the microbial communities of a variety of fermented foods and beverages (14)(15)(16)(17)(18)(19)(20) as well as of raw milk and raw milk cheeses (21)(22)(23)(24)(25)(26). Indeed, this approach has led to identification of a number of genera previously not associated with cheese ecosystems (Prevotella and Helcococcus) or with particular cheese types (Arthrobacter in goat's milk cheese).…”

mentioning

confidence: 99%

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

O’Sullivan

Cotter

O’Sullivan

et al. 2015

Appl Environ Microbiol

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We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

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Dairy Probiotic Products

Camelo‐Silva

Verruck

Luccio

et al. 2023

Microbes in the Food Industry

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High-throughput sequencing of microbial communities in Poro cheese, an artisanal Mexican cheese

Cited by 115 publications

References 31 publications

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

Dairy Probiotic Products

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