Bacteria and yeast microbiota in milk kefir grains from different Italian regions

Garofalo, Cristiana; Osimani, Andrea; Milanović, Vesna; Aquilanti, Lucia; Filippis, Francesca De; Stellato, Giuseppina; Mauro, Simone Di; Turchetti, Benedetta; Buzzini, Pietro; Ercolini, Danilo; Clementi, Francesca

doi:10.1016/j.fm.2015.01.017

Cited by 216 publications

(189 citation statements)

References 63 publications

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“…The following PCR conditions were used: 94°C for 2 min, 35 cycles of 95°C for 20 s, 56°C for 45 s, and 72°C for 5 min, with a final extension at 72°C for 7 min. The fungal community was studied by sequencing of the D1-D2 domain of the 26S rRNA gene amplifying a fragment of 540 bp using the primers NL-1 (5=-GCATATCAATAAGCGGAGGAAAAG-3=) and NL-4 (5=-GGTCCGTGTTTCAAGACGG-3=) (21) as recently reported (54). The 454 adapters were included in the forward primer, followed by a 10-bp sample-specific MID.…”

Section: Methodsmentioning

confidence: 99%

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Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment

Stellato

Filippis

Storia

et al. 2015

Appl Environ Microbiol

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131

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Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA-and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality. Cheese manufacture and ripening are affected by the metabolic activity of different types of microorganisms. When milk of optimal hygienic quality is used, the dairy microbial consortia can be simple when starter cultures are employed, or a higher degree of complexity can occur in the case of natural fermentations. The environmental microbiota from the processing plant has been often addressed as a source of microbes that may play a role in the cheese making (1-4). When lactic acid bacteria (LAB) are included in the environmental microbiota, they may actively contribute to fermentation and ripening of cheese. Conversely, when potential spoilage organisms contaminate the environment, these organisms can play a crucial role because they can be transferred from the environment to intermediates of production and may negatively affect the cheese production process and the quality of the final products. It has been demonstrated that the microbial populations involved in fermentation and ripening are often found on the processing surfaces (1, 3, 5, 6), highlighting the importance of the plant environment in potentially contributing to the microbiota of cheese. Depending on the nature of the microorganisms, the environmental microbiota can exert functional activities important for the fermentative and/or the ripening process but sometimes may also be a hazard for cheese quality and safety (7).The study of the microbial e...

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Section: Methodsmentioning

confidence: 99%

“…PCR mixtures were prepared as described above. The following PCR conditions were used: 95°C for 5 min, followed by 35 cycles of 95°C for 1 min, 52°C for 45 s, and 72°C for 1 min, and then a final extension at 72°C for 7 min and holding at 4°C (54).…”

Section: Methodsmentioning

confidence: 99%

Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment

Stellato

Filippis

Storia

et al. 2015

Appl Environ Microbiol

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131

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“…Since the OTU abundance is proportional to the number of reads obtained, this may lead to an incorrect estimation of OTU abundance (Bokulich and Mills, 2013b; Ercolini, 2013; De Filippis and Ercolini, 2016). Therefore, the use of different targets would be also advisable, such as the 26S (Garofalo et al ., 2015; Stellato et al ., 2015; Wang et al ., 2015) or the 18S rRNA (Liu et al ., 2015b; Minervini et al ., 2015) genes.…”

Section: Monitoring Microbes In Food Fermentationsmentioning

confidence: 99%

Metagenomics insights into food fermentations

Filippis

Parente

2016

Microbial Biotechnology

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191

117

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SummaryThis review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

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“…In the last decade, the introduction of newly developed sequencing strategies, commonly referred to as next-generation DNA sequencing techniques, has substantially revolutionised the study of genomics and molecular biology, being also successfully applied in food microbiology (Mayo et al 2014). However, the recent few studies exploiting and comparing high-throughput sequencing and PCR-DGGE surprisingly demonstrated how the latter technique still represents a valid tool for the profiling of complex food microbial communities (Delgado et al 2013;Garofalo et al 2015).…”

Section: Introductionmentioning

confidence: 99%

PCR-DGGE for the profiling of cheese bacterial communities: strengths and weaknesses of a poorly explored combined approach

Aquilanti

Santarelli

Babini

et al. 2016

Dairy Sci. & Technol.

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Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) represents a still valid molecular tool for the profiling of complex microbial ecosystems, including cheeses. In the present study, a double PCR-DGGE approach has been applied to the investigation of the bacterial diversity of seven cheese models to objectively assess strengths and weaknesses of such an approach. To that end, the bacterial DNA was extracted directly from both the cheese replicates and the bulks of colonies harvested from the serial dilution agar plates of selective solid media used for the enumeration of presumptive lactobacilli, lactococci and thermophilic cocci, respectively. The results overall collected allowed the main bacterial taxa to be identified and roughly quantified. Rough quantification of the main cultivable species represents a strength of the PCR-DGGE approach applied, whereas its main weaknesses were represented by the low degree of selectivity of the conventional growth media used for cultivation of lactic acid bacteria and the underestimation of the effective microbial diversity occurring in the seven cheese models.

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Bacteria and yeast microbiota in milk kefir grains from different Italian regions

Cited by 216 publications

References 63 publications

Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment

Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment

Metagenomics insights into food fermentations

PCR-DGGE for the profiling of cheese bacterial communities: strengths and weaknesses of a poorly explored combined approach

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