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

Abstract

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...

Growth Inhibition of an Opportunistic Yeast Pathogen <i>Trichosporon asahii</i> by <i>Staphylococcus epidermidis</i>

“…[19][20][21][22][23] We purified and analyzed the molecule produced by S. epidermidis that inhibited an opportunistic fungal pathogen, T. asahii, and identified it as lactic acid. We attempted quantitative analysis of lactic acid in the culture supernatant of S. epidermidis by HPLC.…”

Metagenomics insights into food fermentations

“…In other studies, the microbiota was related to raw material origin (Bokulich et al ., 2014a; Rizzello et al ., 2015) or quality (Dolci et al ., 2014; O'Sullivan et al ., 2015; Alessandria et al ., 2016), as well as to development of flavour‐impact compounds (De Pasquale et al ., 2014a, 2016; De Filippis et al ., 2016a). Moreover, food‐related environments were found to harbour a resident microbiota, beneficially involved in dairy (Bokulich and Mills, 2013a; Stellato et al ., 2015; Calasso et al ., 2016), alcoholic (Bokulich et al ., 2012a, 2014b) and sourdough (Minervini et al ., 2015) fermentations, although the presence of potential spoilers was also emphasized in some cases (Bokulich et al ., 2015a; Stellato et al ., 2015). …”

“…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.…”

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d'Arnad

“…Psychrobacter and Vibrio were clearly associated with several matrices, including pasteurized milk (19) and meat (20). Psychrobacter can be involved in food spoilage and is recognized as an undesired genus in food-processing environments (21). It was recently found to be part of the main spoilage in fermented meat.…”