Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk

Rasolofo, Eric Andriamahery; St‐Gelais, Daniel; LaPointe, Gisèle; Roy, Denis

doi:10.1016/j.ijfoodmicro.2010.01.008

Cited by 113 publications

(108 citation statements)

References 55 publications

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“…Corynebacterium variabile is frequently found on cheese (21,23,45); however, it was not found in this study or in the one from Vacheyrou et al (58). Sequences affiliated to Corynebacterium xerosis, as well as Facklamia tabacinasalis, Aerosphaera taetra, and Turicibacter sanguinis, are frequent among clones in the 16S rRNA library and were also detected in milk or cheese (15,23,46). All of these species were dominant among clones identified in farm FD, where the microbial community was not very diversified.…”

Section: Discussioncontrasting

confidence: 63%

Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

Verdier‐Metz¹,

Gagné

Bornes

et al. 2012

Appl Environ Microbiol

132

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The diversity of the microbial community on cow teat skin was evaluated using a culture-dependent method based on the use of different dairy-specific media, followed by the identification of isolates by 16S rRNA gene sequencing. This was combined with a direct molecular approach by cloning and 16S rRNA gene sequencing. This study highlighted the large diversity of the bacterial community that may be found on teat skin, where 79.8% of clones corresponded to various unidentified species as well as 66 identified species, mainly belonging to those commonly found in raw milk (Enterococcus, Pediococcus, Enterobacter, Pantoea, Aerococcus, and Staphylococcus). Several of them, such as nonstarter lactic acid bacteria (NSLAB), Staphylococcus, and Actinobacteria, may contribute to the development of the sensory characteristics of cheese during ripening. Therefore, teat skin could be an interesting source or vector of biodiversity for milk. Variations of microbial counts and diversity between the farms studied have been observed. Moreover, Staphylococcus auricularis, Staphylococcus devriesei, Staphylococcus arlettae, Streptococcus bovis, Streptococcus equinus, Clavibacter michiganensis, Coprococcus catus, or Arthrobacter gandavensis commensal bacteria of teat skin and teat canal, as well as human skin, are not common in milk, suggesting that there is a breakdown of microbial flow from animal to milk. It would then be interesting to thoroughly study this microbial flow from teat to milk.

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Section: Discussioncontrasting

confidence: 63%

Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

Verdier‐Metz¹,

Gagné

Bornes

et al. 2012

Appl Environ Microbiol

132

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“…Interestingly, Alloiococcus has not been described in raw milk previously, having instead being associated with human ear infections (23). Trichococcus has been found in raw milk and dairy waste (24), and Psychrobacter has previously been found in teat apexes (25) and in cheese (26). Again, in the corresponding OP milk samples, soil bacteria such as Flavobacterium, Sphingomonas, and Tumebacillus spp., were detected in higher proportions.…”

Section: Discussionmentioning

confidence: 99%

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Doyle

Gleeson

O’Toole

et al. 2017

Appl Environ Microbiol

132

121

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In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCEThe composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.KEYWORDS farm practices, food chain, food safety, metagenomics, microbial source tracking, raw milk microbiota T he impact of the dairy farm environment on the microbial composition of raw milk and raw milk products has been appreciated for some time (1). There are numerous niches that collectively constitute the dairy farm environment, and these harbor a vast array of microbes. The transfer of microbes from the farm environment to raw milk can be influenced be a number of factors, including farmer hygiene, husbandry practices,

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“…The bacterial community found on pasteurized milk processing membranes had the closest similarity to natural raw milk microflora of the province of Quebec and to pasteurized cheese ecosystems, in comparison to the other fluids filtered (Rasolofo et al 2010;Wolfe et al 2014). Bacilli (Lactococcus sp.…”

Section: The Effect Of Operating Conditionsmentioning

confidence: 95%

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

Chamberland

Lessard

Doyen

et al. 2016

Dairy Sci. & Technol.

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Few data are available concerning the composition of biofilms found at the surface of filtration membranes, which, to some extent, explains the long-term failure of numerous strategies developed to control biofouling. This preliminary study intended to design a metagenomic tool targeting the 16S rRNA gene in order to unravel a general portrait of bacterial communities found on spiral-wound membranes used in the dairy industry. A total of seven spiral-wound membrane elements (ultrafiltration, nanofiltration, or reverse osmosis) at the end of their useful lifetimes were collected from different dairy plants. Targeted analysis of the 16S rRNA genes of the metagenome extracted from the membranes revealed their bacterial diversity via high-throughput sequencing technology (Miseq, Illumina). It was found that the nature of the filtered fluid (milk, whey, water) explained 58.6 % of the variance observed between communities found on membranes. Treatments applied on dairy fluids (milk pasteurization, whey bleaching or whey ultrafiltration) induced a selective pressure that affected the diversity of bacterial communities found on membranes and the proportions of spore-former bacteria among them. This work provides the first complete bacterial portrait of the biofilm composition of spiral-wound membranes used in the dairy industry. It suggests that the nature of the filtered fluid and potentially filtration Dairy Sci. & Technol. (2017)

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Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk

Cited by 113 publications

References 55 publications

Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

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