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Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.

Ceuppens S, Delbeke S, De Coninck D, Boussemaere J, Boon N, Uyttendaele M - Int J Environ Res Public Health (2015)

Bottom Line: Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses.Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas.Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Bioscience Engineering, Department of Food Safety and Food Quality, Laboratory of Food Microbiology and Food Preservation (LFMFP), Ghent University, Ghent 9000, Belgium. siele.ceuppens@ugent.be.

ABSTRACT
Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

No MeSH data available.


Related in: MedlinePlus

Principal component analysis of the NGS data of (A) basil batches I, II and III with different sample preparation methods and (B) storage of basil batches IV and V at different temperatures.
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ijerph-12-10171-f003: Principal component analysis of the NGS data of (A) basil batches I, II and III with different sample preparation methods and (B) storage of basil batches IV and V at different temperatures.

Mentions: Filtration over paper filters to remove plant material and filtration of washing and maceration solutions over a 0.2 µm filter to up-concentrate bacterial densities prior to DNA extraction showed no influence on the DGGE pattern (results not shown), so both filtrations were routinely applied. Unfortunately but not unexpectedly, the main constituents of the basil samples were eukaryotic plant DNA fragments, ranging from 55 % to 99 % (Table 1). As expected, the type of sample preparation (maceration vs. washing) influenced the fraction of eukaryotic DNA, with the more gentle procedure of washing the leaves resulting in a relative increase of microbial DNA of 5.2-fold (basil batch I) and 3.7-fold (basil batch III).In accordance with DGGE clustering, principal component analysis (PCA) of the NGS data showed that the bacterial communities of basil batches I, II and III were very similar following the maceration sample preparation method with a stomacher (Figure 3A). After washing, the samples showed increased variability with basil III being an outlier. Samples derived by washing and by various culture steps from the same basil batch had the tendency to cluster together but were also intermixed with those of other batches, so no clear separation could be made with PCA.


Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.

Ceuppens S, Delbeke S, De Coninck D, Boussemaere J, Boon N, Uyttendaele M - Int J Environ Res Public Health (2015)

Principal component analysis of the NGS data of (A) basil batches I, II and III with different sample preparation methods and (B) storage of basil batches IV and V at different temperatures.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555336&req=5

ijerph-12-10171-f003: Principal component analysis of the NGS data of (A) basil batches I, II and III with different sample preparation methods and (B) storage of basil batches IV and V at different temperatures.
Mentions: Filtration over paper filters to remove plant material and filtration of washing and maceration solutions over a 0.2 µm filter to up-concentrate bacterial densities prior to DNA extraction showed no influence on the DGGE pattern (results not shown), so both filtrations were routinely applied. Unfortunately but not unexpectedly, the main constituents of the basil samples were eukaryotic plant DNA fragments, ranging from 55 % to 99 % (Table 1). As expected, the type of sample preparation (maceration vs. washing) influenced the fraction of eukaryotic DNA, with the more gentle procedure of washing the leaves resulting in a relative increase of microbial DNA of 5.2-fold (basil batch I) and 3.7-fold (basil batch III).In accordance with DGGE clustering, principal component analysis (PCA) of the NGS data showed that the bacterial communities of basil batches I, II and III were very similar following the maceration sample preparation method with a stomacher (Figure 3A). After washing, the samples showed increased variability with basil III being an outlier. Samples derived by washing and by various culture steps from the same basil batch had the tendency to cluster together but were also intermixed with those of other batches, so no clear separation could be made with PCA.

Bottom Line: Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses.Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas.Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Bioscience Engineering, Department of Food Safety and Food Quality, Laboratory of Food Microbiology and Food Preservation (LFMFP), Ghent University, Ghent 9000, Belgium. siele.ceuppens@ugent.be.

ABSTRACT
Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

No MeSH data available.


Related in: MedlinePlus