FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities

Parente, Eugenio; Zotta, Teresa; Ricciardi, Annamaria

doi:10.1101/2022.01.19.476946

Cited by 2 publications

(4 citation statements)

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“…In the present review, the updated version of FMBN 4.1.2 ( Parente et al, 2022 ), integrated with the taxonomy reclassification for the genus Lactobacillus ( Zheng et al, 2020 ) and further recent studies on the raw milk microbiota, has been used. Among the studies available in the database on cow raw milk, those analyzing cow whole raw milk used for cheese production were selected ( De Pasquale et al, 2014 ; Dolci et al, 2014 ; Calasso et al, 2016 ; De Filippis et al, 2016 ; Giello et al, 2017 ; Falardeau et al, 2019 ; Cremonesi et al, 2020 ; Kamimura et al, 2020 ; Nikoloudaki et al, 2021 ; Supplementary Tables 1 , 2 ).…”

Section: Culture-independent Quantificationmentioning

confidence: 99%

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

et al. 2023

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Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: “which and how many LAB are present in cow raw milk used for cheese production?,” this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the “history” of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.

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Section: Culture-independent Quantificationmentioning

confidence: 99%

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

et al. 2023

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“…The marker gene which is most frequently used for bacterial communities is the 16S rRNA gene. Due to the limitations of next generation sequencing methods, hypervariable regions (usually V1-V3, V3-V4 and V4 (Parente et al, 2022; Pollock et al, 2018) are used with amplicon length (after primer removal and merging of paired end sequences for Illumina sequencing) of <450 bp. In order to test the shortcomings of this approach in the study of the ecology of Lactobacillaceae , we retrieved from public databases the 16S rRNA gene sequences of type strains of family Lactobacillaceae and used them to infer phylogenetic trees based on full sequences and hypervariable target regions as described in Materials and Methods.…”

Section: Resultsmentioning

confidence: 99%

“…Starting from version 4.1, FoodMicrobionet includes, as an external resource (https://doi.org/10.5281/zenodo.6954040), R lists containing the ASV for all studies processed using the dada2 pipeline (Parente et al, 2022). Although the ecological significance of ASV is not clear (i.e., there is no convincing proof that they represent different subpopulations within a taxonomic group) they have been used to evaluate microdiversity in some studies (Quijada et al, 2018; Skeie et al, 2019; Zwirzitz et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

“…Our research group has created and maintains the FoodMicrobionet database (Parente et al, 2016), which makes metataxonomic data on the abundance and prevalence of bacteria in foods and food related environments readily accessible. The database has been steadily growing both in size and in functions (Parente et al, 2019, 2022) and is publicly available on both GitHub (https://github.com/ep142/FoodMicrobionet/) and Mendeley data (https://data.mendeley.com/datasets/8fwwjpm79y/6).…”

Section: Introductionmentioning

confidence: 99%

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Metataxonomic insights in the distribution ofLactobacillaceaein foods and food environments

Parente

Zotta

Giavalisco

et al. 2022

Preprint

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Members of the family Lactobacillaceae, which now includes former members of the genera Lactobacillus and Pediococcus, but also member of the family Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9% of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The lifestyle of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

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FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities

Cited by 2 publications

References 49 publications

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Metataxonomic insights in the distribution ofLactobacillaceaein foods and food environments

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