Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Parente, Eugenio; Zotta, Teresa; Giavalisco, Marilisa; Ricciardi, Annamaria

doi:10.1016/j.ijfoodmicro.2023.110124

Cited by 3 publications

(6 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Researchers with the ability to use the R programming language and environment can make the most of FoodMicrobionet and use it extensively for metastudies to test specific hypotheses or even to obtain quantitative comparisons of their own data with those available in FoodMicrobionet. While we have demonstrated this in previous proof of concept papers [ 32 , 34 , 36 , 37 , 49 ], we will add two common use cases below.…”

Section: Resultsmentioning

confidence: 92%

“…We have recently used FoodMicrobionet to explore the distribution of Lactobacillaceae in foods [ 34 ]. The same approach can be easily used to explore the distribution of other microbial groups which play important roles in the safety and spoilage of foods.…”

Section: Resultsmentioning

confidence: 99%

“…The database can be easily accessed using an interactive R Shiny app which is publicly available (Parente, Eugenio (2024), “ShinyFMBN, a Shiny app to access FoodMicrobionet”, Mendeley Data, V9, doi: 10.17632/8fwwjpm79y.9), but both the bacterial and fungal versions of the database are compatible, with minor changes, with scripts developed and used in previous proof of concept papers [ 34 , 36 , 43 ].…”

Section: Methodsmentioning

confidence: 99%

“…Even if the level of sophistication of the database and related software is inferior to other tools, which perform automated searches and analysis on existing repositories or on user-provided projects (like QIITA, MGnify, IMNGS and Microbe Atlas), we feel that the level of annotation of the FoodMicrobionet allows scientists to rapidly access complete information on studies, samples and taxa, integrate them with external resources and rapidly retrieve data for further analysis in a variety of projects. We have demonstrated use cases in a number of recent papers [ 32 , 34 , 35 , 36 , 37 ]. Here, we report on the release of version 5 of FoodMicrobionet, which, for the first time, includes data on fungal microbial communities of food and food environments.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5

Parente,

Ricciardi

2024

Foods

Self Cite

View full text Add to dashboard Cite

Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.

show abstract

Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5

Parente,

Ricciardi

2024

Foods

Self Cite

View full text Add to dashboard Cite

show abstract

“…Species of this genus are commonly detected in various habitats by culture-dependent [4] and -independent [5, 6] methods. A key habitat of members of the genus Lactiplantibacillus seems to be fermented products [7] such as fermented vegetables [8, 9], cereals [10], meat [4] and dairy [4] products where they can dominate these ecosystems, although it is unclear to what extent these are their natural habitats. Additionally, members of this genus are commonly found in a wide range of plant, environmental, vertebrate and invertebrate habitats [11].…”

Section: Introductionmentioning

confidence: 99%

Lactiplantibacillus carotarum AMBF275T sp. nov. isolated from carrot juice fermentation

Eilers,

Dillen,

Van de Vliet

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A novel strain of the genus Lactiplantibacillus , named AMBF275T, was isolated from fermented carrot juice, a salted fermented beverage dominated by lactic acid bacteria. The results of phylogenetic analysis indicated that the 16S rRNA gene of AMBF275T is most similar to the 16S rRNA gene of Lactiplantibacillus garii FI11369T with a sequence similarity of 99.4 %. However, a genome-wide comparison using average nucleotide identity (ANI) revealed that AMBF275T and L. garii FI11369T have an ANI of only 82.35 %. ANI values between AMBF275T and other representative strains of species of the genus Lactiplantibacillus from the Genome Taxonomy Database (GTDB) were even lower than this 82.35 %, indicating that AMBF275T represents a distinct species. We thus propose the name Lactiplantibacillus carotarum sp. nov. for this novel species, with AMBF275T (=LMG 32885T, =CECT 30757T) as the type strain.

show abstract