Probio-Ichnos: A Database of Microorganisms with In Vitro Probiotic Properties

Abstract

Probiotics are live microorganisms that, when consumed in adequate amounts, exert health benefits on the host by regulating intestinal and extraintestinal homeostasis. Common probiotic microorganisms include lactic acid bacteria (LAB), yeasts, and Bacillus species. Here, we present Probio-ichnos, the first manually curated, literature-based database that collects and comprehensively presents information on the microbial strains exhibiting in vitro probiotic characteristics (i.e., resistance to acid and bile, attachment to host epithelia, as well as antimicrobial, immunomodulatory, antiproliferative, and antioxidant activity), derived from human, animal or plant microbiota, fermented dairy or non-dairy food products, and environmental sources. Employing a rigorous methodology, we conducted a systematic search of the PubMed database utilizing the keyword 'probiotic' within the abstracts or titles, resulting in a total of 27,715 studies. Upon further manual filtering, 2207 studies presenting in vitro experiments and elucidating strain-specific probiotic attributes were collected and used for data extraction. The Probio-ichnos database consists of 12,993 entries on the in vitro probiotic characteristics of 11,202 distinct strains belonging to 470 species and 143 genera. Data are presented using a binary categorization approach for the presence of probiotic attributes according to the authors' conclusions. Additionally, information about the availability of the whole-genome sequence (WGS) of strains is included in the database. Overall, the Probio-ichnos database aims to streamline the navigation of the available literature to facilitate targeted validation and comparative investigation of the probiotic properties of the microbial strains.

Keywords: adhesion; antimicrobial activity; antioxidant capacity; antiproliferation; database; immunomodulation; in vitro properties; probiotics; strain specificity.

Figure 1

Overview of the Probio-ichnos database. The Probio-ichnos database is constructed using the available literature on in vitro probiotic properties of strains isolated from human, animal, or plant microbiota, as well as food products and the environment. This data is derived from a total of 2207 publications on 11,202 bacterial and fungal strains examined for basic probiotic attributes: resistance to acid and bile, attachment to host epithelia, as well as antimicrobial, immunomodulatory, antiproliferative, and antioxidant activities. Users can browse the database and search by species or the strain name for all the probiotic traits or for selected attributes. The traits for each strain are scored using a qualitative method based on the authors’ conclusions. The ‘Browse’ and ‘Expand’ functions support the identification of the available literature and genomic information by redirecting the user to the PubMed and the NCBI Assembly databases. All the datasets can be directly downloaded in a JSON format from the ‘Help’ page.

Figure 2

Schematic representation of the data extraction methodology followed for the construction of the Probio-ichnos database.

Figure 3

The ‘Home Page’ of the Probio-ichnos database contains an interactive word cloud depicting the distribution of entries across the different genera. The size of each word is indicative of the number of entries associated with the specific genera.

Figure 4

Entries can be explored in the ‘Browse’ tab of the Probio-ichnos database. (A) The database can be searched using the species or the strain name and/or (B) by selecting specific probiotic attributes. (C) The main table consists of rows that contain a strain and the probiotic properties, the number of studies available, and their PMID. Detailed exploration of a specific strain and its attributes can be achieved by ticking the ‘Explore’ option in the ‘Browse’ tab, highlighted in green. By selecting the ‘Expand’ option, two new tables are generated: (D) a table containing the main results for the specific strain and (E) a table of entries of the individual records. By selecting the unique PMID, the user is redirected to the article from which the data were extracted. Accordingly, the availability of the WGS of strains is indicated in the top table; by clicking on the link, the user is redirected to the NCBI Assembly database.

Figure 5

(A) Data statistics. (B) The distribution of the strains into the seven probiotic categories: resistance to acid, resistance to bile, adhesion/attachment, as well as antimicrobial, immunomodulatory, antiproliferative, and antioxidant capacities. Strains that did not exhibit or were not studied for a specific trait are clustered in ‘Other’.