Database and Bioinformatics Studies of Probiotics

Abstract

Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants. The potential applications of the probiotics data are illustrated by several literature-reported investigations, which have used the relevant information for probing the function and mechanism of the probiotics and for discovering new probiotics. PROBIO can be accessed free of charge at http://bidd2.nus.edu.sg/probio/homepage.htm .

A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch

“…Using PROBIO database to help characterize the contribution of host probiotics is a new trend to improve gut health ( Tao L. et al, 2017 ). In the present study, a total of 128 probiotics were detected and seven changed noticeably with the same trend, which was decreased in the HRDS group compared with the LRDS and MRDS groups.…”

“…For ruminants suffering hindgut acidosis, due to feeding on a higher proportion of grains or concentrate and lesser amounts of fiber and forage, which will increase the flow of fermentable substrate to the hindgut, undigested carbohydrate and microbial products like LPS accumulate in the hindgut ( Gressley et al, 2011 ; Shen et al, 2020a ). Those compounds could cause intestinal mucosa injury and increases expression of cytokines, such as tumor necrosis factor-α and interleukin-1β ( Tao L. et al, 2017 ). Over 99% of the microorganisms colonizing in the intestinal tract are bacteria, which could use the undigested nutrients and non-structural CHO to supply various material for host ruminants, like energy sources, neurotransmitters, and even toxins ( Steele et al, 2016 ; Tao S. Y. et al, 2017 ).…”

Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice

“…TMAO from choline-containing precursors might be reduced by some probiotics [15]. A probiotics database termed PROBIO is a knowledge-based database of probiotics functions and lineages [16]. In this study, clusters of probiotics were annotated for their characteristic sequences by best-hit against a PROBIO database and identified and grouped into 135 probiotics (Figure 4G).…”

Shaping the Future of Probiotics and Prebiotics

“…Advances in bioinformatic platforms and parallel-computing workflows have enhanced our ability to convert the terabytes of sequence data into useable data in a fraction of the time, allowing for generation of probiotic databases and large-scale analyses of probiotic strains [111,112]. Similarly, movement of some software and wrapper programs into more user-friendly graphical user interfaces, rather than only being available through cumbersome command lines, has also helped to remove analysis barriers for probiotic and prebiotic effects.…”