Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN

Abstract

Agroindustrial waste, such as fruit residues, are a renewable, abundant, low-cost, commonly-used carbon source. Biosurfactants are molecules of increasing interest due to their multifunctional properties, biodegradable nature and low toxicity, in comparison to synthetic surfactants. A better understanding of the associated microbial communities will aid prospecting for biosurfactant-producing microorganisms. In this study, six samples of fruit waste, from oranges, mangoes and mixed fruits, were subjected to autochthonous fermentation, so as to promote the growth of their associated microbiota, followed by short-read metagenomic sequencing. Using the DIAMOND+MEGAN analysis pipeline, taxonomic analysis shows that all six samples are dominated by Proteobacteria, in particular, a common core consisting of the genera Klebsiella, Enterobacter, Stenotrophomonas, Acinetobacter and Escherichia. Functional analysis indicates high similarity among samples and a significant number of reads map to genes that are involved in the biosynthesis of lipopeptide-class biosurfactants. Gene-centric analysis reveals Klebsiella as the main assignment for genes related to putisolvins biosynthesis. To simplify the interactive visualization and exploration of the surfactant-related genes in such samples, we have integrated the BiosurfDB classification into MEGAN and make this available. These results indicate that microbiota obtained from autochthonous fermentation have the genetic potential for biosynthesis of biosurfactants, suggesting that fruit wastes may provide a source of biosurfactant-producing microorganisms, with applications in the agricultural, chemical, food and pharmaceutical industries.

Exploring the diversity and functional profile of microbial communities of Brazilian soils with high salinity and oil contamination

“…Pathway analysis was done using KEGG (Kyoto Encyclopedia of Genes and Genomes) [ 33 , 34 ]. Furthermore, we employed an extension of MEGAN6 for functional analysis, employing the BiosurfDB database [ 35 ], which specifically targets genes related to biosurfactant production and biodegradation pathways. Statistical analysis was carried out using STAMP [ 36 ], p-values and confidence intervals were calculated using the two-sided Fisher's exact test and Newcombe-Wilson method, respectively.…”

MeganServer: facilitating interactive access to metagenomic data on a server

“…Together with colleagues in Brazil, we performed short-read metagenomic analysis of six fruit-waste samples to study their potential bio-surfactant bio-synthesis ( Silva et al , 2022 ). Initial metagenomic analysis was performed on a server hosted in Tübingen, Germany, and datasets were then accessed from Sorocaba, Brazil, using MeganServer.…”

Candida krusei M4CK Produces a Bioemulsifier That Acts on Melaleuca Essential Oil and Aids in Its Antibacterial and Antibiofilm Activity

“…In this study, the yeasts were isolated from the fruit B. crassifolia, popularly known as murici; this fruit originates from Central and South America and has been used for food production and folk medicine [18]. The isolation of yeasts with the potential to produce surface-active compounds indicates that the producers of SACs are widely distributed on the surfaces, internally found in the pulp of various fruits and plants, and have the potential for use in emulsifying systems and different biotechnological processes [19,20].…”