Microbiota of Wild Fruits from the Amazon Region of Ecuador: Linking Diversity and Functional Potential of Lactic Acid Bacteria with Their Origin

Abstract

Subtropical wild fruits are a reservoir of microbial diversity and represent a potential source of beneficial microorganisms. Wild fruits provide essential nutrients, minerals, and antioxidants that contribute to human health. Many of these wild fruits are used by indigenous peoples for medicine and food, but there is yet an unexplored potential in the study of their properties and benefits. Wild fruits from the Amazon region and their associated active substances or bacterial communities can prevent disease, provide appropriate nutrition, contribute to new sources of income, and improve lives. Despite its condition as a megabiodiverse country, Ecuador suffers from limited access to its genetic resources, and particularly for research. A total of 41 isolates were obtained from six wild Amazonian fruit species and were molecularly classified into the genera Lactiplantibacillus (31 isolates), Lactococcus (3 isolates), Weissella (3 isolates), and Enterococcus (1 isolate). Three isolates showed large divergence in sequence variability and were not identified by the taxonomic assignment algorithm. Inferred phylogenies on the 16S rRNA gene explained the relationship between lineages and their origin. Carbohydrate metabolism and antimicrobial profiles were evaluated, and the isolates were classified from a functional perspective. Antimicrobial profiles showed a wide-range spectrum against several Gram-positive and Gram-negative bacteria. To our knowledge, this is the first study assessing the diversity of LAB in native tropical fruits from the Amazon region of Ecuador and their promising functional properties. The obtained isolates and their assessed properties are valuable genetic resources to be further investigated for industrial and pharmaceutical applications.

Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance

“…Previously, we showed that LAB strains isolated from wild fruits possess a unique portfolio of enzymes that allow them to metabolize various compounds and present specific metabolic traits as a result of their microenvironmental origin ( Tenea et al, 2020a ). However, the presence of many gene sequences responsible for carbohydrate and amino acid transport and metabolism is considered an important probiotic characteristic.…”

“…Genome analysis showed the presence of the gene glpK_1 , encoded for glycerol kinase, a key enzyme participating in the regulation of glycerol uptake and metabolism. The ability of UTNGt21O strain to metabolize glycerol and to utilize the α-galacto-oligosaccharides (αGOS) family, d-melibiose [α-Gal-(1→6)-Glu], as well as the raffinose-family oligosaccharide (RFO) d-raffinose was previously detected by employing biochemical miniaturized fermentation tests ( Tenea et al, 2020a ). The results suggested the capacity of this strain to adapt to different niches because of its high genome flexibility, which points this strain as good candidates for functional food design or other biotechnological applications.…”

“…Recently, there has been a growing interest in the special use of tropical fruits not only as food but also in the characterization of the microbial population associated with those fruits. In fact, the microbiota associated with wild Amazonian tropical fruits was investigated for the presence of beneficial microorganisms such as LAB ( Tenea et al, 2020a ). Several wild fruits were found as an important source of LAB strains.…”

Genome Characterization of Lactiplantibacillus plantarum Strain UTNGt2 Originated from Theobroma grandiflorum (White Cacao) of Ecuadorian Amazon: Antimicrobial Peptides from Safety to Potential Applications

“…Besides, some strains harbor naturally CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) arrays and Cas associated proteins, which grant the capacity to be converted into a tool for genome editing [ 12 ]. Most LAB species used as probiotics or antimicrobial producers are of human or animal origin, and recently, several scientific documents indicated the probiotic potential of LAB species isolated from unconventional sources such as fruits, vegetables, juices, and grain products [ 8 , 13 , 14 ]. Among Lactobacilli, Lactobacillus plantarum is a potential candidate species [ 1 , 15 , 16 ].…”

“…The characterization of the microbiota of wild tropical fruits draws our attention [ 14 ]. Theobroma grandiflorum , commonly known as white cacao, Amazonian cacao, or copoazú, is a perennial tree typical of the tropical humid forest, which has its origins in the Brazilian Amazon region and belongs to the Malvaceae family.…”