Analysis of Human Gut Microbiota Enzymes for Biotechnological and Food Industrial Applications

Abstract

The human gut microbiota is a complex and dynamic ecosystem, recognized for its valuable and wide array of physiological functions. This study investigated the human gut microbiota as a source of enzymes for innovative applications in the biomedicine, bioremediation, and food and feed biotechnological industries by integrating data from combined in silico and in vitro approaches. A total of 93 easily cultivable strains were selected from a bank of isolated microorganisms generated from the gut microbiota of children under different media and conditions. First, genomic data screening and enzyme interrogation of reference genomes corresponding to the selected species were carried out using a custom bioinformatic searching protocol. The extraction and interpretation of encoding enzymes from the genomic taxa results focused on four major phyla (Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota) and seven genera (Bacillus, Bacteroides, Clostridium, Enterobacter, Enterococcus, Microbacterium, and Staphylococcus) according to their cultivability and biotechnological relevance and interest. A total of 364 enzymes were identified across protein annotations, highlighting amylases, cellulases, inulinases, lipases, proteases, and laccases. Second, phenotypic assays confirmed these main enzymatic activities in 80.6% of 93 isolates. Notable findings included Bacillus species displaying relevant amylase and laccase activity. This study demonstrates the utility of combining genomic annotations with functional assays, offering a robust approach for exploiting gut microbiota enzymes to develop innovative and sustainable biotechnological processes. Moreover, regulatory mechanisms governing enzyme expression in gut resilient microbes are essential steps toward unlocking the full potential of gut microbiota-derived biocatalysts.