Torres-Sánchez Alfonso, Luque Gracia, Ortiz Pilar, Ruiz-Rodríguez Alicia, López-Moreno Ana, Aguilera Margarita
Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain.
Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain.
Foods. 2025 May 18;14(10):1794. doi: 10.3390/foods14101794.
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 (, , , , , , and ) 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 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.
人类肠道微生物群是一个复杂且动态的生态系统，因其具有宝贵且广泛的生理功能而闻名。本研究通过整合计算机模拟和体外实验方法的数据，将人类肠道微生物群作为酶的来源，用于生物医药、生物修复以及食品和饲料生物技术产业的创新应用。从不同培养基和条件下儿童肠道微生物群分离出的微生物库中总共筛选出93株易于培养的菌株。首先，使用定制的生物信息搜索协议对所选物种对应的参考基因组进行基因组数据筛选和酶查询。根据基因组分类结果对编码酶的提取和解读聚焦于四个主要门（芽孢杆菌门、拟杆菌门、放线菌门和假单胞菌门）和七个属（具体属名缺失），依据它们的可培养性以及生物技术相关性和研究价值。通过蛋白质注释总共鉴定出364种酶，其中突出的有淀粉酶、纤维素酶、菊粉酶、脂肪酶、蛋白酶和漆酶。其次，表型分析在93株分离株中的80.6%证实了这些主要酶活性。显著发现包括某些物种显示出相关的淀粉酶和漆酶活性。本研究证明了将基因组注释与功能分析相结合的实用性，为利用肠道微生物群酶开发创新且可持续的生物技术过程提供了一种可靠的方法。此外，控制肠道适应性微生物中酶表达的调控机制是释放肠道微生物群衍生生物催化剂全部潜力的关键步骤。
