Blanco Guillermo, Ruiz Lorena, Tamés Hector, Ruas-Madiedo Patricia, Fdez-Riverola Florentino, Sánchez Borja, Lourenço Anália, Margolles Abelardo
Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain.
Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain.
Microorganisms. 2020 May 13;8(5):723. doi: 10.3390/microorganisms8050723.
Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus , several beneficial effects have been attributed to strains belonging to the subspecies subsp. and subsp. , which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of subsp. and subsp. to gain insight into the characterization and classification of these two subspecies with probiotic interest.
双歧杆菌是人类和许多动物肠道中最丰富的微生物之一。在该属中，属于亚种婴儿双歧杆菌亚种和长双歧杆菌亚种的菌株具有多种有益作用，它们常见于婴儿和成人肠道中。随着这两个亚种测序基因组数量的增加，以及专注于预测糖酵解能力以了解特定碳水化合物降解能力的新型计算工具的出现，我们得以描绘这些细菌潜在的糖苷水解酶（GH），重点关注两个亚种中不同的GH谱。我们对188个已测序的双歧杆菌基因组进行了计算机模拟分析，并描绘了该物种代表中常见的和菌株特异性的GH及GH家族。此外，GH谱分析、基于基因组和基于16S rRNA的聚类分析表明，一些菌株的亚种归属与它们的遗传背景并不完全匹配。此外，对潜在GH成分的分析能够区分出清晰的GH模式。我们进一步讨论了一些GH活性及其与所研究的两个亚种的联系。总体而言，我们的计算机模拟分析对通过考虑婴儿双歧杆菌亚种和长双歧杆菌亚种的GH活性来深入了解这两个具有益生菌研究价值的亚种的特征和分类的适用性提出了一些问题。
