hacksig: a unified and tidy R framework to easily compute gene expression signature scores.

SUMMARY: Hundreds of gene expression signatures have been developed during the last two decades. However, due to the multitude of development procedures and sometimes a lack of explanation for their implementation, it can become challenging to apply the original method on custom data. Moreover, at present, there is no unified and tidy interface to compute signature scores with different single sample enrichment methods. For these reasons, we developed hacksig, an R package intended as a unified framework to obtain single sample scores with a tidy output as well as a collection of manually curated gene signatures and methods from cancer transcriptomics literature. AVAILABILITY AND IMPLEMENTATION: The hacksig R package is freely available on CRAN (https://CRAN.R-project.org/package=hacksig) under the MIT license. The source code can be found on GitHub at https://github.com/Acare/hacksig. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Use of kefir-derived lactic acid bacteria for the preparation of a fermented soy drink with increased estrogenic activity.

Fermented foods are receiving growing attention for their health promoting properties. In particular, there is a growing demand for plant-based fermented foods as dairy alternatives. Considering that soy is a vegetal food rich in nutrients and a source of the phytoestrogen isoflavones, the aim of this study was to select safe food microorganisms with the ability to ferment a soy drink resulting in a final product with an increased estrogenic activity and improved functional properties. We used milk kefir grains, a dairy source of microorganisms with proven health-promoting properties, as a starting inoculum for a soymilk. After 14 passages of daily inoculum in fresh soy drink, we isolated four lactic acid bacterial strains: Lactotoccus lactis subsp. lactis K03, Leuconostc pseudomesenteroides K05, Leuconostc mesenteroides K09 and Lentilactobacillus kefiri K10. Isolated strains were proven to be safe for human consumption according to the assessment of their antibiotic resistance profile and comparative genomics. Furthermore, functional characterization of the bacterial strains demonstrated their ability to ferment sugars naturally present in soybeans and produce a creamy texture. In addition, we demonstrated, by means of a yeast-based bioluminescence reporter system, that the two strains belonging to the genus Leuconostoc increased the estrogenic activity of the soybean drink. In conclusion, the proposed application of the bacterial strains characterized in this study meets the growing demand of consumers for health-promoting vegetal food alternatives to dairy products.