Deep embeddings to comprehend and visualize microbiome protein space.

Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.

Anticancer properties of probiotic yogurt bacteria / Antynowotworowe wlasciwosci probiotycznych bakterii jogurtowych.

The intestinal microflora plays a key role in maintaining homeostasis in the human body. Microbes affect, among others, energy conversion and absorption of nutrients, regulate immune system and help to protect the host organism from pathogenic microorganisms. The balanced composition of the intestinal microflora can be easily disturbed and any changes caused by diet, stress, obesity, diseases of the digestive system or medication may lead to pro-inflammatory immune responses and initiation of disease processes, including cancer. Maintaining intestinal microflora homeostasis is therefore extremely important for human health. In order to restore it, it is most often used to take specimens with appropriate bacterial cultures, i. e. probiotics. Due to the fact that yoghurts are a source of probiotic bacteria, their regular consumption may be a strong point in the prevention of various types of diseases, including civilization diseases and cancer. This article reviews the literature in the area of using yogurt bacteria in the prevention of cancer. Issues addressed in the article relate to the characteristics of yogurt bacteria, beneficial effects of probiotics on human health, anti-cancer properties of yogurt bacteria and their metabolites, i. e. immunoregulation, prevention of bacterial infections, maintenance of cellular connections in the intestine and anti-cancer activity of bacterial metabolites.

Host pathogen interactions in Helicobacter pylori related gastric cancer.

Helicobacter pylori (H. pylori), discovered in 1982, is a microaerophilic, spiral-shaped gram-negative bacterium that is able to colonize the human stomach. Nearly half of the world's population is infected by this pathogen. Its ability to induce gastritis, peptic ulcers, gastric cancer and mucosa-associated lymphoid tissue lymphoma has been confirmed. The susceptibility of an individual to these clinical outcomes is multifactorial and depends on H. pylori virulence, environmental factors, the genetic susceptibility of the host and the reactivity of the host immune system. Despite the host immune response, H. pylori infection can be difficult to eradicate. H. pylori is categorized as a group I carcinogen since this bacterium is responsible for the highest rate of cancer-related deaths worldwide. Early detection of cancer can be lifesaving. The 5-year survival rate for gastric cancer patients diagnosed in the early stages is nearly 90%. Gastric cancer is asymptomatic in the early stages but always progresses over time and begins to cause symptoms when untreated. In 97% of stomach cancer cases, cancer cells metastasize to other organs. H. pylori infection is responsible for nearly 60% of the intestinal-type gastric cancer cases but also influences the development of diffuse gastric cancer. The host genetic susceptibility depends on polymorphisms of genes involved in H. pylori-related inflammation and the cytokine response of gastric epithelial and immune cells. H. pylori strains differ in their ability to induce a deleterious inflammatory response. H. pylori-driven cytokines accelerate the inflammatory response and promote malignancy. Chronic H. pylori infection induces genetic instability in gastric epithelial cells and affects the DNA damage repair systems. Therefore, H. pylori infection should always be considered a pro-cancerous factor.