Interpretable machine learning framework reveals microbiome features of oral disease

Interpretable machine learning reveals microbiome signatures strongly associated with dairy cow milk urea nitrogen

The gut microbiome plays an important role in the healthy and efficient farming of dairy cows. However, high-dimensional microbial information is difficult to interpret in a simplified manner. We collected fecal samples from 161 cows and performed 16S amplicon sequencing. We developed an interpretable machine learning framework to classify individuals based on their milk urea nitrogen (MUN) concentrations. In this framework, we address the challenge of handling high-dimensional microbial data imbalances and identify 9 microorganisms strongly correlated with MUN. We introduce the Shapley Additive Explanations (SHAP) method to provide insights into the machine learning predictions. The results of the study showed that the performance of the machine learning model improved (accuracy = 72.7%) after feature selection on high-dimensional data. Among the 9 microorganisms, g__Firmicutes_unclassified had the greatest impact in the model. This study provides a reference for precision animal husbandry.

Multi-omics analysis of immune-related microbiome and prognostic model in head and neck squamous cell carcinoma

OBJECTIVES

The aim of our study is to explore the transcriptional and microbial characteristics of head and neck cancer's immune phenotypes using a multi-omics approach.

MATERIALS AND METHODS

Employing TCGA data, we analyzed head and neck squamous cell carcinoma (HNSCC) immune cells with CIBERSORT and identified differentially expressed genes using DESeq2. Microbial profiles, obtained from the TCMA database, were analyzed using LEfSe algorithm to identify differential microbes in immune cell infiltration (ICI) subgroups. Random Forest algorithm and deep neural network (DNN) were employed to select microbial features and developed a prognosis model.

RESULTS

We categorized HNSCC into three immune subtypes, finding ICI-2 with the worst prognosis and distinct microbial diversity. Our immune-related microbiome (IRM) model outperformed the TNM staging model in predicting survival, linking higher IRM model scores with poorer prognosis, and demonstrating clinical utility over TNM staging. Patients categorized as low-risk by the IRM model showed higher sensitivity to cisplatin and sorafenib treatments.

CONCLUSIONS

This study offers a comprehensive exploration of the ICI landscape in HNSCC. We provide a detailed scenario of immune regulation in HNSCC and report a correlation between differing ICI patterns, intratumor microbiome, and prognosis. This research aids in identifying prime candidates for optimizing treatment strategies in HNSCC.

CLINICAL RELEVANCE

This study revealed the microbial signatures associated with immunophenotyping of HNSCC and further found the microbial signatures associated with prognosis. The prognostic model based on IRM microbes is helpful for early prediction of patient prognosis and assisting clinical decision-making.

Gut-joint axis: Oral Probiotic ameliorates Osteoarthritis

Osteoarthritis (OA) etiology is multifactorial, and its prevalence is growing globally. The Gut microbiota shapes our immune system and impacts all aspects of health and disease. The idea of utilizing probiotics to treat different conditions prevails. Concerning musculoskeletal illness and health, current data lack the link to understand the interactions between the host and microbiome. We report that S. thermophilus, L. pentosus (as probiotics), and γ-aminobutyric acid (GABA) harbour against osteoarthritis in vivo and alleviate IL-1β induced changes in chondrocytes in vitro. We examined the increased GABA concentration in mice's serum and small intestine content followed by bacterial treatment. The treatment inhibited the catabolism of cartilage and rescued mice joints from degradation. Furthermore, the anabolic markers upregulated and decreased inflammatory markers in mice knee joints and chondrocytes. This study is the first to represent GABA's chondrogenic and chondroprotective effects on joints and human chondrocytes. This data provides a foundation for future studies to elucidate the role of GABA in regulating chondrocyte cell proliferation. These findings opened future horizons to understanding the gut-joint axis and OA treatment. Thus, probiotic/GABA therapy shields OA joints in mice and could at least serve as adjuvant therapy to treat osteoarthritis.