Deep learning enabled integration of tumor microenvironment microbial profiles and host gene expressions for interpretable survival subtyping in diverse types of cancers.

The tumor microbiome, a complex community of microbes found in tumors, has been found to be linked to cancer development, progression, and treatment outcome. However, it remains a bottleneck in distangling the relationship between the tumor microbiome and host gene expressions in tumor microenvironment, as well as their concert effects on patient survival. In this study, we aimed to decode this complex relationship by developing ASD-cancer (autoencoder-based subtypes detector for cancer), a semi-supervised deep learning framework that could extract survival-related features from tumor microbiome and transcriptome data, and identify patients' survival subtypes.

Hidden Links Between Skin Microbiome and Skin Imaging Phenome.

Despite the skin microbiome has been linked to skin health and diseases, its role in modulating human skin appearance remains understudied. Using a total of 1244 face imaging phenomes and 246 cheek metagenomes, we first established three skin age indices by machine learning, including skin phenotype age (SPA), skin microbiota age (SMA), and skin integration age (SIA) as surrogates of phenotypic aging, microbial aging, and their combination, respectively. Moreover, we found that besides aging and gender as intrinsic factors, skin microbiome might also play a role in shaping skin imaging phenotypes (SIPs).

Total phosphorus speciation and transport flux dynamics driven by tidal variations in the Shuidong Bay coastal water during summer, China.

Phosphorus (P) is a vital nutrient for the growth of marine organisms. Tidal cycle had major influence on various biogeochemical parameters of the bay and changed nutrients input with the ebb and flow of the tide. Seawater was collected by synchronous continuous observation during summer in 2021, to investigate tide drives total phosphorus (TP) variation on the concentration, speciation and exchange flux between Shuidong Bay (SDB) and South China Sea (SCS).

Insurance Reimbursement for Special Foods and Phenylalanine Levels in Patients With PKU in China.

Importance: Recent changes in China's social medical insurance reimbursement policy have impacted the financial burden of patients with phenylketonuria (PKU) for special foods. However, whether this policy change is associated with their blood phenylalanine (PHE) concentration is unclear.

Objective: To investigate the association between the reimbursement policy and blood PHE concentration in patients with PKU.

A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau.

The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated.

Gut microbiota and inflammation patterns for specialized athletes: a multi-cohort study across different types of sports.

Regular high-intensity exercise can cause changes in athletes' gut microbiota, and the extent and nature of these changes may be affected by the athletes' exercise patterns. However, it is still unclear to what extent different types of athletes have distinct gut microbiome profiles and whether we can effectively monitor an athlete's inflammatory risk based on their microbiota. To address these questions, we conducted a multi-cohort study of 543 fecal samples from athletes in three different sports: aerobics ( = 316), wrestling ( = 53), and rowing ( = 174).

Niche-Based Microbial Community Assemblage in Urban Transit Systems and the Influence of City Characteristics.

Microbiota residing on the urban transit systems (UTSs) can be shared by travelers and have niche-specific assemblage. However, it remains unclear how the assemblages are influenced by city characteristics, rendering city-specific and microbial-aware urban planning challenging. Here, we analyzed 3,359 UTS microbial samples collected from 16 cities around the world.

Tracing human life trajectory using gut microbial communities by context-aware deep learning.

The gut microbial communities are highly plastic throughout life, and the human gut microbial communities show spatial-temporal dynamic patterns at different life stages. However, the underlying association between gut microbial communities and time-related factors remains unclear. The lack of context-awareness, insufficient data, and the existence of batch effect are the three major issues, making the life trajection of the host based on gut microbial communities problematic.

High-Density Lipoprotein Cholesterol as a Potential Medium between Depletion of Genera and Hypertension under a High-Calorie Diet.

Gut microbial dysbiosis has been associated with hypertension. An extremely high incidence of essential hypertension was found in the Han and the Yugur people who resided in Sunan County in China's nomadic steppes, with little population movement. To investigate gut microbial contributions to this high incidence of hypertension, we recruited a total of 1, 242 Yugur and Han people, who had resided in Sunan County for more than 15 years and accounted for 3% of the local population.

EXPERT: transfer learning-enabled context-aware microbial community classification.

Microbial community classification enables identification of putative type and source of the microbial community, thus facilitating a better understanding of how the taxonomic and functional structure were developed and maintained. However, previous classification models required a trade-off between speed and accuracy, and faced difficulties to be customized for a variety of contexts, especially less studied contexts. Here, we introduced EXPERT based on transfer learning that enabled the classification model to be adaptable in multiple contexts, with both high efficiency and accuracy.

Stage-specific roles of microbial dysbiosis and metabolic disorders in rheumatoid arthritis.

Objective: Rheumatoid arthritis (RA) is a progressive disease including four stages, where gut microbiome is associated with pathogenesis. We aimed to investigate stage-specific roles of microbial dysbiosis and metabolic disorders in RA.

Methods: We investigated stage-based profiles of faecal metagenome and plasma metabolome of 76 individuals with RA grouped into four stages (stages I-IV) according to 2010 RA classification criteria, 19 individuals with osteroarthritis and 27 healthy individuals.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses.

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e.

Microbiome Resilience and Health Implications for People in Half-Year Travel.

Travel entail change in geography and diet, both of which are known as determinant factors in shaping the human gut microbiome. Additionally, altered gut microbiome modulates immunity, bringing about health implications in humans. To explore the effects of the mid-term travel on the gut microbiome, we generated 16S rRNA gene and metagenomic sequencing data from longitudinal samples collected over six months.

Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome.

Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites.

Micro-coevolution of host genetics with gut microbiome in three Chinese ethnic groups.

Understanding the micro-coevolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical studies. To gain insight into the interactions between host genetic variation and the gut microbiome, we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in the same boarding college and representing 3 ethnic groups, Uyghur, Kazakh, and Han Chinese. We found that differences in gut microbiome were greater between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition, functional composition, enterotype stratification, and microbiome genetic differentiation.

Influence of oral nutritional agents rich in soluble dietary fiber on intestinal flora of elderly men with malnutrition.

Objective: Observe the influence of oral nutritional agents rich in soluble dietary (enteral nutritional suspension [TPF-DM]) on intestinal flora of elderly male subjects with malnutrition.

Method: Seventy-eight subjects with good nutrition were considered as the healthy control group. Twenty-eight male subjects who had malnutrition and were older than 70 years were included and randomly divided into the short-term (3 months) intervention group (n = 20) and the long-term (12 months) group (n = 8).

MiR-135a Protects against Myocardial Injury by Targeting TLR4.

Emerging evidence highlights the importance of microRNAs (miRNAs) as functional regulators in cardiovascular disease. This study aimed to investigate the functional significance of miR-135a in the regulation of cardiac injury after isoprenaline (ISO) stimulation and the underlying mechanisms of its effects. Murine models with cardiac-specific overexpression of miR-135a were constructed with an adeno-associated virus expression system.

Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock.

The gut microbiota of intensive care unit (ICU) patients displays extreme dysbiosis associated with increased susceptibility to organ failure, sepsis, and septic shock. However, such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota. We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis.

Microbiome Big-Data Mining and Applications Using Single-Cell Technologies and Metagenomics Approaches Toward Precision Medicine.

With the development of high-throughput sequencing technologies as well as various bioinformatics analytic tools, microbiome is not a "microbial dark matter" anymore. In this review, we first summarized the current analytical strategies used for big-data mining such as single-cell sequencing and metagenomics. We then provided insights into the integration of these strategies, showing significant advantages in fully describing microbiome from multiple aspects.

Stereotypes About Enterotype: the Old and New Ideas.

In 2011, the term "enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view.

Glucose variability aggravates cardiac fibrosis by altering AKT signalling path.

Objective: To study the effect of blood glucose variability on cardiac fibrosis and its mechanism in a model of diabetic cardiomyopathy.

Methods: A total of 45 Sprague Dawley rats were randomly divided into three groups: control, control diabetes mellitus and fluctuated blood glucose groups. Fluctuated blood glucose was induced by daily subcutaneous insulin and intraperitoneal glucose injections at different time points.