Scientific belief in reconstructing healthy ecology with the power of microorganisms

Protein is the cornerstone of life, indispensable for the synthesis of muscles, the immune system, enzymes, and hormones. But just like even the best worker, they can mess up the project if they "work excessive overtime." During normal digestion, protein acts as a diligent "construction worker"; but once intake is excessive, it turns into a rampaging "demolition team" -- not only leaving the gut in a complete mess, but also potentially triggering microbial "riots" and liver/kidney "strikes."

When "a mouthful of rice" enters the mouth, preliminary digestion begins after it is chewed by teeth and mixed with saliva. This journey through the gut is a crucial process for the body to absorb nutrients and maintain life's operations.

If the human body is likened to a vast universe, the gut is its most dynamic "galaxy". Home to approximately 40 trillion microbial inhabitants, their density far surpasses the stars in the Milky Way. They make the small intestine their "main battlefield," engaging in a silent interplay across the folded mucosal plains and villi mountains. This world's "atmosphere" is formed by a mucus barrier, where mucins secreted by epithelial cells hang suspended like stars, simultaneously defending against foreign invaders and nourishing the microbial community. Meanwhile, the intestinal villi and microvilli resemble a dense forest, boasting a surface area of up to 300 square meters, acting as a core hub for energy absorption and signal transmission.

Glycerophospholipid (GPL) perturbance was linked to the pathogenesis of diabetes in animal studies but prospective studies in humans are rare, particularly in Asians. We aimed to investigate the associations between plasma GPLs and incident diabetes and to explore effects of lifestyle on the associations in a Chinese population.

Accompanied with nutrition transition, non-HDL-C levels of individuals in Asian countries has increased rapidly, which has caused the global epicenter of nonoptimal cholesterol to shift from Western countries to Asian countries. Thus, it is critical to underline major genetic and dietary determinants. In the current study of 2,330 Chinese individuals, genetic risk scores (GRSs) were calculated for total cholesterol (TC; GRSTC, 57 SNPs), LDL-C (GRSLDL-C, 45 SNPs), and HDL-C (GRSHDL-C, 65 SNPs) based on SNPs from the Global Lipid Genetics Consortium study. Cholesterol intake was estimated by a 74-item food-frequency questionnaire.

Rapid nutrition transition from plant-based traditional diet to westernized diet has led to dramatically heightening burdens of cardiometabolic diseases in China in past decades. Recently, national surveys reported that poor dietary quality including low marine n-3 fatty acids and high intakes of red meat and processed meat was associated with considerably elevated cardiometabolic deaths. Previous studies mainly from Western population-based cohorts have indicated that not only fat quantity but also quality linked with different cardiometabolic outcomes.

Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. This study aims to define a role for bacterial swarmers in amelioration of intestinal stress.

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper-flagellation have been shown to accompany the swarming phenotype.

Bacterial motility under confinement is relevant to both environmental control and the spread of infection. Here, we report observations on Escherichia coli, Enterobacter sp., Pseudomonas aeruginosa, and Bacillus subtilis when they are confined within a thin layer of water around dispersed micrometer-sized particles sprinkled over a semisolid agar gel. In this setting, E. coli and Enterobacteria orbit around the dispersed particles.

Rare diseases (RDs) may affect individuals in small numbers, but they have a significant impact on a global scale. Accurate diagnosis of RDs is challenging, and there is a severe lack of drugs available for treatment. Pharmaceutical companies have shown a preference for drug repurposing from existing drugs developed for other diseases due to the high investment, high risk, and long cycle involved in RD drug development.

Screening new drug–target interactions (DTIs) by traditional experimental methods is costly and time-consuming. Recent advances in knowledge graphs, chemical linear notations, and genomic data enable researchers to develop computational-based-DTI models, which play a pivotal role in drug repurposing and discovery. However, there still needs to develop a multimodal fusion DTI model that integrates available heterogeneous data into a unified framework.

Knowledge Graph (KG) is becoming increasingly important in the biomedical field. Deriving new and reliable knowledge from existing knowledge by KG embedding technology is a cutting-edge method. Some add a variety of additional information to aid reasoning, namely multimodal reasoning. However, few works based on the existing biomedical KGs are focused on specific diseases.

Postnatal development of the human gut microbiota is linked to healthy growth. Because the number of potential interactions between community components is vast, an unanswered question is what mechanisms determine the form of community assembly (succession). We created a simplified, manipulable in vivo model where bacterial strains cultured from an infant were divided into consortia, representing earlier and later periods in assembly, and introduced in different order into germ-free mice fed infant formula.

Metabolic syndrome is characterized by a constellation of comorbidities that predispose individuals to an increased risk of developing cardiovascular pathologies as well as type 2 diabetes mellitus. The gut microbiota is a new key contributor involved in the onset of obesity-related disorders.

Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA.

Quorum sensing is a chemical communication process that bacteria use to control collective behaviours including bioluminescence, biofilm formation, and virulence factor production. In Vibrio harveyi, five homologous small RNAs (sRNAs) called Qrr1–5, control quorum-sensing transitions. Here, we identify 16 new targets of the Qrr sRNAs. Mutagenesis reveals that particular sequence differences among the Qrr sRNAs determine their target specificities.

The human genome, comprising approximately 20,000 protein-encoding genes, appears surprisingly modest in complexity when juxtaposed with the genomic repertoire of maize, which boasts around 40,000 such genes (Ezkurdia et al. 2014; Jiao et al. 2017). While this comparison highlights the seemingly limited gene count in humans, it is crucial to recognize that a significant portion of our biological functionality extends beyond our own genome.

To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability.

Over the past few decades, most attention to Chinese Cordyceps-associated endogenous microorganism was focused on the fungal community that creates critical bioactive components. Bacterial community associated with Chinese Cordyceps has been previously described; however, most studies were only presenting direct comparisons in the Chinese Cordyceps and its microenvironments. In the current study, our objectives were to reveal the bacterial community structure composition and predict their function.

Immunosenescence refers to age-related declines in the capacity to respond to infections such as influenza (flu). Caloric restriction represents a known strategy to slow many aging processes, including those involving the immune system. More recently, some changes in the microbiome have been described with aging, while the gut microbiome appears to influence responses to flu vaccination and infection.