The advent of generative artificial intelligence (AI) technologies marks a transformative moment for the scientific sphere, unlocking novel avenues to elevate scientific writing's efficiency and quality, expedite insight discovery, and enhance code development processes. Essential to leveraging these advancements is prompt engineering, a method that enhances AI interaction efficiency and quality. Despite its benefits, effective application requires blending researchers' expertise with AI, avoiding overreliance. A balanced strategy of integrating AI with independent critical thinking ensures the advancement and quality of scientific research, leveraging innovation while maintaining research integrity.
Lactobacillus rhamnosus GG (LGG) is a well-studied human-derived probiotic strain. It possesses excellent properties in the maintenance of intestinal homeostasis, immunoregulation and defense against gastrointestinal pathogens in mammals. Zhang et al. report that SpaC pilin of LGG causes intestinal epithelium injury by inducing cell pyroptosis and gut microbial dysbiosis in zebrafish, indicating safety issues of probiotics derived from other species of the host when administrated to aquaculture.
We infer that the maturation of infant resistome is not a random change but a programmed modification in the gut microbiome, which is due to resistance genes being disproportionally distributed across taxa. The decline of overall resistance is possibly due to the diminishment of Pseudomonadota, which is often equipped with antimicrobial resistance genes (ARGs), whereas the transition into table food creates a nutritional niche for Bacteriodota in the infant gut, which is a relatively small reservoir of resistance genes. The maturation of gut resistome is driven by infants’ changing carbohydrate metabolism, which demonstrated an increasing need for carbohydrate-active enzymes from Bacteroidota and decreasing involvements from Pseudomonadota during infancy. AA, auxiliary activities; CAZy, carbohydrate-active enzymes; GH, glycoside hydrolases; GT, glycosyltransferases; PL, polysaccharide lyases.
In the onset of asthenozoospermia (AZS), the presence of six genera of bacteria (Pseudomonas, Serratia, Methylobacterium-Methylorubrum, Uruburuella, Vibrio, and Pseudoalteromonas) in the seminal plasma potentially induces dynamic changes that ultimately diminish the synthesis of hexadecanamide. This reduction in hexadecanamide content in seminal plasma contributes to a subsequent decline in sperm motility. This reduced motility can be attributed to the downregulation of the levels of two key proteins, PAOX and CA2, within sperm cells.
Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform. Here, we developed a DNA data storage platform, named Storage-D, which modularized essential functions for DNA data storage and provided personalized codec choices for users. A new codec algorithm called “Wukong” was specially designed and integrated into the tool, which outperforms previous algorithms in key practical application considerations. By connecting to commercial DNA synthesis and sequencing platform with “Storage-D,” “Diagnosis and treatment protocol for COVID-19 patients” was successfully stored in DNA both in vitro and in vivo. This platform allows for practical and personalized DNA data storage, potentially with a wide range of applications. The web server and codes of the platform are available at http://storage.dailab.xyz:16666/ and https://github.com/DNAstorage-iSynBio/Storage-D/, respectively.
We present a comprehensive exploration of Lachnospiraceae, leveraging an extensive cultured-based genome collection. Phylogenetic analysis reveals previously underestimated taxonomic diversity. A thorough gene set analysis, comprising a 1.5 M gene catalog, sheds light on the functional richness of Lachnospiraceae. Notably, exploration of short-chain fatty acid synthesis pathways highlights their synthetic potential, with strains displaying distinct capacities for butyrate and propionate production. Disease association analysis establishes correlations between Lachnospiraceae strains and atherosclerotic cardiovascular disease and inflammatory bowel disease, offering valuable insights into their potential roles in human health and disease.
Here, both the covalent and noncovalent binding targets of artemisinin at different stages of the intraerythrocytic developmental cycle of Plasmodium falciparum were identified using a photoaffinity probe. The results suggest that interfering with the protein synthesis, glycolysis, and oxidative homeostasis pathways of parasites underlies the antimalarial effects of artemisinin. ABPP, activity-based protein profiling; APP, artemisinin photoaffinity probe; ART, artemisinin; RBC, red blood cell; UV, ultraviolet.
Interactions between nutrient and fungi in cancer development and treatment remain under investigation. In this article, we aim to provide insights into the relationships between fungi and various categories of cancer, mediated by diverse nutrient sensing pathways of fungi in response to external environment. Moreover, we highlight the potential application of fungi-targeted strategies in precision nutrition for both cancer prevention and treatment.
With the rapid development of technologies, including metagenomic and nontargeted or targeted metabolomics, the knowledge of gut microbiota and their related metabolites is constantly growing. Dysfunctions of microorganisms are associated with cardiovascular diseases, and gut microbiota and its associated metabolites are also involved in the pathogenesis of pulmonary hypertension. In addition, pulmonary hypertension might result in the alteration of bacterial flora. Here, we provide a comprehensive landscape of gut microbiota and metabolites in pulmonary hypertension, emphasizing the interplay between microorganisms and hosts in modulating pulmonary hypertension.
Gut microbiota is crucial for a healthy pregnancy, being affected by factors such as hormones, diet, obesity, nicotine, antibiotics, and microplastics. This article emphasizes the impact of gut microbiome changes on pregnancy complications and outcomes, delving into the underlying mechanisms and potential gut microbe-based therapies. Additionally, it explores the contentious issue of bacterial presence in the uterine environment. FGR, fetal growth restriction; HT, hypothyroidism in pregnancy; ICP, intrahepatic cholestasis of pregnancy; PE, pre-eclampsia; GDM, gestational diabetes mellitus; PROM, premature rupture of membranes; PTB, preterm birth.
The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.
In this work, we introduced a siderophore information database (SIDERTE), a digitized siderophore information database containing 649 unique structures. Leveraging this digitalized data set, we gained a systematic overview of siderophores by their clustering patterns in the chemical space. Building upon this, we developed a functional group-based method for predicting new iron-binding molecules with experimental validation. Expanding our approach to the collection of open natural products (COCONUT) database, we predicted a staggering 3199 siderophore candidates, showcasing remarkable structure diversity that is largely unexplored. Our study provides a valuable resource for accelerating the discovery of novel iron-binding molecules and advancing our understanding of siderophores.
The administration of oral antidiabetic drugs (OADs) to patients with type 2 diabetes elicits distinct and shared changes in the gut microbiota, with acarbose and berberine exhibiting greater impacts on the gut microbiota than metformin, vildagliptin, and glipizide. The baseline gut microbiota strongly associates with treatment responses of OADs.
Continuous cropping often results in severe “replant problem,” across various crops due to the autotoxins accumulation, soil acidification, pathogens proliferation, and microbial dysfunction. We unveiled a groundbreaking phenomenon that long-term continuous cropping (LTCC) can alleviate the tobacco replant problem. This mitigation occurs through the enrichment of autotoxin-degrading microbes, and the transformative impact is evident with even a modest application (10%) of LTCC soil to short-term continuous cropping (STCC) soil. Our investigation has pinpointed specific autotoxin-degrading bacteria, particularly the Pseudomonas and Burkholderia species, which exhibit the capacity to alleviate the tobacco replant problem in STCC soil. Their autotoxin-degrading mechanism using axenic culture and soil samples was also conducted via comprehensive analyses of microbiome and transcriptome approach. This research sheds light on the potential of LTCC as a strategic approach for sustainable agriculture, addressing replant problems and promoting the health of cropping systems. UV, ultraviolet; OD, optical density.