mSystems最新文献

Single-cell RNA sequencing (scRNA-seq) technology enables researchers to explore heterogeneity of diverse cell types within complex tissues at the single-cell resolution. Cell annotation, as a crucial step in scRNA-seq data analysis, provides biologically meaningful cell identity information for biological research. With the proliferation of publicly available datasets and the expansion of sequencing data scale, traditional annotation methods reliant on manual marker gene matching have become increasingly cumbersome and time-consuming. Consequently, efficient and convenient automated cell annotation methods are gradually becoming mainstream. In this paper, we propose a single-cell semi-supervised annotation training framework called scSemiPLC, which generates pseudo-labels through clustering and consistency regularization. Specifically, scSemiPLC utilizes existing label information to guide the clustering of unlabeled data. During model training, it assigns pseudo-labels to the unlabeled samples and constrains the prediction of perturbed data to be similar to the pseudo-labels. This strategy addresses the low utilization of unlabeled data caused by the fixed high threshold pseudo-labeling paradigm, offering a new approach for cell annotation in the semi-supervised learning field. Experimental results demonstrate the superior performance of scSemiPLC in annotation accuracy and stability, extraction of biologically meaningful representations, and robustness to the number of cell labels, significantly outperforming classical automatic annotation and mainstream semi-supervised learning methods.

Importance: This work proposes a novel cell annotation training framework, scSemiPLC, which significantly enhances the efficiency and accuracy of annotation by fully leveraging unlabeled data. In the semi-supervised learning component, the framework innovatively generates pseudo-labels through clustering. Subsequently, it evaluates the reliability of these pseudo-labels and assigns corresponding weights, thereby balancing both their quantity and quality. This approach provides new insights into the direction of automatic cell annotation within the realm of semi-supervised learning.

Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.

Importance: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.

Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.

Desiccation-tolerant seeds provide an intriguing system for studying microbial dormancy, which includes reversible inactivation and reactivation in response to stress. Focusing on bacterial responses to desiccation and rehydration, we offer a holistic interpretation of dormancy and quiescence within the seed holobiont, highlighting both parallels and distinctions between microbes and their plant host. Based on pilot evidence, we propose that microbial dormancy supports persistence throughout the life cycle of desiccation-tolerant seeds. Transcriptomic analyses of seed-transmitted bacteria have identified genes implicated in inactivation and the viable-but-nonculturable state. Our analysis of Xanthomonas citri pv. fuscans illustrates this during seed maturation. However, the signals triggering microbial reactivation and the potential reciprocal interactions between seed dormancy and quiescence, and microbial dormancy, remain unknown. Elucidating this interplay within the seed holobiont could enhance plant growth and health either by promoting seed germination through microbial inoculation or by enabling early detection of seed-transmitted phytopathogens.

Enterococcus faecalis, a facultative anaerobic pathogen and common constituent of the gastrointestinal microbiota, must navigate varying iron levels within the host. This study explores its response to iron supplementation in a glutathione-deficient mutant strain (Δgsh). We examined the transcriptomic and metabolic responses of a glutathione synthetase mutant strain (Δgsh) exposed to iron supplementation, integrating these data into a genome-scale metabolic model (GSMM). Our results show that under glutathione deficiency, E. faecalis reduces intracellular iron levels and shifts its transcriptional response to prioritize energy production genes. Notably, basal metabolites, including arginine, increase. The GSMM highlights the importance of arginine metabolism, particularly the arc operon (anaerobic arginine catabolism), as a presumed compensatory mechanism for glutathione deficiency generated during iron exposure. These findings provide insights into how E. faecalis adjusts metal homeostasis and transcriptional/metabolic processes to mitigate the effects of oxidative stress caused by iron.IMPORTANCEIron is essential for bacterial survival, yet its excess can be harmful due to its role in increasing oxidative stress. Enterococcus faecalis, a common member of the human gut microbiota, must carefully balance its iron levels to survive in changing environments. Here, we investigate how E. faecalis compensates for the reduced availability of glutathione, a key antioxidant, when exposed to high iron concentrations. We discovered that E. faecalis lowers its intracellular iron levels when glutathione biosynthesis is disrupted and reprograms its metabolism to prioritize energy production, potentially to fuel stress response mechanisms under iron-induced oxidative conditions. These findings enhance our understanding of bacterial adaptation under oxidative stress and suggest that interfering with arginine metabolic pathways could represent novel strategies to combat E. faecalis infections.

A large annual carbon flux occurs through the surface ocean's labile dissolved organic carbon (DOC) pool, with influx dominated by phytoplankton-derived metabolites and outflux by heterotrophic bacterioplankton uptake. We addressed the dynamics of this carbon flow between microbial primary and secondary producers through analysis of the Thalassiosira pseudonana CCMP1335 endometabolome, a proxy for the labile DOC released upon phytoplankton lysis, as temperature and bacterial presence were altered. Diatom strains acclimated at one of three different temperatures (14°C, 20°C, or 28°C) were cultured either axenically or with the bacterium Ruegeria pomeroyi DSS-3, and their endometabolites analyzed by NMR. Median concentration variation between conditions was ~1.5-fold across all identified endometabolites. Those with roles as osmolytes varied most, exhibiting concentration differences up to 170-fold across conditions with the largest variations triggered by the presence/absence of the heterotrophic bacterium. Differential expression observed for diatom metabolite synthesis pathways suggested changes in synthesis rates as a mechanism for endometabolome remodeling. Consistent with expectations of high turnover by heterotrophic bacteria, endometabolite mean lifetimes in a DOC pool were <2 h to 12 h.

Importance: The role of labile DOC in the transfer of marine carbon between phytoplankton and heterotrophic bacteria was first recognized 40 years ago, yet the identity and dynamics of phytoplankton metabolites entering the labile DOC pool are still poorly known. Using metabolome and transcriptome profiling, we found highly variable composition and concentration of diatom endometabolites, depending on growth conditions and arising over time frames as short as a single growth cycle. This strong response to external conditions, both biotic and abiotic, suggests that the chemical composition of phytoplankton intracellular pools released during lysis shift with ocean conditions. As phytoplankton cell lysis is one of the largest sources of labile dissolved compounds in the ocean, dynamic compositional changes in the metabolites released to heterotrophic bacteria have implications for the fate of surface ocean carbon.

Understanding the role of microbiota on stone surface is essential for developing effective grottoes conservation strategies. However, the ecological feature of microbial communities on stone surfaces has been rarely investigated systematically. In this study, we explored diversity, assembly, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from a microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, Cyanobacteria, and Ascomycota are the dominant phyla. Fundamental metabolic pathways are maintained during the formation of visually distinguishable microbial communities, but gene profiles vary across microbial communities of different colors. Ecological modeling suggests that selective pressure from the harsh stone surface environment fostered the interplay of dispersal limitation and heterogeneous selection during community assembly. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, a higher proportion of habitat specialists, and a sparser network structure. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of the assembly mechanisms and functional potentials of microbial communities on stone cultural heritage surfaces, provides microbial ecological insights for the conservation of these cultural treasures.IMPORTANCEMinimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.

Melioidosis, caused by the soil-dwelling pathogen Burkholderia pseudomallei (Bt), is a severe respiratory infection with limited treatment options. To investigate the host-pathogen metabolic interplay occurring during these intracellular infections, Hicks et al. built upon an in vitro co-culture model they developed with airway epithelial cells and Bt as a surrogate pathogen (D. J. Hicks, N. Aiosa, A. Sinha, O. A. Jaiyesimi, et al., mSystems 10:e00611-25, 2025, https://doi.org/10.1128/msystems.00611-25). Using an untargeted metabolomics approach tailored to central metabolism, they identified several host pathways that were altered during the Bt infection: polyamine biosynthesis, nicotinamide adenine dinucleotide salvage, and the tricarboxylic acid cycle. In addition, they found that several bacterial metabolites, including methylated nucleotide bases, peptidoglycan precursors, and amino acid derivatives, were altered due to Bt infection. These results show that co-culture metabolomics is an effective strategy for identifying host-pathogen metabolic phenotypes resulting from bacterial infections and can uncover new therapeutic strategies to combat melioidosis.

The seed microbiome plays a crucial role in plant health and productivity, yet the extent to which the plant genotype influences its composition remains unclear. We conducted a large-scale study using 100 tomato (Solanum lycopersicum L.) genotypes from 12 geographical locations in China, subjecting all seeds to the same processing to assess seed microbiome plasticity. The plant genotype was identified as the primary factor shaping microbiome structure (R² = 0.56, P = 0.001), followed by geographic location (R² = 0.11, P = 0.001), and insect resistance of the cultivar (R² = 0.07, P = 0.001). A rather small core microbiome of 21 amplicon sequence variants (ASVs) was shared across all tomato genotypes. Ubiquitous seed microbiome members found in 90% of the samples included Pseudomonas, Lactobacillus, Leuconostoc, and Ralstonia. A Random Forest modeling approach showed that tomato traits and their production environment can be predicted via seed microbiome features; core microbiome members, including Lactobacillus and Pseudomonas, were connected to specific tomato traits. This study unveils key factors influencing seed microbiome assembly and emphasizes the crucial role of host traits that can enable new venues for seed microbiomes in plant breeding and sustainable crop production.

Importance: Seeds not only carry the plant's genetic material but also host distinct microbial communities that can influence early plant growth and performance. In a large-scale study involving 100 tomato genotypes collected from 12 geographical locations in China, we examine how plant genotype shapes the seed microbiome. The research findings reveal that plant genotype, more than location or parents' geography, primarily influences microbial community structure (R² = 0.56 vs 0.11). These findings highlight the strong association between host genetics and seed microbiome assembly. Understanding these interactions provides valuable opportunities for integrating microbiome-based strategies into plant breeding and crop improvement programs, ultimately supporting more resilient and sustainable agricultural systems.