npj Biofilms and Microbiomes最新文献

Dietary oligosaccharides are prebiotics that fuel gut microbes, but individual microbiomes may respond differently depending on oligosaccharide structures as well as microbiome composition and function. The extent to which specific gut microbial communities exhibit personalized functional responses to distinct oligosaccharides remains underexplored. We applied a standardized ex vivo microbiome culture, called RapidAIM, coupled with metaproteomics to examine how six structurally diverse oligosaccharides affect the gut microbiota functional response. Our study shows that while human gut microbiomes share some commonalities in utilizing oligosaccharides (e.g. prioritizing dietary fibers over mucin), the fine-scale metabolic and taxonomic responses are highly individualized. Such findings underscore the importance of considering personal microbiome profiles when predicting the outcome of prebiotic interventions. In a broader context, our metaproteomic approach provides a framework for identifying optimal prebiotic choices tailored to individual microbiomes. Ultimately, understanding these personalized responses could inform precision nutrition strategies.

Excessive dieting (ED), a common weight-control strategy, often causes neurological and emotional disturbances, yet its gut-brain interaction mechanisms remain unclear. Employing a short-term dietary (SDR) adult male rabbit model, we found that SDR can induced cerebral cortex up-regulation of the immune-related genes (e.g., C1QC, SAA3) enriched in NF-kappa B signaling pathways, contrasted with down-regulation of sex hormone-related genes (e.g., PRLR, SPA17) implicated in metabolic homeostasis. Furthermore, dysregulated expression of metabolic genes (e.g., PPM1J, GALNT18) in the cecum of the SDR group interacted to impair the immune protection pathways related to intestinal mucosa. Then, SDR significantly increased the cecal Firmicutes/Bacteroidetes ratio (from 3.38 to 5.57) and reduced microbial diversity. Specifically, beneficial bacteria involved in tryptophan metabolism and neurotransmitter synthesis (e.g., Bacteroidales_bacterium, Alistipes_indistinctus) decreased, whereas bile acid-metabolizing bacteria (e.g., Clostridium_sp._CAG:710, Ruminococcus_sp._Marseille-P6503) linked to increase energy metabolism. The top 20 genes from the brain-gut axis analysis (e.g., ITPR1, CAMK4, CDK5R1) were enriched in critical neural pathways like axon guidance, GABAergic synapse, and long-term potentiation. Notably, key neurodevelopmental genes (e.g., GPR37, GPX3) correlated with these microbial shifts, implicating oxidative stress, synaptic plasticity, and mitochondrial function in microbiota-host crosstalk. This study highlights a "microbial-metabolism-neural" axis in SDR, providing novel targets for future obesity intervention strategies.

Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.

Chronic lung infections in cystic fibrosis (CF) patients are associated with Pseudomonas aeruginosa biofilms exhibiting high antibiotic tolerance with no clear explanation. We investigate the role of the biofilm matrix in this antibiotic tolerance using 3D biofilm models based on acetylated alginate and DNA, mimicking mucoid biofilms. Printed from these bioinks seeded with P. aeruginosa (PAO1), these models support robust microcolony formation as observed in vivo and enable high-throughput assessment of antibiotic diffusion and efficacy. Surprisingly, antibiotic diffusion is not significantly impeded by acetylation or DNA incorporation. Despite this, bacterial tolerance increases tremendously upon encapsulation in alginate. Acetylation further enhances tolerance, particularly to tobramycin, ciprofloxacin, and colistin. The addition of DNA mitigates this effect in a drug-specific manner. While mucoid biofilms, in contrast to the biofilm models, show significant retardation of antibiotic penetration, they also get saturated with all tested antibiotics within 20 h. This demonstrates that direct interaction with alginate or DNA does not explain the slow diffusion of antibiotics in mucoid P. aeruginosa biofilms. Our findings challenge the view that diffusion limitation or antibiotics binding by biofilm exopolysaccharides dominate biofilm resilience and highlight the need to target matrix-induced bacterial adaptation in the development of antibiofilm therapies.

Rapid urbanization and dense populations in metropolitan areas increase the risk of tick-borne disease transmission. We profiled 139 RNA libraries of 1697 adult ticks belonging to Haemaphysalis longicornis, Haemaphysalis concinna, Dermacentor silvarum, Dermacentor sinicus, and Rhipicephalus sanguineus, field-collected in the Hebei region. Among 179 viral species, four human pathogens (a novel Bandavirus dabieense genotype, Orthonairovirus nairobiense, Thogotovirus thogotoense, and Xue-Cheng virus) were identified, highlighting potential emerging tick-borne disease threats. Four viruses infecting animals (Lagovirus europaeus, Ovine parvovirus, canine parvovirus, and Psittaciform Parvoviridae sp.) were discovered for the first time in ticks, suggesting the role of ticks as a potential reservoir. Hebei bunya-like virus 1, Dandong tick virus 1, and Zhejiang mosquito virus 3 were genetically closely related to mosquito-associated viruses, suggesting a potential transmission route for these viruses through both mosquitoes and ticks. The diverse tick virome in metropolitan surroundings contained potential human and animal pathogens, highlighting the need for proactive surveillance of emerging tick-borne viruses.

Addressing antibiotic-resistant bacterial biofilm infections without promoting drug resistance is a pressing challenge. Pseudomonas aeruginosa is well known for causing biofilm-associated drug-resistant infections that often lead to treatment failure. In this study, we identified a previously uncharacterized membrane protein ferredoxin encoded by PA1551 using photoaffinity-based biomimetic probes based on our previous dual-acting antibiofilm compound 2-(heptanamido)methyl 3-hydroxy-1,6-dimethylpyridin-4(1H)-one (10d). The precision-targeted ferredoxin PA1551 exhibited excellent effectiveness in various model systems, suppressing bacterial biofilm and virulence, and enhancing the antibacterial effects of tobramycin (Tob, by about 200-fold) and ciprofloxacin (CIP, by 1000-fold) compared to single-dose antibiotic treatments in a mouse model of Pseudomonas aeruginosa wound infection. These results indicate that ferredoxin PA1551 can be used as target to design new antibiofilm drugs for the treatment of Pseudomonas aeruginosa infections, particularly challenging bacterial biofilms.

During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.

Bacteria that colonize the human gut must withstand a variety of stressors, including detergent-like compounds known as bile acids. Here, we investigated how bile acids found in the human cecum and colon impact the behavior of the probiotic strain Escherichia coli Nissle 1917 (EcN). We found that lithocholic acid (LCA), which is a microbiota-derived secondary bile acid, promotes the formation of a distinctive surface-coating biofilm by EcN, including on an organoid-derived model of the human colonic epithelium. Mechanistic investigations revealed that LCA upregulates the production of several components of flagella, which are essential for LCA-induced biofilm formation and form part of the biofilm matrix. Furthermore, LCA-induced biofilm formation helps EcN compete against certain pathogenic strains. Taken together, our findings shed light on how an abundant colonic metabolite influences the behavior of a clinically proven probiotic strain, triggering the formation of biofilms that may contribute to pathogen suppression.

This study examines a subterranean estuary seepage face in China's Sanggou Bay by comparing environmental parameters and microbiome data before and after the COVID-19 lockdown, in order to reveal the regulatory mechanisms of coastal resting on microbial community stability and biogeochemical functions. The results revealed that reduced human activities significantly decreased sediment nutrient loading and shifted organic matter sources from terrestrial- to marine-dominated. This environmental restructuring drove profound microbial community reorganization: while α-diversity indices declined, the relative abundance of core species increased, with marked enhancements in community stability and metabolic efficiency, particularly in pathways related to amino acid metabolism, carbohydrate metabolism, and biogeochemical cycling. The study confirms that a coastal rest period can enhance ecosystem resilience by reducing anthropogenic disturbance, optimizing resource allocation, and activating microbial functional plasticity. These findings suggest that rest periods may represent a potential strategy for supporting ecosystem resilience and sustainability.

Plant-parasitic nematodes (PPNs) pose a significant threat to global crop production, yet their associated viral diversity remains poorly characterized, limiting potential virus-mediated biocontrol strategies. In this study, we investigated PPN-associated viruses using both virome data obtained from ten field populations of potato rot nematode (Ditylenchus destructor) collected in Lulong County (Qinhuangdao city, China), a major sweet potato-producing region, along with 536 publicly available transcriptome datasets from the Sequence Read Archive (SRA) database, collectively encompassing twenty-five PPN species. We identified 94 PPN-associated viruses, representing a 7.9-fold increase over prior records. These viruses span eighteen established families and six unclassified viral groups, including the first discovery of orthomyxo-like viruses, Jingmen viruses, and ormycoviruses in PPNs or nematodes, expanding the possible host ranges of these viral groups. Notably, a clade of yue-like viruses harbored up to 10 introns, surpassing 2-3 introns that were only observed in orthomyxoviruses and certain members of the Mononegavirales. Furthermore, we identified two larger nematode-associated bunyaviruses with the L segments exceeding 12,000 bp, which appear to have acquired a putative cysteine proteinase gene potentially originating from their nematode hosts (possibly Pristionchus spp.). Our findings reveal that natural PPN populations could host an unexpectedly high diversity of RNA viruses, higher than previously recognized. Exploring these viruses provides novel insights into viral evolution and establishes a foundation for utilizing viruses as a potential method for controlling PPN diseases.