Microbiome最新文献

Background: The maternal gut microbiota can modulate host physiological homeostasis through metabolites. Maternal reproductive potential hinges on placental angiogenesis and nutrient transport efficiency, directly determining fetal developmental outcomes. However, the specific molecular mechanisms by which microbial metabolites influence reproductive potential remain to be elucidated. This study aimed to clarify the mechanisms by which maternal gut microbiota affects reproductive potential.

Results: We initially analyzed the metabolic profiles by untargeted metabolomics and the fecal microbiota by 16S rRNA sequencing in sows with different reproductive potential. Sows with high reproductive potential exhibited elevated plasma arginine and fecal thiamine levels. Meanwhile, Lactococcus was enriched in the feces of sows with high reproductive potential. Subsequently, we evaluated the effects of thiamine (a signature metabolite identified) on maternal reproductive potential, gut microbiota, placental angiogenesis, and nutrient transport capacity using a rat model. The results showed that thiamine supplementation in pregnant rats effectively promoted offspring growth and enhanced transplacental thiamine metabolism. Moreover, thiamine modulated maternal gut microbiota composition, increased the abundance of Prevotellaceae Ga6A1 group and Bacteroidale RF16 group unclassified, and promoted butyrate production. We found that thiamine improved placental function by enhancing thiamine-related metabolic enzymes and acetyl-CoA content. It also promoted the migratory capacity of pTr cells. Importantly, thiamine facilitated placental angiogenesis by activating Notch signal transduction, which in turn initiated the PI3K/AKT signaling cascade. Ultimately, this cascade regulated the efficiency of placental nutrient metabolism and the expression of nutrient transporters.

Conclusions: Cumulatively, the gut microbiota regulates early offspring development through metabolite-mediated host interactions. This study provides new evidence that maternal gut microbiota-derived thiamine activates placental Notch signaling to coordinate angiogenesis and nutrient transport, thereby improving pregnancy outcomes. These findings provide novel perspectives and potential actionable strategies for maternal microbial regulation of maternal-fetal health during gestation.

Background: The emerging concept of the pathobiome has revolutionized our understanding of disease etiology by emphasizing the complex interactions between multiple pathogens and their hosts during disease progression. Although significant advancements have been made in characterizing the pathobiome in human, animal, and plant diseases, the pathobiome associated with seaweed diseases remains unexplored. Saccharina japonica, a commercially important farmed seaweed, has increasingly suffered from bleaching disease during its nursery stage, severely compromising the supply of healthy sporelings and sea field cultivation. Despite its significant economic consequences, the pathobiome associated with this bleaching disease and its interactions with the host remain unclear, posing a major challenge for disease control.

Results: Through multi-omics and meta-omics analyses, we identified the pathobiome associated with bleaching disease in S. japonica and elucidated its interactions with the host. The pathobiome is dominated by the core taxa Bin_7 (Glaciecola sp.), Bin_12 (Arenicella sp. 017854775), and Bin_22 (Arenicella sp.), which employ virulence mechanisms such as chemotaxis, motility, and toxin secretion to initiate infection. In response, the host S. japonica activates a multifaceted defense, including mechanisms like cell wall strengthening, reactive oxygen species bursts, and antibiotic production to combat the invading pathobiome. To counteract these host defenses, the core pathobiome taxa upregulate genes associated with antioxidant enzymes and antibiotic resistance, enabling their establishment and persistence within the host.

Conclusions: This study provides the first analysis of the pathobiome in seaweed diseases. By identifying the core taxa of the pathobiome, their virulence mechanisms, and the host defense responses, we elucidate the pathobiome-host interactions underlying S. japonica bleaching disease. These findings significantly advance our understanding of the pathobiome in seaweed diseases and lay the groundwork for developing targeted strategies to control the bleaching disease in seaweed aquaculture. Video Abstract.

Background: Many coastal ecosystems worldwide are impacted by wastewater discharges, which introduce nutrients, pollutants, and allochthonous microbes that can alter microbiome composition and function. Although the severity and distribution of these impacts vary across regions, their potential consequences for key ecological processes remain a concern. The resilience and functional adaptability of native coastal microbiomes are still poorly understood. To study the immediate ecological impact of wastewater discharge on a coastal seawater microbiome, we conducted short-term microcosm experiments, exposing a coastal microbiome to two types of treated wastewater: (i) unfiltered wastewater containing nutrients, pollutants, and allochthonous microbes; and (ii) filtered wastewater containing only nutrients and pollutants.

Results: By integrating multi-omics and metabolic assays, we show that wastewater-derived organic matter and nutrients (mostly ammonia and phosphate) did not alter the taxonomic composition of the coastal microbiota, but triggered reorganization of metabolic pathways in them. We observed enhanced metabolism of proteins, amino acids, lipids, and carbohydrates, particularly of the lineages Alteromonadales, Rhodobacterales, and Flavobacteriales. Glaciecola (Alteromonadales), a copiotroph with antagonistic traits, significantly contributed to these shifts. Conversely, allochthonous taxa like Legionellales and Pseudomonadales had minimal impact. Elevated phosphorus concentrations resulting from wastewater input reduced the synthesis of proteins linked to scavenging phosphorus from organic phosphorus compounds, including alkaline phosphatase activity in native Rhodobacterales and Flavobacteriales, with important ecological implications for phosphorus-depleted coastal ecosystems. Furthermore, the presence of wastewater caused a decline in relative abundance and metabolic activity of Synechococcus, potentially affecting carbon cycling. Yet, the coastal microbiome rapidly respired wastewater-derived dissolved organic carbon, resulting in bacterial growth efficiencies consistent with global coastal averages.

Conclusions: Our findings highlight the capacity of coastal microbiomes to withstand wastewater discharge, with critical implications for assessment of anthropogenic perturbations in coastal ecosystems. However, wastewater-driven changes in metabolic functions and niche utilization within the autochthonous microbial community, impacting phosphorus cycling and potentially affecting carbon cycling, may have long-term consequences for ecosystem functioning. Video Abstract.

Background: The rhizosphere microbiome, as the second genome of plant immunity, forms a critical ecological barrier in plant-pathogen interactions. However, its functional mechanism in resisting the replanting disease pathogenic Fusarium proliferatum MR5 in apples has not been systematically elucidated. This study employed an integrated multi-omics approach to investigate the rhizosphere mechanisms of resistant (CG935) and sensitive (M9T337) apple rootstocks, aiming to uncover the metabolic and microbial interactions underlying apple replant disease resistance.

Results: Multiple omics joint analysis found that the infection of Fusarium proliferatum MR5 triggered the activation of a specific lysine biosynthesis pathway in resistant rootstocks, and the expression levels of key rate limiting enzymes aspartate kinase and dihydrodipicolinate synthase were significantly upregulated by 2.79 ~ 6.81 times compared to M9T337. Along with the metabolic reprogramming process, the efflux of lysine from the rhizosphere increased, and Bacillus with broad-spectrum antibacterial activity were specifically recruited, increasing its relative abundance by 40.73%. In vitro assays demonstrated that the recruited Bacillus suppressed Fusarium spore germination and disrupted mycelial growth through the production of antifungal compounds, including 2,4-di-tert-butylphenol and bacillomycin. Potted experiments have confirmed that the synergistic treatment of Bacillus and lysine significantly reduces the number of pathogenic Fusarium in the rhizosphere, increases soil enzyme activity, and reshapes a more stable rhizosphere bacterial community structure by enhancing the modularity (the degree of modularity in microbial network structure) of the microbial network. This collaborative strategy effectively alleviates the physiological damage of apple seedlings under replanting stress, resulting in a 31.18% increase in plant fresh weight. Field validation experiments further demonstrate that this strategy can promote the growth of replanted apple saplings and reduce the occurrence of apple replant disease.

Conclusions: Our findings elucidate an apple replant disease resistance mechanism in apple rootstocks involving lysine-mediated recruitment of protective Bacillus, which enhances rhizosphere microbiome stability and suppresses soil pathogenic Fusarium. Developed a technology for synergistic control of apple replant disease using Bacillus-lysine. The research results provide theoretical basis and practical solutions for green control of apple replant disease based on precise regulation of rhizosphere microbiome. Video Abstract.

Background: Biocontrols can be used to manage pests while supporting soil health. However, the effects of the biocontrols such as predatory mites on antibiotic resistance in bacterial communities remains largely unknown. Here, we examined long-term field experiments in tea garden soils, combined with global datasets and soil microcosm experiments, to explore the effects and underlying mechanisms of predatory mite treatment on the abundance of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs).

Results: Predatory mite treatment may intensify the predation pressure exerted by bacterial predators on bacterial communities through trophic cascades. This led to genome streamlining and alterations in microdiversity and functions within the bacterial communities. In this process, members of the phylum Actinobacteriota, especially the family Pseudonocardiaceae, demonstrated greater adaptability, with their relative abundance increasing from 25.0 to 41.8%, due to their higher nucleotide diversity and growth rates compared to other bacterial taxa. These taxa served as the primary hosts for ARGs and VFGs, which were also identified in global datasets, playing a key role in promoting the abundance of ARGs and VFGs in soil ecosystems. The possibility of trophic cascade effects of predatory mites on the dispersal of ARGs and VFGs were further validated through soil microcosm experiments.

Conclusions: These findings advance our understanding of bacterial evolutionary trajectories under biocontrols, which is crucial for slowing the spread of antibiotic resistance and promoting sustainable agriculture. Video Abstract.

Background: Pangolins, the world's most trafficked mammals, have emerged as critical subjects of study due to their potential role as intermediate hosts for zoonotic viruses. While previous studies have primarily focused on diseased pangolins, the virome composition of healthy individuals remains largely unexplored.

Results: To address this knowledge gap, we performed comprehensive metatranscriptomic analysis of 83 healthy pangolins, in comparison with virome data of 52 diseased individuals derived from previously published datasets. We identified 51 viral operational taxonomic units (vOTUs) across six mammalian-associated viral families: Parvoviridae, Picornaviridae, Papillomaviridae, Circoviridae, Flaviviridae, and Paramyxoviridae. Notably, we observed recombination in Morbillivirus canis isolate BJ16B35, Canine distemper virus strain PS, and UN_MBA191024-Paramyxoviridae-1 from pangolins and domestic dogs, suggesting cross-species transmission dynamics. Co-infection analysis revealed a strong positive correlation between Copiparvovirus P171T/pangolin/2018 and Pangolin protoparvovirus, suggesting possible shared transmission pathways. Several viruses, including Orthopneumovirus hominis and Orthorubulavirus mammalis, were exclusively detected in diseased pangolins, implicating their potential role in pathogenesis. Zoonotic risk assessment identified 16 vOTUs with high predicted potential for human infection, including Pangolin pestivirus and Manis javanica papillomavirus 1.

Conclusions: Our findings significantly expand our understanding of viral diversity in healthy pangolins and help distinguish commensal viral communities from potentially pathogenic ones. This research underscores the importance of continued wildlife viral surveillance for both conservation and public health preparedness. Video Abstract.

Background: Litchi downy blight (LDB) is a major disease affecting litchi (Litchi chinensis), damaging fruits, inflorescences, and leaves, and significantly hindering the development of the litchi industry in China and globally. Bacillus amyloliquefaciens PP19 has demonstrated significant biocontrol efficacy against LDB, but its mechanism of action remains unclear.

Results: This study used microbiome analysis and bacterial interaction studies to investigate the biocontrol mechanism by which PP19 regulates core microbial communities on litchi exocarps to suppress LDB. First, 16S rRNA diversity analysis revealed that PP19 pretreatment effectively prevented bacterial diversity imbalances caused by Peronophythora litchii infection, maintaining microbial stability by regulating the abundance of specific genera (Actinomycetospora, Paenibacillus, and Spirosoma). Microbial interaction networks and functional prediction revealed that PP19 might modulate bacterial motility pathways, resulting in changes to the abundance of specific microbial communities on litchi exocarps. These changes facilitated the formation of a core microbiome negatively correlated with the abundance of P. litchii. By isolating and genetically identifying 83 cultivable bacterial strains from litchi exocarps and using correlation analysis, 16 candidate strains with potentially significant interactions with PP19 and P. litchii SC18 were identified. Plate antagonism, liquid co-culture, and leaf biocontrol efficacy analyses ultimately identified four representative strains (Sphingomonas sp. F14, Rhizobium sp. F26, Pseudomonas sp. F32, and Enterobacter cloacae F63) with significant interactions with either PP19 or P. litchii. Interaction, motility, and biofilm production analyses showed that PP19 interacted with the four litchi exocarp bacteria to prevent disease through various mechanisms, and enhanced their motility and biofilm production to varying degrees.

Conclusions: PP19 regulates core microbial communities on litchi exocarps, maintaining community stability and enriching interacting strains which together inhibit the growth of P. litchii, thereby achieving biocontrol efficacy. Video Abstract.

Background: The development of the small intestine is crucial during early life, with the gut microbiota and microbe-derived metabolites playing key roles in regulating intestinal epithelial barrier function and overall development. However, the underlying mechanism remains unclear. Here, chicks were used to investigate the influences of early-life crosstalk among bacteria, metabolites, and the host on small intestinal development.

Results: We investigated bacterial succession in the small intestine of broiler chicks at four time points during early development. After 3 days post-hatch, Bacillota became the dominant phylum. At the genus level, Lactobacillus and Ligilactobacillus emerged as the two dominant genera, and their abundance was significantly positively correlated with small intestine weight. Metabolome analysis revealed that indole-3-carboxaldehyde (IAld) is derived from both L. gallinarum C2-16-2 (LG) and L. salivarius D7-21 (LS). Moreover, we found that IAld can be converted into bioactive indole-3-carboxylic acid (ICA) in animals, which exhibited greater biological activity than IAld in vitro. Further chick feeding trials revealed that both bacteria (LG and LS) and metabolites (IAld and ICA) promoted epithelial barrier function and enhanced antioxidant capacity during early life in chicks. Moreover, both IAld and ICA promoted tight junction protein expression and enhanced antioxidant capacity by activating AHR-NRF2 signaling.

Conclusions: These findings suggest that specific bacterial strains (L. gallinarum C2-16-2 and L. salivarius D7-21) and metabolites (IAld and ICA) serve as effective promoters of intestinal epithelial barrier function and antioxidant capacity during early intestinal development in chicks Video Abstract.