Microbiome最新文献

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.

Background: Habitat fragmentation and degradation have led to the critical endangerment of numerous wild plant species. Although significant achievements in the conservation of endangered wild plants in various regions worldwide, the interaction mechanisms between these plants and their associated rhizosphere microorganisms have yet to be fully elucidated.

Results: Here, we present a communication model between the endangered wild plant Qingdao lily (Lilium tsingtauense) and its associated rhizosphere microorganisms. We isolated a rhizosphere fungus, Trichoderma longibrachiatum QDAU 0920, which effectively colonizes the roots of Qingdao lily and significantly promotes root growth. This growth enhancement is mediated by multiple plant hormones, with auxin playing a particularly prominent role. Further investigation revealed that a non-canonical AUX/IAA protein of the LtIAA16 may augment the transcriptional activation activity of LtARF22 by competitively interacting with LtIAA6, LtIAA17, and LtIAA11, thereby facilitating root growth in Qingdao lily. The growth-promoting effects of this interaction were subsequently validated in several other plant species, including tomato, pepper, corn, pumpkin, and cucumber. Notably, T. longibrachiatum QDAU 0920 forms synthetic microbial consortia (SynComs) in conjunction with other Trichoderma and Penicillium species. These SynComs consistently enhance the growth of Qingdao lily as well as other lily species such as L. lancifolium, Lilium 'Avalon Sunset', and Lilium 'Deliana'.

Conclusion: Collectively, these findings underscore the considerable potential of native microorganisms in the development of plant growth-promoting agents and the conservation of endangered plant species. Video Abstract.

Background: The ocular surface microbiome (OSM) in patients with meibomian gland dysfunction (MGD) differs from that of healthy individuals. However, the precise role of OSM in MGD remains unknown. Therefore, we aimed to investigate the mechanism of OSM in the inflammation of MGD and the effects of topical sodium butyrate (SB) treatment in ApoE^-/- mice.

Methods: ApoE^-/- (n = 36) and wild-type C57BL/6J (n = 16) mice served as MGD models and healthy controls, respectively. MGD mice were treated with safety-confirmed concentrations of SB (1, 5, and 10 mM) and PBS for 3 weeks. OSM was analyzed by 16S rRNA gene sequencing (V3-V4). The slit-lamp biomicroscopy, tear cytokines, histopathology (oil red O/PAS/TUNEL staining), and TLR4/MyD88/NF-κB signaling (RT-qPCR, immunohistochemistry, and Western blotting) were evaluated.

Results: Five-month-old ApoE^-/- mice exhibited typical clinical and histological features of MGD. These mice exhibited elevated tear levels of inflammatory cytokines and activation of the TLR4/NF-κB signaling pathway in the MGs and conjunctivae. Treatment with SB improved the corneal fluorescein staining score of MGD. The ApoE^-/- mice demonstrated dysbiosis of OSM, characterized by an increase in Proteobacteria and a decrease in Bacteroidota. Additionally, the relative abundance of Muribacter and Muribacter muris increased in ApoE^-/- mice, while that of Staphylococcus and Staphylococcus lentus decreased, and these alterations were restored by SB treatment. SB also reduced the expression of the TLR4/NF-κB p65 signaling pathway, inflammatory cytokines, and apoptosis in MGs and conjunctival tissues.

Conclusion: ApoE^-/- mice exhibited characteristic features of MGD, accompanied by dysbiosis of OSM. Topical administration of SB modulated the OSM and reduced MGD-associated inflammation. Video Abstract.

Background: The prevalence of calcium oxalate (CaOx) kidney stones is increasing, yet the underlying mechanisms remain incompletely understood. Emerging evidence suggests that gut microbiota-particularly short-chain fatty acid (SCFA)-producing bacteria-may modulate host metabolism and inflammation, thereby influencing stone formation. However, the mechanistic links between gut dysbiosis, metabolic disturbances, and CaOx stone pathophysiology remain to be fully elucidated. This study investigates gut microbiota composition, SCFA levels, and metabolomic alterations in CaOx stone formers (CSF), aiming to uncover potential pathophysiological mechanisms and therapeutic targets.

Results: Among 59 CSF and 60 healthy controls (HC), CSF exhibited significantly reduced microbial richness, with marked depletion of SCFA-producing bacteria such as Faecalibacterium prausnitzii and Eubacterium rectale. This dysbiosis was associated with decreased fecal and plasma SCFA levels, reduced 24-h urinary citrate, and widespread metabolic disturbances, particularly in tryptophan metabolism and the citrate cycle. Plasma SCFA levels were positively correlated with urinary citrate excretion, suggesting a regulatory link within the gut-kidney axis. Mendelian randomization analysis suggested that Bacteroides thetaiotaomicron may be a potential microbial risk factor for stone formation (OR = 1.26, 95% CI: 1.03-1.54, p = 0.028). In a hyperoxaluria rat model, interventions with F. prausnitzii, E. rectale, or sodium butyrate reduced renal CaOx crystal deposition and kidney injury.

Conclusions: Our findings highlight the central role of SCFA-producing bacteria and their metabolites in maintaining metabolic balance and protecting against CaOx stone formation. Gut dysbiosis and reduced SCFA levels appear to drive metabolic changes that contribute to stone development. B. thetaiotaomicron may increase stone risk, while F. prausnitzii, E. rectale, and sodium butyrate show therapeutic potential. These insights support further exploration of microbiome-based strategies for the prevention and personalized management of kidney stones. Video Abstract.

Background: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.

Results: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.

Conclusions: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.

Background: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.

Results: A total of 40 Holstein dairy cows at 21 days to 30 days postpartum were assigned into heathy cows (n = 15), subclinical endometritis cows (n = 12) and clinical endometritis cows (n = 13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.

Conclusion: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.