Microbiome最新文献

Background: Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes' effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns.

Results: Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance.

Conclusions: Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture. Video Abstract.

Background: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.

Results: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for ~ 70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of < 2.9 Mbp and G + C contents of < 40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.

Conclusions: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.

Background: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.

Results: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.

Conclusions: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.

Background: Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on testing sample stabilization protocols to be applied before metaproteomic analysis.

Results: This collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed independently by two mass spectrometry facilities at distinct international locations. Analysis of the mass spectrometric data using two different search engines revealed that the fecal metaproteome profile differed considerably depending on the stabilization method used in terms of richness, alpha and beta diversity, reproducibility, and quantitative distribution of main taxa and functions. Although each method showed unique strengths and weaknesses, a commercial swab-based device stood out for its remarkable reproducibility and ranked highest for most of the metrics measured.

Conclusions: CAMPI-2 allowed a robust evaluation of five different methods for preserving fecal metaproteome samples. The present investigation provides useful data for the design of metaproteomics and multi-omics studies where fecal sampling cannot be immediately followed by long-term storage at - 80 °C. Further optimization of the tested protocols is necessary to improve stabilization efficiency and control bias in the taxonomic and functional profile of the gut microbiome. Video Abstract.

Background: Individuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated bacteriuria and urinary tract infections (UTI). Current identification of these conditions lacks precision, leading to inappropriate antibiotic use, which promotes selection for drug-resistant bacteria. Since infection often leads to dysbiosis in the microbiome and correlates with health status, this study aimed to develop a machine learning-based diagnostic framework to predict potential UTI by monitoring urine and/or catheter microbiome data, thereby minimising unnecessary antibiotic use and improving patient health.

Results: Microbial communities in 609 samples (309 catheter and 300 urine) with asymptomatic and symptomatic bacteriuria status were analysed using 16S rRNA gene sequencing from 27 participants over 18 months. Microbial community compositions were significantly different between asymptomatic and symptomatic bacteriuria, suggesting microbial community signatures have potential application as a diagnostic tool. A significant decrease in local (alpha) diversity was noted in symptomatic bacteriuria compared to the asymptomatic bacteriuria (P < 0.01). Beta diversity measured in weighted unifrac also showed a significant difference (P < 0.05) between groups. Supervised machine learning models were trained on amplicon sequence variant (ASVs) counts and bacterial taxonomic abundances (Taxa) to classify symptomatic and asymptomatic bacteriuria with a repeated tenfold and leave-one-out participant (LOPO) type of cross-validation approaches. Combining urine and catheter microbiome data improved the model performance during repeated tenfold cross-validation, yielding a mean area under the receiver operating characteristic curve (AUROC) of 0.95 (95% CI 93-0.97) and 0.83 (95% CI 0.79-0.89) for ASVs and taxonomic features in the independent held-out test set, respectively. The LOPO cross-validation yielded a mean AUROC of 0.87 (95% CI 0.85-0.89) and 0.79 (95% CI 0.77-0.82) for ASVs and taxa features, respectively. These results suggest the potential of microbiome features in differentiating symptomatic and asymptomatic bacteriuria states.

Conclusions: Our findings demonstrate that signatures within catheter and urine microbiota could serve as tools to monitor the health status of SCI patients. Establishing a classification system based on these microbial signatures could equip physicians with alternative management strategies, potentially reducing UTI episodes and associated hospital costs, thus significantly improving patient quality of life while mitigating the impact of drug-resistant UTI. Video Abstract.

Background: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.

Results: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.

Conclusions: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.

Background: Inflammatory bowel disease (IBD) is a chronic inflammatory disease that has become prevalent worldwide. Excessive expansion of Enterobacteriaceae is a key feature of dysbiosis in IBD patients, which further exacerbates intestinal inflammation. Therefore, inhibiting the dysbiotic expansion of Enterobacteriaceae is a promising strategy for the treatment of IBD. We investigated the effects of Abelmoschus manihot (A. manihot) flowers on the intestinal microbiota during colitis.

Results: We found that A. manihot flowers are capable of ameliorating murine colitis and suppressing Enterobacteriaceae expansion, not by direct action but rather by promoting the growth of Lachnospiraceae, particularly Clostridium bolteae. Bacterial depletion and recolonization confirmed that Clostridium bolteae restored colonic hypoxia via PPAR-γ activation, creating an environment unfavorable for Enterobacteriaceae growth and reducing inflammation. Moreover, intestinal hypoxia is vital for Clostridium bolteae colonization and its effect on Enterobacteriaceae expansion, which involves crosstalk between gut microbe colonization and intestinal oxygen homeostasis.

Conclusion: Overall, our study provides evidence that modulating the gut microbiota to restore intestinal hypoxia is a promising therapeutic strategy for suppressing Enterobacteriaceae proliferation in the inflamed gut and for ameliorating intestinal inflammation, which could be applied to other Enterobacteriaceae-related diseases. Video Abstract.

Background: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.

Results: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.

Conclusions: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.

Background: The plant holobiont concept emphasizes the critical role of the microbiome in host plant health and resilience. Microbial communities have been shown to enhance plant resistance to abiotic stresses, such as drought and salinity, and to mitigate the impact of phytopathogens. Traditional microbiome engineering approaches face challenges due to the complexity of microbial interactions. To overcome these limitations, recent advances in transcriptomics and metataxonomics analyses enable the identification of microbiome-associated phenotypes, co-occurrence networks, and key host genes-microbiome interactions. We present a novel framework combining co-occurrence network analyses and transcriptome-microbiota correlations to identify keystone belowground microorganisms and host genes potentially involved in olive (Olea europaea L.) tolerance to Verticillium wilt, a devastating disease caused by the soil-borne, fungal vascular pathogen Verticillium dahliae Kleb. Our approach aims to identify microbiome-regulating host genes and keystone bacteria and fungi that could be instrumental as genetic and microbiological markers in olive breeding programs.

Results: In the root endosphere, cultivars qualified as tolerant to Verticillium wilt of olive (VWO) exhibited an enrichment of the bacterial genera Actinophytocola, Kibdelosporangium and Nocardia. Keystone taxa analyses revealed clearly different profiles when comparing the microbial co-occurrence networks of the VWO-tolerant genotypes with those varieties described as susceptible to V. dahliae. Thus, tolerant cultivars harbored bacteria predominantly displaying negative interactions with the mycobiome. In contrast, VWO-susceptible cultivars displayed microbial hubs with positive fungal correlations. Transcriptomic analyses of olive roots identified 1,143 differentially expressed genes (DEGs), with 309 upregulated genes in tolerant cultivars, highlighting biological processes like defense response, carbohydrate metabolism, and amino acid transport. Key microbial taxa (Actinophytocola, Kibdelosporangium, Nocardia, Aquabispora, and Fusarium) strongly correlated with DEGs associated with plant defense.

Conclusions: Keystone microbial taxa, particularly Actinophytocola and Nocardia, are proposed to play an important role against V. dahliae within the indigenous olive root microbiota under natural conditions. Moreover, our findings underscore the importance of studying keystone taxa along with essential host plant genes to holistically understand plant-microbiota interactions and explore their potential in disease management. This integrative approach provides insights into the complex dialogue taking place between the host plant and its microbiota, offering potential targets for microbiome engineering to enhance olive resilience against VWO. Video Abstract.

Background: Planktonic microalgae deploy multifaceted responsive and adaptive strategies against anthropogenic pollutants; however, current understanding of antibiotic resistance mechanisms remains predominantly focused on intrinsic physiological adaptations. While microalgae maintain intimate relationships with the phycosphere microbiome, the ecological roles of these associated microbes in mediating host adaptation to polluted environments are inadequately characterized.

Results: We identified a phycosphere microbiome-involved antibiotic resistance mechanism in Dictyosphaerium sp., a pollution-tolerant Chlorophyta microalgae exhibiting remarkable enrofloxacin (ENR) tolerance. Microalgal growth displayed initial inhibition followed by significant promotion under 5 mg/L ENR exposure. This resilience was associated with the restructuring of phycosphere microbiome, characterized by Porphyrobacter enrichment and functional enhancement of algal fitness-promoting pathways, including upregulation of cobalamin biosynthesis genes (log₂FC = 7.76) and a 33.3-fold increase in extracellular B₁₂ accumulation. Consequently, we isolated the ENR-selected microbial taxa to elucidate their roles in microalgal stress adaptation. Co-culturing axenic Dictyosphaerium sp. with Porphyrobacter enhanced microalgal growth by 36.5% after 8-day ENR exposure, whereas non-dominant bacteria exhibited negligible effects. Based on the transcriptomic and metabolomic analyses of the algal system when Porphyrobacter was dominant, we subsequently compared the growth of axenic microalgae with and without B vitamin (B₁, B₆, B₇, B₁₂) supplementation. Experimental validation demonstrated the pivotal role of B₁₂-producing Porphyrobacter in enhancing microalgal ENR adaptation through (i) stimulating extracellular polymeric substances production and subsequently enhancing ENR removal via EPS-mediated adsorption and (ii) alleviating intracellular oxidative stress via elevating superoxide dismutase and peroxidase activities and reducing malondialdehyde levels. Additionally, this B₁₂-producing bacteria/B₁₂-mediated adaptability exhibited cross-species conservation, improving ENR resistance in Chlorella vulgaris and Scenedesmus quadricauda, with analogous protection observed under ciprofloxacin and norfloxacin exposures.

Conclusion: Collectively, our findings establish stress-induced enrichment of B₁₂-producing Porphyrobacter within the phycosphere microbiome as a pivotal mechanism underlying microalgal antibiotic adaptation. This insight facilitates the rational development of microalgae-microbiome systems for enhanced wastewater treatment and sustainable bioproduction, with applications in aquatic feed supplementation, biofuel production, and biofertilizer development. Video Abstract.