Inter-kingdom Network Research Articles

Fungal mycobiome dysbiosis in choledocholithiasis concurrent with cholangitis.

The gut mycobiome might have an important influence on the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to characterize the fungal mycobiome profiles, explore the correlation and equilibrium of gut interkingdom network among bacteria-fungi-metabolites triangle in CCs. In a retrospective case-control study, we recruited patients with CC (n = 25) and healthy controls (HCs) (n = 25) respectively to analyze the gut fungal dysbiosis. Metagenomic sequencing was employed to characterize the gut mycobiome profiles, and liquid chromatography/mass spectrometry (LC/MS) analysis was used to quantify the metabolites composition. The Shannon index displayed a reduction in fungal α-diversity in CCs compared to HCs (p = 0.041), and the overall fungal composition differed significantly between two groups. The dominant 7 fungi species with the remarkable altered abundance were identified (LDA score > 3.0, p < 0.05), including CC-enriched Aspergillus_niger and CC-depleted fungi Saccharomyces_boulardii. In addition, the correlations between CC-related fungi and clinical variables in CCs were analyzed. Moreover, the increased abundance ratio of Basidiomycota-to-Ascomycota and a dense linkage of bacteria-fungi interkingdom network in CCs were demonstrated. Finally, we identified 30 markedlyaltered metabolites in CCs (VIP > 1.0 and p < 0.05), including low level of acetate and butyrate, and the deeper understanding on the complexity of bacteria-fungi-metabolites triangle involving bile inflammation was verified. Our investigation demonstrated a distinct gut fungal dysbiosis in CCs and proposed that, beyond bacteria, the more attention should be paid to significantly potential influence of fungi and bacteria-fungi-metabolites triangle interkingdom interactions on pathogenesis of CC.

Interkingdom network analyses reveal microalgae and protostomes as keystone taxa involved in nutrient cycling in large freshwater lake sediment.

Few studies have explored the role of interkingdom interactions between bacteria and microeukaryotes in nutrient cycling in lake ecosystems. We conducted sediment sampling from 40 locations covering Hongze Lake and analyzed their chemical properties. Intra- and interkingdom networks were constructed using 16S and 18S rRNA gene amplicon sequencing. Microeukaryotic intranetworks were more complex in spring than in autumn, while no clear variation in the complexity of bacterial intranetworks was found between autumn and spring. Larger and more complex bacterial-microeukaryotic bipartite networks emerged in spring than in autumn, correlated with lower carbon, nitrogen, and phosphorus levels in spring, likely resulting in intense microbial competition. Bacteria and microeukaryotes played different topological roles in interkingdom networks, with microeukaryotes contributing to the networks' greater complexity. Seven keystone modules were identified in spring and autumn nutrient cycling. Importantly, keystone taxa in these modules belonged to photoautotrophic microalgae or predatory protostomes, indicating that these organisms are key drivers in lake sediment nutrient cycling. Our results suggested that nutrient content variation in autumn and spring changes interkingdom networks' topological structure between bacteria and microeukaryotes. Microalgae and protostomes are essential in freshwater lake nutrient cycling and may be targeted to modulate nutrient cycling in large freshwater ecosystems.

Altered gut bacterial–fungal interkingdom networks in children and adolescents with depression

BackgroundMost studies of the gut–brain axis have focused on bacteria; little is known about commensal fungi. Children and adolescents with depression were reported to have gut bacterial microbiota dysbiosis, but the role of the mycobiota has not been evaluated. MethodsFaecal samples were obtained from 145 children and adolescents with depression and 110 age- and gender-matched healthy controls. We analysed the fungal microbiota, including in terms of their associations with the gut microbiota, and subjected the internal transcribed spacer 2 (ITS2) rRNA gene to mitochondrial sequencing. ResultsOur findings revealed unaltered fungal diversity, but altered taxonomic composition, of the faecal fungal microbiota in the children and adolescents with depression. Key fungi such as Saccharomyces and Apiotrichum were enriched in the depressed patients, while Aspergillus and Xeromyces showed significantly decreased abundance. Interestingly, the bacterial–fungal interkingdom network was markedly altered in the children and adolescents with depression, and mycobiome profiles were associated with different bacterial microbiomes. LimitationThe cross-sectional design precluded the establishment of a causal relationship between the gut mycobiota and the children and adolescents with depression. ConclusionsThe gut mycobiome is altered in the children and adolescents with depression. Our findings suggest that fungi play an important role in the balance of the gut microbiota and may help identify novel therapeutic targets for depression.

A18 INTERKINGDOM DYNAMICS AND NUTRITION ARE ASSOCIATED WITH DIVERGENT MATURATIONAL PATTERNS OF THE INFANT BACTERIAL AND FUNGAL GUT MICROBIOME

Abstract Background Early life has been identified as a critical window, during which time deviations from typical patterns of gut microbiome maturation have been associated with adverse health outcomes later in life. In the first 2-3 years of life, the infant gut microbiome undergoes ecological shifts characterized by increasing bacterial alpha diversity and variable changes in fungal alpha diversity. Research has shown not all infants follow these maturational trends, but our understandings of the factors linked to atypical microbiome maturation patterns are limited. Purpose We assessed bacterial and fungal gut microbiome maturation in early life to determine if atypical maturational patterns were observed in otherwise healthy infants and identify factors associated with these patterns. Method In 100 infants from the CHILD Cohort Study, we assessed the bacterial and fungal gut microbiome in stool samples collected at 3 and 12 months of age using 16S and ITS2 Illumina sequencing, respectively. We performed untargeted metabolomics on urine samples collected at 3 and 12 months using liquid chromatography-mass spectrometry/mass spectrometry. Microbiome and metabolomic measures were evaluated by ecological and multivariate analyses using RStudio. Result(s) Gut microbiome analyses revealed 24% and 20% of infants displayed atypical alpha diversity trajectories in the first year of life for bacteria or fungi, respectively. Atypical patterns were linked to reduced abundance of Bacteroides and increased Candida at 3 months. Functional analysis revealed an atypical bacterial alpha diversity trend was associated with elevated urinary trimethylamine N-oxide, creatine, indole acetic acid, and 2-furoylglycine, and an atypical fungal trend was associated with elevated urinary lactate. Using decision trees, the strongest predictors of atypical alpha diversity trends were interkingdom dynamics, breastfeeding duration, and maternal diet during pregnancy. Logistic regression revealed an atypical bacterial trend was positively associated with delivery via C-section and inversely associated with exclusive breastfeeding at 3 months, and an atypical fungal trend was positively associated with gestational consumption of artificially sweetened beverages and inversely associated with prenatal antibiotics. Interkingdom network analyses revealed the gut microbiome of infants with an atypical bacterial or fungal alpha diversity trend displayed a greater number of interkingdom interactions reflective of a less stable or immature gut microbiome. Conclusion(s) Our findings reveal a substantial proportion of infants display atypical patterns of gut microbiome maturation in the first year of life. While known microbiome-modifying factors were important determinants of maturational patterns, these factors were generally less influential than interkingdom influences. Together, this highlights the importance of interkingdom analyses at the individual level to generate more nuanced understandings of maturational trajectories in early life. Please acknowledge all funding agencies by checking the applicable boxes below CIHR, Other Please indicate your source of funding; Alberta Children's Hospital Research Institute Disclosure of Interest None Declared

Deciphering the microbial diversity associated with healthy and wilted Paeonia suffruticosa rhizosphere soil.

Plant health is closely related to the soil, where microorganisms play a critical and unique role. For instance, Paeonia suffruticosa is an emerging woody oil crop in China with attractive development and utilization prospects. However, black root rot causes wilting of the aboveground plant parts, which significantly affected its seed yield and quality. Studies found that soil microorganisms are critical in maintaining plant health, but how changes in the soil microbial communities affect the healthy and diseased oil peony is unclear. Therefore, our present study used high throughput sequencing and BIOLOG to analyze the rhizosphere soil microbial communities of healthy and diseased oil peonies. Our results revealed that the physical and chemical properties of the soil of the diseased plants had changed, with the ability to metabolize the carbon source being enhanced. Moreover, our research highlighted that the oil peony-infecting fungal pathogenic genus (Fusarium, Cylindrocarpon, and Neocosmospora) was closely associated with oil peony yield reduction and disease aggravation. Further network analysis demonstrated that the bacterial and fungal networks of the diseased plants were more complex than those of the healthy plants. Finally, the inter-kingdom network among the diseased plants further indicated that the lesions destroyed the network and increased the intraspecific correlation between the fungal groups.

Microbial Multitrophic Communities Drive the Variation of Antibiotic Resistome in the Gut of Soil Woodlice (Crustacea: Isopoda).

Multitrophic communities inhabit in soil faunal gut, including bacteria, fungi, and protists, which have been considered a hidden reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of research focusing on the relationships between ARGs and multitrophic communities in the gut of soil faunas. Here, we studied the contribution of multitrophic communities to variations of ARGs in the soil woodlouse gut. The results revealed diverse and abundant ARGs in the woodlouse gut. Network analysis further exhibited strong connections between key ecological module members and ARGs, suggesting that multitrophic communities in the keystone ecological cluster may play a pivotal role in the variation of ARGs in the woodlouse gut. Moreover, long-term application of sewage sludge significantly altered the woodlice gut resistome and interkingdom communities. The variation portioning analysis indicated that the fungal community has a greater contribution to variations of ARGs than bacterial and protistan communities in the woodlice gut after long-term application of sewage sludge. Together, our results showed that changes in gut microbiota associated with agricultural practices (e.g., sewage sludge application) can largely alter the gut interkingdom network in ecologically relevant soil animals, with implications for antibiotic resistance, which advances our understanding of the microecological drivers of ARGs in terrestrial ecosystem.

Microbial Diversity Analyses of Fertilized Thitarodes Eggs and Soil Provide New Clues About the Occurrence of Chinese Cordyceps.

Chinese cordyceps is a well-known fungus-larva complex with medicinal and economic importance. At present the occurrence of Chinese cordyceps has not been fully illuminated. In this study, the microbial diversities of fertilized Thitarodes eggs from sites A (high occurrence rates of Chinese cordyceps), B (low occurrence rates), and C (no Chinese cordyceps) were analyzed using 16S rRNA and ITS gene-sequencing technique. The previous sequencing data of soil from the same sites were conjointly analyzed. The results showed that bacterial communities among the eggs were significantly different. The bacterial diversity and evenness were much higher on site A. Wolbachia was overwhelmingly predominant in the eggs of sites B and C, while Spiroplasma showed preference on site A. The fungal between-group differences in the eggs were not as significant as that of bacteria. Purpureocillium in Cordyceps-related families showed preference on site A. Wolbachia, Spiroplasma, and Purpureocillium were inferred to be closely related to Chinese cordyceps occurrence. Intra-kingdom and inter-kingdom network analyses suggest that closer correlations of microbial communities (especially closer fungal positive correlations) in fertilized eggs might promote Chinese cordyceps occurrence. Besides, metabolic pathway analysis showed that in fertilized eggs or soil the number of bacterial metabolic pathways with significant differences in every comparison between two sites was greater than that of fungi. Collectively, this study provides novel information about the occurrence of Chinese cordyceps, contributing to the large-scale artificial cultivation of Chinese cordyceps.

Deciphering the intra- and inter-kingdom networks of microbiota in the pit mud of Chinese strong-flavor liquor

Microbes have central roles in the pit mud (PM) ecosystems and flavor formation, yet specific ecological interactions and keystone taxa among these taxa are largely unknown. Here, we used network analyses to explore the PM microbial intra- and inter-kingdom networks based on Illumina MiSeq sequencing data. The results showed that Firmicutes (mainly Caproiciproducens, Lactobacillus and Bacillus), Ascomycota (mainly Thermoascus, Eurotium and Aspergillus) and Euryarchaeota (mainly Methanobacterium, Methanosarcina, Methanobrevibacter and Methanocorpusculum) were the most dominant taxa detected in PM microbiota. The complexity of PM bacterial networks was much higher than that of fungal and archaeal networks, the hubs were mainly derived from bacteria rather than fungi and archaea in each inter-kingdom network, and the positive correlations dominated in bacterial (>75%), fungal (>90%) and inter-kingdom (>80%) networks. In addition, Mantel test showed that PM properties, especially pH, humic acid, available P and organic matter, were closely correlated with compositional structure of microbial communities and their main ecological clusters. The findings will contribute to a better understanding of PM microbiome structure and the ecological rules guiding community assembly, and have important implications for manipulating microbial resources and controlling PM environmental factors for pit management and sustainable brewing.

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production.

The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Disease-induced changes in plant microbiome assembly and functional adaptation

BackgroundThe plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.ResultsThe amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants.ConclusionsTogether, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture.DwWQb6Dg7ZT1-tarvfq632Video abstract

Plant developmental stage drives the differentiation in ecological role of the maize microbiome

BackgroundPlants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.ResultsOur results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage.ConclusionsOur results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.2NpR2QgL41qVHhBsXo3pXwVideo

Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis

Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.

Diversity and Co-Occurrence Patterns of Soil Bacterial and Fungal Communities of Chinese Cordyceps Habitats at Shergyla Mountain, Tibet: Implications for the Occurrence.

Chinese Cordyceps is a well-known medicinal larva-fungus symbiote distributed in the Qinghai-Tibetan Plateau and adjacent areas. Previous studies have involved its artificial cultivation but commercial cultivation is difficult to perform because the crucial factors triggering the occurrence of Chinese Cordyceps are not quite clear. The occurrence of Chinese Cordyceps is greatly affected by the soil environment, including the soil’s physicochemical and microecological properties. In this study, the effects of these soil properties on the occurrence of Chinese Cordyceps were investigated. The results show that the physicochemical properties, including easily oxidizable organic carbon (EOC), soil organic carbon (SOC), humic acid carbon (HAC), humin carbon (HMC), and pH, might be negatively related to the occurrence of Chinese Cordyceps, and soil water content (SWC) might be positively related. Several soil physicochemical parameters (pH, SOC, HMC, HAC, available potassium (APO), available phosphorus (APH), microbial biomass carbon (MBC), and the ratio of NH4+ to NO3− (NH4+/NO3−)) and microbial properties interact and mix together, which might affect the occurrence of Chinese Cordyceps. Soil microbial community structure was also a possible factor, and a low level of bacterial and fungal diversity was suitable for the occurrence of Chinese Cordyceps. The intra-kingdom network revealed that a closer correlation of the bacterial community might help the occurrence of Chinese Cordyceps, while a closer correlation of the fungal community might suppress it. The inter-kingdom network revealed that the occurrence rate of Chinese Cordyceps might be negatively correlated with the stability of the correlation state of the soil habitat. In conclusion, this study shows that soil physicochemical properties and microbial communities could be greatly related with the occurrence of Chinese Cordyceps. In addition, soil physicochemical properties, the level of bacterial and fungal diversity, and correlations of bacterial and fungal communities should be controlled to a certain level to increase the production of Chinese Cordyceps in artificial cultivation.

Altered Bacterial-Fungal Interkingdom Networks in the Guts of Ankylosing Spondylitis Patients.

Intestinal bacterial dysbiosis has been increasingly linked to ankylosing spondylitis (AS), which is a prototypic and best studied subtype of spondyloarthritis (SpA). Fungi and bacteria coexist in the human gut and interact with each other. Although they have been shown to contribute actively to health or disease, no studies have investigated whether the fungal microbiota in AS patients is perturbed. In this study, fecal samples from 22 AS patients, with clinical and radiographic assessments, and 16 healthy controls (HCs) were collected to systematically characterize the gut microbiota and mycobiota in AS patients by 16S rRNA gene- and ITS2-based DNA sequencing. Our results showed that the microbiota of AS patients was characterized by increased abundance of Proteobacteria and decreased Bacteroidetes, which was contributed by enrichment of Escherichia-Shigella, Veillonella, Lachnospiraceae NK4A136 group, and reduction of Prevotella strain 9, Megamona, and Fusobacterium. The gut mycobiota of AS patients was characterized by higher levels of Ascomycota, especially the class of Dothideomycetes, and decreased abundance of Basidiomycota, which was mainly contributed by the decease of Agaricales. Compared to HCs, decreased ITS2/16S biodiversity ratios and altered bacterial-fungal interkingdom networks were observed in AS patients. Compared with nonsteroidal anti-inflammatory drugs (NSAIDs), treating AS patients with biological agents induced obvious changes in the gut mycobiota, and this result was highly associated with disease activity indexes, including AS disease activity index (ASDAS) C-reactive protein (asCRP), erythrocyte sedimentation rate (ESR), and Bath AS disease activity index (BASDAI). In addition, altered mycobiota in AS patients was also found associated with the degree of radiographic damage. IMPORTANCE The human gut is colonized by diverse fungi (mycobiota), and fungi have long been suspected in the pathogenesis of SpA. Our study unraveled a disease-specific interkingdom network alteration in AS, suggesting that fungi, or the interkingdom interactions between bacteria and fungi, may play an essential role in AS development. However, our study is limited by sample size, and in-depth mechanism studies and additional large-scale investigations characterizing the gut mycobiome in AS patients are needed to form a foundation for research into the relationship between mycobiota dysbiosis and AS development.

Respiratory Mycobiome and Microbiome in Cystic Fibrosis: First Evidence for Inter-Kingdom Network During Acute Pulmonary Exacerbation

Background: Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. While CF respiratory tract is now considered as a polymicrobial niche, advances in high-throughput sequencing (NGS) have paved the way to microbiota and mycobiota analysis. However, none of these NGS studies have characterized both communities during CF pulmonary exacerbation (CFPE). Methods: Using NGS, thirty-three sputa isolated from patients with and without CFPE were successfully sequenced targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to detect significant correlations in compositional data. Findings: We confirmed that respiratory function decline was significantly associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as significantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by our correlation network. Interpretation: For the first time, we proposed a version of the ecological Climax/Attack model that includes documented mycobiome data. Such combinations of omics and ecological approaches will help us to understand better the physiopathology of CF lung disease, and to improve therapeutic management of this critical clinical state.- Funding Statement: LD has received a research grant from Vaincre La Mucoviscidose (RF20160501626); LEV's salary was provided by Genoscreen Company. All these funders had no role in article design, decision to publish, or preparation of the manuscript. Declaration of Interests: The authors declared no conflict of interest. Ethics Approval Statement: MucoFong study was approved by the institutional ethics committees of Lille University Hospital (Reference Number: CPP-06/84), and a written informed consent was provided by all participants.

Vibrio vulnificus quorum-sensing molecule cyclo(Phe-Pro) inhibits RIG-I-mediated antiviral innate immunity

The recognition of pathogen-derived ligands by pattern recognition receptors activates the innate immune response, but the potential interaction of quorum-sensing (QS) signaling molecules with host anti-viral defenses remains largely unknown. Here we show that the Vibrio vulnificus QS molecule cyclo(Phe-Pro) (cFP) inhibits interferon (IFN)-β production by interfering with retinoic-acid-inducible gene-I (RIG-I) activation. Binding of cFP to the RIG-I 2CARD domain induces a conformational change in RIG-I, preventing the TRIM25-mediated ubiquitination to abrogate IFN production. cFP enhances susceptibility to hepatitis C virus (HCV), as well as Sendai and influenza viruses, each known to be sensed by RIG-I but did not affect the melanoma-differentiation-associated gene 5 (MDA5)-recognition of norovirus. Our results reveal an inter-kingdom network between bacteria, viruses and host that dysregulates host innate responses via a microbial quorum-sensing molecule modulating the response to viral infection.

Microbiome Medicine: This Changes Everything

Microbiome Medicine: This Changes Everything

Fungal microbiota dysbiosis in IBD

ObjectiveThe bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce....