In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies

Mikrobiota-abhängige Umprogrammierung des transkriptionellen Profils von Salmonella Typhimurium in vivo

Salmonella enterica infection is one of the major causes of food-borne diseases in both developing and developed countries. Salmonella possess gene repertoire that allow it to outcompete the inherent commensal bacteria and evade the immune system in the host digestive tract to cause infection. Hence it is highly essential to identify the Salmonella gene signatures that could be associated with its infection and gut-microbial signatures that could protect against Salmonella infection. In the current study, we introduce a novel operon-based expression profile analysis approach that enabled us to identify functionally coordinated gene signatures characterizing Salmonella virulence. We also performed an association study between the gene expression profiles of Salmonella and gut microbiota in colonized mouse models. The association study was made feasible by the development of a novel, improved host-specific reference catalogue for colonized mouse models. For further improving the ability of this host-specific gene reference catalogue in identifying the potential microbes and their functional potentials that were highly expressed in the host-gut environment, we devised a novel strategy in this study, by linking the MGS Bins and the 16S rRNA genes. This method highlighted that even a sparse amount of 16S rRNA sequences could be efficiently used to infer taxonomic annotations with improved resolution. By comparing Salmonella in vivo gene expression profiles to in vitro growth, we identified that colonization of the intestinal environment as well as competition induces specific expression signatures. We observed that Salmonella adjusts its transcriptional machinery in order to compete for nutrients with the host’s microbiota, thereby adapting to its environment. Specifically, adaptations to variable availability of nutrients such as mono/disaccharides and co-factors were highlighted by differential expression of uptake and utilization systems and correspondingly, of non-coding small RNAs, which regulate sugar-phosphate stress and carbon-storage activities in vivo. Our data supports the observation that Salmonella is a metabolically highly flexible enteropathogen employing different transcriptional sub-systems to adapt to the host. We performed a Salmonella-gut microbiota association study to identify the microbial gene signatures that could be associated in inhibiting Salmonella overgrowth (protection). We observed that the abundance of microbiota-derived nutrients like succinate could be associated with Salmonella infection in host gut ecosystem. This study highlights the significance of deciphering the gut microbial complexity in providing protection against enteropathogenic infections.Eine Hauptursache für Lebensmittelinfektionen und Durchfallerkrankungen weltweit stellt das Pathogen Salmonella eneterica dar. Salmonellen besitzten eine Reihe von Genen die es Ihnen erlaubt, die umgebende Darmflora und die Immunantwort des Wirtes zu umgehen und sich erfolgreich im Versauungstrakt zu etablieren. Folglich ist es von essentieller Bedeutung mögliche Gensignaturen zu identifizieren, die für die Infektion von Salmonella ursächlich oder mit der Resistenz gegenüber Infektionen durch die Mikrobiota assoziiert sind. In dieser Studie stellen wir eine neue Operon-basierte Expressionsprofil Analyse Methode vor, die es erlaubt funktionell koordinierte Gensignaturen zu identifizieren, die mit der Virulenz von Salmonella assoziiert sind. Dafür wurde eine Assoziationsstudie zwischen dem Genexpressionsprofil von Salmonella und der Darmmikrobiota in ausgewählten Mausmodellen durchgeführt, für die ein neuartiger, wirts-spezifischer Genreferenzkatalog für die verwendeten Mausmodelle erstellt wurde. Zur Optimierung dieses spezifischen Genkatalogs zur Identifikation von potentiell wichtigen Bakterien und ihren Eigenschaften wurde ein neues Konzept entwickelt, bei der MGS Bins mit den zugehörigen 16S rRNA Genen verknüpft wurden. Diese Methode erlaubt es auch eine geringe Anzahl an 16S rRNA Sequenzen effizient für die taxonomische Annotierung zu nutzen und somit eine verbesserter Auflösung zu erzielen Durch den Vergleich von Salmonella Genexpressionsprofilen unter in vivo und in vitro Wachstumsbedingungen konnte gezeigt werden, dass die Kolonisation sowie die Kompetition mit anderen Darmbakterien dass die Kolonisation sowie die Kompetition mit anderen Darmbakterien im Darm spezifische Expressionssignaturen induzieren. im Darm spezifische Expressionssignaturen induzieren. Salmonella ist in der Lage seine Transkriptionsmaschinerie anzupassen, um mit der Darmmikrobiota um vorhandene Nährstoffe konkurrieren und sich der vorhandenen Umgebung anzupassen. Insbesondere konnte die variable Anpassung zur Verwertung von Mono-/ Disacchariden, Co-Faktoren, und die Regulation von Aufnahme- und Verwertungssysteme durch differenzierte Expression spezifischer kleiner, nicht-kodierender RNAs, die für die Närhstoffspeicherung essentiell sind, unter in vitro Bedingungen gezeigt werden. Diese Daten stützen die Einschätzung, dass Salmonella ein metabolisch hochflexibler Darmerreger ist, der die Expression verschiedener transkriptionaler Subsysteme nutzt, um sich an spezifische Wirtbedingungen anzupassen. Um mikrobielle Gensignaturen zu identifizieren, die mit einer Inhibition von Salmonella Wachstum (Kolonisationsresistenz) assoziiert sind, wurde eine weitere Assoziationsstudie zwischen Salmonella und der Darmmikrobiota durchgeführt. Dabei konnte beobachtet werden, dass die Menge an mikrobiell produzierten, verfügbaren Nährstoffen wie Succinaten mit Infektionen von Salmonella im Darm korrelliert. Diese Ergebnisse heben hevor, wie bedeutend neue Ansätze zur Entschlüsselung von komplexen mikrobiellen Gemeinschaften im Darm sind, die einen Schutz gegen Infektionen mit Enteropathogenen gewährleisten

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models

Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host’s environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome “dark matter” and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome

Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism

International audienceGut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease

In vitro interaction network of a synthetic gut bacterial community.

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies