Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome.

Shotgun metagenomic sequencing has the potential to provide bacterial strain-level resolution which is of key importance to tackle a host of clinical questions. While bioinformatic tools that achieve strain-level resolution are available, thorough benchmarking is needed to validate their use for less investigated and low biomass microbiomes like those from the upper respiratory tract. We analyzed a previously published data set of longitudinally collected nasopharyngeal samples from Bangladeshi infants (Microbiota and Health study) and a novel data set of oropharyngeal samples from Swiss children with cystic fibrosis. Data from bacterial cultures were used for benchmarking the parameters of StrainPhlAn 3, a bioinformatic tool designed for strain-level resolution. In addition, StrainPhlAn 3 results were compared with metagenomic assemblies derived from StrainGE and newly derived whole-genome sequencing data. After optimizing the analytical parameters, we compared StrainPhlAn 3 results to culture gold standard methods and achieved sensitivity values of 87% (Streptococcus pneumoniae), 80% (Moraxella catarrhalis), 75% (Haemophilus influenzae), and 57% (Staphylococcus aureus) for 420 nasopharyngeal and 75% (H. influenzae) and 46% (S. aureus) for 260 oropharyngeal samples. Comparing the phylogenetic tree of the core genome of 50 S. aureus isolates with a corresponding marker gene tree generated by StrainPhlAn 3 revealed a striking similarity in tree topology for all but three samples indicating adequate strain resolution. In conclusion, a comparison of StrainPhlAn 3 results to data from bacterial cultures revealed that strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA when parameters are carefully optimized to fit low biomass microbiomes.IMPORTANCEThe usage of 16S rRNA gene sequencing has become the state-of-the-art method for the characterization of the microbiota in health and respiratory disease. The method is reliable for low biomass samples due to prior amplification of the 16S rRNA gene but has limitations as species and certainly strain identification is not possible. However, the usage of metagenomic tools for the analyses of microbiome data from low biomass samples is not straight forward, and careful optimization is needed. In this work, we show that by validating StrainPhlAn 3 results with the data from bacterial cultures, the strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA being present when parameters are carefully optimized to fit low biomass microbiomes. This work further proposes that strain retention analyses are feasible, at least for more abundant species. This will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease

Computational Approaches for a Healthier Microbiome

Our gut flora, the microbiome, plays an indispensable role in our health. Changes in the microbiome have been linked to an increasing list of diseases. Metagenomics is a technique that allows the sequencing of microbiomes directly from samples, giving valuable insight into the composition and functional potential of microbial populations. The analysis of metagenomic data is complex and depends on the availability of reference genomes. This work describes computational methods that allow the analysis of microbiomes with a lack of reference genomes by assembling genomes from the metagenomic data. We demonstrate how our methods can be used to infer the functional potential of a microbiome and how they allow us to link each function to the responsible species. We could predict changes in metabolites that were confirmed by targeted measurements. The mouse is the most used model for studying the impact of microbiota on its host. However, the species living in the mouse gut remain poorly characterized. By analyzing all publicly available metagenomes from the mouse gut, we created a comprehensive catalog of all bacterial species commonly living in the gut of laboratory mice. We assembled over 30'000 bacterial genomes, as well as the sequences from viruses and plasmids. Our catalog effectively answers the need for reference genomes for this microbiome. It allows efficient analysis of mouse gut metagenomes at the species and subspecies level. We discovered that mice and humans harbor a largely distinct set of species in their gastrointestinal tracts, an analysis which was hereto unfeasible.Notre flore intestinale, le microbiote, joue un rôle indispensable dans notre santé. Des changements dans le microbiote sont associés à une liste croissante de maladies. La métagénomique est une technique qui permet le séquençage de microbiotes directement à partir d'échantillons, donnant un aperçu utile de la composition et du potentiel fonctionnel des populations microbiennes. L'analyse des données métagénomiques est complexe et dépend de la disponibilité de génomes de référence. Ce travail décrit des méthodes de calcul qui permettent l'analyse de microbiotes lors d’un manque de génomes de référence en assemblant des génomes à partir des données métagénomiques. Nous démontrons comment nos méthodes peuvent être utilisées pour déduire le potentiel fonctionnel d'un microbiote et comment elles nous permettent de lier chaque fonction à l'espèce responsable. Nous avons pu prédire des changements dans les métabolites qui ont été confirmés par une analyse ciblée. La souris est le modèle le plus utilisé pour étudier l'impact du microbiote sur son hôte. Cependant, les espèces vivant dans l'intestin de la souris restent mal caractérisées. En analysant tous les métagénomes de l'intestin de la souris en libre accès, nous avons créé un catalogue complet de toutes les espèces bactériennes vivant couramment dans l'intestin des souris de laboratoire. Nous avons assemblé plus de 30'000 génomes bactériens, ainsi que les séquences de virus et de plasmides. Notre catalogue répond efficacement au besoin de génomes de référence pour ce microbiote. Il permet une analyse efficace des métagénomes intestinaux de souris au niveau des espèces et des sous-espèces. Nous avons découvert que les souris et les humains hébergent un ensemble d'espèces largement distinct dans leur système digestif, une analyse qui n’était jusqu'à présent pas réalisable

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41’798 genomes cluster into 1’573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for the analysis of new and reanalysis of existing datasets at an unprecedented depth.</p

Common traits between the beige fat-inducing stimuli

Adipose tissues play an essential role in regulating the metabolic homeostasis and can be found in almost all parts of the body. Excessive adiposity leads to obesity and can contribute to metabolic and other disorders. Adipocytes show remarkable plasticity in their function, which can be pushed toward energy storage, or energy expenditure — a `browning' of fat. Browning is controlled by the cellular milieu of the adipose tissue, with sympathetic innervation and by immune responses as key integrators of the signals that promote browning. Here, we describe the latest contributions to our understanding of how different metabolic stimuli can shape the adipocyte function. We especially focus on the role of the gut microbiota and the negative energy balance in regulating the browning

ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers

broadinstitute/StrainGE: StrainGE 1.3.9

&lt;ul&gt; &lt;li&gt;[FIX] KeyError in straingst cluster with newer version of Pandas (#12)&lt;/li&gt; &lt;/ul&gt

broadinstitute/StrainGE: StrainGE 1.3.9

&lt;ul&gt; &lt;li&gt;[FIX] KeyError in straingst cluster with newer version of Pandas&lt;/li&gt; &lt;/ul&gt

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh

A T4-like coliphage cocktail was given with different oral doses to healthy Bangladeshi children in a placebo-controlled randomized phase I safety trial. Fecal phage detection was oral dose dependent suggesting passive gut transit of coliphages through the gut. No adverse effects of phage application were seen clinically and by clinical chemistry. Similar results were obtained for a commercial phage preparation (Coliproteus from Microgen/Russia). By 16S rRNA gene sequencing, only a low degree of fecal microbiota conservation was seen in healthy children from Bangladesh who were sampled over a time interval of 7 days suggesting a substantial temporal fluctuation of the fecal microbiota composition. Microbiota variability was not associated with the age of the children or the presence of phage in the stool. Stool microbiota composition of Bangladeshi children resembled that found in children of other regions of the world. Marked variability in fecal microbiota composition was also seen in 71 pediatric diarrhea patients receiving only oral rehydration therapy and in 38 patients receiving coliphage preparations or placebo when sampled 1.2 or 4 days apart respectively. Temporal stability of the gut microbiota should be assessed in case-control studies involving children before associating fecal microbiota composition with health or disease phenotypes

Functional Gut Microbiota Remodeling Contributes to the Caloric Restriction-Induced Metabolic Improvements

Caloric restriction (CR) stimulates development of functional beige fat and extends healthy lifespan. Here we show that compositional and functional changes in the gut microbiota contribute to a number of CR-induced metabolic improvements and promote fat browning. Mechanistically, these effects are linked to a lower expression of the key bacterial enzymes necessary for the lipid A biosynthesis, a critical lipopolysaccharide (LPS) building component. The decreased LPS dictates the tone of the innate immune response during CR, leading to increased eosinophil infiltration and anti-inflammatory macrophage polarization in fat of the CR animals. Genetic and pharmacological suppression of the LPS-TLR4 pathway or transplantation with Tlr4 bone-marrow-derived hematopoietic cells increases beige fat development and ameliorates diet-induced fatty liver, while Tlr4 or microbiota-depleted mice are resistant to further CR-stimulated metabolic alterations. These data reveal signals critical for our understanding of the microbiota-fat signaling axis during CR and provide potential new anti-obesity therapeutics