Latest Articles
Research Article | Host-Microbe BiologyThe Adenoids but Not the Palatine Tonsils Serve as a Reservoir for Bacteria Associated with Secretory Otitis Media in Small ChildrenOur findings that the microbiome differs between crypts of the adenoids and crypts of the palatine tonsils, including the relative abundances of potential pathogens such as Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella...
Research Article | Ecological and Evolutionary ScienceA Novel Sparse Compositional Technique Reveals Microbial PerturbationsBy accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this...
Editor's Pick Research Article | Ecological and Evolutionary ScienceUnique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine BacteriaMarine microbes must manage variation in their chemical, physical, and biological surroundings. Because they directly link bacterial physiology to environmental changes, TCS systems are crucial to the bacterial cell. This study surveyed TCS systems in a large number of marine bacteria and identified key phylogenetic and lifestyle patterns in environmental sensing. We found evidence that, in comparison with bacteria as a whole, marine...
Research Article | Molecular Biology and PhysiologyOxidative Pathways of Deoxyribose and Deoxyribonate CatabolismDeoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified...
Perspective | Ecological and Evolutionary ScienceBridging the Holistic-Reductionist Divide in Microbial EcologyMicrobial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace.
Research Article | Novel Systems Biology TechniquesMetabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic ModelingCombating antimicrobial resistance has been highlighted as a critical global health priority. Due to the drying drug discovery pipeline, polymyxins have been employed as the last-line therapy against Gram-negative “superbugs”; however, the detailed mechanisms of antibacterial killing remain largely unclear, hampering the improvement of polymyxin therapy. Our integrative modeling using the constructed genome-scale metabolic model i...
Research Article | Host-Microbe BiologyAlterations in Gut Glutamate Metabolism Associated with Changes in Gut Microbiota Composition in Children with Autism Spectrum DisorderMultiple lines of evidence suggest that the gut microbiota may play an important role in the pathogenesis of ASD, but the specific mechanism is still unclear. Through a comprehensive gut metagenomic and metabolome study of children with ASD, alterations in gut metabolite composition were found in children with ASD, and these alterations were linked to changes in gut microbiota composition. This may give us a deeper understanding of the...
Methods and Protocols | Novel Systems Biology TechniquesCalour: an Interactive, Microbe-Centric Analysis ToolCalour allows us to identify interesting microbial patterns and generate novel biological hypotheses by interactively inspecting microbiome studies and incorporating annotation databases and convenient statistical tools. Calour can be used as a first-step tool for microbiome data exploration.
Research Article | Applied and Environmental ScienceFeed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed IntakeThe impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in...
Commentary | Host-Microbe BiologyA Significant Expansion of Our Understanding of the Composition of the Human MicrobiomeShotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set.