Latest Articles
Commentary | Novel Systems Biology TechniquesPathovar TranscriptomesArchetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-...
Editor's Pick Research Article | Novel Systems Biology TechniquesTranscriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing ConditionsRecent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC...
Research Article | Host-Microbe BiologyThe Skin Microbiome of Cohabiting CouplesOur work characterizes the influence of cohabitation as a factor influencing the composition of the skin microbiome. Although the body site and sampled individual were stronger influences than other factors collected as metadata in this study, we show that modeling of detected microbial taxa can help with correct identifications of cohabiting partners based on skin microbiome profiles using machine learning approaches. These results...
Editor's Pick Research Article | Host-Microbe BiologyMetabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic MoleculesMetabolomics is the ultimate tool for studies of microbial functions under any specific set of environmental conditions (D. S. Wishart, Nat Rev Drug Discov 45:473–484, 2016, https://doi.org/10.1038/nrd.2016.32). This is a great advance over studying genes alone, which only inform about metabolic potential. Approximately 25,000 compounds have been chemically characterized thus far;...
Editor's Pick Research Article | Applied and Environmental ScienceInsights into Butyrate Production in a Controlled Fermentation System via Gene PredictionsThis study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system....
Commentary | Host-Microbe BiologyParasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host InteractionsUnderstanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.
Research Article | Applied and Environmental ScienceNon-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space StationThe International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed...
Editor's Pick Research Article | Host-Microbe BiologyMulti-omics Analysis of Periodontal Pocket Microbial Communities Pre- and PosttreatmentPeriodontal disease affects the majority of adults worldwide and has been linked to numerous systemic diseases. Despite decades of research, the reasons for the substantial differences among periodontitis patients in disease incidence, progressivity, and response to treatment remain poorly understood. While deep sequencing of oral bacterial communities has greatly expanded our comprehension of the microbial diversity of periodontal...
Research Article | Molecular Biology and PhysiologyThe Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function PredictionsIdentification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogen S. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions for...
Research Article | Molecular Biology and PhysiologyCombining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroidesKnowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in...