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Editor's Pick Research Article | Host-Microbe BiologyModerate Exercise Has Limited but Distinguishable Effects on the Mouse MicrobiomeThe bacteria that live in our gut have a complex yet vital relationship with our health. Environmental factors that influence the gut microbiome are of great interest, as recent research demonstrates that these microbes, mostly bacteria, are important for normal host physiology. Diseases such as obesity, diabetes, inflammatory bowel disease, and colon cancer have also been linked to shifts in the microbiome. Exercise is known to have...
Methods and Protocols | Novel Systems Biology TechniquesPaperBLAST: Text Mining Papers for Information about HomologsWith the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about...
Research Article | Host-Microbe BiologyFluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in MiceFluoride has been added to drinking water and dental products since the 1950s. The beneficial effects of fluoride on oral health are due to its ability to inhibit the growth of bacteria that cause dental caries. Despite widespread human consumption of fluoride, there have been only two studies of humans that considered the effect of fluoride on human-associated microbial communities, which are increasingly understood to play important...
Editor's Pick Research Article | Host-Microbe BiologyClostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut MicrobiomesInfection by the bacterium Clostridium difficile causes an inflammatory diarrheal disease which can become life threatening and has grown to be the most prevalent nosocomial infection. Susceptibility to C. difficile infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study, we demonstrated that C. difficile...
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.