Latest Articles
Research Article | Novel Systems Biology TechniquesDefining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association StudiesIdentifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-metabolome association studies, comprehensively measuring both the composition of species and the concentration of metabolites across a set of microbial community samples and then testing for...
Editor's Pick Methods and Protocols | Novel Systems Biology TechniquesThe Generalized Matrix Decomposition Biplot and Its Application to Microbiome DataBiplots that simultaneously display the sample clustering and the important taxa have gained popularity in the exploratory analysis of human microbiome data. Traditional biplots, assuming Euclidean distances between samples, are not appropriate for microbiome data, when non-Euclidean distances are used to characterize dissimilarities among microbial communities. Thus, incorporating information from non-Euclidean distances into a biplot...
Research Article | Ecological and Evolutionary ScienceDiverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA LineageThe RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups....
Research Article | Host-Microbe BiologyGut Microbiota Dysbiosis Is Associated with Altered Bile Acid Metabolism in Infantile CholestasisLiver health, fecal bile acid (BA) concentrations, and gut microbiota composition are closely connected. BAs and the microbiome influence each other in the gut, where bacteria modify the BA profile, while intestinal BAs regulate the growth of commensal bacteria, maintain the barrier integrity, and modulate the immune system. Previous studies have found that the co-occurrence of gut microbiota dysbiosis and BA metabolism alteration is...
Research Article | Molecular Biology and PhysiologyGlobal Screening of Genomic and Transcriptomic Factors Associated with Phenotype Differences between Multidrug-Resistant and -Susceptible Candida haemulonii StrainsA comprehensive, multi-omic survey was performed to disclose the genetic backgrounds and differences between multidrug-resistant and -susceptible C. haemulonii strains. Genes were identified with mutations or significant expression differences in multidrug-resistant compared to multidrug-susceptible strains, which were mainly involved in multidrug resistance, stress...
Research Article | Molecular Biology and PhysiologyRapid and Concomitant Gut Microbiota and Endocannabinoidome Response to Diet-Induced Obesity in MiceThe intestinal microbiota and the expanded endocannabinoid system, or endocannabinoidome, have both been implicated in diet-induced obesity and dysmetabolism. This study aims at identifying the potential interactions between these two fundamental systems—which form the gut microbiota-endocannabinoidome axis—and their involvement in the establishment of diet-induced obesity and related metabolic complications. We report here time- and...
Research Article | Molecular Biology and PhysiologyGenomewide and Enzymatic Analysis Reveals Efficient d-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloidesThe switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant biomass, warranting the identification of microorganisms with broader catabolic capacity and characterization of their unique biochemical pathways. d-Galacturonic acid is a plant...
Research Article | Novel Systems Biology TechniquesCharacterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in ChinaThe gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to...
Research Article | Applied and Environmental ScienceQuantifying Methane and Methanol Metabolism of “Methylotuvimicrobium buryatense” 5GB1C under Substrate LimitationMethanotrophic metabolism has been under investigation for decades using biochemical and genetic approaches. Recently, a further step has been taken toward understanding methanotrophic metabolism in a quantitative manner by means of flux balance analysis (FBA), a mathematical approach that predicts fluxes constrained by mass balance and a few experimental measurements. However, no study has previously been undertaken to experimentally...
Research Article | Host-Microbe BiologyThe Effects of Crude Oil and Dispersant on the Larval Sponge HolobiontLarvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the...