Otto X. Cordero
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View article: Niche partitioning by resource size in the gut microbiome
Niche partitioning by resource size in the gut microbiome Open
Niche partitioning promotes diversity of the human gut microbiota. However, the molecular basis of resource specialization and niche separation in the gut remains poorly understood. Here we show that structural differences in glycan transp…
View article: A universal surface functionalization technique to chemically enhance live microbial cells
A universal surface functionalization technique to chemically enhance live microbial cells Open
Microbial surface functionalization is a powerful strategy for endowing microbes with novel, non-genetic functions. However, existing methods are often species-specific, limited in scope, and compromise cell viability. Here, we present a u…
View article: Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer
Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer Open
Chitin is a major structural component of arthropod exoskeletons, and an important carbon and nitrogen source in marine environments. Chitin degradation, which proceeds similarly under both oxic and anoxic conditions, produces chitooligosa…
View article: Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer
Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer Open
Chitin is a major structural component of arthropod exoskeletons, and an important carbon and nitrogen source in marine environments. In anoxic sediments, its degradation generates chitooligosaccharides and N-acetylglucosamine (GlcNAc), wh…
View article: Microbiome determinants of productivity in aquaculture of whiteleg shrimp
Microbiome determinants of productivity in aquaculture of whiteleg shrimp Open
Aquaculture holds immense promise for addressing the food needs of our growing global population. Yet, a quantitative understanding of the factors that control its efficiency and productivity has remained elusive. In this study, we address…
View article: Vitamin auxotrophies shape microbial community assembly on model marine particles
Vitamin auxotrophies shape microbial community assembly on model marine particles Open
Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism represents only a small fraction of the biosynthetic repertoire of microbes: metabolites such…
View article: Climate change and Vibrio vulnificus dynamics: A blueprint for infectious diseases
Climate change and Vibrio vulnificus dynamics: A blueprint for infectious diseases Open
Climate change is having increasingly profound effects on human health, notably those associated with the occurrence, distribution, and transmission of infectious diseases. The number of disparate ecological parameters and pathogens affect…
View article: Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function Open
Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach …
View article: The development of ecological systems along paths of least resistance
The development of ecological systems along paths of least resistance Open
A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context. Classic e…
View article: Spatially structured microbial consortia and their role in food fermentations
Spatially structured microbial consortia and their role in food fermentations Open
View article: Targeted hypermutation of putative antigen sensors in multicellular bacteria
Targeted hypermutation of putative antigen sensors in multicellular bacteria Open
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolut…
View article: Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function Open
Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach …
View article: Biological sources and sinks of dimethylsulfide disentangled by an induced bloom experiment and a numerical model
Biological sources and sinks of dimethylsulfide disentangled by an induced bloom experiment and a numerical model Open
Dimethylsulfide (DMS) is a climatically active trace gas promoting cloud formation. The biochemical precursor of DMS, dimethylsulfoniopropionate (DMSP), is a phytoplankton metabolite and a source of reduced sulfur for many microbial specie…
View article: Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities
Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities Open
Microbial communities perform essential ecosystem functions such as the remineralization of organic carbon that exists as biopolymers. The first step in mineralization is performed by biopolymer degraders, which harbor enzymes that can bre…
View article: Vitamin auxotrophies shape microbial community assembly in the ocean
Vitamin auxotrophies shape microbial community assembly in the ocean Open
Microbial community assembly is governed by trophic interactions that mediate the transfer of carbon sources and biomass building blocks between species. However, central metabolism corresponds to only a small fraction of the biosynthetic …
View article: Targeted hypermutation of putative antigen sensors in multicellular bacteria
Targeted hypermutation of putative antigen sensors in multicellular bacteria Open
Diversity-generating retroelements (DGRs) are used by bacteria, archaea and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evoluti…
View article: Genome content predicts the carbon catabolic preferences of heterotrophic bacteria
Genome content predicts the carbon catabolic preferences of heterotrophic bacteria Open
View article: Mapping gut bacteria into functional niches reveals the ecological structure of human gut microbiomes
Mapping gut bacteria into functional niches reveals the ecological structure of human gut microbiomes Open
Microbiomes are an essential contributor to the metabolic activity in the human gastrointestinal tract. The fermentation of otherwise indigestible nutritional components like dietary fibers relies on a complex interplay of metabolic pathwa…
View article: Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance
Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance Open
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of fre…
View article: Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle
Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle Open
Marine picocyanobacteria Prochlorococcus and Synechococcus , the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of pi…
View article: Mutation-induced infections of phage-plasmids
Mutation-induced infections of phage-plasmids Open
Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show that segregational drift and loss-of-function mutations play key roles in the i…
View article: Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities
Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities Open
Microbial communities perform essential ecosystem functions such as the remineralization of organic carbon that exists as biopolymers. The first step in mineralization is performed by biopolymer degraders, which harbor enzymes that can bre…
View article: A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01
A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01 Open
A genome-scale metabolic model of V. splendidus 1A01 was reconstructed in this work. We offer solutions to the technical problems associated with model reconstruction for a marine bacterial strain like V. splendidus 1A01, which arise large…
View article: Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria Open
Polysaccharide breakdown by bacteria requires the activity of enzymes that degrade polymers either intra- or extra-cellularly. The latter mechanism generates a localized pool of breakdown products that are accessible to the enzyme producer…
View article: Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms
Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms Open
View article: Mutation-induced infections of phage-plasmids
Mutation-induced infections of phage-plasmids Open
Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show segregational drift and loss- of-function mutations play key roles in the infec…
View article: Annotation-free discovery of functional groups in microbial communities
Annotation-free discovery of functional groups in microbial communities Open
Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa, whose abundance is more stable and better associated with metabolic fluxes than that of any individual taxon. However, identifying t…
View article: Fundamental metabolic strategies of heterotrophic bacteria
Fundamental metabolic strategies of heterotrophic bacteria Open
Through their metabolism, heterotrophic microbes drive carbon cycling in many environments (1). These microbes consume (and produce) hundreds to thousands of different metabolic substrates, begging the question of what level of description…
View article: Historical contingencies and phage induction diversify bacterioplankton communities at the microscale
Historical contingencies and phage induction diversify bacterioplankton communities at the microscale Open
In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers o…
View article: Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles
Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles Open