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Special Issue Perspective | Applied and Environmental ScienceMoving towards a Robust Definition for a “Healthy” Indoor MicrobiomeBuildings of the future should be designed to support human health, both by promoting the presence of beneficial microbes and by reducing exposure to harmful ones. However, we still do not have a robust definition of what constitutes a “healthy” indoor microbiome.
Special Issue Perspective | Novel Systems Biology TechniquesDetermining Microbial Niche Breadth in the Environment for Better Ecosystem Fate PredictionsIntegrated omics applied to microbial communities offers a great opportunity to analyze the niche breadths (i.e., resource and condition ranges usable by a species) of constituent populations, ranging from generalists, with a broad niche breadth, to specialists, with a narrow one. In this context, extracellular metabolomics measurements describe resource spaces available to microbial populations; dedicated analyses of metagenomics data...
Special Issue Perspective | Applied and Environmental ScienceA “Cultural” Renaissance: Genomics Breathes New Life into an Old CraftSometimes, to move ahead, you must take a look at where you have been. Culturing microbes is a foundational underpinning of microbiology.
Special Issue Perspective | Ecological and Evolutionary ScienceClonal yet Different: Understanding the Causes of Genomic Heterogeneity in Microbial Species and Impacts on Public HealthWhy are members of a microbial species not the same? They may be clonal, but microbial populations are often composed of multiple cocirculating lineages distinguished by large phenotypic and genetic differences. Species and the mechanisms of speciation have been notoriously challenging to study in microbes owing to pervasive horizontal gene flow, widespread geographical distribution, and cryptic ecological niches that structure...
Special Issue Perspective | Ecological and Evolutionary ScienceRole of Multiple Infections on Immunological Variation in Wild PopulationsA central challenge in the fields of evolutionary immunology and disease ecology is to understand the causes and consequences of natural variation in host susceptibility to infectious diseases. As hosts progress from birth to death in the wild, they are exposed to a wide variety of microorganisms that influence their physical condition, immune system maturation, and susceptibility to concurrent and future infection.
Special Issue Perspective | Ecological and Evolutionary ScienceTowards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data IntegrationThe investigation of microbial community dynamics is hampered by low resolution, a lack of control, and a small number of replicates. These deficiencies can be tackled with defined communities grown under well-controlled conditions in high-throughput automated cultivation devices.
Special Issue Perspective | Host-Microbe BiologyConsidering the Other Half of the Gut Microbiome: BacteriophagesBacteriophages, viruses specific to bacteria, regulate bacterial communities in all known microbial systems. My research aims to determine how they interact with the trillions of bacteria found in the human gut.
Special Issue Perspective | Host-Microbe BiologyBovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle SystemsThe mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and...
Special Issue Perspective | Host-Microbe BiologyMissing a Phage: Unraveling Tripartite Symbioses within the Human GutTripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating...
Special Issue Perspective | Synthetic BiologyReconciling Ecological and Engineering Design Principles for Building MicrobiomesSimplified microbial communities, or “benchtop microbiomes,” enable us to manage the profound complexity of microbial ecosystems. Widespread activities aiming to design and control communities result in novel resources for testing ecological theories and also for realizing new biotechnologies.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative ApproachesA grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states.
Special Issue Perspective | Host-Microbe BiologyThe Vibrio-Squid Symbiosis as a Model for Studying Interbacterial CompetitionThe symbiosis between Euprymna scolopes squid and its bioluminescent bacterial symbiont, Vibrio fischeri, is a valuable model system to study a natural, coevolved host-microbe association. Over the past 30 years, researchers have developed and optimized many experimental methods to study both...
Special Issue Perspective | Ecological and Evolutionary ScienceMicrobial Metazoa Are Microbes TooMicrobial metazoa inhabit a certain “Goldilocks zone,” where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths.
Special Issue Perspective | Ecological and Evolutionary ScienceA Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection.
Special Issue Perspective | Host-Microbe BiologyMicrobiomes, Community Ecology, and the Comparative MethodMicrobiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. In my research on the evolution and ecology of avian microbiomes, I use two complementary frameworks: the microbiome as a community and the microbiome as a trait of the host.
Special Issue Perspective | Synthetic BiologyNatural Products and Synthetic Biology: Where We Are and Where We Need To GoThe biosynthetic talent of microorganisms has been harnessed for drug discovery for almost a century. Microbial metabolites not only account for the majority of antibiotics available today, but have also led to anticancer, immunosuppressant, and cholesterol-lowering drugs.
Special Issue Perspective | Molecular Biology and PhysiologyToward a Better Understanding of Species Interactions through Network BiologyWithin the last decade, there has been an explosion of multi-omics data generated for several microbial systems. At the same time, new methods of analysis have emerged that are based on inferring networks that link features both within and between species based on correlation in abundance.
Special Issue Perspective | Host-Microbe BiologyMetaproteomics: Much More than Measuring Gene Expression in Microbial CommunitiesMetaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.
Special Issue Perspective | Therapeutics and PreventionRigorous Statistical Methods for Rigorous Microbiome ScienceHigh-throughput sequencing has facilitated discovery in microbiome science, but distinguishing true discoveries from spurious signals can be challenging. The Statistical Diversity Lab develops rigorous statistical methods and statistical software for the analysis of microbiome and biodiversity data.
Special Issue Perspective | Ecological and Evolutionary ScienceAdvancing Genome-Resolved Metagenomics beyond the ShotgunExploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required...
Special Issue Perspective | Clinical Science and EpidemiologyTowards Translational Epidemiology: Next-Generation Sequencing and Phylogeography as Epidemiological Mainstays...Next-generation sequencing, coupled with the development of user-friendly software, has achieved a level of accessibility that is revolutionizing the way we approach epidemiological investigations. We can sequence pathogen genomes and conduct phylogenetic analyses to assess transmission, identify from which country or city a pathogen originated, or which contaminated potluck item resulted in widespread foodborne illness.
Special Issue Perspective | Applied and Environmental ScienceSoil Viruses: A New HopeAs abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput ToolsVirus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion.
Special Issue Perspective | Host-Microbe BiologyNew Approaches to Microbiome-Based TherapiesOver the last decade, our understanding of the composition and functions of the gut microbiota has greatly increased. To a large extent, this has been due to the development of high-throughput genomic analyses of microbial communities, which have identified the critical contributions of the microbiome to human health.
Special Issue Perspective | Novel Systems Biology TechniquesStrengthening Insights in Microbial Ecological Networks from Theory to ApplicationsNetworks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assembly.
Special Issue Perspective | Host-Microbe BiologyThe Significance of Microbial Symbionts in Ecosystem ProcessesIt is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained.
Special Issue Perspective | Host-Microbe BiologyDigitalizing the Microbiome for Human HealthThe microbiome has recently joined the club of endocrine entities of the human body that are involved in homeostasis and disease. Microbiome characterizations are now typically included in longitudinal and cross-sectional population studies, associations with microbiome features have been made for almost any human disease, and the molecules by which the microbiome functionally contributes to host physiology are being elucidated.
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Special Issue Perspective | Applied and Environmental ScienceCulturing the Uncultured: Risk versus RewardIsolation of new microorganisms is challenging, but cultures are invaluable resources for experimental validation of phenotype, ecology, and evolutionary processes. Although the number of new isolates continues to grow, the majority of cultivars still come from a limited number of phylogenetic groups and environments, necessitating investment in new cultivation efforts.
Special Issue Perspective | Ecological and Evolutionary ScienceThe Power of Metabolism for Predicting Microbial Community DynamicsQuantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.
Special Issue Perspective | Synthetic BiologyToward Autonomous Antibiotic DiscoveryMachines hold the potential to replace humans in many societal endeavors, and drug discovery is no exception. Antibiotic innovation has been stalled for decades, which has coincided with an alarming increase in multidrug-resistant bacteria.
Special Issue Perspective | Applied and Environmental ScienceDetermining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom BarriersMicroorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth.
Special Issue Perspective | Host-Microbe BiologyDefining Microbiome Health through a Host LensWe are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state.
Special Issue Perspective | Therapeutics and PreventionMoving Microbiome Science from the Bench to the Bedside: a Physician-Scientist PerspectiveThe recognition over the past decade that nearly all diseases are associated with changes in the microbiome has raised hope that microbiome-based therapeutics may cure many human ailments. Billions of dollars are being poured into microbiome-oriented biotech companies, and the coming years will undoubtedly witness the approval of the first generation of these products.
Special Issue Perspective | Ecological and Evolutionary ScienceExploring the Evolution of Virulence Factors through Bioinformatic Data MiningThe molecular evolution of virulence factors is a central theme in our understanding of bacterial pathogenesis and host-microbe interactions. Using bioinformatics and genome data mining, recent studies have shed light on the evolution of important virulence factor families and the mechanisms by which they have adapted and diversified in function.
Special Issue Perspective | Applied and Environmental SciencePrecision Food Safety: a Paradigm Shift in Detection and Control of Foodborne PathogensThe implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology.
Special Issue Perspective | Host-Microbe BiologyMissing Links: the Role of Primates in Understanding the Human MicrobiomeThe gut microbiome can influence host energy balances and metabolic programming. While this information is valuable in a disease context, it also has important implications for understanding host energetics from an ecological and evolutionary perspective.
