The importance of host physical niches for the stability of gut microbiome composition.

Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts.

Cellular and molecular organization of the Drosophila foregut.

The animal foregut is the first tissue to encounter ingested food, bacteria, and viruses. We characterized the adult Drosophila foregut using transcriptomics to better understand how it triages consumed items for digestion or immune response and manages resources. Cell types were assigned and validated using GFP-tagged and Gal4 reporter lines.

Master regulators of biological systems in higher dimensions.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present, generating higher-order interactions.

First-passage-time statistics of growing microbial populations carry an imprint of initial conditions.

In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of exponential growth we show power-law relationships that relate variability in the time required to reach a threshold population size to growth rate and inoculum size. Population-growth experiments in E.

A chemically-defined growth medium to support Lactobacillus-Acetobacter sp. community analysis.

Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of the fruit fly Drosophila melanogaster. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growth.

Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund.

A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition.

Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life.

How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored.

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota.

The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization.

From worms to humans: Understanding intestinal lipid metabolism via model organisms.

The intestine is responsible for efficient absorption and packaging of dietary lipids before they enter the circulatory system. This review provides a comprehensive overview of how intestinal enterocytes from diverse model organisms absorb dietary lipid and subsequently secrete the largest class of lipoproteins (chylomicrons) to meet the unique needs of each animal. We discuss the putative relationship between diet and metabolic disease progression, specifically Type 2 Diabetes Mellitus.

Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome.

The intestines of animals are colonized by commensal microbes, which impact host development, health, and behavior. Precise quantification of colonization is essential for studying the complex interactions between host and microbe both to validate the microbial composition and study its effects. Drosophila melanogaster, which has a low native microbial diversity and is economical to rear with defined microbial composition, has emerged as a model organism for studying the gut microbiome.

Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities.

The optimisation of synthetic and natural microbial communities has vast potential for emerging applications in medicine, agriculture and industry. Realising this goal is contingent on a close correlation between theory, experiments, and the real world. Although the temporal pattern of resource supply can play a major role in microbial community assembly, resource dynamics are commonly treated inconsistently in theoretical and experimental research.

Whole Animal Feeding FLat (WAFFL): a complete and comprehensive validation of a novel, high-throughput fly experimentation system.

Non-mammalian model organisms have been essential for our understanding of the mechanisms that control development, disease, and physiology, but they are underutilized in pharmacological and toxicological phenotypic screening assays due to their low throughput in comparison with cell-based screens. To increase the utility of using Drosophila melanogaster in screening, we designed the Whole Animal Feeding FLat (WAFFL), a novel, flexible, and complete system for feeding, monitoring, and assaying flies in a high-throughput format. Our 3D printed system is compatible with inexpensive and readily available, commercial 96-well plate consumables and equipment.

Nutrient encryption and the diversity of cobamides, siderophores, and glycans.

Encryption makes information available only to those with the decoding key. We propose that microbes, living in a chemical environment, encrypt nutrients, thereby making them available only to those with the decoding enzymes, such as their kin. Examples of encrypted nutrients include cobamides, which are expensive to make and valuable for microbial fitness.

Higher-order microbiome interactions and how to find them.

The complexity of microbial communities suggests prevalent interactions involving more than just pairs of species. These so-called higher-order interactions may reveal new molecules that enable bacteria to deal with complex environments. This forum article discusses how higher-order interactions can be detected and why molecular biologists might care.

Microbiome-by-ethanol interactions impact Drosophila melanogaster fitness, physiology, and behavior.

The gut microbiota can affect how animals respond to ingested toxins, such as ethanol, which is prevalent in the diets of diverse animals and often leads to negative health outcomes in humans. Ethanol is a complex dietary factor because it acts as a toxin, behavioral manipulator, and nutritional source, with both direct effects on the host as well as indirect ones through the microbiome. Here, we developed a model for chronic, non-intoxicating ethanol ingestion in the adult fruit fly, , and paired this with the tractability of the fly gut microbiota, which can be experimentally removed.

Stochastic microbiome assembly depends on context.

Observational studies reveal substantial variability in microbiome composition across individuals. Targeted studies in gnotobiotic animals underscore this variability by showing that some bacterial strains colonize deterministically, while others colonize stochastically. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism , interactions between bacteria can affect the microbiome assembly process, contributing to a baseline level of microbiome variability even among isogenic organisms that are identically reared, housed, and fed.

Genetic Rescue of the Highly Inbred Norwegian Lundehund.

Augmenting the genetic diversity of small, inbred populations by the introduction of new individuals is often termed "genetic rescue". An example is the Norwegian Lundehund, a small spitz dog with inbreeding-related health problems that is being crossed with three Nordic breeds, including the Norwegian Buhund. Conservation breeding decisions for the (typically) small number of outcrossed individuals are vital for managing the rescue process, and we genotyped the Lundehund ( = 12), the Buhund ( = 12), their crosses (F1, = 7) and first-generation backcrosses to the Lundehund (F2, = 12) with >170,000 single nucleotide polymorphism loci to compare their levels of genetic diversity.

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance.

Predicting antibiotic efficacy within microbial communities remains highly challenging. Interspecies interactions can impact antibiotic activity through many mechanisms, including alterations to bacterial physiology. Here, we studied synthetic communities constructed from the core members of the fruit fly gut microbiota.

Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila.

Cell- and tissue-level processes often occur across days or weeks, but few imaging methods can capture such long timescales. Here, we describe Bellymount, a simple, noninvasive method for longitudinal imaging of the Drosophila abdomen at subcellular resolution. Bellymounted animals remain live and intact, so the same individual can be imaged serially to yield vivid time series of multiday processes.

Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of .

Cilia and flagella are ideal model organelles in which to study the general question of organelle size control. Flagellar microtubules are steady-state structures whose size is set by the balance of assembly and disassembly. Assembly requires intraflagellar transport (IFT), and measurements of IFT have shown that the rate of entry of IFT particles into the flagellum is a decreasing function of length.

Cluster partitions and fitness landscapes of the Drosophila fly microbiome.

The concept of genetic epistasis defines an interaction between two genetic loci as the degree of non-additivity in their phenotypes. A fitness landscape describes the phenotypes over many genetic loci, and the shape of this landscape can be used to predict evolutionary trajectories. Epistasis in a fitness landscape makes prediction of evolutionary trajectories more complex because the interactions between loci can produce local fitness peaks or troughs, which changes the likelihood of different paths.

Microbiome interactions shape host fitness.

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of and reveal that interactions between bacteria shape host fitness through life history tradeoffs.