scholarly journals Meta-analysis of Diets Used in Drosophila Microbiome Research and Introduction of the Drosophila Dietary Composition Calculator (DDCC)

2020 ◽  
Vol 10 (7) ◽  
pp. 2207-2211 ◽  
Author(s):  
Danielle N. A. Lesperance ◽  
Nichole A. Broderick
Keyword(s):  
Meta Analysis ◽  
Dietary Composition ◽  
Nutritional Content ◽  
Web Based ◽  
Future Studies ◽  
Microbiome Composition ◽  
Wide Range ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Nutrition is a major factor influencing many aspects of Drosophila melanogaster physiology. However, a wide range of diets, many of which are termed “standard” in the literature, are utilized for D. melanogaster research, leading to inconsistencies in reporting of nutrition-dependent phenotypes across the field. This is especially evident in microbiome studies, as diet has a pivotal role in microbiome composition and resulting host-microbe interactions. Here, we performed a meta-analysis of diets used in fly microbiome research and provide a web-based tool for researchers to determine the nutritional content of diets of interest. While our meta-analysis primarily focuses on microbiome studies, our goal in developing these resources is to aid the broader community in contextualizing past and future studies across the scope of D. melanogaster research to better understand how individual lab diets can contribute to observed phenotypes.

scholarly journals Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC)

2020 ◽  
Author(s):  
Danielle N.A. Lesperance ◽  
Nichole A. Broderick
Keyword(s):  
Meta Analysis ◽  
Standard Diet ◽  
Dietary Composition ◽  
Community Resources ◽  
Nutritional Content ◽  
Web Based ◽  
Microbiome Composition ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

AbstractWhile the term standard diet is commonly used in studies using Drosophila melanogaster, more often than not these diets are anything but standard, making it difficult to contextualize results in the broader scope of the field. This is especially evident in microbiome studies, despite diet having a pivotal role in microbiome composition and resulting host-microbe interactions. Here, we performed a meta-analysis of diets used in fly microbiome research and provide a web-based tool for researchers to determine the nutritional content of diets of interest. Our goal is for these community resources to aid in contextualizing both past and future microbiome studies (with utility to other fields as well) to better understand how individual lab diets can contribute to observed phenotypes.

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals Health and disease markers correlate with gut microbiome composition across thousands of people

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ohad Manor ◽  
Chengzhen L. Dai ◽  
Sergey A. Kornilov ◽  
Brett Smith ◽  
Nathan D. Price ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Lifestyle Factors ◽  
Clinical Markers ◽  
Human Gut ◽  
Microbiome Composition ◽  
Targeted Interventions ◽  
Human Gut Microbiome ◽  
Host Diet ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Abstract Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.

scholarly journals Candidate pathogenicity islands in the genome of ‘CandidatusRickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2806 ◽  
Author(s):  
YaDong Wang ◽  
Christopher Chandler
Keyword(s):  
Genomic Island ◽  
Genomic Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Photorhabdus Luminescens ◽  
Future Studies ◽  
Terrestrial Isopod ◽  
Microbe Interactions ◽  
Host Microbe Interactions

The bacterial genusRickettsiellabelongs to the order Legionellales in the Gammaproteobacteria, and consists of several described species and pathotypes, most of which are considered to be intracellular pathogens infecting arthropods. Two members of this genus,R. grylliandR. isopodorum, are known to infect terrestrial isopod crustaceans. In this study, we assembled a draft genomic sequence forR. isopodorum, and performed a comparative genomic analysis withR. grylli. We found evidence for several candidate genomic island regions inR. isopodorum, none of which appear in the previously availableR. grylligenome sequence.Furthermore, one of these genomic island candidates inR. isopodorumcontained a gene that encodes a cytotoxin partially homologous to those found inPhotorhabdus luminescensandXenorhabdus nematophilus(Enterobacteriaceae), suggesting that horizontal gene transfer may have played a role in the evolution of pathogenicity inRickettsiella. These results lay the groundwork for future studies on the mechanisms underlying pathogenesis inR. isopodorum, and this system may provide a good model for studying the evolution of host-microbe interactions in nature.

scholarly journals Integrative developmental ecology: a review of density-dependent effects on life-history traits and host-microbe interactions in non-social holometabolous insects

2020 ◽  
Vol 34 (5) ◽  
pp. 659-680 ◽  
Author(s):  
Anh The Than ◽  
Fleur Ponton ◽  
Juliano Morimoto
Keyword(s):  
Population Dynamics ◽  
Life History ◽  
Life History Traits ◽  
Larval Density ◽  
Future Research ◽  
Density Dependent ◽  
Integrative Framework ◽  
Wide Range ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Abstract Population density modulates a wide range of eco-evolutionary processes including inter- and intra-specific competition, fitness and population dynamics. In holometabolous insects, the larval stage is particularly susceptible to density-dependent effects because the larva is the resource-acquiring stage. Larval density-dependent effects can modulate the expression of life-history traits not only in the larval and adult stages but also downstream for population dynamics and evolution. Better understanding the scope and generality of density-dependent effects on life-history traits of current and future generations can provide useful knowledge for both theory and experiments in developmental ecology. Here, we review the literature on larval density-dependent effects on fitness of non-social holometabolous insects. First, we provide a functional definition of density to navigate the terminology in the literature. We then classify the biological levels upon which larval density-dependent effects can be observed followed by a review of the literature produced over the past decades across major non-social holometabolous groups. Next, we argue that host-microbe interactions are yet an overlooked biological level susceptible to density-dependent effects and propose a conceptual model to explain how density-dependent effects on host-microbe interactions can modulate density-dependent fitness curves. In summary, this review provides an integrative framework of density-dependent effects across biological levels which can be used to guide future research in the field of ecology and evolution.

scholarly journals Making the invisible visible: exploring host–microbiome interactions across different taxa using data-driven 3D visualization

2021 ◽  
Author(s):  
Susanne H. Landis ◽  
Tom Duscher ◽  
Thomas C.G. Bosch
Keyword(s):  
3D Visualization ◽  
Interactive Media ◽  
Visual Communication Design ◽  
Microbiome Research ◽  
Scientific Poster ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions ◽  
Using Data ◽  
User Friendly

The importance of microbiome research is rapidly gaining momentum for understanding its role in development, evolution, ecology, health and disease. Recent progress in community and single-cell genomic approaches has provided an unprecedented amount of information on the abundance and ecology of microbes in different host organisms and turned them into metaorganisms. A metaorganism is a host and its complete microbial community which is commonly referred to as the microbiome. Over half the cells in a human body are not human but belong to the multitude of species that compose our microbiome. However, linkages between metaorganisms from different taxa and their in situ level of intraspecific dependence (be it growth, division or metabolic activity) are much more scarce. Visualization therefore is crucial for understanding host–microbe interactions as well as overarching concepts in different host organisms. Here we introduce an innovative user-friendly method for interactive visualization of microbiome multi-omics data. The new communication format combines science and visual communication design. Interactive media are used to transform scientific findings on host–microbe interactions in an intuitive way. The method provides access to additional layers of information that cannot be visualized using a traditional platform. We demonstrate the usefulness of this visualization approach using the interactive scientific poster ‘Digital Meta’, which is designed to support not only interdisciplinary co-working but also communication with the general public.

scholarly journals Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

2019 ◽  
Vol 116 (40) ◽  
pp. 20025-20032 ◽  
Author(s):  
Seth M. Rudman ◽  
Sharon Greenblum ◽  
Rachel C. Hughes ◽  
Subhash Rajpurohit ◽  
Ozan Kiratli ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
Microbiome Composition ◽  
Adaptive Process ◽  
Population Genomic ◽  
Polygenic Adaptation ◽  
Microbial Group ◽  
Genomic Adaptation ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host–microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.

scholarly journals The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions

2019 ◽  
Author(s):  
Veronica Roman-Reyna ◽  
Dale Pinili ◽  
Frances Nikki Borja ◽  
Ian Lorenzo Quibod ◽  
Simon C. Groen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Cropping Systems ◽  
Field Trials ◽  
The Philippines ◽  
Microbiome Composition ◽  
Relative Contribution ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Composition Structure ◽  
Genomic Regions

AbstractUnderstanding the factors that influence the outcome of crop interactions with microbes is key to managing crop diseases and improving yield. While the composition, structure and functional profile of crop microbial communities are shaped by complex interactions between the host, microbes and the environment, the relative contribution of each of these factors is mostly unknown. Here, we profiled the community composition of bacteria across leaves of 3,024 rice (Oryza sativa) accessions from field trials in China and the Philippines using metagenomics. Despite significant differences in diversity between environments, the structure and metabolic profiles of the microbiome appear to be conserved, suggesting that microbiomes converge onto core functions. Furthermore, co-occurrence analysis identified microbial hubs that regulate the network structure of the microbiome. We identified rice genomic regions controlling the abundance of these hubs, enriched for processes involved in stress responses and carbohydrate metabolism. We functionally validated the importance of these processes, finding that abundance of hub taxa was different in rice mutants with altered cellulose and salicylate accumulation, two major metabolites at the host-microbe interactions interface. By identifying key host genomic regions, host traits and hub microbes that govern microbiome composition, our study opens the door to designing future cropping systems.

scholarly journals The Lung Microbiome during Health and Disease

2021 ◽  
Vol 22 (19) ◽  
pp. 10872
Author(s):  
Kazuma Yagi ◽  
Gary B. Huffnagle ◽  
Nicholas W. Lukacs ◽  
Nobuhiro Asai
Keyword(s):  
Molecular Techniques ◽  
Microbial Composition ◽  
Healthy Human ◽  
Lung Microbiome ◽  
Large Numbers ◽  
Human Lungs ◽  
Culture Independent ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Healthy human lungs have traditionally been considered to be a sterile organ. However, culture-independent molecular techniques have reported that large numbers of microbes coexist in the lung and airways. The lungs harbor diverse microbial composition that are undetected by previous approaches. Many studies have found significant differences in microbial composition between during health and respiratory disease. The lung microbiome is likely to not only influence susceptibility or causes of diseases but be affected by disease activities or responses to treatment. Although lung microbiome research has some limitations from study design to reporting, it can add further dimensionality to host-microbe interactions. Moreover, there is a possibility that extending understanding to the lung microbiome with new multiple omics approaches would be useful for developing both diagnostic and prognostic biomarkers for respiratory diseases in clinical settings.

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