scholarly journals Missing Links: the Role of Primates in Understanding the Human Microbiome

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Katherine R. Amato
Keyword(s):  
Life History ◽  
Life History Theory ◽  
Human Microbiome ◽  
Cultural Influences ◽  
Microbiome Research ◽  
Allocation Patterns ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Host Life ◽  
Energy Balances

ABSTRACT The 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. Here I argue that gut microbial influences on host life history—the timing of events that make up an organism's life—are an overlooked but robust area of study given that variation in life history is linked directly to host energetic budgets and allocation patterns. Additionally, while cultural influences on life history complicate the exploration of these links in humans, nonhuman primates represent an alternative system in which more robust associations can be made. By integrating human and nonhuman primate microbiome research within the context of life history theory, we will be able to more effectively pinpoint microbial contributions to host phenotypes. This information will improve our understanding of host-microbe interactions in health and disease and will transform the fields of ecology and evolution more generally.

scholarly journals Ecological rules for the assembly of microbiome communities

PLoS Biology ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. e3001116
Author(s):  
Katharine Z. Coyte ◽  
Chitong Rao ◽  
Seth Rakoff-Nahoum ◽  
Kevin R. Foster
Keyword(s):  
Evolutionary Biology ◽  
Human Microbiome ◽  
Published Data ◽  
Host Feeding ◽  
Assembly Process ◽  
Microbe Interactions ◽  
One Step ◽  
Diverse Community ◽  
Host Microbe Interactions ◽  
Microbial Community Assembly

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome—with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these “assembly maps” reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable—and can provide metabolic benefits to the host—but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe–microbe and host–microbe interactions are important for the trajectory of microbiome assembly.

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 Macronutrients mediate the functional relationship between Drosophila and Wolbachia

2015 ◽  
Vol 282 (1800) ◽  
pp. 20142029 ◽  
Author(s):  
Fleur Ponton ◽  
Kenneth Wilson ◽  
Andrew Holmes ◽  
David Raubenheimer ◽  
Katie L. Robinson ◽  
...  
Keyword(s):  
Life History ◽  
Life History Theory ◽  
General Interest ◽  
Nutritional Geometry ◽  
New Strategy ◽  
Host Diet ◽  
Bacterial Endosymbionts ◽  
Host Life ◽  
Protection Against Infection

Wolbachia are maternally inherited bacterial endosymbionts that naturally infect a diverse array of arthropods. They are primarily known for their manipulation of host reproductive biology, and recently, infections with Wolbachia have been proposed as a new strategy for controlling insect vectors and subsequent human-transmissible diseases. Yet, Wolbachia abundance has been shown to vary greatly between individuals and the magnitude of the effects of infection on host life-history traits and protection against infection is correlated to within-host Wolbachia abundance. It is therefore essential to better understand the factors that modulate Wolbachia abundance and effects on host fitness. Nutrition is known to be one of the most important mediators of host–symbiont interactions. Here, we used nutritional geometry to quantify the role of macronutrients on insect– Wolbachia relationships in Drosophila melanogaster . Our results show fundamental interactions between diet composition, host diet selection, Wolbachia abundance and effects on host lifespan and fecundity. The results and methods described here open a new avenue in the study of insect– Wolbachia relationships and are of general interest to numerous research disciplines, ranging from nutrition and life-history theory to public health.

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.

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 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 Old and new models for studying host-microbe interactions in health and disease:C. difficileas an example

2017 ◽  
Vol 312 (6) ◽  
pp. G623-G627 ◽  
Author(s):  
Vincent B. Young
Keyword(s):  
Human Health ◽  
Bacterial Communities ◽  
Human Microbiome ◽  
Model Systems ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Indigenous Microbiota ◽  
Pathogenic Microbes ◽  
Host Microbe Interactions ◽  
Insight Into

There has been an explosion of interest in studying the indigenous microbiota, which plays an important role in human health and disease. Traditionally, the study of microbes in relationship to human health involved consideration of individual microbial species that caused classical infectious diseases. With the interest in the human microbiome, an appreciation of the influence that complex communities of microbes can have on their environment has developed. When considering either individual pathogenic microbes or a symbiotic microbial community, researchers have employed a variety of model systems with which they can study the host-microbe interaction. With the use of studies of infections with the toxin-producing bacterium Clostridium difficile as a model for both a pathogen and beneficial bacterial communities as an example, this review will summarize and compare various model systems that can be used to gain insight into the host-microbe interaction.

Invertebrate systems for hypothesis-driven microbiome research

2013 ◽  
Vol 1 (1) ◽  
Author(s):  
Irene L.G. Newton ◽  
Kathy B. Sheehan ◽  
Fredrick J. Lee ◽  
Melissa A. Horton ◽  
Randy D. Hicks
Keyword(s):  
Genetic Diversity ◽  
Host Specificity ◽  
Transmission Dynamics ◽  
Functional Equivalence ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

AbstractA number of novel, invertebrate systems have emerged as excellent models for the study of microbiomes. Due to their small size, evolutionary diversity, ease of culture, and – in many cases – relatively simple gut communities, invertebrates of many different orders can be tools to drive hypothesis-driven microbiome research. In this review we highlight several host systems amenable to microbiota analyses and specific questions that can be easily addressed in those systems. These questions address functional equivalence across similar habitats, host-specificity and coevolution of host-microbe interactions, and acquisition and transmission dynamics of host-associated communities. We propose that host systems be chosen based on the question of interest, and that insect systems are excellent tools for the vast behavioral, ecological, and genetic diversity that allows them to address a variety of these questions.

scholarly journals Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions

2018 ◽  
Vol 115 (10) ◽  
pp. 2461-2466 ◽  
Author(s):  
Emrah Altindis ◽  
Weikang Cai ◽  
Masaji Sakaguchi ◽  
Fa Zhang ◽  
Wang GuoXiao ◽  
...  
Keyword(s):  
Growth Factors ◽  
Human Insulin ◽  
Genetic Material ◽  
Human Microbiome ◽  
Insulin Receptors ◽  
Dna Encoding ◽  
Downstream Signaling ◽  
Increase Glucose Uptake ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Viruses are the most abundant biological entities and carry a wide variety of genetic material, including the ability to encode host-like proteins. Here we show that viruses carry sequences with significant homology to several human peptide hormones including insulin, insulin-like growth factors (IGF)-1 and -2, FGF-19 and -21, endothelin-1, inhibin, adiponectin, and resistin. Among the strongest homologies were those for four viral insulin/IGF-1–like peptides (VILPs), each encoded by a different member of the family Iridoviridae. VILPs show up to 50% homology to human insulin/IGF-1, contain all critical cysteine residues, and are predicted to form similar 3D structures. Chemically synthesized VILPs can bind to human and murine IGF-1/insulin receptors and stimulate receptor autophosphorylation and downstream signaling. VILPs can also increase glucose uptake in adipocytes and stimulate the proliferation of fibroblasts, and injection of VILPs into mice significantly lowers blood glucose. Transfection of mouse hepatocytes with DNA encoding a VILP also stimulates insulin/IGF-1 signaling and DNA synthesis. Human microbiome studies reveal the presence of these Iridoviridae in blood and fecal samples. Thus, VILPs are members of the insulin/IGF superfamily with the ability to be active on human and rodent cells, raising the possibility for a potential role of VILPs in human disease. Furthermore, since only 2% of viruses have been sequenced, this study raises the potential for discovery of other viral hormones which, along with known virally encoded growth factors, may modify human health and disease.

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