The Gut Microbiome: Connecting Spatial Organization to Function

Tropini, Carolina; Earle, Kristen A.; Huang, Kerwyn Casey; Sonnenburg, Justin L.

doi:10.1016/j.chom.2017.03.010

Cited by 513 publications

(453 citation statements)

References 105 publications

(145 reference statements)

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“…( 2016), Martino, Ma and Leulier ( 2017), Smith et al. ( 2017), Tropini, Earle, Huang and Sonnenburg ( 2017); excretory system: King and Goldstein (1985), Buechner (2002), Gautam, Verma and Tapadia ( 2017); sleep and circadian system: Raizen et al. ( 2008); Trojanowski and Raizen (2016); Miyazaki, Liu and Hayashi ( 2017); others: Micchelli and Perrimon (2006), Ohlstein and Spradling (2006), Chaturvedi, Reichert, Gunage and VijayRaghavan ( 2017), Gunage, Dhanyasi, Reichert and VijayRaghavan (2017)…”

Section: Research Organisms For Agingmentioning

confidence: 99%

The African turquoise killifish: A research organism to study vertebrate aging and diapause

Brunet²

2018

Aging Cell

135

118

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SummaryThe African turquoise killifish has recently gained significant traction as a new research organism in the aging field. Our understanding of aging has strongly benefited from canonical research organisms—yeast, C. elegans, Drosophila, zebrafish, and mice. Many characteristics that are essential to understand aging—for example, the adaptive immune system or the hypothalamo‐pituitary axis—are only present in vertebrates (zebrafish and mice). However, zebrafish and mice live more than 3 years and their relatively long lifespans are not compatible with high‐throughput studies. Therefore, the turquoise killifish, a vertebrate with a naturally compressed lifespan of only 4–6 months, fills an essential gap to understand aging. With a recently developed genomic and genetic toolkit, the turquoise killifish not only provides practical advantages for lifespan and longitudinal experiments, but also allows more systematic characterizations of the interplay between genetics and environment during vertebrate aging. Interestingly, the turquoise killifish can also enter a long‐term dormant state during development called diapause. Killifish embryos in diapause already have some organs and tissues, and they can last in this state for years, exhibiting exceptional resistance to stress and to damages due to the passage of time. Understanding the diapause state could give new insights into strategies to prevent the damage caused by aging and to better preserve organs, tissues, and cells. Thus, the African turquoise killifish brings two interesting aspects to the aging field—a compressed lifespan and a long‐term resistant diapause state, both of which should spark new discoveries in the field.

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Section: Research Organisms For Agingmentioning

confidence: 99%

The African turquoise killifish: A research organism to study vertebrate aging and diapause

Brunet²

2018

Aging Cell

135

118

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“…[52,53] However, microbial communities adapt to their physical environment and availability to nutrients. [60][61][62] Ultimately, and in line with the ambition to generate new treatment regimens for lifestylerelated diseases using microbial intervention, the impact of microbial biogeographical localization on host physiology and disease merits further studies. Gut microbial composition, in terms of aerobes and anaerobes, most likely also adapt to these differences.…”

Section: Gut Microbe-host Interactions Are Optimized By Their Biogeogmentioning

confidence: 99%

When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes

2019

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Animals exist as biodiverse composite organisms that include microbial residents, eukaryotic cells, and organs that collectively form a human being. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body or the holobiont secures growth, health, and reproduction. As such, the survival of a holobiont is dependent on the maintenance of biological order including metabolic homeostasis by tight regulation of the communication between its eukaryotic and prokaryotic residents. In this review an overview and perspective are provided on the bidirectional communication between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships between the components of the holobiont. An emphasis is placed on exemplifying microbiome-mediated effects on host functions-aiming to integrate microbiome functionality to host physiology, be it health or disease. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex transkingdom interactions are provided. We Nurture an Intricate Relationship with Our Symbiotic MicrobesHumans and their indigenous microbiomes are uniquely symbiotic in a number of facets. Indeed, many human genes are homologous to bacterial genes that are predominant in

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“…fibers), that exist in the distal gut. Development of higher throughput methods for imaging and quantifying the spatial distribution of different taxa within the gut (Tropini et al, 2017) would allow tests of the following concepts. These particles serve as an important site of attachment for saccharolytic organisms so that they can harvest particle-associated glycans and share the products of their digestion with syntrophic partners who also reside on these particles.…”

Section: Defining the Nutrient Content Of Food: A Key Missing ‘Ingredmentioning

confidence: 99%

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage

Barratt

Lebrilla

Shapiro

et al. 2017

Cell Host & Microbe

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Analytic advances are enabling more precise definitions of the molecular composition of key food staples incorporated into contemporary diets and how the nutrient landscapes of these staples vary as a function of cultivar and food processing methods. This knowledge, combined with insights about the interrelationship between consumer microbiota configurations and biotransformation of food ingredients, should have a number of effects on agriculture, food production and strategies for improving the nutritional value of foods and health status. These effects include decision-making about which cultivars of current or future food staples to incorporate into existing and future food systems, and which components of waste streams from current or future food manufacturing processes have nutritional value that is worth capturing. They can also guide which technologies should be applied, or need to be developed, to produce foods that support efficient microbial biotransformation of their ingredients into metabolic products that sustain health.

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The Gut Microbiome: Connecting Spatial Organization to Function

Cited by 513 publications

References 105 publications

The African turquoise killifish: A research organism to study vertebrate aging and diapause

The African turquoise killifish: A research organism to study vertebrate aging and diapause

When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage

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