Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics

Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics

Author: Patrick Smyth

Publisher:

Published: 2021

Total Pages:

ISBN-13:

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The gut microbiome and its metabolic processes are dynamic systems. Surprisingly, our understanding of gut microbiome dynamics is limited. Here we report a metaproteomic workflow that involves protein stable isotope probing (protein-SIP) and identification/quantification of partially labeled peptides. We also developed a package, which we call MetaProfiler, that corrects for false identifications and performs phylogenetic and time series analysis for the study of microbiome dynamics. From the stool sample of five mice that were fed with 15-N hydrolysate from Ralstonia eutropha, we identified 15,297 non-redundant unlabeled peptides of which 10,839 of their heavy counterparts were quantified. These peptides revealed incorporation profiles over time that were different between and within taxa, as well as between and within clusters of orthologous groups (COGs). Our study helps unravel the complex dynamics of protein synthesis and bacterial dynamics in the mouse gut microbiome.


Phage Therapy: Past, Present and Future

Phage Therapy: Past, Present and Future

Author: Stephen T. Abedon

Publisher: Frontiers Media SA

Published: 2017-09-05

Total Pages: 394

ISBN-13: 2889452514

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Historically, the first observation of a transmissible lytic agent that is specifically active against a bacterium (Bacillus anthracis) was by a Russian microbiologist Nikolay Gamaleya in 1898. At that time, however, it was too early to make a connection to another discovery made by Dmitri Ivanovsky in 1892 and Martinus Beijerinck in 1898 on a non-bacterial pathogen infecting tobacco plants. Thus the viral world was discovered in two of the three domains of life, and our current understanding is that viruses represent the most abundant biological entities on the planet. The potential of bacteriophages for infection treatment have been recognized after the discoveries by Frederick Twort and Felix d’Hérelle in 1915 and 1917. Subsequent phage therapy developments, however, have been overshadowed by the remarkable success of antibiotics in infection control and treatment, and phage therapy research and development persisted mostly in the former Soviet Union countries, Russia and Georgia, as well as in France and Poland. The dramatic rise of antibiotic resistance and especially of multi-drug resistance among human and animal bacterial pathogens, however, challenged the position of antibiotics as a single most important pillar for infection control and treatment. Thus there is a renewed interest in phage therapy as a possible additive/alternative therapy, especially for the infections that resist routine antibiotic treatment. The basis for the revival of phage therapy is affected by a number of issues that need to be resolved before it can enter the arena, which is traditionally reserved for antibiotics. Probably the most important is the regulatory issue: How should phage therapy be regulated? Similarly to drugs? Then the co-evolving nature of phage-bacterial host relationship will be a major hurdle for the production of consistent phage formulae. Or should we resort to the phage products such as lysins and the corresponding engineered versions in order to have accurate and consistent delivery doses? We still have very limited knowledge about the pharmacodynamics of phage therapy. More data, obtained in animal models, are necessary to evaluate the phage therapy efficiency compared, for example, to antibiotics. Another aspect is the safety of phage therapy. How do phages interact with the immune system and to what costs, or benefits? What are the risks, in the course of phage therapy, of transduction of undesirable properties such as virulence or antibiotic resistance genes? How frequent is the development of bacterial host resistance during phage therapy? Understanding these and many other aspects of phage therapy, basic and applied, is the main subject of this Topic.


Temporal Dynamics of the Skin Microbiome in Disease

Temporal Dynamics of the Skin Microbiome in Disease

Author: Michael Austin Loesche

Publisher:

Published: 2016

Total Pages: 306

ISBN-13:

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The skin is colonized by communities of bacteria, fungi, and viruses, collectively referred to as the skin microbiome. These microbial communities are shaped by the topology and diseases of the skin. Dysbiosis of the cutaneous microbiome has been associated with several ailments of the skin including atopic dermatitis, acne, rosacea, psoriasis, and chronic wounds. However, our understandings of the processes by which these microbes initiate, maintain, or modulate skin diseases is lacking. Moreover, previous research on the topic has largely been limited by cross-sectional study designs, neglecting the natural dynamism of microbial communities. Here we present a comprehensive analysis of the temporal dynamics of the skin microbiome in various diseases. In the first section, we characterize the diversity and dynamics of both bacterial and fungal communities colonizing chronic wounds and its associations with clinical outcomes. In a study of 100 subjects with diabetic foot ulcers, we sampled the wound microbiota in 2-week intervals until healing, amputation of 26 weeks of follow-up. We demonstrate the high levels of community instability in chronic wounds and expose the positive association between wound healing community instability. We also reveal the effect of antibiotic perturbation on the microbiota. The fungal component was found to have associations with various bacteria and clinical outcomes. Our results should inform the design of future studies and provides evidence that microbial dynamics may be an effective biomarker for identifying high-risk ulcers. The second section investigates the body-site specific effects of psoriasis on the skin microbiome and how it responds to therapy. We reveal these patterns in a study of 114 subjects, across 6 body sites, and over 112 weeks of follow-up. The effect of psoriatic lesions was found to be mild and body-site specific. In contrast, ustekinumab treatment was found to induce moderate shifts in microbial composition, including an increase in atypical skin bacteria and inter-individual heterogeneity. These results suggest that the effect of psoriasis lesions is secondary to the effect the broad effects of the immune environment. Together the work presented in this thesis represents a significant advancement in our understanding of the microbial dynamics of the skin and their associations with human health.


Temporal Microbiome Dynamics

Temporal Microbiome Dynamics

Author: Celeste Allaband

Publisher:

Published: 2022

Total Pages: 0

ISBN-13:

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Microbial life is all around us and inside us in an unseen vast and varied ecosystem. For the past several decades, the microbiome field has attempted to characterize this microscopic web of life using next generation sequencing technology. It turns out that the number of host organism cells is generally outnumbered by the number of microbial cells that live on and within them. Moreover, these microbes collectively have two orders of magnitude more genes than their host organism. While the host organism's genome stays constant during its life, the microbial community and its associated genes change much more frequently. Since microbial lifespans are sometimes measured in minutes, selective pressures in the host micro-environments can rapidly affect the evolution and gene content of the microorganisms present. Over the course of a lifetime, the host winds up with a unique set of microbes selected to fit their unique individual environment, from immune system quirks to specialized diets to biological rhythms. However, despite biological rhythms having always played a role in host behavior and survival, the impact of time on health has been a widely neglected realm until recently. The basic argument of this thesis is that time is an underappreciated but critical variable that impacts both experimental study design as well as host health.


Environmental Chemicals, the Human Microbiome, and Health Risk

Environmental Chemicals, the Human Microbiome, and Health Risk

Author: National Academies of Sciences, Engineering, and Medicine

Publisher: National Academies Press

Published: 2018-03-01

Total Pages: 123

ISBN-13: 0309468698

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A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.


Skin Microbiome Handbook

Skin Microbiome Handbook

Author: Nava Dayan

Publisher: John Wiley & Sons

Published: 2020-09-01

Total Pages: 432

ISBN-13: 1119592232

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The book provides a comprehensive detailed summary of current status on skin microbiome research in health and disease as well as key regulatory and legal aspects. In the past decade, interest and technology have greatly advanced to unravel the nature and effect of skin microbiome on our health. Diseases such as atopic dermatitis and acne are at the forefront of this research, but also other conditions such as skin cancer are under investigation. In addition, mapping of the skin microbiome has gone from basic to more detailed with attempts to correlate it to various ages, ethnicities and genders. In parallel to mapping it, a great deal of research is dedicated to understanding its functionality and communication (and hence effect) on human cells. The Skin Microbiome Handbook is a summary of current status of knowledge, research tools and approaches in skin microbiome, in health and disease. It contains the following categories: healthy skin microbiome and oral-skin interaction; skin microbiome observational research; skin microbiome in disequilibrium and disease; skin's innate immunity; testing and study design; regulatory and legal aspects for skin microbiome related products. The 18 chapters of the book are written by carefully selected leaders in the academia and industry exhibiting extensive experience and understanding in the areas of interest.


Bugs as Drugs

Bugs as Drugs

Author: Robert A. Britton

Publisher: John Wiley & Sons

Published: 2020-07-02

Total Pages: 514

ISBN-13: 1555819702

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Examining the enormous potential of microbiome manipulation to improve health Associations between the composition of the intestinal microbiome and many human diseases, including inflammatory bowel disease, cardiovascular disease, metabolic disorders, and cancer, have been elegantly described in the past decade. Now, whole-genome sequencing, bioinformatics, and precision gene-editing techniques are being combined with centuries-old therapies, such as fecal microbiota transplantation, to translate current research into new diagnostics and therapeutics to treat complex diseases. Bugs as Drugs provides a much-needed overview of microbes in therapies and will serve as an excellent resource for scientists and clinicians as they carry out research and clinical studies on investigating the roles the microbiota plays in health and disease. In Bugs as Drugs, editors Robert A. Britton and Patrice D. Cani have assembled a fascinating collection of reviews that chart the history, current efforts, and future prospects of using microorganisms to fight disease and improve health. Sections cover traditional uses of probiotics, next-generation microbial therapeutics, controlling infectious diseases, and indirect strategies for manipulating the host microbiome. Topics presented include: How well-established probiotics support and improve host health by improving the composition of the intestinal microbiota of the host and by modulating the host immune response. The use of gene editing and recombinant DNA techniques to create tailored probiotics and to characterize next-generation beneficial microbes. For example, engineering that improves the anti-inflammatory profile of probiotics can reduce the number of colonic polyps formed, and lactobacilli can be transformed into targeted delivery systems carrying therapeutic proteins or bioengineered bacteriophage. The association of specific microbiota composition with colorectal cancer, liver diseases, osteoporosis, and inflammatory bowel disease. The gut microbiota has been proposed to serve as an organ involved in regulation of inflammation, immune function, and energy homeostasis. Fecal microbiota transplantation as a promising treatment for numerous diseases beyond C. difficile infection. Practical considerations for using fecal microbiota transplantation are provided, while it is acknowledged that more high-quality evidence is needed to ascertain the importance of strain specificity in positive treatment outcomes. Because systems biology approaches and synthetic engineering of microbes are now high-throughput and cost-effective, a much wider range of therapeutic possibilities can be explored and vetted.


The Human Microbiome, Diet, and Health

The Human Microbiome, Diet, and Health

Author: Food Forum

Publisher: National Academies Press

Published: 2013-02-27

Total Pages: 197

ISBN-13: 030926586X

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The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge of the human microbiome, its role in human health, its interaction with the diet, and the translation of new research findings into tools and products that improve the nutritional quality of the food supply. The Human Microbiome, Diet, and Health: Workshop Summary summarizes the presentations and discussions that took place during the workshop. Over the two day workshop, several themes covered included: The microbiome is integral to human physiology, health, and disease. The microbiome is arguably the most intimate connection that humans have with their external environment, mostly through diet. Given the emerging nature of research on the microbiome, some important methodology issues might still have to be resolved with respect to undersampling and a lack of causal and mechanistic studies. Dietary interventions intended to have an impact on host biology via their impact on the microbiome are being developed, and the market for these products is seeing tremendous success. However, the current regulatory framework poses challenges to industry interest and investment.


Spatiotemporal Modeling of Microbial Communities

Spatiotemporal Modeling of Microbial Communities

Author: Liat Shenhav

Publisher:

Published: 2020

Total Pages: 102

ISBN-13:

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Microbial communities can undergo rapid changes, that can both cause and indicate host disease, rendering longitudinal microbiome studies key for understanding microbiome-associated disorders. However, most standard statistical methods, based on random samples, are not applicable for addressing the methodological and statistical challenges associated with repeated, structured observations of a complex ecosystem. Therefore, to elucidate how and why our microbiome varies in time, and whether these trajectories are consistent across humans, we developed new methods for modeling the temporal and spatial dynamics of microbial communities. We developed a method to identify 'time-dependent' microbes (Shenhav et al., PLoS Computational Biology 2019) and showed that their temporal patterns differentiate between the developing microbial communities of infants and those of adults. We also developed models to deconvolute the dynamics of microbial community formation. Using these methods, we found significant differences between vaginally- and cesarean-delivered infants in terms of initial colonization and succession of their gut microbial community (Shenhav et al., Nature Methods 2019) as well as the trajectories of these communities in the first years of life (Martino*, Shenhav* et al., Nature Biotechnology). These models, designed to identify and predict time-dependent patterns, will help researchers better understand the temporal nature of the human microbiome from the time of its formation at birth and throughout life.