Download or read book Statistical Analysis of Microbiome Data with R written by Yinglin Xia and published by Springer. This book was released on 2018-10-06 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.

Download or read book The Gut Skin Axis Interaction of Gut Microbiome and Skin Diseases written by Jianmin Chai and published by Frontiers Media SA. This book was released on 2024-06-13 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: More and more evidence has demonstrated that gut microbiome plays critical roles in modulating the development of diseases beyond the gastrointestinal tract, including skin disorders such as psoriasis. The new conception ‘gut-skin axis’ refers to the bidirectional relationship between the gut microbiome and skin health. Several mechanisms, such as intestinal barrier, inflammatory mediators, and metabolites, have been proposed for gut-skin axis. Currently, there have been various studies regarding the presence of the gut-skin axis and its resulting inflammatory effect due to gut microbiome imbalance. In addition, dysbiosis of the skin and gut microbiota is also observed in skin disorders. Therefore, understanding the gut-skin axis, especially in terms of microbiome modulation, is important for the gut and skin health, which may lead to development of novel therapies for skin disease.

Download or read book Statistical Analysis of Microbiome Data written by Somnath Datta and published by Springer Nature. This book was released on 2021-10-27 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.

Download or read book Animal social behaviour and gut microbiome written by Lifeng Zhu and published by Frontiers Media SA. This book was released on 2023-09-06 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Oral Microbiome is a Key Factor in Oral and Systemic Health written by Florence Carrouel and published by Frontiers Media SA. This book was released on 2022-03-10 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Exploring the Bee Microbiome Distributions Interactions and Functions written by Hao Zheng and published by Frontiers Media SA. This book was released on 2023-09-12 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Nutritional Physiology and Gut Microbiome written by Jia Yin and published by Frontiers Media SA. This book was released on 2023-06-22 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: The gut microbiota is the largest symbiotic ecosystem in the host and has been demonstrated to play an important role in maintaining intestinal homeostasis. The symbiotic relationship between the microbiota and the host is mutually beneficial. The host provides important habitat and nutrients for the microbiome. The gut microbiota supports the development of the metabolic system and the intestinal immune system's maturation. Intestinal microbes ingest dietary components such as carbohydrates, proteins, and lipids, and the metabolites are reported to directly or indirectly affect human health. Therefore, there is an inseparable relationship between the gut microbiota and the nutrition of the host.

Download or read book Soil microbiome community and functional succession mechanism driven by different factors in agricultural ecology written by Bin Huang and published by Frontiers Media SA. This book was released on 2023-09-29 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Female Reproductive Tract Microbiome Gatekeeper for Sexual and Reproductive Health written by Mariya Ivanova Petrova and published by Frontiers Media SA. This book was released on 2023-03-21 with total page 267 pages. Available in PDF, EPUB and Kindle. Book excerpt: An optimal female reproductive tract (FRT) microbiome represents a cornerstone for successful reproductive and sexual health. Although understanding the link between the microbiota and our health is the focus of a growing number of research programs and research has advanced in the last decade, the FRT microbiome remains relatively poorly defined. This is despite it being one of the most critical factors impacting fertility and the health of the future generation. Important gaps in our knowledge remain about women-specific microbial niches, such as the lower FRT. The vaginal microbiome of healthy women is almost exclusively dominated by Lactobacillus species, making these species synonymous with vaginal health. Largely thanks to their capacity to produce high levels of lactic acid, lactobacilli are thought to inhibit most invading bacterial and viral pathogens. Nonetheless, the dogma that all Lactobacillus species are key beneficial species in the vaginal niche has been questioned, based on the association with disease for some of the major players in the niche, for example L. iners, particularly in non-European or Caucasian cohorts. Further, the ability of other (mostly anaerobic) species besides lactobacilli, to maintain similar homeostasis in the vaginal niche raises the question of what we define as optimal or healthy vaginal microbiota. Answering this question is essential since a non-optimal or dysbiotic vaginal microbiome has been linked to the acquisition of sexually transmitted infections (STIs), infertility, and adverse pregnancy outcomes. To confront these healthcare challenges we should be able to distinguish between an optimal and non-optimal microbiome. With the advance of sequence-based technologies, as well as other omics methodologies, including metaproteomics, metabolomics and culturomics, we are now able to begin to correlate the presence, as well as the activities, of specific organisms and microbial communities with health or disease. However, we are only beginning to understand the complexity of interactions between bacterial community members with each other and the human host. A better understanding of these relationships within this specialized environmental niche and in relation to female sexual and reproductive health is critical for the development of novel diagnostics and therapeutics to create and maintain an optimal FRT microbiome.

Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. - Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies - Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose - Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Download or read book The Oral Microbiome in an Ecological Perspective written by Egija Zaura and published by Frontiers Media SA. This book was released on 2015-07-27 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: The oral cavity harbors an immense diversity of microorganisms, including bacteria, fungi, archaea, protozoa and viruses. At health, oral microbial community is thought to be in a state of homeostasis, even after numerous perturbations (e.g., toothbrushing, food intake) a day. The breach in this homeostasis can occur for instance if the perturbations become too excessive (e.g., frequent carbohydrate intake leading to acidification of the community) or the host is compromised (e.g., inadequate immune response resulting in persistent inflammation of periodontal tissue). Aggressive antimicrobial therapy (e.g., antibiotics in case of periodontal disease or preventive antibiotic therapy before and after dental extractions) is commonly applied with all the negative consequences of this approach. So far little is known on the interplay between the environmental, host and microbial factors in maintaining an ecological balance. What are the prerequisites for a healthy oral ecosystem? Can we restore an unbalanced oral microbiome? How stable is the oral microbiome through time and how robust it is to external perturbations? Gaining new insights in the ecological factors sustaining oral health will lead to conceptually new therapies and preventive programs. Recent advances in high throughput technologies have brought microbiology as a science to a new era, allowing an open-ended approach instead of focusing on few opportunistic pathogens. With this topic we would like to integrate the current high-throughput ‘omics’ tools such as metagenomics, metatranscriptomics, metaproteomics or metabolomics with biochemical, physiological, genetic or clinical parameters within the oral microbial ecosystem. We aim to address questions underlying the regulation of the ecological balance in the oral cavity by including the following areas: • Ecology of oral microbiome at health • Ecology of oral microbiome under oral diseases • Ecology of oral microbiome during non-oral diseases • Shifts in the oral microbiome by therapeutic approaches (e.g., antimicrobials, replacement therapy, pre- and probiotics) • Modeling of oral ecological shifts (e.g., animal models, in vitro microcosm models) • Complex inter- and intra-kingdom interactions (e.g., bacterial-fungal-host) related to oral ecology • Environmental (e.g., diet, tobacco), host-related (e.g., immune response, saliva composition and flow) and biotic (e.g., bacterial competition) factors influencing oral ecology • Geographic variation in oral microbial ecology and diversity

Download or read book Oral Microbiome and Inflammation Connection to Systemic Health written by Tomomi Hashizume-Takizawa and published by Frontiers Media SA. This book was released on 2022-01-04 with total page 119 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Plant Microbiome Interactions Mechanisms of Action and Applications Volume II written by Alok Kumar Srivastava and published by Frontiers Media SA. This book was released on 2022-06-27 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Compositional Data Analysis written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2011-09-19 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is difficult to imagine that the statistical analysis of compositional data has been a major issue of concern for more than 100 years. It is even more difficult to realize that so many statisticians and users of statistics are unaware of the particular problems affecting compositional data, as well as their solutions. The issue of ``spurious correlation'', as the situation was phrased by Karl Pearson back in 1897, affects all data that measures parts of some whole, such as percentages, proportions, ppm and ppb. Such measurements are present in all fields of science, ranging from geology, biology, environmental sciences, forensic sciences, medicine and hydrology. This book presents the history and development of compositional data analysis along with Aitchison's log-ratio approach. Compositional Data Analysis describes the state of the art both in theoretical fields as well as applications in the different fields of science. Key Features: Reflects the state-of-the-art in compositional data analysis. Gives an overview of the historical development of compositional data analysis, as well as basic concepts and procedures. Looks at advances in algebra and calculus on the simplex. Presents applications in different fields of science, including, genomics, ecology, biology, geochemistry, planetology, chemistry and economics. Explores connections to correspondence analysis and the Dirichlet distribution. Presents a summary of three available software packages for compositional data analysis. Supported by an accompanying website featuring R code. Applied scientists working on compositional data analysis in any field of science, both in academia and professionals will benefit from this book, along with graduate students in any field of science working with compositional data.

Download or read book Modeling and Analysis of Compositional Data written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2015-02-17 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling and Analysis of Compositional Data presents a practical and comprehensive introduction to the analysis of compositional data along with numerous examples to illustrate both theory and application of each method. Based upon short courses delivered by the authors, it provides a complete and current compendium of fundamental to advanced methodologies along with exercises at the end of each chapter to improve understanding, as well as data and a solutions manual which is available on an accompanying website. Complementing Pawlowsky-Glahn’s earlier collective text that provides an overview of the state-of-the-art in this field, Modeling and Analysis of Compositional Data fills a gap in the literature for a much-needed manual for teaching, self learning or consulting.

Download or read book Microbial Landscape Ecology Highlights on the Invisible Corridors written by Cendrine Mony and published by Frontiers Media SA. This book was released on 2021-11-26 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Gastrointestinal Nutrients Microbiome Host Interactions in Livestock written by Jinxin Liu and published by Frontiers Media SA. This book was released on 2024-02-01 with total page 616 pages. Available in PDF, EPUB and Kindle. Book excerpt: