Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
Gongchao JingLu LiuZengbin WangYufeng ZhangQian LiChunxiao GaoMeng ZhangMin LiZhenkun ZhangXiaohan LiuJian XuXiaoquan Su
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Abstract:
A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile.This POSTnote examines what is known about the human microbiome and the diseases and conditions linked to it. The note then describes interventions to modify the human microbiome and examines the issues raised by their use and by microbiome research more generally.
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The study of the human microbiome or community of microorganisms and collection of genomes found in the human body is one of the fastest growing research areas because many diseases are reported to be associated with microbiome imbalance or dysbiosis. With the improvement in novel sequencing techniques, researchers are now generating millions of sequences of different sites from the human body and evaluating specific differences in microbial communities. The importance of microbiome constituency is so relevant that several consortia like the Human Microbiome project (HMP) and Metagenomics of the Human Intestinal Tract (MetaHIT) project are focusing mainly on the human microbiome. The aim of this review is to highlight points of research in this field, mainly focusing on particular factors that modulate the microbiome and important insights into its potential impact on our health and well-being.
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Dysbiosis
Inflammatory Bowel Diseases
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Objectives/Hypothesis The human microbiome represents the collective genomes and gene products of microbes living within and on humans. The objective of this review is to provide a summary of the current microbiome literature pertaining to otolaryngology–head and neck surgery. Data Source Ovid MEDLINE. Methods Scientific publications with clinical correlates. Results Human microbiome studies have been facilitated by culture‐independent, high‐throughput sequencing methods. Data from the Human Microbiome Project has shown that the composition of the human microbiome is specific to each body site and that each individual has a unique microbiome. Alterations in the human microbiome are associated with some disease states; thus, novel therapeutic strategies are being developed based on concepts and findings stemming from microbiome research. Conclusions Although a growing body of research shows potential significance of the human microbiome for human health and disease, there is a paucity of microbiome studies in otolaryngology. More studies are required to increase our understanding of the indigenous microbiota and their effects on diseases of the head and neck. Level of Evidence Laryngoscope , 124:1352–1357, 2014
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The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug–microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.
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The Human Microbiome Project began 10 years ago, leading to a signifi cant growth in understanding of the role the human microbiome plays in health and disease.In this article, we explain with an emphasis on the lung, the origins of microbiome research.We discuss how 16S rRNA gene sequencing became the fi rst major molecular tool to examine the bacterial communities present within the human body.We highlight the pitfalls of molecular-based studies, such as false fi ndings resulting from contamination, and the limitations of 16S rRNA gene sequencing.Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a signifi cant infl uence on many illnesses.We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions.In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood.We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.
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The human microbiome, the collection of trillions of microbes living in and on the human body, is not random, and scientists believe that it plays a role in many basic life processes. As science continues to explore and better understand the identities and activities of the microbial species comprising the human microbiome, microbiologists hope to draw connections between microbiome composition, host genetics, and human health. FAQ: Human Microbiome addresses this growing area of research.
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Human body is a habitat for a large number of microorganisms, called microbiome. Microbiome has been recognized as a key factor in understanding human health and diseases. Bacteria are a major component of most of human body including gut. The study of human microbiome has been accelerated by the invention of next generation sequencing and bioinformatics. Application of the concept and techniques used in microbial ecology to microbiome allows us to understand the role and effects of microbiome, especially gut microbiome to human health and diseases. In this presentation, the principles of human microbiome and related methodology will be explained.
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