Microbiome a promising and fascinating subject in the modern Biology. It integrates the microbial communities in human, animal, plant and environment. In human, the microbiota associated with gut, skin, genital organs, oral and respiratory organs. Plant microbial community is referred as ‘holobiont’ exerted in maintenance and health of the plants further it influenced its role in the animal health and environment. The contents of the Microbiome and Host Interactions book covered all area and new research trends in the fields of plant, animal, human and environmental microbiomes and their interactions. This book covered the details about the microbiome in soil environment to polar (Antartic) microbiota, microbiome role in health and disease, microbiota functions in Caenorhabditis elegans, mycobiome in agroecosystem, rice root and actinorhizal root nodule microbiome, speleothems, microbiome of marine shallow water hydrothermal vents. Moreover, this book also provides a comprehensive account on advanced Next-Generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing and understand nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial and archaeal communities using QIIME software (Quantitative Insights Into Microbial Ecology). Salient features: Summarize the recent insight in the Microbiome and host interactions in distinct habitat including antarctic, hydrothermal vents water, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forest and mangroves. Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, multivariate analysis commonly used for microbiome analysis. Describe the probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, microbial communities in the reproductive tract of human and animals. Information presented in a reachable way for valuable to students, teachers, researchers, microbiologists, computational biologist and other professionals who interested to strengthen and enlarge their knowledge about microbiome analysis by with Next-Generation DNA Sequencing in different branches of sciences.