Microbiome-Host Interactions

Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont," and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment. The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans, and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents. Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology). FEATURES Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences

1. An Insight of Microbiome Science [T. Savitha, A. Sankaranarayanan, and Ashraf Y. Z. Khalifa] Section I: Omics and Computational Techniques Used for Microbiome Analysis 2. Multi-Omics: Overview, Challenges, and Applications [Sushant Parab and Federico Bussolino] 3. Computational Techniques Used for Microbial Diversity Analysis [Dattatray S. Mongad, Nikeeta S. Chavan, and Yogesh S. Shouche] 4. Downstream Analysis and Visualization-Knowledge Discovery – Alpha and Beta Diversity [Murali Sankar Perumal and Shreedevasena Sakthibalan] 5. Biostatistics Including Multivariate Analysis Commonly Used for Microbiome Analysis/Study [Priyanka Sarkar] Section II: Human Microbiome 6. Structure and Functional Role of Microbiome Associated with Specific Organs of Healthy Individuals [Shanmugaraj Gowrishankar, Arumugam Kamaladevi, and Shunmugiah Karutha Pandian] 7. Structure and Function of Healthy Human Microbiome: Role in Health and Disease [Sunil Banskar and Shrikant Bhute] 8. Human Microbiome’s Role in Disease [Sahabram Dewala and Yogesh S. Shouche] 9. Role of Human Gut Microbiome in Health and Disease [Nazar Reehana, Mohamed Yousuff Mohamed Imran, Nooruddin Thajuddin, and Dharumadurai Dhanasekaran] 10. The Role of Probiotics and Prebiotics in the Composition of the Gut Microbiota and Their Influence on Inflammatory Bowel Disease, Obesity, and Diabetes [Rafael Resende Maldonado, Ana Lúcia Alves Caram, Daniela Soares de Oliveira, Eliana Setsuko Kamimura and Mônica Roberta Mazalli, and Elizama Aguiar-Oliveira] 11. Skin Microbiome, Its Impact on Dermatological Diseases, and Intervention of Probiotics [Mitesh Dwivedi, Firdosh Shah, and Prashant S. Giri] 12. Role of Dysregulation of the Human Oral and Gastrointestinal Microbiome in Chronic Inflammatory Disease [Diana R. Cundell and Manuela Tripepi] 13. Microbiome in Women Reproductive Health [C. Anchana Devi, T. Ramani Devi, and Pavithra Amritkumar] 14. Crosstalk between Bacteria and Host Immune System with Special Emphasis on Foodborne Pathogens [A.A.P. Milton, G. BhuvanaPriya, M. Angappan, S. Ghatak, and Vivek Joshi] Section III: Animal Microbiome 15. Reproductive Tract Microbiome in Animals: Physiological versus Pathological Condition [R. Vikram, Vivek Joshi, A. A. P. Milton, M. H. Khan, and K. P. Biam] 16. Community Structures of Fecal Actinobacteria in Animal Gastrointestinal System [Selvanathan Latha and Dharumadurai Dhanasekaran] 17. Microbiota Functions in Caenorhabditis elegans [Arun Kumar, Somarani Dash, and Mojibur R. Khan] 18. Impact of Microbial Communities on the Female Reproductive Tract of Bovine [M. Srinivasan, J. Helan Chandra, M.S. Murugan, C. Manikkaraja, D. Dhanasekaran, and G. Archunan] Section IV: Plant Microbiome 19. Insights into the Structure, Function, and Dynamics of Rice Root and Rhizosphere-Associated Microbiome [Ekramul Islam and Kiron Bhakat] 20. Mangrove Ecosystem and Microbiome [Snehal O. Kulkarni and Yogesh S. Shouche] 21. Role of the Mycobiome in Agroecosystems [Ahmed Abdul Haleem Khan] 22. Root Nodule Microbiome from Actinorhizal Casuarina Plant [Narayanasamy Marappa, Dhanasekaran Dharumadurai, and Thajuddin Nooruddin] 23. Growth Promotion Utility of the Plant Microbiome [S. Kalaiselvi and A. Panneerselvam] Section V: Environmental Microbiome 24. Microbiome of Speleothems – Secondary Mineral Deposits [D. Mudgil] 25. Microbiome of Marine Shallow-Water Hydrothermal Vents [Raju Rajasabapathy, Chellandi Mohandass, Ana Colaço, and Rathinam Arthur James] 26. Diversity and Bioprospecting Potentials of Antarctic (Polar) Microbes [B. Abirami, K. Manigundan, M. Radhakrishnan, V. Gopikrishnan, P.V. Bhaskar, T. Shanmugasundaram, and Syed G. Dastager] 27. Alterations in Microbial Community Structure and Function in Response to Azo Dyes [Sandhya Nanjani and Hareshkumar Keharia] 28. Soil Microbiome [Govindan Nadar Rajivgandhi, Vimala RTV, Govindan Ramachandran, Natesan Manoharan, and Wen Jun-Li]

D. Dhanasekaran is an Associate Professor in the Department of Microbiology, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India. He has experience in the fields of actinobacteriology and mycology. His current research focuses on microbiome profiling of actinorhizal root nodules, lichen, poultry gut, and cattle reproductive system. He was awarded UGC-Raman Postdoctoral Fellowship and worked in the Department of Molecular, Cellular, and Biomedical Sciences at the University of New Hampshire, Durham, USA. He has qualified the Tamil Nadu State Eligibility Test (SET) for Lectureship in Life Science. He has deposited around 106 nucleotide sequences and 7 metagenome sequences; drafted genome sequence of Blastococcus sp. CT_GayMR20 in GenBank and five bioactive compounds in PubChem; and published 105 research and review articles—including one paper in Nature Group Journal Scientific Report—and 23 book chapters. He has an h-index of 25 with total citations of 1995 as per Google Scholar. He has edited seven books on Antimicrobial Compounds: Synthetic and Natural Compounds, Microbial Control of Vector Borne Diseases, Fermented Food Products, CRC Press, Taylor & Francis Group, New York, Fungicides for Plant and Animal Diseases, Actinobacteria: Basics and Biotechnological Applications, Algae-Organisms for Imminent Biotechnology, Microbial Biofilms – Importance and Applications under in-tech open access publisher Eastern Europe. He has guided 12PhD candidates and organized several national-level symposia, conference, and workshop programs. He has received research funding from the Department of Biotechnology, University Grant Commission, Indian Council for Medical Research and International Foundation for Science, Sweden; International Society for Microbial Ecology, The Netherlands; and Tamil Nadu State Council for Science and Technology. He is a member of the American Society for Microbiology, North American Mycology Association, Mycological Society of India, National Academy of Biological Sciences, Society for Alternatives to Animal Experiments, and a member of several editorial boards in national, international journals, doctoral committee member, board of study member in microbiology, and reviewer in the scientific journals and research grants. As per the reports of Indian Journal of Experimental Biology, 51, 2013, Dr. Dhanasekaran is rated second among the top five institutions in the field of actinobacteria research in India. Dhiraj Paul is a Scientist at the National Center for Microbial Resources (NCMR-NCCS), Pune. Previously, he was a scientist (DST, Govt. of India Fast-track fellowship) at the Microbial Ecology Laboratory, NCCS, Pune, India. He earned a PhD at the Environmental Microbiology Laboratory, Department of Biotechnology, IIT Kharagpur, India. He has published his findings in reputed journals such as mSystems, AEM, Bioresource Technology, PLOS One, Geomicrobiology, Water research, Frontiers in Microbiology, and Microbiology. He also edited the books and authors of a number of book chapters of CRC Press and Springer. He has expertise in microbial ecology, geomicrobiology, microbial diversity, and metagenomics. He has received an AMI Young Scientist Award, DST Young Scientist, and a number of fellowships (CSIR, GATE, DBT) in life sciences. Presently, he is working on microbial ecology of hypersaline Lonar Lake ecosystem, deep biosphere, and human microbiome using multiomics approaches. N. Amaresan is an Assistant Professor at C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Gujarat. He has over 15 years of experience in teaching and research, and made several original and novel discoveries, especially in various allied fields of microbiology, mainly plant–microbe interactions, bioremediation, plant pathology, and others. For his original discoveries on agriculturally important microorganisms, he has received Young Scientist Awards by Association of Microbiologists of India and National Academy of Biological Sciences. He was also awarded a visiting scientist fellowship from National Academy of India to learn advanced techniques and Early Career Research Award by Department of Science and Technology, Government of India. He has handled many funded projects sponsored by DST, DBT, GEMI, etc. He has published more than 70 research articles and books of national and international repute. He also deposited over 500 bacterial 16S rDNA and fungal ITS rDNA sequences in the GenBank (NCBI, EMBL, and DDBJ), and also preserved over 150 microbial germplasms in various culture collection centers of India. A. Sankaranarayanan has been associated since 2015 with C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat of Gujarat State of India. He has experience in the fields of fermented food products and antimicrobial activity of herbal and nanoparticles against pathogens. His research focuses on microbes in fermented food products and removal of bacteria from foo