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Shailza Singh - Metagenomic Systems Biology: Integrative Analysis of the Microbiome

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Shailza Singh Metagenomic Systems Biology: Integrative Analysis of the Microbiome
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Metagenomic Systems Biology: Integrative Analysis of the Microbiome: summary, description and annotation

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The book serves as an amalgamation of knowledge and principles used in the area of systems and synthetic biology, and targets inter-disciplinary research groups. The readers from diversified areas would be benefited by the valuable resources and information available in one book. Microbiome projects with efficient data handling can fuel progress in the area of microbial synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. The different chapters of the book reviews a broad range of topics, including food microbiome in ecology, use of microbiome in personalized medicine, machine learning in biomedicine. The book also describes ways to harness and exploit the incredible amounts of genomic data.

The book is not only limited to medicine but also caters to the needs of environmentalists, biochemical engineers etc. It will be of interest to advanced students and researchers in life sciences, computational biology, microbiology and other inter-disciplinary areas.

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Book cover of Metagenomic Systems Biology Editor Shailza Singh - photo 1
Book cover of Metagenomic Systems Biology
Editor
Shailza Singh
Metagenomic Systems Biology
Integrative Analysis of the Microbiome
1st ed. 2020
Logo of the publisher Editor Shailza Singh Computational and Systems - photo 2
Logo of the publisher
Editor
Shailza Singh
Computational and Systems Biology Lab, National Centre for Cell Science, Pune, Maharashtra, India
ISBN 978-981-15-8561-6 e-ISBN 978-981-15-8562-3
https://doi.org/10.1007/978-981-15-8562-3
Springer Nature Singapore Pte Ltd. 2020
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd.

The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore

Contents
Pragya Misra and Shailza Singh
Rashmi Dahiya , Taj Mohammad and Md. Imtaiyaz Hassan
Aditya Narayan , Ajeet Singh and Shailesh Kumar
Anindita Paul and Sushma Singh
Santanu Sasidharan , K. Divakar and Prakash Saudagar
Deepika Goyal , Manali Vaijanapurkar , Eden Jacques , Janmejay Pandey and Om Prakash
Preeti Rathi , Deepanshu Verma , Ashutosh Singh and Neha Garg
Ashok Bankar , Laxmi Jadhav and Vrushali Phalke
Malathi Srinivasan
About the Editor
Shailza Singh

is Scientist E and In-Charge of Bioinformatics and High Performance Computing Facility at National Centre for Cell Science, Pune. Her lab focuses on systems and synthetic biology of infectious disease leishmaniasis, wherein she is trying to integrate the action of regulatory circuits, cross talk between pathways and non-linear kinetics of biochemical processes through mathematical modeling. The hypotheses laid down through theoretical approaches are validated in in vitro and in vivo systems. Currently, she has started working in the area of Precision Oncology.

She is the recipient of several awards such as RGYI, DST-Young Scientist, INSA Bilateral Exchange, SAKURA Exchange Program etc. She is the reviewer of various international journals of repute like Scientific Reports, PlosOne, Molecular Biosystems, Oncotarget, BMC Systems Biology, Parasites and Vectors, ACS Journal of Natural products etc. She also serves as reviewers for various national and international grants like DST, DBT, CSIR, RCUK etc. She has guided a number of MTech, MSc. and PhD students.

Springer Nature Singapore Pte Ltd. 2020
S. Singh (ed.) Metagenomic Systems Biology https://doi.org/10.1007/978-981-15-8562-3_1
1. Gut Microbiome in Microbial Pathogenicity
Pragya Misra
(1)
National Centre for Cell Science, NCCS Complex, Ganeshkhind, SPPU Campus, Pune, India
Shailza Singh
Email:
Abstract

Gut microbiota with diverse population has gained a lot of attention in the last decade. This microbial population along with maintaining homeostasis in gut also shapes the immune system in gut by interacting with various arms of the immune system. It has an important role in development of gut-associated lymphoid tissues (GALTs), regulating the Th17 cells development by intrinsic mechanism along with their importance in differentiation of Th17 cells in lamina propria. It has also been observed that host-intestinal T cell mutualism is also maintained by Treg-cell response generated due to microbial colonization. Along with this, in this chapter, we have focussed on mechanism by which these commensal confer resistance to various infections. Deciphering all this knowledge about gut-host interaction, the present chapter aims at understanding how to modulate gut microbiome for personalized medicine. It is well proven that microbiome acts as an important player in drug response variability or toxicity for various diseases. This provides a lead to understand ways by which microbiome could be used as a target for improving the efficacy of drugs along with safety by manipulating its composition. Various strategies have been adapted for this such as pathogen-specific approach, faecal microbiota transplantation (FMT), removing specific strain or species of a bacteria, inhibiting metabolic function of gut microbiota enzymes, introducing engineered strains in the gut and genetically modifying bacterial cells present in the gut. Thorough evaluation of all the available literature made us give our insight which suggests that developing microbial therapeutics which could be well adapted in the specific body environment is necessary for its efficient activity. Based on this observation, we suggest that construction of synthetic circuits which could be functionally active in in vivo conditions along with establishing regulatory frameworks for safety could be fruitful approach.

Keywords
Gut microbiota Gut immune system Drug metabolism Drug toxicity Faecal microbiota Personalized medicine
Abbreviations
GALTs

Gut-associated lymphoid tissues

LTi

Lymphoid tissue inducer

ILFs

Isolated lymphoid follicles

AID

Activation-induced cytidine deaminase

EHEC

Enterohaemorrhagic E. coli

FXR

Farnesoid X receptor

CDDL

Cytidine deaminase

CDI

C. difficile infection

FMT

Faecal microbiota transplantation

1.1 Introduction

Gut microbiota comprises of diverse microbial population that is present in the intestine. This microbial population is of immense benefits to the host; most importantly, it shapes the gut immune system (Round and Mazmanian ). Many available sugar components present in the large intestine are not digested by host, these two enzymes help in breakdown of complex polysaccharides as an energy source, and this is the reason that bacteria of order Bacteroidales and Clostridiales are dominantly present in intestine. This type of co-evolution has been developed between the host and microbes through millions of years, wherein microbes help in various physiological processes of host and in turn they are benefited for their nutritional requirements. Along with these metabolic advantages, host microbiota helps in various other functions as discussed above to shape the immune system.

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