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VOLUME ONE HUNDRED AND NINETY TWO
PROGRESS IN
MOLECULAR BIOLOGY
AND TRANSLATIONAL
SCIENCE
Human Microbiome in Health and
Disease - Part B
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VOLUME ONE HUNDRED AND NINETY TWO
PROGRESS IN
MOLECULAR BIOLOGY
AND TRANSLATIONAL
SCIENCE
Human Microbiome in Health and
Disease - Part B
Edited by
BHABATOSH DAS
Molecular Genetics Laboratory, Infection and Immunology
Division, Translational Health Science and Technology
Institute, Faridabad, Haryana, India
VIJAI SINGH
Department of Biosciences, School of Science,
Indrashil University, Rajpur, Mehsana, India
Academic Press is an imprint of Elsevier
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or mechanical, including photocopying, recording, or any information storage and retrieval system,
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This book and the individual contributions contained in it are protected under copyright by the
Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and experience
broaden our understanding, changes in research methods, professional practices, or medical
treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating
and using any information, methods, compounds, or experiments described herein. In using such
information or methods they should be mindful of their own safety and the safety of others, including
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To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume
any liability for any injury and/or damage to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas
contained in the material herein.
ISBN: 978-0-323-91210-5
ISSN: 1877-1173
Contributors xi
Preface xv
1. Introduction 2
2. Community structure of gut-microbiota 4
3. Gut microbiome is a potential reservoir of antibiotic-resistant genes 7
4. Microbiome: Accumulated effects of antibiotic exposure 9
5. Factors affecting gut resistome and spread of ARGs 11
6. Gut microbiome: A well-known transporter of antibiotic resistance gene 13
7. Different approaches to study and understand human gut-resistome 22
8. Conclusion and future perspective 24
Acknowledgment 25
Conflict of interest 25
References 25
Further reading 31
1. Introduction 34
2. Diseases associated with dysbiosis 36
3. Protective role of the host microbiota during diseases 40
4. Targeting the gut microbiota during digestive diseases 42
5. Conclusion and future perspectives 45
References 46
v
vi Contents
Index 331
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Contributors
Ramesh Agarwal
Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
Swati Aggarwal
Regional Centre for Biotechnology, Faridabad, Haryana, India
Taruna Ahrodia
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Vineet Ahuja
Department of Gastroenterology and Human Nutrition, All India Institute of Medical
Sciences, New Delhi, India
Md Jahangir Alam
Department of Biotechnology, National Institute of Pharmaceutical Education and Research
(NIPER), Guwahati, Assam, India
Krishnamohan Atmakuri
Bacterial Pathogenesis Lab, Infection and Immunology Division, Translational Health
Science and Technology Institute, Faridabad, India
Sanjay K. Banerjee
Department of Biotechnology, National Institute of Pharmaceutical Education and Research
(NIPER), Guwahati, Assam, India
Krishna Singh Bisht
Regional Centre for Biotechnology, Faridabad, Haryana, India
Santanu Chattopadhyay
Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
Meenal Chawla
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Bhabatosh Das
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Amit Ghosh
ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
Aeshna Gupta
School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
Rashi Gupta
Department of Microbiology, Institute of Home Economics, University of Delhi, India
xi
xii Contributors
Bharti Kandiyal
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Shashi Kumari
DBT-Translational Health Science and Technology Institute, Faridabad, India
Shruti Lal
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Tushar Kanti Maiti
Regional Centre for Biotechnology, Faridabad, Haryana, India
Indra Mani
Department of Microbiology, Gargi College, University of Delhi, New Delhi, India
G. Balakrish Nair
Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
Lekshmi Narendrakumar
Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health
Science and Technology Institute, Faridabad, India
Angitha N. Nath
Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
Archana Pant
Regional Centre for Biotechnology, Faridabad, Haryana, India
Deepjyoti Paul
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
Vaishnavi Puppala
Department of Biotechnology, National Institute of Pharmaceutical Education and Research
(NIPER), Guwahati, Assam, India
Thandavarayan Ramamurthy
ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
Animesh Ray
Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
R.J. Retnakumar
Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala; Manipal Academy of Higher
Education, Karnataka, India
M. Jeeva Sankar
Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
Vijai Singh
Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana,
Gujarat, India
Contributors xiii
Kiyoshi Takeda
Laboratory of Immune Regulation, Department of Microbiology and Immunology,
Graduate School of Medicine, Osaka University, Suita, Japan
Shravan K. Uppulapu
Department of Biotechnology, National Institute of Pharmaceutical Education and Research
(NIPER), Guwahati, Assam, India
Jyoti Verma
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
J.R. Yodhaanjali
Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health
Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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Preface
xv
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CHAPTER ONE
Contents
1. Introduction 2
2. Community structure of gut-microbiota 4
2.1 Phyla bacteroidetes 5
2.2 Phyla Firmicutes 6
2.3 Phyla actinobacteria 6
2.4 Phyla proteobacteria 7
3. Gut microbiome is a potential reservoir of antibiotic-resistant genes 7
4. Microbiome: Accumulated effects of antibiotic exposure 9
5. Factors affecting gut resistome and spread of ARGs 11
5.1 Application of antibiotics in farm animals 11
5.2 Diet and its consequence on resistome 12
5.3 AMR genes in waste and effluent 13
5.4 Tourism and migratory birds 13
6. Gut microbiome: A well-known transporter of antibiotic resistance gene 13
7. Different approaches to study and understand human gut-resistome 22
7.1 Culture-based approach 22
7.2 Molecular biology-based approach 22
8. Conclusion and future perspective 24
Acknowledgment 25
Conflict of interest 25
References 25
Further reading 31
Abstract
The human gastrointestinal tract is home to a complex and dynamic community of
microorganisms known as gut microbiota, which provide the host with important met-
abolic, signaling, and immunomodulatory functions. Both the commensal and patho-
genic members of the gut microbiome serve as reservoirs of antimicrobial-resistance
genes (ARG), which can cause potential health threats to the host and can transfer
Progress in Molecular Biology and Translational Science, Volume 192 Copyright # 2022 Elsevier Inc. 1
ISSN 1877-1173 All rights reserved.
https://doi.org/10.1016/bs.pmbts.2022.07.009
2 Deepjyoti Paul and Bhabatosh Das
the ARGs to the susceptible microbes and into the environment. Antimicrobial resis-
tance is becoming a major burden on human health and is widely recognized as a
global challenge. The diversity and abundance of ARGs in the gut microbiome are
variable and depend on the exposure to healthcare-associated antibiotics, usage of anti-
biotics in veterinary and agriculture, and the migration of the population. The transfer
frequency of the ARGs through horizontal gene transfer (HGT) with the help of mobile
genetic elements (MGEs) like plasmids, transposons, or phages is much higher among
bacteria living in the GI tract compared to other microbial ecosystems. HGT in gut bac-
teria is facilitated through multiple gene transfer mechanisms, including transformation,
conjugation, transduction, and vesicle fusion. It is the need of the hour to implement
strict policies to limit indiscriminate antibiotic usage when needed. Developing rapid
diagnostic tests for resistance determination and alternatives to antibiotics like vaccina-
tion, probiotics, and bacteriophage therapy should have the highest priority in the
research and development sectors. Collective actions for sustainable development
against resistant pathogens by promoting endogenous gut microbial growth and diver-
sity through interdisciplinary research and findings are key to overcoming the current
antimicrobial resistance crisis.
Abbreviations
AMR antimicrobial resistance
ARDB antibiotic resistance gene database
ARGO antibiotic resistance gene online
ARGs antimicrobial-resistance genes
CADRD comprehensive antibiotic resistance database
ESBLs extended-spectrum beta-lactamases
HGT horizontal gene transfer
MDR multidrug resistance
MGEs mobile genetic elements
1. Introduction
The human microbiome is considered a complex ecosystem of micro-
bial communities where multiple organisms comprising bacteria, archaea,
viruses, and protists reside mostly on the environmentally exposed surfaces
of the human body. Microbial communities in the human body are more
dynamic and diverse, and the interactions among the microbes may be sym-
biotic or pathogenic, as observed in healthy individuals and patients suffering
from microbiome associated health disorders. The balance among these
microorganisms within the microbiome is complicated and is continually
developing defense mechanisms against each other, leading to a real “arms
race.”1 The term “microbiome” was originally described as the ecological
community of commensal, symbiotic, and pathogenic microorganisms
Gut microbiome and AMR 3
Cable-laying, 150.
Cables, telegraph, 144.
Cell, voltaic, 29.
Clocks, electric, 124.
Coherer, the, 183.
Commutator, 70.
Compass, magnetic, 52.
Condenser, 63.
Conductors, 6.
Conduit system, 83.
Convectors, 109.
Cookers, electric, 110.
Creed telegraph, 137.
Crookes, Sir W., 230.
Current, electric, 30.
Faraday, 66.
Finsen light treatment, 243.
Franklin, Benjamin, 19.
Frictional electricity, 2.
Furnace, electric, 111.
Galvani, 27.
Galvanometer, 59.
Glass, 4.
Goldschmidt system, 197.
Great Eastern, the, 148.
Ohm, 33.
Oil radiator, 110.
Ozone, 23, 247.
Ozone ventilation, 249.
Petrol, motor, ignition in, 253.
Photographophone, the, 173.
Pile, voltaic, 28.
Pipe locator, 266.
Plant culture, electric, 258.
Polarization, 31.
Pollak-Virag telegraph, 137.
Positive electricity, 5.
Poulsen, Waldemar, 171, 197.
Poultry, electro-culture of, 264.
Power stations, 75.
Preece, wireless experiments, 180.
Primary and secondary coils, 62.
Radiator, 109.
Railways, electric, 87;
use of wireless, 211.
Resistance, 33.
Röntgen rays, 228, 242.
Searchlights, 98.
Ships, use of wireless, 206.
Siphon recorder, the, 252.
Sparking plug, 154.
Static electricity, 7.
Stations, wireless, 204.
Steinheil telegraph, 130.
Submarine telegraphy, 144.
Submarine telephony, 169.
Surface contact system, 83.
Volt, 33.
Voltaic electricity, 28, 129, 290.
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