Investigating Human Diseases with the Microbiome

Investigating Human Diseases with the Microbiome

Metagenomics Bench to Bedside

1st Edition - February 23, 2022

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  • Author: Huijue Jia
  • Paperback ISBN: 9780323913690
  • eBook ISBN: 9780323913706

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Investigating Human Diseases with the Microbiome: Metagenomics Bench to Bedside is a summary of underlying principles for human health and disease studies from a microbiome point-of-view. From birth to old age, microbiomes in fecal, oral/nasal, vaginal, and skin samples contain important information that can predict disease risks in the future. Tissue samples also contain microbes that are relevant for diseases. The microbiome connects genetic and environmental factors and is poised to greatly facilitate precision medicine, including prevention, diagnosis and effective treatment of many complex diseases. Based in traditional microbiology and adding a more wholistic view of the advent of high-throughput sequencing, this reference poses the key questions of the total number of microbial cells and their distribution in the human body while also considering concepts from macroecology and from causal reasoning. An entire chapter is dedicated to methods, providing hands-on information for important considerations when collecting samples for metagenomic studies.

Key Features

  • Provides a consistent framework for the study of the microbiome at various body sites based on over 10 years of human microbiome studies
  • Consolidates relevant information for readers looking to get an idea of microbes for human health, elucidating why one might want to include the study of the microbiome in current or future research efforts
  • Provides technical considerations for designing and carrying out microbiome research and applications


Academic Researchers and Clinicians who are interested in collecting samples and incorporating the human microbiome into their study, on both diseased and healthy populations; Those inspired to offer metagenomic tests, e.g. in dental clinics, in gyms, food and dietary supplements companies transitioning into a healthier and high-tech public image

Table of Contents

  • Cover image
  • Title page
  • Table of Contents
  • Copyright
  • Acknowledgment
  • 1: The supraorganism
  • Abstract
  • 1.1: New discoveries with new technology— A historical account
  • 1.2: How many microbial cells can a human body have?
  • 1.3: Viral particles in the human body
  • 1.4: Microbiome in other species
  • 1.5: Microbiome from ancient times
  • 1.6: Summary
  • 2: Microbiota
  • Abstract
  • 2.1: Trophic levels in macroecology
  • 2.2: Microbiome stability, diversity, and richness
  • 2.3: De novo assembly of microbiota and robustness against invasions
  • 2.4: Types of habitats for the skin microbiome
  • 2.5: Forces shaping the oral microbiome
  • 2.6: A stable gut microbiome
  • 2.7: “Enterotypes” and the Serengeti rules?
  • 2.8: Summary
  • 3: Collecting samples for metagenomics
  • Abstract
  • 3.1: Nonmicrobial components in the sample that could influence DNA extraction and sequencing amount
  • 3.2: Beware of contamination in each step, from stools to low-biomass samples
  • 3.3: Reagents that prevent microbial growth after sampling
  • 3.4: DNA extraction for metagenomic samples
  • 3.5: Sequencing amount
  • 3.6: Taxonomic and functional profiles, absolute abundance
  • 3.7: Sample size for metagenome-wide association studies
  • 3.8: Summary
  • 4: Epidemiology in the human body
  • Abstract
  • 4.1: Analogy to COVID-19
  • 4.2: Sources of potential pathogens in the infant gut
  • 4.3: Ectopic presence of commensal microbes
  • 4.4: Get to where it matters for the disease
  • 4.5: Interkingdom interactions in the microbiome in diseases
  • 4.6: Other omics data that hint at a difference in microbiome
  • 4.7: Summary
  • 5: The evolving microbial taxonomy
  • Abstract
  • 5.1: Approaching a closed reference set for routine applications
  • 5.2: Sparser data with increasing taxonomic resolution
  • 5.3: Evolutionary history below the species level
  • 5.4: Whole-cell modeling to predict functional differences from genomic differences?
  • 5.5: Summary
  • 6: Blurring the line between opportunistic pathogens and commensals
  • Abstract
  • 6.1: Causal reasoning 101
  • 6.2: Levels of existing evidence for the human microbiome and diseases
  • 6.3: From microbes to molecules
  • 6.4: Summary
  • 7: Metagenomics from bench to bedside and from bedside to bench
  • Abstract
  • 7.1: Metagenomics for decision-making in diagnosis and treatment
  • 7.2: Further research to be inspired by clinical practice
  • 7.3: Potential to modify existing categorization of diseases with knowledge of the microbiome
  • 7.4: Summary
  • 8: A microbiome record for life
  • Abstract
  • 8.1: Proactive sampling of the microbiome at important time periods
  • 8.2: From genetic risk to the prevention of diseases
  • 8.3: Summary
  • Index

Product details

  • No. of pages: 226
  • Language: English
  • Copyright: © Academic Press 2022
  • Published: February 23, 2022
  • Imprint: Academic Press
  • Paperback ISBN: 9780323913690
  • eBook ISBN: 9780323913706

About the Author

Huijue Jia

Dr. Huijue Jia PhD has been pushing the boundaries of human microbiome and disease studies since returning back to China and joining BGI-Shenzhen by the end of 2012, and is the Director of the Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research where applies her extensive knowledge of the academic, clinical, and the corporate trends within the metagenomic field. She is a Co-Chair of the Million Microbiome of Humans Project (MMHP), the largest microbiome consortium after government funding ended for Metagenomics of the Human Intestinal Tract (MetaHIT) in Europe and then integrative Human Microbiome Project (iHMP) in the U.S. She is responsible for over 30 publications in this area of research with over 50% of them in the top citation percentile. She has served as Scientific Editor on Nature Communications and has contributed to reviews, commentaries, and other book projects.

Affiliations and Expertise

Director, Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen; Mentor for graduate students, BGI Education Center, University of Chinese Academy of Sciences

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