Biophysical Reviews

, Volume 11, Issue 1, pp 55–65 | Cite as

Host and microbiome multi-omics integration: applications and methodologies

  • Qing Wang
  • Kaicen Wang
  • Wenrui Wu
  • Eleni Giannoulatou
  • Joshua W. K. Ho
  • Lanjuan LiEmail author


The study of the microbial community—the microbiome—associated with a human host is a maturing research field. It is increasingly clear that the composition of the human’s microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry–based metabolomics, we are able to comprehensively sequence the microbiome—the metagenome—and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.


Microbiome Genome Epigenome Transcriptome Metabolome Network analysis Big data 


Compliance with ethical standards


Funding was provided by the National Natural Science Foundation of China (grant nos. 81330011, 81330014, 81790631, 81790633, 81570512 and 81121002), the Science Fund for Creative Research Groups of the National Natural Science Foundation of China (grant no. 81721091), and the National Basic Research Program of China (973 program) (grant no. 2013CB531401). This work was also supported in part by funds from the New South Wales Ministry of Health, a National Health and Medical Research Council Career Development Fellowship (1105271 to JWKH) and the National Heart Foundation (Future Leader Fellowship 100848 to JWKH and 101204 to EG).

Conflict of interest

Qing Wang declares that she has no conflict of interest. Kaicen Wang declares that she has no conflict of interest. Wenrui Wu declares that she has no conflict of interest. Eleni Giannoulatou declares that she has no conflict of interest. Joshua W. K. Ho declares that he has no conflict of interest. Lanjuan Li declares that he/she has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Qing Wang
    • 1
    • 2
    • 3
  • Kaicen Wang
    • 1
    • 2
  • Wenrui Wu
    • 1
    • 2
  • Eleni Giannoulatou
    • 3
    • 4
  • Joshua W. K. Ho
    • 3
    • 4
    • 5
  • Lanjuan Li
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
  2. 2.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhouChina
  3. 3.Victor Chang Cardiac Research InstituteDarlinghurstAustralia
  4. 4.St Vincent’s Clinical SchoolUniversity of New South WalesSydneyAustralia
  5. 5.School of Biomedical Sciences, Li Ka Shing Faculty of MedicineThe University of Hong KongPokfulamChina

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