Microbial source tracking using metagenomics and other new technologies

Shahbaz Raza, Jungman Kim, Michael J. Sadowsky, Tatsuya Unno

Research output: Contribution to journalReview articlepeer-review

9 Scopus citations


The environment is under siege from a variety of pollution sources. Fecal pollution is especially harmful as it disperses pathogenic bacteria into waterways. Unraveling origins of mixed sources of fecal bacteria is difficult and microbial source tracking (MST) in complex environments is still a daunting task. Despite the challenges, the need for answers far outweighs the difficulties experienced. Advancements in qPCR and next generation sequencing (NGS) technologies have shifted the traditional culture-based MST approaches towards culture independent technologies, where community-based MST is becoming a method of choice. Metagenomic tools may be useful to overcome some of the limitations of community-based MST methods as they can give deep insight into identifying host specific fecal markers and their association with different environments. Adoption of machine learning (ML) algorithms, along with the metagenomic based MST approaches, will also provide a statistically robust and automated platform. To compliment that, ML-based approaches provide accurate optimization of resources. With the successful application of ML based models in disease prediction, outbreak investigation and medicine prescription, it would be possible that these methods would serve as a better surrogate of traditional MST approaches in future.

Original languageEnglish (US)
Pages (from-to)259-269
Number of pages11
JournalJournal of Microbiology
Issue number3
StatePublished - Mar 2021

Bibliographical note

Funding Information:
This work was supported by the Research Program funded by the Korea Disease Control and Prevention Agency (2020-ER5408-00). This research was also supported by the Minnesota Agricultural Experiment Station and the Basic Science Research Program to Research Institute for Basic Sciences (RIBS) of Jeju National University through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2019R1A6A1A10072987).

Publisher Copyright:
© 2021, The Microbiological Society of Korea.


  • fecal pollution
  • machine learning
  • metagenomics
  • microbial source tracking
  • next generation sequencing

PubMed: MeSH publication types

  • Journal Article
  • Review


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