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Updated: Nov 24, 2025
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data
Shuai Wang1, Yiqi Jiang1, Shuaicheng Li1
1Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong.
Motivation:
The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain.
Results:
These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B.coprocola in the gut microbiota of CRC.
Availabilityand Implementation:
https://github.com/wshuai294/PStrain.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
