Unexpected cross-species contamination in genome sequencing projects

Area of Science:

• Genomics
• Bioinformatics
• Microbiome Analysis

Background:

• Genome sequencing data can contain DNA from contaminating organisms introduced during sample collection or preparation.
• These contaminants may persist in public databases, leading to erroneous search results and confusion.
• Accurate genome assembly and data integrity are crucial for reliable biological research.

Purpose of the Study:

• To identify and characterize microbial contaminants within a draft genome assembly of the domestic cow (Bos taurus).
• To investigate potential misannotations in public genome databases by examining a specific Neisseria gonorrhoeae genome.
• To emphasize the importance of validating anomalous DNA findings in genomic datasets.

Main Methods:

• Utilized efficient microbiome analysis software to scan the draft genome assembly of Bos taurus.
• Identified small contigs suspected of originating from microbial contaminants.
• Performed verification of identified sequences, including cross-referencing with host and microbial genomes.

Main Results:

• Successfully identified 173 small contigs likely originating from microbial contaminants in the Bos taurus draft genome.
• Discovered that the Neisseria gonorrhoeae TCDC-NG08107 genome contained multiple sequences derived from cow and sheep genomes.
• Highlighted instances where putative complete genomes contained significant host-derived DNA.

Conclusions:

• Genome sequencing projects must implement rigorous quality control to detect and remove contaminating DNA.
• The presence of host DNA in microbial genomes underscores the need for careful validation of genomic data.
• Relying solely on comparisons with existing draft or finished genomes for anomaly detection can be unreliable.