Comprehensive analysis of prokaryotes in environmental water using DNA microarray analysis and whole genome amplification

Detection of Mycobacterium ulcerans subsp. shinshuense DNA from a water channel in familial Buruli ulcer cases in Japan

AIM

To determine if Mycobacterium ulcerans subsp. shinshuense is present in the common living environment in a case of familial concurrent occurrence of Buruli ulcer in Japan.

MATERIALS & METHODS

Environmental samples were collected primarily from a water channel in the patient's residence. A combination of whole-genome amplification, touchdown PCR and DNA sequencing was used to detect M. ulcerans subsp. shinshuense DNA.

RESULTS

M. ulcerans subsp. shinshuense DNA was detected in a crayfish sampled in July, but not in other samples including a crayfish sampled in October.

CONCLUSION

These findings support an association between contaminated aquatic environments and Buruli ulcer in Japan. The data also suggest dynamic seasonal appearance of the pathogen in the environment may contribute to the seasonal variation of Buruli ulcer occurrence in Japan.

New perspectives on microbial community distortion after whole-genome amplification

Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the effects of WGA on 31 different microbial communities from five biotopes that also included low-biomass samples from drinking water and groundwater. Our findings provide evidence that microbiome segregation by biotope was possible despite WGA treatment. Nevertheless, samples from different biotopes revealed different levels of distortion, with genomic GC content significantly correlated with WGA perturbation. Certain phylogenetic clades revealed a homogenous trend across various sample types, for instance Alpha- and Betaproteobacteria showed a decrease in their abundance after WGA treatment. On the other hand, Enterobacteriaceae, an important biomarker group for fecal contamination in groundwater and drinking water, were strongly affected by WGA treatment without a predictable pattern. These novel results describe the impact of WGA on low-biomass samples and may highlight issues to be aware of when designing future metagenomic studies that necessitate preceding WGA treatment.