Abstract
Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.
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Acknowledgements
We gratefully acknowledge Dr. Narjol Gonzalez-Escalona for contributing V. parahaemolyticus genomes. This work is supported by the National Key Research & Development Program of China (No. 2017YFC1601503, 2016YFC1200100 and 2017YFC1200800), Sanming Project of Medicine in Shenzhen (No. SZSM201811071) and the National Natural Science Foundation of China (No. 31770001). J. Martinez-Urtaza is funded by Natural Environment Research Council (NERC) project (No. NE/P004121/1). D.F. is funded by a Medical Research Council Fellowship as part of the MRC CLIMB consortium for microbial bioinformatics (grant number MR/M501608/1).
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YC, DF, and RY designed the study and coordinated the project; XP, LY, JM, QH, and DY contributed strains for analysis; CY, XP, YW, NC, YQS, YJS, YY, MJ, CQ, DF, and YC analyzed the data; EF, JM, and DZ provided insightful comments, DF and YC wrote the manuscript. All authors approved the final version of the manuscript.
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Yang, C., Pei, X., Wu, Y. et al. Recent mixing of Vibrio parahaemolyticus populations. ISME J 13, 2578–2588 (2019). https://doi.org/10.1038/s41396-019-0461-5
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DOI: https://doi.org/10.1038/s41396-019-0461-5
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