Moore Foundation grantee Katherine Pollard of the J. David Gladstone Institutes and University of California, San Francisco, has developed a new tool to examine genetic differences within bacterial species to study genetic differences in bacteria between mothers and infants.
Direct microbial sequencing of environmental samples, such as from ocean water, hospital surfaces and the human gut have illuminated the vast number of microbes present in our world. What's more, microbial species can be genetically diverse: within a given bacterial species, gene content can vary by 50 percent or more.
To understand the genetic differences in the microbes present on mothers and infants, Pollard and her colleagues developed a tool, called MIDAS, for rapidly profiling differences in gene content and single nucleotide variants across bacterial strains.
Previous studies suggested that mother and infant microbiomes become more similar over the first year of life. By examining rare genetic differences, Pollard's team found that early colonizing strains are transferred from the mother to the infant, but that late colonizing strains are different and likely are acquired from the environment.
"The maturation of the infant gut microbiome over the first year gives the impression of ongoing transmissions from the mother," said Pollard, a grantee through the foundation's Marine Microbiology Initiative. "But the genetic variants in the bacteria show that the acquired strains are often not the same as the mother's."
The researchers also applied MIDAS to marine samples collected at varying depths across the world's oceans. Most prevalent marine bacteria had differences in gene content that were strongly associated with geography. Additional work will be needed to distinguish whether genetic differences between locations are the result of adaptation or genetic drift within the species, said Pollard.
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