If you've wondered how metagenomics works, metagenomics documents past and present infections by sequencing DNA from the pathogens and from the people. Researchers recently identified a disease that may have plagued 700-year-old skeleton, an infection with a bactium found in consuming unpasteurized dairy products. European researchers have recovered a genome of the bacterium Brucella melitensis from a 700-year-old skeleton found in the ruins of a Medieval Italian village. You may wish to check out the abstract of the research, "Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics," published online July 15, 2014 in mBio®, the online open-access journal of the American Society for Microbiology.
The authors describe using a technique called shotgun metagenomics to sequence DNA from a calcified nodule in the pelvic region of a middle-aged male skeleton excavated from the settlement of Geridu in Sardinia, an island off the coast of Italy. Geridu is thought to have been abandoned in the late 14th century. Shotgun metagenomics allows scientists to sequence DNA without looking for a specific target. Metagenomics sheds light on the emergence, evolution and spread of microbial pathogens, whether the health condition happened tens of thousands of years ago, a few hundred years ago, or currently.
From this sample, the researchers recovered the genome of Brucella melitensis, which causes an infection called brucellosis in livestock and humans. In humans, brucellosis is usually acquired by ingesting unpasteurized dairy products or from direct contact with infected animals. Symptoms include fevers, arthritis and swelling of the heart and liver. The disease is still found in the Mediterranean region.
"Normally when you think of calcified material in human or animal remains you think about tuberculosis, because that's the most common infection that leads to calcification," says senior study author Mark Pallen, PhD, according to a July 15, 2014 news release, "Little too late: Researchers identify disease that may have plagued 700-year-old skeleton." Pallen is a professor of microbial genomics at Warwick Medical School in Coventry, England. "We were a bit surprised to get Brucella instead."
The skeleton contained 32 hardened nodules the size of a penny in the pelvic area, though Pallen says it's unclear if they originated in the pelvis, or higher up in the chest or other body part
In additional experiments, the research team showed that the DNA fragments extracted had the appearance of aged DNA – they were shorter than contemporary strands, and had characteristic mutations at the ends. They also found that the medieval Brucella strain, which they called Geridu-1, was closely related to a recent Brucella strain called Ether, identified in Italy in 1961, and two other Italian strains identified in 2006 and 2007.
Pallen and others have used shotgun metagenomics before to detect pathogens in contemporary and historical human material. Last summer, he published a report in the New England Journal of Medicine describing the recovery of tuberculosis genomes from the lung tissue of a 215-year-old mummy from Hungary. He also has identified Eschericia coli from stool samples during a 2011 outbreak in Germany.
Pallen's team is now testing the technique on a range of additional samples, including historical material from Hungarian mummies; Egyptian mummies; a Korean mummy from the 16th or 17th century; and lung tissue from a French queen from the Merovingian dynasty, which ruled France from the 5th to 8th centuries; as well as contemporary sputum samples from the Gambia in Africa.
Metagenomics documents past and present infections
"Metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution and spread of microbial pathogens," Pallen says, according to the news release. "We're cranking through all of these samples and we're hopeful that we're going to find new things."
The Sardinia Region and Warwick Medical School supported the study. mBio® is an open access online journal published by the American Society for Microbiology to make microbiology research broadly accessible. The focus of the journal is on rapid publication of cutting-edge research spanning the entire spectrum of microbiology and related fields. It can be found online at the mBio® website.