In the Journals

Microbiome ‘fingerprint’ shows donor microbes persist in fecal transplant recipients

Specific microbial strains from donors colonized and persisted for up to 2 years in patients who received fecal microbiota transplantation for recurrent Clostridium difficile infection, according to recent study results.

“Our study provides new insights into the dynamics of the reconstitution of the gastrointestinal microbe community structure following fecal microbiota transplantation,” investigators wrote.

While 16S rRNA sequencing can identify microbial species and their prevalence in the gut microbiome, it cannot follow an individual strain from donor to recipient. Therefore, to better understand what happens to specific strains of donor microbes in FMT recipients, researchers from University of Alabama at Birmingham developed a strategy that uses the unique single nucleotide variants of gut microbes to detect related microbes in fecal samples collected from the same individual at different times.

“It essentially is a personalized microbiome ‘fingerprint,’” Ranjit Kumar, PhD, research scientist in the UAB Center for Clinical and Translational Science Informatics Institute, said in a press release.

This “window-based similarity approach” compares variants “in short, consecutive windows of DNA sequences spanning the bacterial genome,” according to the release. Elliot J. Lefkowitz, PhD, a professor in the UAB Department of Microbiology and director of UAB CCTS Informatics, added that the method extends “the resolution of what we can detect in the gut microbiome, not to just the genus or species, but to individual strain detection.”

The investigators used this strategy to compare microbiome sequences from the stool samples of six donors and seven FMT recipients who were treated for recurrent CDI at UAB. The samples were collected 1 to 6 months after FMT, and two of the seven recipients had additional samples available that were collected at 2 years.

The researchers detected donor microbes in all seven FMT recipients, which persisted up to 2 years in the two recipients for whom additional samples were available. The most common donor microbe identified in recipients was Bacteroides spp., though the researchers observed differences in overall patterns of donor microbial species, which highlights “the complexity of microbial ecology in the gastrointestinal tract environment,” according to the press release.

In addition to nine species of Bacteroides, the researchers found donor-to-recipient microbes also included two species of Alistipes and Parabacteroides, and one species of Acidaminococcus, Akkermansia, Barnesiella, Coprococcus, Eubacterium, Faecalibacterium, Prevotella and Ruminococcus.

While this novel strategy may help explain why FMT is so effective for treating recurrent CDI, it could also, in the long-term, help identify changes in the gut microbiome to predict diseases like diabetes, obesity, ulcerative colitis or Parkinson’s disease, according to the press release.

“Disruption of the gut microbial community structure can impact the overall health of the host and result in or exacerbate metabolic diseases,” Casey D. Morrow, PhD, professor emeritus in the UAB Department of Cell, Developmental and Integrative Biology, said in the press release. “Our microbiome fingerprint method will form the cornerstone of a personalized medicine approach to improve human health by providing an early warning system to detect disruption of the gut microbial community structure. This early warning system could be used to signal the use of interventions, such as microbe transplants, designed to maintain the gut microbe community structure necessary for efficient metabolic function needed for human health.” – by Adam Leitenberger

Disclosures: The researchers report no relevant financial disclosures.

Specific microbial strains from donors colonized and persisted for up to 2 years in patients who received fecal microbiota transplantation for recurrent Clostridium difficile infection, according to recent study results.

“Our study provides new insights into the dynamics of the reconstitution of the gastrointestinal microbe community structure following fecal microbiota transplantation,” investigators wrote.

While 16S rRNA sequencing can identify microbial species and their prevalence in the gut microbiome, it cannot follow an individual strain from donor to recipient. Therefore, to better understand what happens to specific strains of donor microbes in FMT recipients, researchers from University of Alabama at Birmingham developed a strategy that uses the unique single nucleotide variants of gut microbes to detect related microbes in fecal samples collected from the same individual at different times.

“It essentially is a personalized microbiome ‘fingerprint,’” Ranjit Kumar, PhD, research scientist in the UAB Center for Clinical and Translational Science Informatics Institute, said in a press release.

This “window-based similarity approach” compares variants “in short, consecutive windows of DNA sequences spanning the bacterial genome,” according to the release. Elliot J. Lefkowitz, PhD, a professor in the UAB Department of Microbiology and director of UAB CCTS Informatics, added that the method extends “the resolution of what we can detect in the gut microbiome, not to just the genus or species, but to individual strain detection.”

The investigators used this strategy to compare microbiome sequences from the stool samples of six donors and seven FMT recipients who were treated for recurrent CDI at UAB. The samples were collected 1 to 6 months after FMT, and two of the seven recipients had additional samples available that were collected at 2 years.

The researchers detected donor microbes in all seven FMT recipients, which persisted up to 2 years in the two recipients for whom additional samples were available. The most common donor microbe identified in recipients was Bacteroides spp., though the researchers observed differences in overall patterns of donor microbial species, which highlights “the complexity of microbial ecology in the gastrointestinal tract environment,” according to the press release.

In addition to nine species of Bacteroides, the researchers found donor-to-recipient microbes also included two species of Alistipes and Parabacteroides, and one species of Acidaminococcus, Akkermansia, Barnesiella, Coprococcus, Eubacterium, Faecalibacterium, Prevotella and Ruminococcus.

While this novel strategy may help explain why FMT is so effective for treating recurrent CDI, it could also, in the long-term, help identify changes in the gut microbiome to predict diseases like diabetes, obesity, ulcerative colitis or Parkinson’s disease, according to the press release.

“Disruption of the gut microbial community structure can impact the overall health of the host and result in or exacerbate metabolic diseases,” Casey D. Morrow, PhD, professor emeritus in the UAB Department of Cell, Developmental and Integrative Biology, said in the press release. “Our microbiome fingerprint method will form the cornerstone of a personalized medicine approach to improve human health by providing an early warning system to detect disruption of the gut microbial community structure. This early warning system could be used to signal the use of interventions, such as microbe transplants, designed to maintain the gut microbe community structure necessary for efficient metabolic function needed for human health.” – by Adam Leitenberger

Disclosures: The researchers report no relevant financial disclosures.