A Citizen Scientist Makes Her Mark in Microbiome Research
A Citizen Scientist Makes Her Mark in Microbiome Research

A Citizen Scientist Makes Her Mark in Microbiome Research

The BioCollective, a company that transforms whole stool samples into microbial metadata, is developing the US’s first national microbiome reference material.

Amy Schleunes
Amy Schleunes
Jun 1, 2020

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The first thing Martha Carlin noticed was a faraway look in her husband’s eyes. It was a subtle change, she says, something only a wife would see. She happened to be reading Lucky Man by Michael J. Fox at the time, and began to wonder about some of the symptoms she’d observed in her husband: his loss of facial expressions, his quivering pinky finger, his trembling tongue. An appointment with an internist led to an appointment with a neurologist, who confirmed Carlin’s worst fears. In the fall of 2002, her husband John was diagnosed with Parkinson’s disease. He was 44 years old.

Carlin and her collaborators were convinced that stool held much more information than one small scoop could capture.

Carlin spent the next seven years reading everything she could find on Parkinson’s. A consultant skilled at identifying breakpoints in businesses, Carlin concluded that the disease is “a systems problem,” she says, a collapse of the body’s ecosystem. Much of what she had learned implicated the gut, including the finding that constipation is one of the earliest symptoms of Parkinson’s, often emerging 10 years or more before a diagnosis. In late 2014, Carlin read a study that identified a specific imbalance in the composition of Parkinson’s patients’ gut microbiomes, suggesting that changes in the gut microbiota could be an important biomarker for the disease. “That is it,” she remembers thinking. “The gut is the general ledger of the body.”

She quit her consulting job and enlisted the help of Jack Gilbert, a microbiome expert then at the University of Chicago. Carlin paid Gilbert, who serves on The Scientist’s editorial advisory board, to analyze her and her husband’s stool samples, and also donated $30,000 to cover part of the salary of one of his postdocs. Together, she and Gilbert pored over the microbiome literature. They kept coming across mentions of certain microbial genes that were overexpressed in conditions such as Parkinson’s and autism, suggesting “functional similarities at a systems level,” Carlin says. It seemed logical to her that investigating such complex conditions would require looking at the whole community of bacteria in the living system.

At the time, however, microbiologists weren’t really focusing on whole microbial communities, says Carlin. Instead, most research involved taking small samples of stool and analyzing 16S ribosomal RNA. She and her collaborators were convinced that stool held much more information than one small scoop could capture. They proposed collecting the whole stool, homogenizing it, and cataloging all the bacteria in the sample using whole-genome sequencing. That approach, Carlin says, yields 2–8 gigabytes of genetic data per sample, compared to the few kilobytes produced with 16S sequencing. There wasn’t any company set up to process stool in this way, so she decided to start her own.

NEW APPROACH: In 2015, Martha Carlin founded The BioCollective and began work on a stool-collecting kit that could help microbiome researchers standardize their work.
Adam Beach Photography

Carlin founded The BioCollective in 2015, and within a year she and her team had designed and patented the BioCollector Kit, an “ick-free” paper hammock that catches the entire stool, which is then shipped to the lab, homogenized, and aliquoted into identical portions. Aided by publicity from a handful of bloggers, the team collected samples from hundreds of people. Carlin also targeted Parkinson’s support groups. Researchers soon asked to use the kits, too—among them scientists at the Dana-Farber Cancer Institute and San Francisco–based biotech company Siolta Therapeutics. 

For microbiologists, the appeal of The BioCollective’s approach lies in both its easy collection method and its potential to standardize the field by providing a reliable control against which to compare other human gut microbiome samples. Microbiome research suffers from a high degree of variability, says Scott Jackson, a biochemist who leads the Complex Microbial Systems Group at the National Institute of Standards and Technology (NIST) and partners with The Bio-Collective. Variation in methodology crops up everywhere, “from how you extract DNA to how you build your [DNA] library” he says. Two different labs analyzing the same stool sample will often get “very different results.” If researchers could agree on a single reference standard, with a known taxonomic composition, he argues, they would be able to “understand reproducibility—or the lack thereof—across laboratories.”

Jonathan Jacobs, a gastroenterologist and microbiome researcher at the University of California, Los Angeles, who has not collaborated with Carlin or The BioCollective, agrees that a “reference standard would be helpful in assessing the variation across different labs and for the labs to monitor technical changes over time in their own pipelines.” 

As Carlin and her team continued to develop TruMatrix, their signature reference standard, they were simultaneously studying samples in their bank, which holds stools from nearly 1,000 people, including some multi-year samples in the Parkinson’s cohort. Her team has created a computational model called BioFlux to predict how gut bacteria will react to various chemicals. Carlin says the model could be used to study how pharmaceuticals, nutraceuticals, and different foods influence the micro-biome of Parkinson’s patients. 

In early 2018, the company released SugarBuster, a probiotic that The Bio-Collective notes may help boost gastrointestinal concentrations of the sugar alcohol mannitol. Some research has suggested that mannitol can inhibit the formation of amyloid fibrils, an early sign of Parkinson’s, in a Drosophila model of the disease. The probiotic has not been evaluated in clinical trials, although Carlin says the team is planning a trial in diabetes patients later this year. And in February 2020, The BioCollective was awarded a $1.2 million Fast Track Grant from the National Institute of General Medical Sciences (NIGMS) to develop the first national microbiome reference standard.

But not everyone thinks that standard reference material for the human microbiome will impact microbiological research. Mayo Clinic gastrointestinal researcher Purna Kashyap, who has not collaborated with The BioCollective, cautions that this reference will need “a buy-in from the microbiome community.” He adds that he would be more convinced of its value if Carlin’s team were to conduct research showing that the company’s reference microbiome, which contains hundreds if not thousands of different bacteria, yields results that contradict previous studies when used as an experimental control instead of a standard mock community of 10 to 20 species of bacteria. Jacobs also questions the research implications of using The BioCollective’s reference: “I’m not aware of data demonstrating that this [reference standard] has a significant effect in actual studies,” he says.

In addition to working with NIGMS, Carlin is now collaborating with NIST, the International Life Sciences Institute, Caltech microbiologist Sarkis Mazmanian, and numerous other researchers, although her partnership with Gilbert has ended for now. “We’re looking at how systems work together,” she says, “and how people work together,” adding that the scientific community could benefit from more openness and information sharing. 

Nearly 18 years after receiving his diagnosis, John is boxing, biking, and leading Parkinson’s support groups. He no longer needs the support of a cane to walk, and his scores in the Uniform Parkinson’s Disease Rating Scale, which measures motor and non-motor symptoms, have improved over the last three years. 

Carlin is determined to keep moving forward, just as she is dedicated to John and their shared belief that his disease is not a death sentence. The answer lies in the gut, she’s convinced, and she’ll keep searching until she finds it.