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gut bacteria

Understanding gut bacteria: forces for good (and sometimes evil)

gut bacteria

In a paper published Sept. 11, 2019, in PLOS ONE, a multi-institutional research team led by George Washington University (GW) faculty found 157 different types of organisms (eight phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) living inside the guts of healthy volunteers.

Back in 2015, an interdisciplinary group of research scientists made their case during a business pitch competition: They want to create a subscription-based service, much like 23andMe, through which people could send in samples for detailed analyses. The researchers would crunch that big data fast, using a speedy algorithm, and would send the consumer a detailed report.

But rather than ancestry testing via cheek swab, the team sought to determine the plethora of diverse bacterial species that reside inside an individual’s gut in their ultimate aim to improve public health.

Hiroki Morizono, Ph.D., a member of that team, contributed detailed knowledge of Bacteroides, a key organism amid the diverse array of bacterial species that co-exist with humans, living inside our guts. These symbiotic bacteria convert the food we eat into elements that ensure their well-being as well as ours.

“Trillions of bacteria live in the gut. Bacteroides is one of the major bacterial species,” says Morizono, a principal investigator in the Center for Genetic Medicine Research at Children’s National in Washington, D.C. “In our guts they are usually good citizens. But if they enter our bloodstream, they turn evil; they’re in the wrong place. If you have a bacteroides infection, the mortality rate is 19%, and they resist most antibiotic treatments.”

The starting point for their project – as well as step one for better characterizing the relationship between gut bacteria and human disease – is taking an accurate census count of bacteria residing there.

In a paper published Sept. 11, 2019, in PLOS ONE, a multi-institutional research team led by George Washington University (GW) faculty did just that, finding 157 different types of organisms (eight phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) living inside the guts of healthy volunteers.

The study participants were recruited through flyers on the GW Foggy Bottom campus and via emails.  They jotted down what they ate and drank daily, including the brand, type and portion size. They complemented that food journal by providing fecal samples from which DNA was extracted. Fifty fecal metagenomics samples randomly selected from the Human Microbiome Project Phase I research were used for comparison purposes.

“The gut microbiome inherently is really, really cool. In the process of gathering this data, we are building a knowledge base. In this paper, we’re saying that by looking at healthy people, we should be able to establish a baseline about what a normal, healthy gut microbiome should look like and how things may change under different conditions,” Morizono adds.

And they picked a really, really cool name for their bacteria abundance profile: GutFeelingKB.

“KB is knowledge base. Our idea, it’s a gut feeling. It’s a bad joke,” he admits. “Drosophila researchers have the best names for their genes. No other biology group can compete. We, at least, tried.”

Next, the team will continue to collect samples to build out their bacteria baseline, associate it with clinical data, and then will start looking at the health implications for patients.

“One thing we could use this for is to understand how the bacterial population in the gut changes after antibiotic treatment. It’s like watching a forest regrow after a massive fire,” he says. “With probiotics, can we do things to encourage the right bacteria to grow?”

In addition to Morizono, study co-authors include Lead Author Charles H. King, and co-authors Hiral Desai, Allison C. Sylvetsky, Jonathan LoTempio, Shant Ayanyan, Jill Carrie, Keith A. Crandall, Brian C. Fochtman, Lusine Gasparyan, Naila Gulzar, Najy Issa, Lopa Mishra, Shuyun Rao, Yao Ren, Vahan Simonyan, Krista Smith and Senior Author, Raja Mazumder, all of George Washington University; Paul Howell and Sharanjit VedBrat, of KamTek Inc.; Konstantinos Krampis, of City University of New York; Joseph R. Pisegna, of VA Greater Los Angeles Healthcare System; and Michael D. Yao, of Washington DC VA Medical Center.

Financial support for research described in this post was provided by the National Science Foundation under award number 1546491 and the National Institutes of Health National Center for Advancing Translational Sciences under award number UL1TR000075.

Murray Pollack

Exploring accurate data use that supports clinical judgment

Murray Pollack

A new research collaboration between Children’s National Health System and KenSci seeks to understand how current data streams in health care can be used to enhance clinical decision making. The partnership seeks to develop personalized data-driven dynamic outcomes prediction for individual patients.

“These data are all around us in clinical medicine,” says Murray Pollack, M.D., MBA, of Children’s National Center for Translational Research. “Our goal for this project is to apply machine learning and statistical modeling to apply that data in ways that will enhance the work of the patient’s medical providers.”

“Since the mid-80s we have been able to predict mortality risks in pediatric ICUs using risk scores. In most cases these scores are used for quality assessment.,” Dr. Pollack continues. “Our collaborative goals are to study the temporal variation in data, taking the first step towards dynamic risk scoring for pediatric ICUs.”

“We see tremendous possibilities for how this wealth of data can be used safely and securely to supplement the clinician’s judgment,” says Hiroki Morizono, Ph.D., director of Biomedical Informatics at the Children’s National Center for Genetic Medicine Research. “This type of modeling, if successful, could perhaps predict an individual patient’s likelihood for deterioration or improvement.”

Over the course of one year, the two groups will come together and apply KenSci’s prediction platform to test different models and compare their accuracy to previous iterations developed at Children’s National.

Ankur Teredesai, KenSci’s co-founder, chief technology officer and professor at the University of Washington Tacoma, acknowledged the strategic nature of this collaboration, “Time is our best ally if integrated appropriately with other variables in healthcare machine learning and AI. Adding dynamism holds tremendous promise to be assistive for critical care. Caregivers in Pediatric ICUs serve the most vulnerable patients in our population, and this collaboration advances KenSci’s vision to be the best system of intelligence for healthcare.

Read KenSci’s press release about the partnership.

Cas9-mediated correction of metabolic liver disease

AAV.CRISPR-SaCas9

In vivo gene correction of the OTC locus in the mouse liver by AAV.CRISPR-SaCas9. Source: Nature Publishing Group copyright 2016.

What’s known

A deficiency of the enzyme ornithine transcarbamylase (OTC) in humans causes life-threatening hyperammonemic crises.  The OTC gene enables the body to make an enzyme that is a critical player in the urea cycle, a process that ensures excess nitrogen is excreted by the kidneys. Left unchecked, accumulating nitrogen becomes a toxic form of ammonia. Infants with OTC deficiency can suffer their first metabolic crisis as newborns. Up to 50 percent die or sustain severe brain injury, and survivors typically need a liver transplant by age 1. Gene therapy could cure OTC deficiency, but currently used viruses, such as adeno-associated virus (AAV), are not optimal in the neonatal setting.

What’s new

A research team led by Children’s National Health System and the University of Pennsylvania reasoned that the newborn liver may be an ideal setting for AAV-mediated gene correction using CRISPR-Cas9 gene editing. They intravenously infused two AAVs into two-day-old mice with partial OTC deficiency. One AAV expressed Cas9 and the other expressed a guide RNA and a donor OTC DNA. This resulted in correction of the mutation in 10 percent of liver cells and increased survival in mice challenged with a high-protein diet, which normally exacerbates disease. After consuming a high-protein diet for one week, the treated newborns had a 40 percent reduction in ammonia compared with the untreated group. The correction appears to last long term. The study “provides evidence for efficacy of gene editing in neonatal onset OTC deficiency,” says Mark L. Batshaw, M.D., Physician-In-Chief and Chief Academic Officer at Children’s National, and a study co-author. “This study provides convincing evidence for efficacy of in vivo genome editing in an authentic animal model of a lethal human metabolic disease,” the research team concludes.

Questions for future research

Q: More than 400 mutations can cause OTC deficiency, and each would require a separate gene-editing approach. Is it possible instead to insert the OTC genome using CRISPR-Cas9 to correct the disorder irrespective of the mutation?
Q: Will such gene editing also work in adult animal models of the OTC disorder?
Q: Do these encouraging results in animals translate to efficacy in infants?

Source: Yang, Y., L. Wang, P. Bell, D. McMenamin, Z. He, J. White, H. Yu, C. Xu, H. Morizono, K. Musunuru, M.L. Batshaw and J.M. Wilson. “A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice.” Published Feb. 1, 2016 by Nature Biotechnology.