Targeting gut microbes may reverse effects of childhood malnutrition

Healthy microbes, breast milk component suggest new treatment approach, mouse study shows

A child being examined by a doctor.
Manipulating the makeup of microbes in the gut has the potential to provide new ways to treat and ultimately help prevent childhood malnutrition. The research involved studying gut microbes from children living in Malawi, where malnutrition is a significant problem. (Photo: Lucy Bollinger/Washington University)

The tens of trillions of microbes living in the gut are major players in human health. So-called friendly intestinal bacteria promote health, but disruptions in our resident microbes also have been linked to childhood malnutrition, an underlying cause of death for some 2.7 million children annually.

Now, two studies published Feb. 18 — one in Science and the other in Cell — both led by Washington University School of Medicine in St. Louis, show that effects of gut bacteria reach far beyond the gastrointestinal tract, influencing development of distant tissues, including muscle, bone and brain. Further, the research indicates that manipulating the makeup of microbes in the gut has the potential to provide new ways to treat and ultimately help prevent childhood malnutrition.

Both studies, led by Jeffrey I. Gordon, MD, the Dr. Robert J. Glaser Distinguished University Professor and director of Washington University’s Center for Genome Sciences and Systems Biology, involved an international team of scientists and were carried out in germ-free mice with gut microbes transferred from either healthy or malnourished young children living in Malawi, in Africa. Collaborators included the University of California at Davis, University of Malawi, University of Tampere and Duke University, among other institutions.

The Science study implicates underdeveloped gut microbial communities as a cause of childhood malnutrition, rather than an effect, and identifies specific microbes that direct healthy growth. The study in Cell demonstrates that a component of human breast milk interacts with gut microbes in ways that may help promote healthy growth and metabolism in malnourished children.

“This research provides a microbial view of human development and suggests potential new therapies for malnutrition that target gut microbes in order to promote healthy growth,” said Gordon, who also directs Washington University’s Center for Gut Microbiome and Nutrition Research. “Current ‘ready-to-use’ therapeutic foods have reduced mortality from malnutrition, but these children continue to show lingering long-term effects, including stunted growth, impaired neurodevelopment and dysfunctional immune systems.”

Work by Gordon’s team reveals likely explanations for these persistent maladies: a failure of a malnourished child’s gut microbial community — known as the microbiota — to develop along a normal, healthy trajectory, and a failure of current treatments to permanently repair and restore proper functions mediated by gut microbes, such as synthesizing vitamins and nutrients.

Findings in Science:

Working with colleagues in Malawi, Finland and the United States, the study’s first author, Laura V. Blanton, PhD, who carried out the research as a graduate student in Gordon’s lab, identified a scenario of microbial community development that is shared among healthy children and develops in the first two years of life. Having defined normal development, she determined that malnourished children have defects in this developmental scenario, leaving them with gut microbial communities that look younger than what would be expected based on their chronological ages.

To determine whether this persistent immaturity of the gut microbiota was a cause rather than an effect of malnutrition, Blanton modeled the gut microbes of Malawian children in young mice that were still actively growing and that were born without gut microbes of their own (germ-free mice). Some young mice received gut bacteria from healthy children, and others received gut microbes from malnourished children. Like their human counterparts transitioning to solid foods, these young mice ate a Malawian diet — primarily corn flour cooked with vegetables, peanuts and kidney beans. On its own, this diet does not meet nutritional requirements for humans or mice. The researchers then monitored the growth of the mice over the next month.

“The impaired growth we see in malnourished children was transmitted to the mice that received gut microbes from these children,” said Gordon. “These differences in growth between the different groups of mice occurred even though they were consuming the same amount of food. The only difference between the groups was in the makeup of their human microbial communities.”

And the disparities went beyond size. With imaging studies, the researchers found that most of the increased weight of the mice with healthy microbes was in the form of lean body mass, characteristic of healthy growth, rather than fat mass. The researchers also found better skeletal development in the mice with healthy microbes and healthier metabolism in their livers, muscles and brains.

The researchers also identified members of the healthy microbiota whose presence correlated to more robust growth. In a series of experiments, they determined that good bacteria could compensate for growth impairments seen in mice receiving malnourished microbial communities. The researchers saw this effect when they let mice that received microbial communities from healthy infants and children live together with mice that had received communities from undernourished individuals. Like other rodents, mice consume each other’s feces and thereby exchange gut bacteria.

“In this battle of good microbes versus bad, good triumphed,” Gordon said. “Beneficial growth-promoting microbes established themselves in the guts of cagemates containing microbiota from undernourished infants and prevented poor growth.”

The researchers cultured these organisms and showed that adding two of them, Ruminococcus gnavus and Clostridium symbiosum, directly to unhealthy gut microbes and giving this mixture to mice also corrected growth impairments and metabolic abnormalities typical of mice harboring a malnourished child’s microbiota alone.

Findings in Cell:

Compared with mothers of healthy infants, those with undernourished infants had breast milk with lower levels of sugars that carry sialic acid, the researchers found. Other research has linked sialic acid to brain development. First author Mark R. Charbonneau, PhD, carried out this research as a graduate student in Gordon’s lab along with colleagues at the University of California at Davis, University of Malawi and University of Tampere in Finland.

Because of the difficulty obtaining significant quantities of human breast milk, the researchers looked for these sugars in cow’s milk. They found them but at 20-fold lower concentrations. Colleagues at the University of California at Davis and Hilmar Cheese Co. in Hilmar, Calif., purified these sugars from whey produced during cheese manufacturing. Charbonneau then studied the effects of these sialylated bovine milk oligosaccharides (S-BMOs). He did so using young mice that had been colonized with gut bacteria from a malnourished Malawian child. One group of these mice received a Malawian diet supplemented with S-BMO; a second group received the Malawian diet plus a different type of sugar commonly added to infant formula but that does not contain sialic acid. A third group received the unsupplemented Malawian diet alone.

The group eating the diet supplemented with S-BMO showed significantly better growth than the other two groups, despite the fact that all of the diets contained the same number of calories. The benefit of this supplement also was dependent on the presence of gut bacteria, as the growth promotion produced by S-BMO disappeared when given to germ-free mice reared under sterile conditions.

Like the Science study, the Cell study demonstrated that the improved growth produced by S-BMO supplementation went beyond size, with mice gaining significantly more lean body mass, and experiencing improvements in skeletal development and a better metabolic profile in the blood, brain and liver.

In a final series of experiments, the researchers reproduced their results in piglets that were born germ-free and then colonized with the malnourished child’s gut microbial community. As in the mouse experiments, the piglets were fed the Malawian diet with or without S-BMO. The piglets were studied because their physiologic and metabolic properties are closer to humans than mice.

“The next steps we are actively pursuing are development of new microbiota-directed food interventions that enhance the representation and beneficial functions of the growth-promoting gut microbes we have identified,” Gordon said. “We hope that these next-generation, food-based interventions will produce durable repair of microbiota immaturity in malnourished children and produce better long-term clinical outcomes.”

In addition to Washington University, other institutions involved in the research were: University of Malawi, University of California-Davis, University of Tampere in Finland, Duke University, Centre National de la Recherche Scientifique and Aix-Marseille Université in France, King Abdulaziz University in Saudi Arabia, Russian Academy of Sciences in Moscow, Sanford Burnham Prebys Medical Discovery Institute in La Jolla, Calif., and the Hilmar Cheese Co., in California.

Work presented in the Science paper was supported by the Bill and Melinda Gates Foundation; the National Institutes of Health (NIH), grant number DK30292; and the Office of Health, Infectious Diseases and Nutrition, Bureau for Global Health, U.S. Agency for International Development, under the terms of cooperative agreement no. AID-OAA-A-12-00005, through the Food and Nutrition Technical Assistance III Project managed by FHI 360. Data management and statistical analysis for the iLiNS-DYAD-M clinical study also were funded by the Academy of Finland, grant number 252075; and by the Medical Research Fund of Tampere University Hospital, grant number 9M004. Micro-CT analysis was performed in the Washington University Musculoskeletal Research Center, which is supported by NIH grant P30 AR057235. Additional support was provided by NIH predoctoral training grants T32 AI007172 and T32 GM007067 and from the Lucille P. Markey Special Emphasis Pathway in Human Pathobiology; and by the Russian Science Foundation, grant 14-14-00289. Collection of the human specimens included in this study was approved by the University of Malawi College of Medicine Research Ethics Committee.
Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan Y, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, Gordon JI. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science. Feb. 18, 2016
Work presented in the Cell paper was supported in part by the Bill and Melinda Gates Foundation; the National Institutes of Health (NIH), grant numbers DK30292, DK70977 and P30 AR057235; the Office of Health, Infectious Diseases and Nutrition, Bureau for Global Health, USAID under terms of Cooperative Agreements GHN-A-00-08- 00001-00 and AID-OAA-A-12-00005, through the Food and Nutrition Technical Assistance II and III Projects (FANTA) managed by the Academy for Educational Development (AED) and FHI 360. Data management and statistical analysis for the iILNS-DYAD-M clinical study were supported by the Academy of Finland, grant number 252075; and the Medical Research Fund of Tampere University Hospital, grant number 9M004. Gordon is a co-founder of Matatu Inc., a company characterizing the role of diet-by-microbiota interactions in animal health. Three authors are co-founders of Evolve Biosystems Inc., a company focused on diet-based manipulation of the gut microbiota.
Charbonneau MR, O’Donnell D, Blanton LV, Totten SM, Davis JCC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR, Muehlbauer MJ, Ilkayeva O, Wu C, Struckmeyer T, Barile D, Mangani C, Jorgensen J, Fan Y, Maleta K, Dewey KG, Ashorn P, Newgard CB, Lebrilla C, Mills DA, Gordon JI. Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition. Cell. Feb. 18, 2016.
Washington University School of Medicine’s 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is one of the leading medical research, teaching and patient-care institutions in the nation, currently ranked sixth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.

Originally published by the School of Medicine