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Fundamental Knowledge of Microbes Shedding New Light on Human Health

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A laboratory researching the human microbiome
Caption: Human microbiome research requires teamwork. Kimberly Jefferson (second from left), a leader of the Multi-Omic Microbiome Study—Pregnancy Initiative, joins some of the team at Virginia Commonwealth University, Richmond. Credit: Courtesy of Kimberly Jefferson

Basic research in biology generates fundamental knowledge about the nature and behavior of living systems. It is generally impossible to predict exactly where this line of scientific inquiry might lead, but history shows that basic science almost always serves as the foundation for dramatic breakthroughs that advance human health. Indeed, many important medical advances can be traced back to basic research that, at least at the outset, had no clear link at all to human health.

One exciting example of NIH-supported basic research is the Human Microbiome Project (HMP), which began 12 years ago as a quest to use DNA sequencing to identify and characterize the diverse collection of microbes—including trillions of bacteria, fungi, and viruses—that live on and in the healthy human body.

The HMP researchers have subsequently been using those vast troves of fundamental data as a tool to explore how microbial communities interact with human cells to influence health and disease. Today, these explorers are reporting their latest findings in a landmark set of papers in the Nature family of journals. Among other things, these findings shed new light on the microbiome’s role in prediabetes, inflammatory bowel disease, and preterm birth. The studies are part of the Integrative Human Microbiome Project.

If you’d like to keep up on the microbiome and other basic research journeys, here’s a good way to do so. Consider signing up for basic research updates from the NIH Director’s Blog and NIH Research Matters. Here’s how to do it: Go to Email Updates, type in your email address, and enter. That’s it. If you’d like to see other update possibilities, including clinical and translational research, hit the “Finish” button to access Subscriber Preferences.

As for the recent microbiome findings, let’s start with the prediabetes study [1]. An estimated 1 in 3 American adults has prediabetes, detected by the presence of higher than normal fasting blood glucose levels. If uncontrolled and untreated, prediabetes can lead to the more-severe type 2 diabetes (T2D) and its many potentially serious side effects [2].

George Weinstock, The Jackson Laboratory for Genomic Medicine, Farmington, CT, Michael Snyder, Stanford University, Palo Alto, CA, and colleagues report that they have assembled a rich new data set covering the complex biology of prediabetes. That includes a comprehensive analysis of the human microbiome in prediabetes.

The data come from monitoring the health of 106 people with and without prediabetes for nearly four years. The researchers met with participants every three months, drawing blood, assessing the gut microbiome, and performing 51 laboratory tests. All this work generated millions of molecular and microbial measurements that provided a unique biological picture of prediabetes.

The picture showed specific interactions between cells and microbes that were different for people who are sensitive to insulin and those whose cells are resistant to it (as is true of many of those with prediabetes). The data also pointed to extensive changes in the microbiome during respiratory viral infections. Those changes showed clear differences in people with and without prediabetes. Some aspects of the immune response also appeared abnormal in people who were prediabetic.

As demonstrated in a landmark NIH study several years ago [2], people with prediabetes can do a lot to reduce their chances of developing T2D, such as exercising, eating healthy, and losing a modest amount of body weight. But this study offers some new leads to define the biological underpinnings of T2D in its earliest stages. These insights potentially point to high value targets for slowing or perhaps stopping the systemic changes that drive the transition from prediabetes to T2D.

The second study features the work of the Inflammatory Bowel Disease Multi’omics Data team. It’s led by Ramnik Xavier and Curtis Huttenhower, Broad Institute of MIT and Harvard, Cambridge, MA. [4]

Inflammatory bowel disease (IBD) is an umbrella term for chronic inflammations of the body’s digestive tract, such as Crohn’s disease and ulcerative colitis. These disorders are characterized by remissions and relapses, and the most severe flares can be life-threatening. Xavier, Huttenhower, and team followed 132 people with and without IBD for a year, collecting samples of their gut microbiomes every other week along with biopsies and blood samples for a total of nearly 3,000 samples.

By integrating DNA, RNA, protein, and metabolic analyses, they followed precisely which microbial species were present. They could also track which biochemical functions those microbes were capable of performing, and which functions they actually were performing over the course of the study.

These data now offer the most comprehensive view yet of functional imbalances associated with changes in the microbiome during IBD flares. These data also show how those imbalances may be altered when a person with IBD goes into remission. It’s also noteworthy that participants completed questionnaires on their diet. This dataset is the first to capture associations between diet and the gut microbiome in a relatively large group of people over time.

The evidence showed that the gut microbiomes of people with IBD were significantly less stable than the microbiomes of those without IBD. During IBD activity, the researchers observed increases in certain groups of microbes at the expense of others. Those changes in the microbiome also came with other telltale metabolic and biochemical disruptions along with shifts in the functioning of an individual’s immune system. The shifts, however, were not significantly associated with people taking medications or their social status.

By presenting this comprehensive, “multi-omic” view on the microbiome in IBD, the researchers were able to single out a variety of new host and microbial features that now warrant further study. For example, people with IBD had dramatically lower levels of an unclassified Subdoligranulum species of bacteria compared to people without the condition.

The third study features the work of The Vaginal Microbiome Consortium (VMC). The study represents a collaboration between Virginia Commonwealth University, Richmond, and Global Alliance to Prevent Prematurity and Stillbirth (GAPPS). The VMC study is led by Gregory Buck, Jennifer Fettweis, Jerome Strauss,and Kimberly Jefferson of Virginia Commonwealth and colleagues.

In this study, part of the Multi-Omic Microbiome Study: Pregnancy Initiative, the team followed up on previous research that suggested a potential link between the composition of the vaginal microbiome and the risk of preterm birth [5]. The team collected various samples from more than 1,500 pregnant women at multiple time points in their pregnancies. The researchers sequenced the complete microbiomes from the vaginal samples of 45 study participants, who gave birth prematurely and 90 case-matched controls who gave birth to full-term babies. Both cases and controls were primarily of African ancestry.

Those data reveal unique microbial signatures early in pregnancy in women who went on to experience a preterm birth. Specifically, women who delivered their babies earlier showed lower levels of Lactobacillus crispatus, a bacterium long associated with health in the female reproductive tract. Those women also had higher levels of several other microbes. The preterm birth-associated signatures also were associated with other inflammatory molecules.

The findings suggest a link between the vaginal microbiome and preterm birth, and raise the possibility that a microbiome test, conducted early in pregnancy, might help to predict a woman’s risk for preterm birth. Even more exciting, this might suggest a possible way to modify the vaginal microbiome to reduce the risk of prematurity in susceptible individuals.

Overall, these landmark HMP studies add to evidence that our microbial inhabitants have important implications for many aspects of our health. We are truly a “superorganism.” In terms of the implications for biomedicine, this is still just the beginning of what is sure to be a very exciting journey.

References:

[1] Longitudinal multi-omics of host-microbe dynamics in prediabetes. Zhou W, Sailani MR, Contrepois K, Sodergren E, Weinstock GM, Snyder M, et. al. Nature. 2019 May 29.

[2] National Diabetes Statistics Report, 2017, Center for Disease Control and Prevention (Atlanta, GA)

[3] Long-term effects of lifestyle intervention or metformin on diabetes development and microvascular complications over 15-year follow-up: the Diabetes Prevention Program Outcomes Study. Diabetes Prevention Program Research Group.Lancet Diabetes Endocrinol.2015 Nov;3(11):866-875.

[4] Multi-omics of the gut microbial ecosystem in inflammatory bowel disease. Lloyd-Price J, Arze C. Ananthakrishnan AN, Vlamakis H, Xavier RJ, Huttenhower C, et. al. Nature. 2019 May 29.

[5] The vaginal microbiome and preterm birth. Fettweis JM, Serrano MG, Brooks, JP, Jefferson KK, Strauss JF, Buck GA, et al. Nature Med. 2019 May 29.

Links:

Insulin Resistance & Prediabetes (National Institute of Diabetes and Digestive and Kidney Diseases/NIH)

Crohn’s Disease (NIDDK/NIH)

Ulcerative colitis (NIDDK/NIH)

Preterm Labor and Birth: Condition Information (Eunice Kennedy Shriver National Institute of Child Health and Human Development/NIH)

Global Alliance to Prevent Prematurity and Stillbirth (Seattle, WA)

NIH Integrative Human Microbiome Project

NIH Human Microbiome Project

NIH Support:

Prediabetes Study: Common Fund; National Institute of Dental and Craniofacial Research; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Human Genome Research; National Center for Advancing Translational Sciences

Inflammatory Bowel Disease Study: Common Fund; National Institute of Diabetes and Digestive and Kidney Diseases; National Center for Advancing Translational Sciences; National Institute of Human Genome Research; National Institute of Dental and Craniofacial Research

Preterm Birth Study: Common Fund; National Institute of Allergy and Infectious Diseases; Eunice Kennedy Shriver National Institute of Child Health and Human Development


Oral Insulin Delivery: Can the Tortoise Win the Race?

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Turtle shape compared to capsule shape
Caption: The African leopard tortoise’s shape inspired a new insulin-injecting “pill” (right). Credit: Alex Abramson

People with diabetes often must inject insulin multiple times a day to keep their blood glucose levels under control. So, I was intrigued to learn that NIH-funded bioengineers have designed a new kind of “pill” that may someday reduce the need for those uncomfortable shots. The inspiration for their design? A tortoise!

The new “pill”—actually, a swallowable device containing a tiny injection system—is shaped like the shell of an African leopard tortoise. In much the same way that the animal’s highly curved shell enables it to quickly right itself when flipped on its back, the shape of the new device is intended to help it land in the right position to inject insulin or other medicines into the stomach wall.

The hunt for a means to deliver insulin in pill form has been on ever since insulin injections first were introduced, nearly a century ago. The challenge in oral delivery of insulin and other “biologic” drugs—including therapeutic proteins, peptides, or nucleic acids—is how to get these large biomolecules through the highly acidic stomach and duodenum, where multiple powerful digestive enzymes reside, and into the bloodstream unscathed. Past efforts to address this challenge have met with only limited success.

In a study published in the journal Science, a team, led by Robert Langer at Massachusetts Institute of Technology, Cambridge, and Giovanni Traverso, Brigham and Women’s Hospital, Harvard Medical School, Boston, took a new approach to the problem by developing a tiny, ingestible injection system [1]. They call their pea-sized device SOMA, short for “self-orienting millimeter-scale applicator.”

In designing SOMA, the researchers knew they had to come up with a design that would orient the injection apparatus correctly. So they looked to the African leopard tortoise. They knew that, much like a child’s “weeble-wobble” toy, this tortoise can easily right its body if tipped over due to its low center of gravity and highly curved shell. With the shape of the tortoise shell as a starting point, the researchers used computer modeling to perfect their design. The final result features a partially hollowed-out, polymer-and-steel capsule that houses a tiny, spring-loaded needle tipped with compressed, freeze-dried insulin. There is also a dissolvable sugar disk to hold the needle in place until the time is right.

Here’s how it works: once a SOMA is swallowed and reaches the stomach, it quickly orients itself in a way that its needle-side rests against the stomach wall. After the protective sugar disk dissolves in stomach acid, the spring-loaded needle tipped with insulin is released, injecting its load of insulin into the stomach wall, from which it enters the bloodstream. Meanwhile, the spent SOMA device passes on through the digestive system.

The researchers’ tests in pigs have shown that a single SOMA can successfully deliver insulin doses of up to 3 milligrams, comparable to the amount a human with diabetes might need to inject. The tests also showed that the device’s microinjection did not damage the animals’ stomach tissue or the muscles surrounding the stomach. Because the stomach is known for being insensitive to pain, researchers expect that people receiving insulin via SOMA wouldn’t feel a thing, but much more research is needed to confirm both the safety and efficacy of the new device for human use.

Meanwhile, this fascinating work serves as a reminder that when it comes to biomedical science, inspiration sometimes can come from the most unexpected places.

Reference:

[1] An ingestible self-orienting system for oral delivery of macromolecules. Abramson A, Caffarel-Salvador E, Khang M, Dellal D, Silverstein D, Gao Y, Frederiksen MR, Vegge A, Hubálek F, Water JJ, Friderichsen AV, Fels J, Kirk RK, Cleveland C, Collins J, Tamang S, Hayward A, Landh T, Buckley ST, Roxhed N, Rahbek U, Langer R, Traverso G. Science. 2019 Feb 8;363(6427):611-615.

Links:

Diabetes (National Institute of Diabetes and Digestive and Kidney Diseases/NIH)

Langer Lab (MIT, Cambridge)

Giovanni Traverso (Brigham and Women’s Hospital, Harvard Medical School, Boston)

NIH Support: National Institute of Biomedical Imaging and Bioengineering


The Actin Superhighway

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Actin Superhighway

Credit: Andrew Lombardo and David Warshaw, University of Vermont, Burlington

What looks like a traffic grid filled with roundabouts is nothing of the sort: It’s actually a peek inside a tiny microchamber that models a complex system operating in many of our cells. The system is a molecular transportation network made of the protein actin, and researchers have reconstructed it in the lab to study its rules of the road and, when things go wrong, how it can lead to molecular traffic accidents.

This 3D super-resolution image shows the model’s silicone beads (circles) positioned in a tiny microfluidic-chamber. Suspended from the beads are actin filaments that form some of the main cytoskeletal roadways in our cells. Interestingly, a single dye creates the photo’s beautiful colors, which arise from the different vertical dimensions of a microscopic image: 300 nanometers below the focus (red), at focus (green), and 300 nanometers above the focus (blue). When a component spans multiple dimensions—such as the spherical beads—all the colors of the rainbow are visible. The technique is called 3D stochastic optical reconstruction microscopy, or STORM [1].


Building a Smarter Bandage

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Smart Bandage

Credit: Tufts University, Medford, MA

Smartphones, smartwatches, and smart electrocardiograms. How about a smart bandage?

This image features a prototype of a smart bandage equipped with temperature and pH sensors (lower right) printed directly onto the surface of a thin, flexible medical tape. You also see the “brains” of the operation: a microprocessor (upper left). When the sensors prompt the microprocessor, it heats up a hydrogel heating element in the bandage, releasing drugs and/or other healing substances on demand. It can also wirelessly transmit messages directly to a smartphone to keep patients and doctors updated.

While the smart bandage might help mend everyday cuts and scrapes, it was designed with the intent of helping people with hard-to-heal chronic wounds, such as leg and foot ulcers. Chronic wounds affect millions of Americans, including many seniors [1]. Such wounds are often treated at home and, if managed incorrectly, can lead to infections and potentially serious health problems.


Does Gastric Bypass Reduce Cardiovascular Complications of Diabetes?

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Doctor with patient

Thinkstock/IPGGutenbergUKLtd

For obese people with diabetes, doctors have increasingly been offering gastric bypass surgery as a way to lose weight and control blood glucose levels. Short-term results are often impressive, but questions have remained about the long-term benefits of such operations. Now, a large, international study has some answers.

Soon after gastric bypass surgery, about 50 percent of folks not only lost weight but they also showed well-controlled blood glucose, cholesterol, and blood pressure. The good news is that five years later about half of those who originally showed those broad benefits of surgery maintained that healthy profile. The not-so-good news is that the other half, while they generally continued to sustain weight loss and better glucose control, began to show signs of increasing risk for cardiovascular complications.


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