Why do some people live to be 100? Intestinal bacteria may hold the answer

We are pursuing the dream of eternal life. We fast to stay healthy. And each year, we spend billions of kroner on treatment to make sure we stay alive. But some people turn 100 years old all by themselves. Why is that?

Researchers from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen have set out to find the answer.

Studying 176 healthy Japanese centenarians, the researchers learned that the combination of intestinal bacteria and bacterial viruses of these people is quite unique.

"We are always eager to find out why some people live extremely long lives. Previous research has shown that the intestinal bacteria of old Japanese citizens produce brand new molecules that make them resistant to pathogenic -- that is, disease-promoting -- microorganisms. And if their intestines are better protected against infection, well, then that is probably one of the things that cause them to live longer than others," says Postdoc Joachim Johansen, who is first author of the new study.

Among other things, the new study shows that specific viruses in the intestines can have a beneficial effect on the intestinal flora and thus on our health.

"Our intestines contain billions of viruses living of and inside bacteria, and they could not care less about human cells; instead, they infect the bacterial cells. And seeing as there are hundreds of different types of bacteria in our intestines, there are also lots of bacterial viruses," says Associate Professor Simon Rasmussen, last author of the new study.

Joachim Johansen adds that aside from the important, new, protective bacterial viruses, the researchers also found that the intestinal flora of the Japanese centenarians is extremely interesting.

"We found great biological diversity in both bacteria and bacterial viruses in the centenarians. High microbial diversity is usually associated with a healthy gut microbiome. And we expect people with a healthy gut microbiome to be better protected against aging related diseases," says Joachim Johansen.

Once we know what the intestinal flora of centenarians looks like, we can get closer to understanding how we can increase the life expectancy of other people. Using an algorithm designed by the researchers, they managed to map the intestinal bacteria and bacterial viruses of the centenarians.

"We want to understand the dynamics of the intestinal flora. How do the different kinds of bacteria and viruses interact? How can we engineer a microbiome that can help us live healthy, long lives? Are some bacteria better than others? Using the algorithm, we are able to describe the balance between viruses and bacteria," says Simon Rasmussen.

And if the researchers are able to understand the connection between viruses and bacteria in the Japanese centenarians, they may be able to tell what the optimal balance of viruses and bacteria looks like.

Optimising intestinal bacteria

More specifically, the new knowledge on intestinal bacteria may help us understand how we should optimise the bacteria found in the human body to protect it against disease.

"We have learned that if a virus pays a bacterium a visit, it may actually strengthen the bacterium. The viruses we found in the healthy Japanese centenarians contained extra genes that could boost the bacteria. We learned that they were able to boost the transformation of specific molecules in the intestines, which might serve to stabilise the intestinal flora and counteract inflammation," says Joachim Johansen, and Simon Rasmussen adds:

"If you discover bacteria and viruses that have a positive effect on the human intestinal flora, the obvious next step is to find out whether only some or all of us have them. If we are able to get these bacteria and their viruses to move in with the people who do not have them, more people could benefit from them."

Even though this requires more research, the new insight is significant, because we are able to modify the intestinal flora.

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Your baby's gut is crawling with unknown viruses

Babies tumble about with more than 200 previously unknown viral families within their intestines. This large number comes as a surprise to researchers from the University of Copenhagen and COPSAC, who closely studied the diapers of 647 Danish babies and made the first mapping of its kind. These viruses most likely play an important role in protecting children from chronic diseases.

Viruses are usually associated with illness. But our bodies are full of both bacteria and viruses that constantly proliferate and interact with each other in our gastrointestinal tract. While we have known for decades that gut bacteria in young children are vital to protect them from chronic diseases later on in life, our knowledge about the many viruses found there is minimal.

A few years back, this gave University of Copenhagen professor Dennis Sandris Nielsen the idea to delve more deeply into this question. As a result, a team of researchers from COPSAC (Copenhagen Prospective Studies on Asthma in Childhood) and the Department of Food Science at UCPH, among others, spent five years studying and mapping the diaper contents of 647 healthy Danish one-year-olds.

"We found an exceptional number of unknown viruses in the faeces of these babies. Not just thousands of new virus species -- but to our surprise, the viruses represented more than 200 families of yet to be described viruses. This means that, from early on in life, healthy children are tumbling about with an extreme diversity of gut viruses, which probably have a major impact on whether they develop various diseases later on in life," says Professor Dennis Sandris Nielsen of the Department of Food Science, senior author of the research paper about the study, now published in Nature Microbiology.

The researchers found and mapped a total of 10,000 viral species in the children's faeces -- a number ten times larger than the number of bacterial species in the same children. These viral species are distributed across 248 different viral families, of which only 16 were previously known. The researchers named the remaining 232 unknown viral families after the children whose diapers made the study possible. As a result, new viral families include names like Sylvesterviridae, Rigmorviridae and Tristanviridae.

Bacterial viruses are our allies

"This is the first time that such a systematic an overview of gut viral diversity has been compiled. It provides an entirely new basis for discovering the importance of viruses for our microbiome and immune system development. Our hypothesis is that, because the immune system has not yet learned to separate the wheat from the chaff at the age of one, an extraordinarily high species richness of gut viruses emerges, and is likely needed to protect against chronic diseases like asthma and diabetes later on in life," states Shiraz Shah, first author and a senior researcher at COPSAC.

Ninety percent of the viruses found by the researchers are bacterial viruses -- known as bacteriophages. These viruses have bacteria as their hosts and do not attack the children's own cells, meaning that they do not cause disease. The hypothesis is that bacteriophages primarily serve as allies:

"We work from the assumption that bacteriophages are largely responsible for shaping bacterial communities and their function in our intestinal system. Some bacteriophages can provide their host bacterium with properties that make it more competitive by integrating its own genome into the genome of the bacterium. When this occurs, a bacteriophage can then increase a bacterium's ability to absorb e.g. various carbohydrates, thereby allowing the bacterium to metabolise more things," explains Dennis Sandris Nielsen, who continues:

"It also seems like bacteriophages help keep the gut microbiome balanced by keeping individual bacterial populations in check, which ensures that there are not too many of a single bacterial species in the ecosystem. It's a bit like lion and gazelle populations on the savannah."

Shiraz Shah adds:

"Previously, the research community mostly focused on the role of bacteria in relation to health and disease. But viruses are the third leg of the stool and we need to learn more about them. Viruses, bacteria and the immune system most likely interact and affect each other in some type of balance. Any imbalance in this relationship most likely increases the risk of chronic disease."

The remaining ten percent of viruses found in the children are eukaryotic -- that is, they use human cells as hosts. These can be both friends and foes for us:

"It is thought-provoking that all children run around with 10-20 of these virus types that infect human cells. So, there is a constant viral infection taking place, which apparently doesn't make them sick. We just know very little about what's really at play. My guess is that they're important for training our immune system to recognise infections later. But it may also be that they are a risk factor for diseases that we have yet to discover," says Dennis Sandris Nielsen.

Could play an important role in inflammatory diseases

The researchers have yet to discover where the many viruses in the one-year-olds come from. Their best answer thus far is the environment:

"Our gut is sterile until we are born. During birth, we are exposed to bacteria from the mother and environment. It is likely that some of the first viruses come along with these initial bacteria, while many others are introduced later via dirty fingers, pets, dirt that kids put in their mouths and other things in the environment," says Dennis Sandris Nielsen.

As Shiraz Shah points out, the entire field of research speaks to a huge global health problem:

"A lot of research suggests that the majority of chronic diseases that we're familiar with -- from arthritis to depression -- have an inflammatory component. That is, the immune system is not working as it ought to -- which might be because it wasn't trained properly. So, if we learn more about the role that bacteria and viruses play in a well-trained immune system, it can hopefully lead us to being able to avoid many of the chronic diseases that afflict so many people today."

The research groups have begun investigating the role of gut viruses in relation to a number of different diseases that occur in childhood, such as asthma and ADHD.

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The future of replacement organs is (quite possibly) here: Robust human intestinal organoids created in a lab

Researchers from Tokyo Medical and Dental University (TMDU) find that spheroids grown in suspension mature into human intestinal organoids when transferred to a bioreactor and differentiate into complex intestinal tissue upon transplantation.

Growing human body parts in the lab is a common trope of horror movies and sci-fi books. But growing miniature organ-like tissues in the lab is already within our reach. Researchers from Japan have developed a new approach that enables intestinal mini-organs to be grown more easily and efficiently in the lab. This holds immense promise for regenerative medicine.

In a study published in November in Cell Reports Methods, researchers from Tokyo Medical and Dental University (TMDU) reveal that applying a few specialized lab techniques yields intestine-like tissues of predictable size and composition.

Organoids are organ-like balls of cells that are grown in the lab from spheroids (even smaller balls) of human cells and mimic the properties of the organ from which the "seed" cell was taken. Organoids are used for studying organ function in a lab setting and are also promising tools in the field of regenerative medicine.

"There are established methods for growing human intestinal organoids (HIOs) from induced pluripotent stem cells (iPSCs)," states Junichi Takahashi, first author of the study. "However, these techniques are challenging to perform. They result in spheroids of varying sizes and are limited by the growth conditions, which can result in deformed and unhealthy spheroids over time."

To develop a more robust and consistent way to generate HIOs, the researchers explored the use of cell culture plates made with an ultra-low attachment polymer to encourage the cells to detach and grow in suspension. They also tested the effects of growing the resulting spheroids in a bioreactor, a specialized incubator that keeps the growth medium constantly flowing to improve the health of the cells.

"Using our technique, we were able to grow spheroids of a predictable, consistent size that could be modified by modulating the number of cells seeded into the plates," says Tomohiro Mizutani, corresponding author of the study. "Furthermore, transferring the spheroids to a bioreactor allowed them to grow even larger, into healthy HIOs."

These organoids were surrounded by mesenchyme, which is a type of tissue found between organs in the human body. Importantly, when the organoids were transplanted into mice, they continued to grow and differentiate, developing a complex tissue architecture reflecting that of mature intestine. "Our findings show that intestinal tissue can be generated from iPSC-derived HIOs by inducing spheroids in suspension and maturing them in a bioreactor," says Takahashi.

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Robotic drug capsule can deliver drugs to gut

One reason that it's so difficult to deliver large protein drugs orally is that these drugs can't pass through the mucus barrier that lines the digestive tract. This means that insulin and most other "biologic drugs" -- drugs consisting of proteins or nucleic acids -- have to be injected or administered in a hospital.

A new drug capsule developed at MIT may one day be able to replace those injections. The capsule has a robotic cap that spins and tunnels through the mucus barrier when it reaches the small intestine, allowing drugs carried by the capsule to pass into cells lining the intestine.

"By displacing the mucus, we can maximize the dispersion of the drug within a local area and enhance the absorption of both small molecules and macromolecules," says Giovanni Traverso, the Karl van Tassel Career Development Assistant Professor of Mechanical Engineering at MIT and a gastroenterologist at Brigham and Women's Hospital.

In a study appearing today in Science Robotics, the researchers demonstrated that they could use this approach to deliver insulin as well as vancomycin, an antibiotic peptide that currently has to be injected.

Shriya Srinivasan, a research affiliate at MIT's Koch Institute for Integrative Cancer Research and a junior fellow at the Society of Fellows at Harvard University, is the lead author of the study.

Tunneling through

For several years, Traverso's lab has been developing strategies to deliver protein drugs such as insulin orally. This is a difficult task because protein drugs tend to be broken down in acidic environment of the digestive tract, and they also have difficulty penetrating the mucus barrier that lines the tract.

To overcome those obstacles, Srinivasan came up with the idea of creating a protective capsule that includes a mechanism that can tunnel through mucus, just as tunnel boring machines drill into soil and rock.

"I thought that if we could tunnel through the mucus, then we could deposit the drug directly on the epithelium," she says. "The idea is that you would ingest this capsule and the outer layer would dissolve in the digestive tract, exposing all these features that start to churn through the mucus and clear it."

The "RoboCap" capsule, which is about the size of a multivitamin, carries its drug payload in a small reservoir at one end and carries the tunnelling features in its main body and surface. The capsule is coated with gelatin that can be tuned to dissolve at a specific pH.

When the coating dissolves, the change in pH triggers a tiny motor inside the RoboCap capsule to start spinning. This motion helps the capsule to tunnel into the mucus and displace it. The capsule is also coated with small studs that brush mucus away, similar to the action of a toothbrush.

The spinning motion also helps to erode the compartment that carries the drug, which is gradually released into the digestive tract.

"What the RoboCap does is transiently displace the initial mucus barrier and then enhance absorption by maximizing the dispersion of the drug locally," Traverso says. "By combining all of these elements, we're really maximizing our capacity to provide the optimal situation for the drug to be absorbed."

Enhanced delivery

In tests in animals, the researchers used this capsule to deliver either insulin or vancomycin, a large peptide antibiotic that is used to treat a broad range of infections, including skin infections as well as infections affecting orthopedic implants. With the capsule, the researchers found that they could deliver 20 to 40 times more drug than a similar capsule without the tunneling mechanism.

Once the drug is released from the capsule, the capsule itself passes through the digestive tract on its own. The researchers found no sign of inflammation or irritation in the digestive tract after the capsule passed through, and they also observed that the mucus layer reforms within a few hours after being displaced by the capsule.

Another approach that some researchers have used to enhance oral delivery of drugs is to give them along with additional drugs that help them cross through the intestinal tissue. However, these enhancers often only work with certain drugs. Because the MIT team's new approach relies solely on mechanical disruptions to the mucus barrier, it could potentially be applied to a broader set of drugs, Traverso says.

"Some of the chemical enhancers preferentially work with certain drug molecules," he says. "Using mechanical methods of administration can potentially enable more drugs to have enhanced absorption."

While the capsule used in this study released its payload in the small intestine, it could also be used to target the stomach or colon by changing the pH at which the gelatin coating dissolves. The researchers also plan to explore the possibility of delivering other protein drugs such as GLP1 receptor agonist, which is sometimes used to treat type 2 diabetes. The capsules could also be used to deliver topical drugs to treat ulcerative colitis and other inflammatory conditions by maximizing the local concentration of the drugs in the tissue to help treat the inflammation.

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Heart of our evolution discovered: 380-million-year-old heart

Researchers have discovered a 380-million-year-old heart -- the oldest ever found -- alongside a separate fossilised stomach, intestine and liver in an ancient jawed fish, shedding new light on the evolution of our own bodies.

The new research, published today in Science, found that the position of the organs in the body of arthrodires -- an extinct class of armoured fishes that flourished through the Devonian period from 419.2 million years ago to 358.9 million years ago -- is similar to modern shark anatomy, offering vital new evolutionary clues.

Lead researcher John Curtin Distinguished Professor Kate Trinajstic, from Curtin's School of Molecular and Life Sciences and the Western Australian Museum, said the discovery was remarkable given that soft tissues of ancient species were rarely preserved and it was even rarer to find 3D preservation.

"As a palaeontologist who has studied fossils for more than 20 years, I was truly amazed to find a 3D and beautifully preserved heart in a 380-million-year-old ancestor," Professor Trinajstic said.

"Evolution is often thought of as a series of small steps, but these ancient fossils suggest there was a larger leap between jawless and jawed vertebrates. These fish literally have their hearts in their mouths and under their gills -- just like sharks today."

This research presents -- for the first time -- the 3D model of a complex s-shaped heart in an arthrodire that is made up of two chambers with the smaller chamber sitting on top.

Professor Trinajstic said these features were advanced in such early vertebrates, offering a unique window into how the head and neck region began to change to accommodate jaws, a critical stage in the evolution of our own bodies.

"For the first time, we can see all the organs together in a primitive jawed fish, and we were especially surprised to learn that they were not so different from us," Professor Trinajstic said.

"However, there was one critical difference -- the liver was large and enabled the fish to remain buoyant, just like sharks today. Some of today's bony fish such as lungfish and birchers have lungs that evolved from swim bladders but it was significant that we found no evidence of lungs in any of the extinct armoured fishes we examined, which suggests that they evolved independently in the bony fishes at a later date."

The Gogo Formation, in the Kimberley region of Western Australia where the fossils were collected, was originally a large reef.

Enlisting the help of scientists at the Australian Nuclear Science and Technology Organisation in Sydney and the European Synchrotron Radiation Facility in France, researchers used neutron beams and synchrotron x-rays to scan the specimens, still embedded in the limestone concretions, and constructed three-dimensional images of the soft tissues inside them based on the different densities of minerals deposited by the bacteria and the surrounding rock matrix.

This new discovery of mineralised organs, in addition to previous finds of muscles and embryos, makes the Gogo arthrodires the most fully understood of all jawed stem vertebrates and clarifies an evolutionary transition on the line to living jawed vertebrates, which includes the mammals and humans.

Co-author Professor John Long, from Flinders University, said: "These new discoveries of soft organs in these ancient fishes are truly the stuff of palaeontologists' dreams, for without doubt these fossils are the best preserved in the world for this age. They show the value of the Gogo fossils for understanding the big steps in our distant evolution. Gogo has given us world firsts, from the origins of sex to the oldest vertebrate heart, and is now one of the most significant fossil sites in the world. It's time the site was seriously considered for world heritage status."

Co-author Professor Per Ahlberg, from Uppsala University, said: "What's really exceptional about the Gogo fishes is that their soft tissues are preserved in three dimensions. Most cases of soft-tissue preservation are found in flattened fossils, where the soft anatomy is little more than a stain on the rock. We are also very fortunate in that modern scanning techniques allow us to study these fragile soft tissues without destroying them. A couple of decades ago, the project would have been impossible."

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How the intestine replaces and repairs itself

To act as a robust barrier against pathogens while also absorbing needed nutrients, the lining of the intestines must regenerate on a daily basis to remain equal to the task. The intestine's resident stem cells are responsible for meeting this need for constant repair and replenishment, but each stem cell faces decisions that depend on the overall conditions of the intestine and the needs of the moment. Bad decisions and poor coordination could result in intestinal diseases or cancer.

A new study suggests that stem cells are able to integrate cues from their surroundings and coordinate their behavior across the tissue through networks of vasculature in their close vicinity.

Rockefeller scientists found that lymphatic capillaries -- fine vessels that transport immune cells and drain fluids from tissues -- represent a signaling hub that communicates with stem cells to regulate their activity. With molecular guidance from the lymphatics, the stem cells produce daughter cells to repopulate the intestinal lining or self-renew to restock the stem cell reserve.

The findings, published in the journal Cell Stem Cell, provide new insights about primary intestinal components whose disrupted communication may contribute to intestinal disorders, such as inflammatory bowel disease. "The key to treating these diseases will be to figure out who talks to whom in this ecosystem and how we can reset the communication networks," says Rachel Niec, a clinical scholar in the laboratory of Elaine Fuchs.

Communications in the crypt

The intestinal stem cells reside in so-called crypts, found at the base of densely packed indentations in the intestinal lining. The stem cells may renew and stay in the crypt, or differentiate into specialized cells, which then migrate out of the crypt to replenish the gut lining. "To understand how stem cells balance self-renewal with differentiation, we needed a more complete picture of crypt niches," says Marina Schernthanner, a graduate student in the Fuchs lab.

To zoom in on the crypt, the team used a suite of techniques, including single-cell and spatial transcriptomics, which allowed them to identify cell types at specific locations and study their signaling molecules. The results showed that lymphatic capillaries, which form an intimate connection with the stem cells in the crypt, produce a number of proteins known to be important for stem cell functioning.

One previously underappreciated protein, REELIN, emerged as a top candidate for mediating communications between lymphatics and stem cells. By manipulating the amount of REELIN in lab-grown intestinal organoid cultures in some experiments and genetically suppressing it in mice in others, the researchers found that REELIN directly governs the regenerative behavior of intestinal stem cells.

The involvement of the lymphatic system in stem cell functioning is a relatively new concept. A previous study by the Fuchs team revealed that lymphatics are also closely involved with stem cells of the skin and play a key role in hair regeneration. There, however, it is the hair follicle stem cells that signal to lymphatic capillaries. By controlling their interactions with lymphatics, the stem cells synchronize hair regeneration across the tissue. "This suggests that lymphatics may be a conserved feature of stem cell niches, but their relationship to stem cells are likely tailored around the needs of each tissue," Niec says.

From Science Daily

Scientists map entire human gut at single cell resolution

If you get nervous, you might feel it in your gut. If you eat chili, your gut might revolt, but your friend can eat anything and feel great. You can pop ibuprofen like candy with no ill effects, but your friend's belly might bleed and might get no pain relief. Why is this? The quick answer is because we're all different. The next questions are how different exactly, and what do these differences mean for health and disease? Answering these is much more difficult, but the UNC School of Medicine lab of Scott Magness, PhD, is revealing some interesting scientific answers.

For the first time, the Magness lab used entire human GI tracts from three organ donors to show how cell types differ across all regions of the intestines, to shed light on cellular functions, and to show gene expression differences between these cells and between individuals.

This work, published in Cellular and Molecular Gastroenterology and Hepatology, opens the door to exploring the many facets of gut health in a much more precise manner at greater resolution than ever before.

"Our lab showed it's possible to learn about each cell type's function in important processes, such as nutrient absorption, protection from parasites, and the production of mucus and hormones that regulate eating behavior and gut motility," said Magness, associate professor in the Joint UNC-NC State Department of Biomedical Engineering and senior author of the paper. "We also learned how the gut lining might interact with the environment through receptors and sensors, and how drugs could interact with different cell types."

The Sensitive Gut

Think of a typical pharmaceutical commercial voiceover when the voice actor pleasantly recites possible side effects, such as diarrhea, vomiting, intestinal bleeding, and other unpleasant collateral damage. Well, the Magness lab is attempting to understand why those side effects happen, down to the level of individual cells, their functions, their locations, and their genes.

For this research, the Magness lab focused on the epithelium: the single-cell thick layer separating the inside of the intestines and colon from everything else. Like other cell populations and the microbiota, the epithelium is incredibly important to human health, and for years scientists have been exploring it. But until now, researchers could only take tiny biopsies the size of grains of rice from a few parts of the digestive tract, usually from the colon or limited regions of the small intestine.

"Such exploration would be like looking at the United States from space but only investigating what's going on in Massachusetts, Oklahoma, and California," Magness said. "To really learn about the country, we'd want to see everything."

Magness leaned on co-first authors, postdoctoral fellow Joseph Burclaff, PhD, and graduate student, Jarrett Bliton, both trainees in the Magness lab.

"Not only do we want to identify where the cells are located, but we want to know exactly which cell types do what, and why," Burclaff said. "So, staying with the map analogy, we don't want to just say, 'oh, there's North Carolina'. We want to know where to get the best barbecue. We want a ground level view to know as much as possible."

In the past, researchers would mash up those rice-sized biopsies to identify all epithelial cell types and learn some general features of these cells. Magness's approach was to sample thousands of individual cells from every part of the lower digestive tract (small intestine and colon) to create an atlas and then study the potential roles of these cells through the genes that each cell expresses. Knowing all of this would deepen scientific knowledge about the gut epithelium and hopefully encourage other scientists to explore each cell's function in biology, in disease, and in the unfortunate scenario of pharmaceutical side effects.

To do such a deep individual cell dive, Magness needed two things: better technology and the entire digestive tracts of humans.

The Biology of Data

UNC-Chapel Hill acquired state-of-the-art RNA sequencing technology several years ago for the creation of the Advanced Analytics Core Facility through the UNC Center for Gastrointestinal Disease and Biology, which developed the scientific and intellectual heft -- research faculty, staff, postdocs, and students -- to use state-of-the-art equipment.

The Magness Group acquired human digestive tracts through a research agreement with organ donor services at HonorBridge. When intestines are harvested for transplant and if they are not claimed by higher-priority groups, HonorBridge staff coordinates with the Magness Group to donate the transplant-grade organs for research.

Six to eight hours after harvest, the Magness lab receives intact intestinal tracts, each about 15 to 30 feet long. They remove the epithelial layer, which is one long connected piece of tissue despite being only one cell thick. Then the researchers use enzymes to break down the epithelium into individual cells. For this study, they repeated this for organs from three separate donors.

Using sequencing technology to characterize gene expression, the Magness group first extracts RNA from each cell while keeping each cell separate, and then they run single-cell sequencing, which takes a snapshot of which genes each intestinal cell is expressing and how much.

"The picture we get from each cell is a mosaic of all the different types of genes the cells make and this complement of genes creates a 'signature' to tell us what kind of cell it is and potentially what it is doing," Magness said. "Is it a stem cell or a mucous cell or a hormone-producing cell or an immune-signaling cell?

Burclaff added, "We were able to see the differences in cell types throughout the entire digestive tracts, and we can see different gene expression levels in the same cell types from three different people. We can see the different sets of genes turned on or off in individual cells. This is how, for instance, we might begin to understand why some people form toxicity to certain foods or drugs and some people don't."

A major problem with this kind of research is the sheer amount of data produced. The single cell sequencing picks up about 11,000 'reads', or individual samples of gene products in just one cell, and in many thousands of individual cells, each with different combinations of the 20,000-plus human genes that are turned on or off. This creates almost 140,000,000 data points for all the 12,590 cells in the study that have to be put into a visualizable format so that scientists can make sense of the vast amount of information.

"The human brain can only comprehend two dimensions, three is challenging," Magness said. "Add time, and it's even trickier to comprehend what a single cell is up to. The amount of data our experiments produced was basically millions of dimensions all at once."

Bliton devised computational techniques to filter the data to produce a manageable data set that included cell populations from all portions of the GI tract. Then, based on what Magness and other researchers had already learned of each cell type, Bliton could computationally identify each cell type from each region. He then plotted these data in a manner that humans can understand and interpret.

Reining in the immense data allowed the scientists to learn a lot about each cell type. Consider the tuft cell, discovered 40 years ago and so named because they look as if they have tufts of hair on their surface. Turns out these tuft cells express similar genes as those on taste buds on the tongue. Other researchers discovered that these tuft cells sensed worm infections and sent signals to the immune system to begin waging war. The Magness lab showed that tuft cells exhibit a set of genes thought to be important for sensing and "tasting" other kinds of intestinal content so it can signal the immune system if need be. This would represent a much broader function than sensing if there's a parasite in your gut or not.

"Not only did we describe every single cell type and every single gene they express individually, but we also looked at potential functions," Burclaff said. "If you look at intestinal mucus, which is a complex mixture that protects the cells, we show which cells express various mucin proteins, how much, and in which regions of the digestive tract. We looked at where specific enzymes that digest food are expressed. We looked at cells with anti-inflammatory gene expression and synapse genes where the gut is probably connected to nerves so it can talk to the rest of the body. We looked at aquaporins, proteins involved in transferring water through the intestinal membrane."

What the Magness group found was a whole new level of variation in potential functions that had not previously been appreciated through mashing up biopsy samples.

The researchers explored all epithelial receptors -- the cell surface proteins used to communicate with other cells and molecules and with the environment of the gut. Magness and colleagues could see which receptors were expressed the most and in which cell types, painting a new picture of how cells might interact with gut contents such as nutrients, microbes, toxins, and drugs.

"As far as we know, we're the first to do this kind of analysis across the length of the human gut from three full donors," Bliton said. "We can look at each cell type and predict which pharmaceuticals might affect which cell type individually."

For instance, there's a class of drugs to treat inflammatory bowel disease; they're designed to hit specific targets, certain immune cells that trigger inflammation. But the Magness lab learned that some epithelial cells express the same genes as those in the immune cells that are intended to be the target. This finding indicates there could be "off-target" effects in epithelial cells that are not intended and could lead to side-effects.

"This was not known," Burclaff said. "Lots of drugs have bad GI side effects. And it could be because the drugs are affecting individual cells along the entire length of the GI tract. We show where these receptors are most expressed and in which cell types."

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