In the early 1900s, scientists discovered that each person belonged to one of four blood types. Now they have discovered a new way to classify humanity: by bacteria. Each human being is host to thousands of different species of microbes. Yet a group of scientists now report just three distinct ecosystems in the guts of people they have studied.
Whatever the cause of the different enterotypes, they may end up having discrete effects on people’s health. Gut microbes aid in food digestion and synthesize vitamins, using enzymes our own cells cannot make. Dr. Bork and his colleagues have found that each of the types makes a unique balance of these enzymes. Enterotype 1 produces more enzymes for making vitamin B7 (also known as biotin), for example, and Enterotype 2 more enzymes for vitamin B1 (thiamine). The discovery of the blood types A, B, AB and O had a major effect on how doctors practice medicine. They could limit the chances that a patient’s body would reject a blood transfusion by making sure the donated blood was of a matching type. The discovery of enterotypes could someday lead to medical applications of its own, but they would be far down the road. “Some things are pretty obvious already,” Dr. Bork said. Doctors might be able to tailor diets or drug prescriptions to suit people’s enterotypes, for example. Or, he speculated, doctors might be able to use enterotypes to find alternatives to antibiotics, which are becoming increasingly ineffective. Instead of trying to wipe out disease-causing bacteria that have disrupted the ecological balance of the gut, they could try to provide reinforcements for the good bacteria. “You’d try to restore the type you had before,” he said. Dr. Bork notes that more testing is necessary. Researchers will need to search for enterotypes in people from African, Chinese and other ethnic origins. He also notes that so far, all the subjects come from industrial nations, and thus eat similar foods. “This is a shortcoming,” he said. “We don’t have remote villages.”
The discovery of enterotypes follows on years of work mapping the diversity of microbes in the human body — the human microbiome, as it is known. The difficulty of the task has been staggering. Each person shelters about 100 trillion microbes. (For comparison, the human body is made up of only around 10 trillion cells.) But scientists cannot rear a vast majority of these bacteria in their labs to identify them and learn their characteristics. As genetics developed, scientists learned how to study the microbiome by analyzing its DNA. Scientists extracted DNA fragments from people’s skin, saliva and stool. They learned how to recognize and discard human DNA, so that they were left with genes from the microbiome. They searched through the remaining DNA for all the variants of a specific gene and compared them with known species. In some cases, the variants proved to be from familiar bacteria, like E. coli. In other cases, the gene belonged to a species new to science.
These studies offered glimpses of a diversity akin to a rain forest’s. Different regions of the body were home to different combinations of species. From one person to another, scientists found more tremendous variety. Many of the species that lived in one person’s mouth, for example, were missing from another’s. Scientists wondered if deeper studies would reveal a unity to human microbiomes. Over the past few years, researchers have identified the genomes — the complete catalog of genes — of hundreds of microbe species that live in humans. Now they can compare any gene they find with these reference genomes. They can identify the gene’s function, and identify which genus of bacteria the microbe belongs to. And by tallying all the genes they find, the scientists can estimate how abundant each type of bacteria is.
In the recent work, Dr. Bork and his team carried out an analysis of the gut microbes in 22 people from Denmark, France, Italy and Spain. Some of their subjects were healthy, while others were obese or suffered from intestinal disorders like Crohn’s disease. Dr. Bork and his colleagues searched for fragments of DNA corresponding to the genomes of 1,511 different species of bacteria. The researchers combined their results with previous studies of 13 Japanese individuals and 4 Americans. The scientists then searched for patterns. “We didn’t have any hypothesis,” Dr. Bork said. “Anything that came out would be new.” Still, Dr. Bork was startled by the result of the study: all the microbiomes fell neatly into three distinct groups. And, as Dr. Bork and his colleagues reported on Wednesday in the journal Nature, each of the three enterotypes was composed of a different balance of species. People with type 1, for example, had high levels of bacteria called Bacteroides. In type 2, on the other hand, Bacteroides were relatively rare, while the genus Prevotella was unusually common. “You can cut the data in lots of different ways, and you still get these three clusters,” Dr. Bork said. Dr. Bork and his colleagues found confirmation of the three enterotypes when they turned to other microbiome surveys, and the groups continue to hold up now that they have expanded their own study to 400 people.
The geographic distribution and bacterial diversity of the included samples. (Credit: Tito et al. Insights from Characterizing Extinct Human Gut Microbiomes. PLoS ONE, 2012; 7 (12): e51146 DOI: 10.1371/journal.pone.0051146)
Bacterial Ecology That Lives On Humans Has Changed in Last 100 Years / Dec. 13, 2012
A University of Oklahoma-led study has demonstrated that ancient DNA can be used to understand ancient human microbiomes. The microbiomes from ancient people have broad reaching implications for understanding recent changes to human health, such as what good bacteria might have been lost as a result of our current abundant use of antibiotics and aseptic practices. Cecil M. Lewis Jr., professor of anthropology in the OU College of Arts and Sciences and director of the OU Molecular Anthropology Laboratory, and Raul Tito, OU Research Associate, led the research study that analyzed microbiome data from ancient human fecal samples collected from three different archaeological sites in the Americas, each dating to over 1000 years ago. In addition, the team provided a new analysis of published data from two samples that reflect rare and extraordinary preservation: Otzi the Iceman and a soldier frozen for 93 years on a glacier.
“The results support the hypothesis that ancient human gut microbiomes are more similar to those of non-human primates and rural non-western communities than to those of people living a modern lifestyle in the United States,” says Lewis. “From these data, the team concluded that the last 100 years has been a time of major change to the human gut microbiome in cosmopolitan areas. Dietary changes, as well as the widespread adoption of various aseptic and antibiotic practices have largely benefited modern humans, but many studies suggest there has been a cost, such as a recent increase in autoimmune related risks and other health states,” states Lewis. “We wish to reveal how this co-evolutionary relationship between humans and bacteria has changed, while providing the foundation for interventions to reconstruct what has been lost. One way to do this is to study remote communities and non-human primates. An alternative path is to look at ancient samples and see what they tell us,” Lewis says. “An argument can be made that remote traditional communities are not truly removed from modern human ecologies. They may receive milk or other food sources from the government, which could alter the microbial ecology of the community. Our evolutionary cousins, non-human primates are important to consider. However, the human-chimp common ancestor was over six million years ago, which is a lot of time for microbiomes to evolve distinct, human signatures.”
Retrieving ancient human microbiome data is complementary to these studies. However, studying ancient microbiomes is not without problems. Assuming DNA preserves, there is also a problem with contamination and modification of ancient samples, both from the soil deposition, and from other sources, including the laboratory itself. “In addition to laboratory controls in our study, we use an exciting new quantitative approach called source tracking developed by Dan Knights from Rob Knight’s Laboratory at the University of Colorado in Boulder, which can estimate how much of the ancient microbiome data is consistent with the human gut, rather than other sources, such as soil,” explains Lewis. “We discovered that certain samples have excellent gut microbiome signatures, opening the door for deeper analyses of the ancient human gut, including a better understanding of the ancient humans themselves, such as learning more about their disease burdens, but also learning more about what has changed in our gut today.”
Three nations divided by common gut bacteria
by Ed Yong / May 9, 2012
A child from the village of Chamba in rural Malawi has very little in common with one living in the city of Philadelphia in the USA. They eat different food, speak different languages, and enjoy different lifestyles. But they are both united by the fact that they are vessels for teeming hordes of bacteria. These children, like all of us, are home to trillions of bacteria and other microbes. These passengers outnumber our own cells by ten to one, and their genes outnumber ours by a hundred to one. Collectively, they’re known as the microbiome, and they are as much a part of us as any one of our own organs. Theybreak down our food, safeguard our health, and affect our minds. And they have become intensely fashionable.
Microbiome research is booming, fuelled by the realisation that these microbes might provide a deeper understanding of our bodies, and new ways of diagnosing or treating diseases. But,with some exceptions, most microbiome studies have focused on wealthy populations from Europe, North America and Japan. There’s a risk that the bacteria of people from the developing world will be ignored.
Tanya Yatsunenko has led one of the largest efforts yet to remedy that problem. Working with Rob Knight and Jeffrey Gordon, she amassed an international collection of faecal samples and studied the gut microbes of people three diverse populations: 100 Guahibo people from the Venezuelan Amazon; 115 people from four Malawian villages; and 316 people from three American cities. The recruits ranged from newborn babies to 70-year-old adults. “The paper represents a heroic effort,” says David Relman, who studies the microbiome at Stanford University. “It’s the most definitive cross-culture and multi-age assessment of the human microbiome to date.” First, the similarities. Yatsunenko found that in all three countries, newborn babies have the greatest variety of gut bacteria, both in the species and the genes they carry. As they grow up, especially in their first three years, their microbiomes diversify, while the differences between individuals shrink. This means that adults end up with more diverse gut communities compared to babies, but more similar ones compared to each other. No one really knows why this happens, although studies are afoot to find out. But for now, it tells us that the microbiome matures along a “consistent developmental program”, according to Knight.
The guts of babies are dominated by Bifidobacterium – the group that’s commonly found in probiotic foods. They’re also loaded with genes for producing folate, an essential B-vitamin that’s involved in creating and repairing DNA. These folate-making genes decline as babies grow up, and get more of the vitamin from their diets. At the same time, the genes for making other vitamins, like B1, B7 and especially B12, become more common. “This similarity across cultures in building up the gut microbiome in childhood has been touched on before but it’s much more convincing here,” says Peer Bork, from theEuropean Molecular Biology Laboratory. As adults, microbiomes fell along a spectrum, whose extremes are characterised by two groups: Bacteroides or Prevotella. There’s a trade-off between them, so people either have aBacteroides-rich gut or a Prevotella-rich one. Note that these aren’t necessarily the most common microbes around; they’re just the most distinctive.
Now, the differences. The genetic variation within human populations is greater than the variation between them. The same is true of our microbiomes. That being said, Yatsunenkodid find distinct differences between the microbes of all three countries, and especially between the Americans and the other two. These differences seemed to be largely driven by different diets. For example, Malawian and Venezuelan babies had more gut genes for making vitamin B2 compared to American ones. The vitamin is found in breast milk, meat and dairy products, and it may be that American babies (whose mothers eat more dairy and meat) get more vitamin B2 than those from the other countries. The Malawian and Venezuelan babies also had more genes for harvesting the readily available sugars in breast milk, although these dwindle away as they get older. As their diet shifts towards high-fibre foods like corn and cassava, their gut bacteria become loaded with genes for breaking down more complex sugars and starches. For American babies, the opposite is true. With a lifelong diet of refined sugars ahead of them, the genes for harvesting these nutrients become moreabundant as they get older. And since they eat high-protein diets, their gut bacteria become rife with genes for breaking down amino acids.
Yatsunenko also found differences at the level of individual species. For example, Malawian and Venezuelan gut communities contained more Prevotella microbes. This fits with the results from previous studies, which showed thatpeople who eat a high-fat or high-protein diet (including European children) tend towards the Bacteroides end of the spectrum, while those who eat lots of carbohydrates (includingvillagers from Burkina Faso) lie at Prevotella end. These differences could well be due to other aspects of the volunteers’ lifestyles, but it’s telling that they mirror the differences between meat-eating and plant-eating mammals. Just like the Americans, carnivore microbiomes are also packed with protein-busting genes, while herbivore microbiomes are rich in the starch-breaking genes that are common in Malawaians and Venezuelans guts.
Results like these are invaluable. At a time when we’re thinking of manipulating the microbiome to improve our health, it’s vital that we understand how our microbial partners are affected by our age, diet and culture. We need to expand our knowledge of the microbiome beyond the confines of the Western world. Yatsunenko’s study is certainly a step in the right direction, but even she describes it as a “demonstration project”. We need many more such studies, with more volunteers from all parts of the world. There’s a certain urgency to this work. As many parts of the world shift towards a western lifestyle, there’s a risk that we might lose important reservoirs of bacterial diversity. The microbiomes of the world are becoming increasingly gentrified, and we need to study them while we still can. Early studies gave us the opening lines to the microbiome story, and this study fleshes out a few more themes and characters. There are still many chapters left to write.
Reference: Yatsunenko, Rey, Manary, Trehan, Dominguez-Bellos, Contreras, Magris, Hidalgo, Baldassanos, Anokhin, Heath, Warner, Reeder, Kuczynski, Caproraso, Lozupone, Lauber, Clemente, Knights, Knight & Gordon. 2012. Human gut microbiome viewed across age and geography. Nature http://dx.doi.org/10.1038/nature11053
An extra word on splitters and lumpers: Canny readers might notice that I talk about a spectrum of microbiomes dominated by Prevotella and Bacteroides. This differs from the conclusions of a study I covered in 2011, which suggested thatgut microbiomes can be classified into three discrete ‘enterotypes’, characterised by Bacteroides, Prevotella andRuminococcus (more recently replaced byMethanobrevibacter). So, one continuous spectrum, or three distinct clusters? News of this debate emerged at a Paris conference in March, and I covered the story for Nature. Head over there for the full details. In the meantime, Peer Bork, who led the original enterotype study, mentioned to me that the technique that Yatsunenko used might miss out some rarer microbes such as Methanobrevibacter. As such, the third enterotype might be invisible. He has a study in the pipeline that bolsters the enterotype concept. This debate, it seems, will continue for a while.
BREAST MILK ECOLOGY
Breast Milk Contains More Than 700 Species of Bacteria, Spanish Researchers Find / Jan. 4, 2013
Spanish researchers have traced the bacterial microbiota map in breast milk, which is often the main source of nourishment for newborns. The study has revealed a larger microbial diversity than originally thought: more than 700 species. The breast milk received from the mother is one of the factors determining how the bacterial flora will develop in the newborn baby. However, the composition and the biological role of these bacteria in infants remain unknown. A group of Spanish scientists have now used a technique based on massive DNA sequencing to identify the set of bacteria contained within breast milk called microbiome. Thanks to their study, pre- and postnatal variables influencing the micriobial richness of milk can now be determined. Colostrum is the first secretion of the mammary glands after giving birth. In some of the samples taken of this liquid, more than 700 species of these microorganisms were found, which is more than originally expected by experts. The results have been published in the American Journal of Clinical Nutrition. “This is one of the first studies to document such diversity using the pyrosequencing technique (a large scale DNA sequencing determination technique) on colostrum samples on the one hand, and breast milk on the other, the latter being collected after one and six months of breastfeeding,” explain the coauthors, María Carmen Collado, researcher at the Institute of Agrochemistry and Food Technology (IATA-CSIC) and Alex Mira, researcher at the Higher Public Health Research Centre (CSISP-GVA). The most common bacterial genera in the colostrum samples were Weissella, Leuconostoc, Staphylococcus, Streptococcus and Lactococcus. In the fluid developed between the first and sixth month of breastfeeding, bacteria typical of the oral cavity were observed, such as Veillonella, Leptotrichia and Prevotella. “We are not yet able to determine if these bacteria colonise the mouth of the baby or whether oral bacteria of the breast-fed baby enter the breast milk and thus change its composition,” outline the authors.
The heavier the mother, the fewer the bacteria
The study also reveals that the milk of overweight mothers or those who put on more weight than recommended during pregnancy contains a lesser diversity of species. The type of labour also affects the microbiome within the breast milk: that of mothers who underwent a planned caesarean is different and not as rich in microorganisms as that of mothers who had a vaginal birth. However, when the caesarean is unplanned (intrapartum), milk composition is very similar to that of mothers who have a vaginal birth. These results suggest that the hormonal state of the mother at the time of labour also plays a role: “The lack of signals of physiological stress, as well as hormonal signals specific to labour, could influence the microbial composition and diversity of breast milk,” state the authors.
Help for the food industry
Given that the bacteria present in breast milk constitute one of initial instances of contact with microorganisms that colonise the infant’s digestive system, the researchers are now working to determine if their role is metabolic (it helps the breast-fed baby to digest the milk) or immune (it helps to distinguish beneficial or foreign organisms). For the authors, the results have opened up new doors for the design of child nutrition strategies that improve health. “If the breast milk bacteria discovered in this study were important for the development of the immune system, its addition to infant formula could decrease the risk of allergies, asthma and autoimmune diseases,” conclude the authors.
MICROBE SPURS OBESITY
This microbe is making you fat
by Annalee Newitz / Dec 21, 2012
The difference between an obese person and a thinner one may not be just diet. Certain microbes that live naturally in our guts may contribute a great deal to whether we become obese and develop obesity-related illnesses such as diabetes. A study published this week demonstrated that a person suffering from obesity was also suffering from extremely elevated levels of a group of gut bacteria called Enterobacter. In fact, Enterobacter comprised 35% of the bacteria in this person’s colon.
When Enterobacter die or suffer damage to their cell walls, they release endotoxins, substances that often provoke a strong immune response in other cells. And these immune responses can cause inflammation that tips over into hypertension, diabetes, hyperglycemia, and even colitis. Once the experimental subject had lost over 50 kg, the amount of Enterobacter in their gut became so small as to be undetectable — and they stopped suffering the effects of hypertension and hyperglycemia. The researchers attribute this transformation to a shift in diet. A high fat diet leads to a population explosion in these bacteria, who release a lot of endotoxins into the body. In their study, the researchers discovered that mice with Enterobacter in their systems rapidly became obese when fed on a high-fat diet; mice with Enterobacter who ate regular chow did not. What this suggests is that Enterobacter could promote obesity in people with a high fat diet, and also might make their obesity far more deadly. Previously, other research teams have found that high fat diets seem to interact with other gut microbes to cause inflammatory diseases like colitis.
Every human contains millions of microbes throughout our bodies, most of which contribute significantly to keeping us healthy. All those microbes put together are called a microbiome — it’s sort of like an ecosystem of microbes. We each have a slightly different microbiome. Scientists have identified several distinct types of human microbiome, and there may be many more. People unlucky enough to have Enterobacter in their microbiomes may be more susceptible to obesity-related diseases, and indeed to obesity itself.
Iguana. Green iguanas establish their intestinal microbiomes by feeding first on soil and later on the feces of adult iguanas. (Credit: © Sebastian Duda / Fotolia)
PARASITES AFFECT HOST BEHAVIOR
Animals’ Microbial Communities Linked to Their Behavior / Oct. 11, 2012
New research is revealing surprising connections between animal microbiomes — the communities of microbes that live inside animals’ bodies — and animal behavior, according to a paper by University of Georgia ecologist Vanessa O. Ezenwa and her colleagues. The article, just published in the Perspectives section of the journal Science, reviews recent developments in this emerging research area and offers questions for future investigation. The paper grew out of a National Science Foundation-sponsored workshop on new ways to approach the study of animal behavior. Ezenwa, an associate professor in the UGA Odum School of Ecology and College of Veterinary Medicine department of infectious diseases, and her coauthors were interested in the relationship between animal behavior and beneficial microbes. Most research on the interactions between microbes and their animal hosts has focused on pathogens, Ezenwa said. Less is known about beneficial microbes or animal microbiomes, but several recent studies have begun to explore these connections. “We know that animal behavior plays a critical role in establishing microbiomes,” she said. “Once they’re established, the microbiomes then influence animal behavior in lots of ways that have far-reaching consequences. That’s what we were trying to highlight in this article.”
Bumble bees, for example, obtain the microbes they need through social contact with nest mates, including consuming their nest mates’ feces-a not uncommon method for animals to acquire microbes. Green iguanas establish their intestinal microbiomes by feeding first on soil and later on the feces of adult iguanas. “There are a lot of behaviors that animals might have that allow them to get the different microbes they need at different points of their lives,” Ezenwa said. Microbes, in their turn, influence a wide range of animal behaviors, including feeding, mating and predator-prey interactions. One recent study found that fruit flies prefer to mate with others that have microbiomes most similar to their own. Another found that African malaria mosquitoes were less attracted to humans who had a greater diversity of microbes on their skin, possibly because certain microbes produce chemicals that repel these mosquitoes. Other studies have focused on understanding the mechanisms by which microbes influence behavior. “Recent experiments have been able to assess the molecules that are involved in communication between microbes in the gut and the brain of mice, showing that microbes are associated with shifts in things like depression and anxiety in these mice,” she said. “There are huge implications in the role these microbes play in regulating neural function.” Ezenwa’s own work involves investigating how social behavior and interactions between organisms might increase their likelihood of acquiring parasites and pathogens. She is starting a new project examining animal behavior and microbiomes in relation to infectious disease. “As in the example of the bumble bees, behavior might control the microbes an animal acquires, and those microbes might then influence the animal’s vulnerability to pathogens,” she said.
Biotech Startup uBiome Aims to Sequence the Bacteria that Call Our Bodies Home
by David J. Hill / 12/28/12
When you look at your body in the mirror, most of what you consider to be “you” actually isn’t you, at least not in a biological sense. That’s because there are approximately 10 bacterial cells for every single human cell in the body. Startling, yes, but that’s just the tip of the iceberg. Each human body may contain hundreds of thousands of species of bacteria, providing over 350 times the number of genes that is within our own genome,according to an article from Scientific American published last June. As we consider the issues of health and longevity, the big questions that naturally arise are, what exactly are all these bacteria and what relationship does each have with human physiology? That’s not exactly an easy problem, but fortunately efforts to more rigorously study the bacteria in the body, also known as the microbiome, are underway in research laboratories around the world. Now, a startup called uBiome has recently launched a project on Indiegogo to map human microbiomes through crowdsourced funding and open up sequencing to a much larger pool of people. With a minimum pledge of $79 to the project, users will receive a kit to obtain samples from their body in order to have their microbiome sequenced. Now, the kit comes with cotton swabs to remove samples of bacterial flora from the mouth, ear, nose, genitalia, or GI tract. Users submit the kit and complete a survey about themselves, and once sequenced, uBiome provides the results, an analysis of what the data mean, charts that compare the user’s microbiome to others in the database, and finally the latest research about the bacteria identified. In the press release, cofounder Zachary Apte said, “We have two aims with uBiome. First, we want to make the science and the technology available to everyone. Now anyone can have their microbiome sequenced. Second, we want to curate the world’s largest microbiome dataset. Citizen science is the answer.”
With an initial target of 1,000 users, the project so far has nearly 600 backers who have donated enough to receive at least one GI microbiome kit. To receive kits that will enable sequencing at all five different sites, a pledge of $335 is required, and few have opted for the level of mapping. Though dependent on large numbers of participants to be meaningful, the kind of gross comparative analysis that uBiome provides can be qualitatively insightful. For instance, users could see how their microbioome compares to those in the same geographical region. As the website points out, people who suffer from diabetes or irritable bowel disorder can see how their microflora compare to others with the same conditions. Or perhaps those who are on restricted diets, such as low carb or gluten free, could glean insight into how successful they are with their food choices based on the kinds of bacteria in their GI tracts. Finally, there’s also the issue of excesses, like alcohol or coffee, that could show users how their choices are impacting the microecosystems within their bodies. Analysis of microbiome data could give users insight about what’s going on inside their bodies that cannot be measured by current medical practices. Whether any of this information will be able to be tied to specific research that suggests a lifestyle change is in order remains to be seen. But as the human microbiome continues to be researched, more discoveries are bound to make this personal data meaningful. “We believe the biological information era is going to follow the same trend that the internet did,” said uBiome cofounder Jessica Richman in the press release. “When citizens became empowered to explore the internet via search engines like Google, usage skyrocketed. With uBiome, people can explore their personal metagenome from home.” It’s a bit overwhelming to realize just how little is understood still about the human body. In fact, it was only a few years ago that doctors at Duke University Medical School proposed a beneficial function of the appendix, long thought of as a vestigial organ left over from evolutionary development. Their theory is that the appendix replenishes good bacteria into the gut, which is vital after things like diarrhea effectively slough the top layer of cells from the GI tract, including bacteria that help to digest consumed food. Without an appendix, a person’s GI flora repopulate more slowly, and it’s unclear what effects that has on health.
Crowdsourcing the mapping of human microflora can be exactly the kind of complement that researchers need to advance the understanding of this complex problem. Sequencing all of the bacteria in the human body is a monumental task, akin to the Human Genome Project and its challenges. Since 2007, the NIH has been overseeing the Human Microbiome Project, an effort to sequence the microbiomes of 250 volunteers by 200 scientists worldwide. To do this, new kinds of data analysis methods are being developed, and it would be useful to test these against a larger, independent pool that uBiome could acquire. Understanding how bacterial flora relates to human health will likely be a diverse, multidecade endeavor that is full of surprises. Toward that effort, uBiome’s approach offers another way for people to both learn more about their bodies and contribute to important studies. Perhaps one day, we’ll be as equally (if not more) concerned about what the 90 percent of the non-human cells in our bodies are up to as we are about our own genomes. It seems fair since we are providing them room and board, after all.