Global Microbiome Conservancy scales up
by Fatima Husain
Researcher Ainara Sistiaga shares food processing methods with a Hadza woman and her child. Photo credit: Christopher Corzett
As global human gut microbiome diversity dwindles, a non-profit collaboration between scientists around the world is racing to collect, catalog, and preserve the full biodiversity of human gut bacteria before they disappear. The collaboration, the Global Microbiome Conservancy, began over conversations between three postdoctoral researchers at MIT, Ainara Sistiaga, Mathilde Poyet, and Mathieu Groussin.
“We all know about the DNA composition of these [bacterial] communities but we don’t have access to the bacteria themselves,” says Groussin, who studies the evolutionary and ecological processes that change the human gut microbiome in the Alm Lab. “We thought [preserving the bacteria themselves] was definitely something to do that could help make a difference regarding conservation and biodiversity issues.”
The goal of the collaboration is simple: to collect and preserve the full diversity of bacteria that live in the gut of humans. The bacterial biodiversity of “both major and minority populations in many different countries in South America, Africa and Asia have been overlooked, and we know very little about them,” Groussin says, “so we want to put them on the map and have them represented in this initiative.”
To achieve global microbiome representation, the Conservancy aims to isolate 100,000 bacterial strains from fecal samples collected across 30 countries around the world within the next 2-3 years. Research in the collaboration involves traveling around the world and interacting with local populations and scientists to collect and analyze data. “We want to interact with the local people and the populations we enroll [in the collaboration] because we want to learn from them and experience what they are living … we know that the environment is the dominant factor shaping microbiomes,” Groussin says.
The Conservancy has highlighted particular countries and groups of people who may have diverse gut microbiota and aims to isolate the particular strains of bacteria responsible for that biodiversity.
And that biodiversity is at risk.
“Globalization, antibiotic use, and Western diets are spreading all across the world. All these are factors that decrease the biodiversity in the gut,” says Sistiaga, who uses organic geochemical techniques to reveal the hidden histories of human evolution in the Summons Lab in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS).
“For the first time, we are doing a very comprehensive study of microbiome,” Sistiaga says. Part of her research in particular involves exploring the lipids, or fats, associated with the human gut microbiome. “We have extensively studied the relationship between microbes and lipids in environment for a long time in organic geochemistry, but we don’t know anything about microbes in the gut … It’s going to provide a lot of basic science that is going to be essential for the future of this field,” she adds.
In addition to laying the foundation for studying lipids in the gut, the collection, classification, and preservation of gut bacterial species in pure cultures may be important for human health in the future.
“This is an invisible biodiversity we are neglecting to preserve … we want to make sure that the [bacterial] legacies we leave behind are at least as good as the ones we inherited.”
A herder overlooks his livestock from the pastoral Datoga community. Photo credit: Christopher Corzett
NASA’s Curiosity rover has found evidence of complex organic matter preserved in the topmost layers of the Martian surface, scientists report today in the journal Science.
While the new results are far from a confirmation of life on Mars, scientists believe they support earlier hypotheses that the Red Planet was once clement and habitable for microbial life. However, whether such life ever existed on Mars remains the big unknown.
Since Curiosity landed on Mars in 2012, the rover has been exploring Gale Crater, a massive impact crater roughly the size of Connecticut and Rhode Island, for geological and chemical evidence of the chemical elements and other conditions necessary to sustain life. Almost exactly a year ago, NASA reported the discovery of such evidence in the form of an ancient lake that would have been suitable for microbial life to not only survive but flourish.
Now, scientists have found signs of complex, macromolecular organic matter in samples of the crater’s 3-billion-year-old mudstones — layers of mud and clay that are typically deposited on the floors of ancient lakes. Curiosity sampled mudstone in the top 5 centimeters from the Mojave and Confidence Hills localities within Gale Crater. The rover’s onboard Sample Analysis at Mars (SAM) instrument analyzed the samples by heating then in an oven under a flow of helium. Gases released from the samples at temperatures over 500 degrees Celsius were carried by the helium flow directly into a mass spectrometer. Based on the masses of the detected gases, the scientists could determine that the complex organic matter consisted of aromatic and aliphatic components including sulfur-containing species such as thiophenes.
MIT News checked in with SAM team member Roger Summons, the Schlumberger Professor of Geobiology in the Department of Earth, Atmospheric and Planetary Sciences, and a co-author on the Science paper, about what the team’s findings might mean for the possibility of life on Mars.
Q: What organic molecules did you find, and how do they compare with anything that is found or produced on Earth?
A: The new Curiosity study is different from the previous reports that identified small molecules composed of carbon, hydrogen, and chlorine. Instead, SAM detected fragments of much larger molecules that had been broken up during the high-temperature heating experiment. Thus, SAM has detected “macromolecular organic matter” otherwise known as kerogen. Kerogen is a name given to organic material that is present in rocks and in carbonaceous meteorites. It is generally present as small particles that are chemically complex with no easily identified chemical entities. One analogy I use is that it is something like finding very finely powdered coal-like material distributed through a rock. Except that there were no trees on Mars, so it is not coal. Just coal-like.
The problem with comparing it to anything on Earth is that Curiosity does not have the highly sophisticated tools we have in our labs that would allow a deeper evaluation of the chemical structure. All we can say from the data is that there is complex organic matter similar to what is found in many equivalent aged rocks on the Earth.
Q: What could be the possible sources for these organic molecules, biological or otherwise?
A: We cannot say anything about its origin. The significance of the finding, however, is that the results show organic matter can be preserved in Mars surface sediments. Previously, some scientists have said it would be destroyed by the oxidation processes that are active at Mars’ surface. It is also significant because it validates plans to return samples from Mars to Earth for further study.
Q: The Curiosity rover found the first definitive evidence of organic matter on Mars in 2014. Now with these new results, what does this all say about the possibility that there is, or was life on Mars?
A: Yes, previously, Curiosity found small organic molecules containing carbon, hydrogen, and chlorine. Again, without having a Mars rock in a laboratory on Earth for more detailed study, we cannot say what processes formed these molecules and whether they formed on Mars or somewhere in the interstellar medium and were transported in the form of carbonaceous meteorites. Unfortunately, the new findings do not allow us to say anything about the presence or absence of life on Mars now or in the past. On the other hand, the finding that complex organic matter can be preserved there for more than 3 billion years is a very encouraging sign for future exploration. “Preservation” is the key word, here. It means that, one day, there is potential for more sophisticated instrumentation to detect a wider range of compounds in Mars samples, including the sorts of molecules made by living organisms, such as lipids, amino acids, sugars, or even nucleobases.
The original article appeared in MIT News on June 7, 2018.
Source: Jennifer Chu, MIT News
Dr. Ainara Sistiaga from the Summons Lab was recently interviewed by Horizon Magazine on the evolution of human diets.
By studying mummies, researchers want to establish how our gut bacteria has changed over time. Image credit – ‘MNH – Mumie Frau 1’ by Wolfgang Sauber is licenced under CC-S.A 3.0
Mummified bodies from Egypt and the Canary Islands are having their digestive tracts tested and compared to living people in order to reveal how the bacteria in our guts has changed over the centuries and how it varies between people with different diets.
It’s part of a recent wave of research into what’s known as the gut microbiome – the collection of bacteria that live in our digestive system – which also includes looking at how these bacteria influence obesity. It is thought that the more diverse the mix of bacteria in your gut, the healthier you are.
“Western populations have already lost 30 % of the biodiversity of their gut microbiome,” said Spanish scientist Dr Ainara Sistiaga. She is examining mummies from Egypt and the Canary Islands to better understand the microbiome of our ancestors.
“We are discovering every day how important our microbiome is to our biology, even our mood, and many diseases are related to gut bacteria,” said Dr Sistiaga.
Yet little is known about how this vital microbial cargo changed during our evolution and as we moved from being hunter-gatherers to farmers and to a diet rich in processed food. It could be hugely beneficial to know what sorts of bacteria lived inside our ancestors and what we have lost, says Dr Sistiaga.
Right now scientists do not have the tools to understand the microbiome of people from bygone times, but this is a goal of Dr Sistiaga’s EU-funded research project, MIND THE GUT. She will search for tell-tale lipid compounds, proteins and DNA from bacteria in the bodies of mummies and people today.
“Lipids stay around for longer and might tell us which gut bacteria were around,” explained Dr Sistiaga, who is affiliated with the Massachusetts Institute of Technology, in the US, and the University of Copenhagen, Denmark.
She will study two types of mummies. First, she’ll take small samples from the gut of mummies preserved on the Canary Islands which date from before the Spanish conquest of the 15th century. Those from the island of Tenerife were pastoralists, while those from Gran Canaria were likely farmers. They mostly date from between the 9th and 13th century.
The other type are Nubian mummies from Egypt in the British Museum who were people who died in the Nubian desert around the 9th to 10th century and were naturally mummified by the dry conditions there.
Dr Sistiaga will compare the microbiome of mummies to the hunter-gathering Hadza group living in Tanzania and a separate pastoralist community called Datoga living nearby. “This study will help us understand what a healthy microbiome is and how it adapts to different environments, diets and lifestyles,” she said. She previously studied organic compounds from Neanderthal waste, which showed that they ate plants.
Health lessons for modern times might come from this bio-archaeology project, which will also examine human waste to identify signatures, or biochemical markers, from the gut microbiome.
“The main goal though is to provide tools to better understand our ancestral microbiome,” said Dr Sistiaga. “Some traditional populations still have strains that help them face challenges, such as extreme cold or rotten food or other difficult situations. If we can get more information on the benefits of all these bacteria, we might be able to be more resilient to challenges ourselves.”
Each of us carries in our gut a two-kilo microbial horde that is part and parcel of our biology. The work of these microorganisms – which could number 100 trillion individual cells – is recognised as essential to our health.
Scientists have learned that you can either host a diverse and healthy collection of intestinal bugs or perhaps a more minimalist, unhealthy collection. A high-fat Western diet can encourage an unhealthy microbiome, which often is found in those who are overweight. Worryingly, this situation is linked to diabetes, high blood pressure, inflammation and cardiovascular disease. Therefore, anything we can do to promote healthy bugs in our guts is a plus.
Those who eat lots of fruit and vegetables carry around lots of an odd-sounding intestinal bacterium, Akkermansia muciniphila. This mucus-eating bug was first isolated in 2004 by a team working under Professor Willem de Vos at Wageningen University in the Netherlands. It makes up 5 % of bugs in a healthy gut, but in overweight people, it can be almost entirely absent.
“This bacteria lives close to intestinal cells in the colon,” said Professor Patrice D. Cani at the Université catholique de Louvain, in Belgium.
What makes this bug truly interesting is what happens when it is fed to obese mice. It reduces their weight gain, cuts down on their bad cholesterol and dampens inflammation. Human studies hint at benefits too: obese people with more of this bacteria in their gut at the start of a six-week diet displayed better metabolic and heart health readings at the end.
Prof. Cani is now running an EU-supported trial – Microbes4U – to see if feeding this bacteria to people improves health metrics such as blood sugar, cholesterol levels and low-grade inflammation. Patients consume the bacteria daily for 12 weeks and are monitored for safety and tolerance first, then weight gain or loss, inflammation, circulating fats and insulin resistance.
They receive a sachet that contains either a placebo, one billion or 10 billion living bacteria, or 10 billion pasteurised bacteria. Prof. Cani and Prof. de Vos previously reported that pasteurisation boosted the effectiveness of A. muciniphila in reducing fat gain and controlling blood sugar levels in mice. The trial aims to gain insights for a larger study.
There is already much evidence that diet impacts the gut microbiome. “A diet high in dietary fibre, fruits and vegetables contain compounds like polyphenols that we know are food for our microbes,” Prof. Cani said.
Worryingly, an unhealthy microbiome chips away at our gut barrier. “The change caused by a high-fat, low-fibre diet changes the gut microbiome and causes leakage of some bacteria and pro-inflammatory compounds into the blood,” Prof. Cani explained.
The weakened gut barrier allows compounds to leak into the blood that ramp up inflammation and are linked to metabolic syndrome: high blood sugar, abnormal cholesterol and high body fat. This increases your risk of heart disease, stroke and diabetes.
Anything that lessens this unhealthy cycle would be a huge gain for the health of European citizens. “We do not claim that this one bacteria can reverse obesity,” Prof. Cani said. “But even reducing cholesterol in people would be a success.” Strong scientific evidence would be needed before the bug could be used to boost health, most likely as a food supplement.
Provided by: Horizon: The EU Research & Innovation Magazine
(The photographs above showing the location (a) and detail of the preserved uropygial gland (b: before sampling in the unprepared fossil; c: after sampling in the prepared fossil.)
A recent study by postdoc fellow Shane O’Reilly from Summons Lab on fossil organic molecules provides palaeontologists with important new insight into how animal soft tissues fossilize and the importance of fats,or lipids, in that process.
The analysis of particularly well-preserved preen gland from a 48-million-year-old bird fossil has resulted in the discovery of original wax molecules within it. The research, led by former EAPS postdoc fellow Shane O’Reilly (now at University College Dublin) and MIT Professor Roger Summons, collaborating with researchers in the School of Biological Sciences at the University of Bristol in the United Kingdom, and the Senckenberg Natural History museum in Frankfurt, Germany, is published today in Proceedings of the Royal Society B.
The fossil O’Reilly and Summons analysed is from the famous Messel locality in Germany, a trove of fossils from the Eocene and a place well known for the exceptional detail of its preserved birds, mammals, fish, reptiles, insects and plants.
In particular, the site is famous for the preservation of melanin seen in many of the animals found there and even the structural iridescence of beetle and moth fossils. Finding intact avian preening glands and the wax molecules within them, however, is an exciting new development.
Birds use their preening glands in maintaining their feathers. By secreting an oily substance onto their bill, the action of preening helps make feathers more waterproof, maintain their health and durability and even protect them from microbial degradation.
Jakob Vinther, a palaeobiologist, has been working for a long time with researchers at the Senckenberg Natural History museum in Frankfurt, Germany, on the preservation of melanin in birds and mammals from the Messel Shale. An ornithologist at the museum, Gerald Mayr, had noted preservation of the preening glands in some birds from Messel and together they realized that if wax from a fossilized gland could be extracted and analysed it would help shed light on how the gland came to be preserved. “Usually, only melanin is preserved in these sorts of fossils; all the keratin and other proteins are lost,” Vinther says. “We know that some fats, or lipids, may be preserved as they have been observed in extracts of sediments and fossil plants. We could therefore expect to find that the waxy material could be extremely well preserved and give us new insights into what may also preserve in vertebrate fossils.” However, at that time, to aid in their conservation, all previously collected samples of fossilized preening glands had been embedded in resin plates coated with varnish, complicating analysis.
So, when a field crew from Senckenberg working to excavate in Messel discovered a new bird fossil containing a preserved wax gland Vinther immediately contacted his colleague at the Massachusetts Institute of Technology (MIT), Roger Summons, and a postdoc in his lab, Shane O’Reilly, who were equally excited to undertake the study of the fossil bird wax.
The Senckenberg preparator, Michael Ackermann, painstakingly collected the fossilised wax, (which could be scooped out of the fossil “like cold butter”) and carefully wrapped it in sterile aluminium foil for the journey to MIT.
When the material was analysed in the Summons Lab alongside control samples from the sediment and the preserved feathers associated with the bird fossil, a clear pattern emerged: the preening gland preserved the waxy molecules produced by the bird in beautiful detail.
“By studying the molecular fossils within the fossil, and picking out the molecules coming from the sediment, we could clearly see that a portion of the original molecules that make up preen oil were preserved within the fossil gland” said O’Reilly.
The sediment that hosts the fossil is a so-called oil shale, was full of various fossil lipid molecules from dead plant and algal matter, while the lipids from the preening gland contained longer carbon chain lengths that the ones in the surrounding sediment and even more complex structures that were entirely absent from the sediment.
The next step in this work will be to look for fossil preening glands in dinosaurs. “The research is a milestone for palaeontologists.” Vintner says. “We have discovered preserved wax material in a bird and it is likely that we can look for the origin of this important gland and see if dinosaurs also used oil glands to preen their feathers.”
Article Source: Shane O’Reilly, Roger Summons, Gerald Mayr and Jakob Vinther (2017), Preservation of uropygial gland lipids in a 48-million-year-old bird, Proc. R. Soc. B 20171050, doi: 10.1098/rspb.2017.1050
Dr. Xiaolei Liu has been a postdoctoral associate and a research scientist in Roger’s lab for the last 3 years. Xiaolei received his PhD degree at the University of Bremen with Dr. Kai-Uwe Hinrichs. Afterwards, he continued in the same lab before joining the Summons Lab in 2014. Xiaolei has contributed significantly to this lab and has helped manage the lab since 2016. Xiaolei recently accepted the offer from the University of Oklahoma (OU) to be a tenure-track professor. http://www.ou.edu/mcee/geology/people/faculty/xiaolei_liu.html. The Summons Lab wishes him all the best with his new career.
Dr. Xiaowen Zhang received her PhD in 2017. She pioneered the use of compound specific radiocarbon analysis in tracking permafrost thawing in the past. She also worked on permafrost thawing in Arctic Alaska and the associated climatic feedbacks. After completing her PhD, she joined the Summons Lab. For her postdoctoral research, she will primarily focus on the abiotic synthesis of lipids. Her research could potentially answer how the earliest lipids were synthesized on Earth.
Angel Mojarro is a new PhD student, co-advised by Roger Summons and Maria Zuber. His research is focused on human exploration and the search for life of Mars. In Summons Lab, he will analyze organic molecules from rock/soil samples and extract information about life from them.
The front cover of the latest issue of Journal Applied and Environmental Microbiology featured the research work from Summons Lab on the synthesis of methylated hopanoids by cyanobacterium Nostoc punctiforme ATCC 29133S. This work discovered that by deleting the hpnP gene, Nostoc Punctiforme is not able to synthesize all 2-methylhopanoids, however, it produces much higher levels of two bacteriohopanepentol isomers than the wild type. The ΔhpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the ΔhpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions.
Cover photograph: Scanning electron micrograph of the cyanobacterium Nostoc punctiforme ATCC 29133S forming akinetes (resting cells that are larger and rounder in morphology) under conditions of phosphate deprivation. N. punctiforme has a complex life cycle, in which, based on environmental signals, vegetative cells can differentiate into N2-fixing heterocysts, akinetes, or motile hormogonia. N. punctiforme ATCC 29133 was originally isolated from a symbiotic association with the gymnosperm cycad Macrozamia sp.; the 29133S strain is a spontaneous mutant that grows more rapidly and homogenously in liquid, producing slow hormogonia. (See related article at e00777–17.) (Copyright © 2017 American Society for Microbiology. All Rights Reserved.)
Summons Lab recent research features two publications in Nature and PNAS with funding support from the Simons Foundation Origins of Life Collaboration program.
Recently, David Gold published his paper entitled “Paleoproterozoic sterol biosynthesis and the rise of oxygen” in Nature. Sterol biosynthesis signals aerobic metabolic processes by eukaryotes. However, there has been debates on the earliest emergence of eukaryotes, with time ranging from Archean to meso-proterozoic. Here, he used a molecular clock approach to improve constrains on the evolution of sterol biosynthesis. He found the maximum marginal probability for eukaryal sterol biosynthesis genes is around 2.31 Gyr ago, in align with the evidence of the Great Oxidation Event. This study further indicated that the simple sterol biosynthesis existed well before the diversification of eukaryotes and is tied to the first widespread availability of molecular oxygen in the ocean-atmosphere system.
Gareth Izon published his work entitled “Biological regulation of atmosphere chemistry en route to planetary oxygenation” in PNAS and provided us evidence on the presence of organic-haze pre-GOE. It has been proposed that enhanced methane fluxes to Earth’s early atmosphere could have altered atmospheric chemistry, initiating a hydrocarbon-rich haze reminiscent of Saturn’s moon, Titan. In this study, he tested and refined the “haze hypothesis” to refine the structure and timing of haze development. The persistence of haze requires a sustained biological driver, with methane fluxes controlled by the relative availability of organic carbon and sulfate. This study implied that the presence of haze could have had a significant impact on the escape of hydrogen from the atmosphere, contributing to the terminal oxidation ~2.4 GYr ago.
Summons Lab group retreat was held in Jackson, NH. This lab retreat brought together most of current lab members and a former lab member, Shane O’Reilly. Everyone shared their on-going research, all with common objectives in attempting to better understand earth history. Topics were broad and spanned origin of life to modern biogeochemical processes. The group retreat was very successful and it was clear that all involved got insights and ideas from the presentations.
Ainara giving presentation on seeking new biomarkers to understand the role of gut microbiome in human evolution
Everyone is happy about the snow.
Dr. Ross Williams has been a PhD researcher in Roger’s lab for the last 5 years. Ross recently received his PhD degree in Geochemistry at MIT. His research focus has been on paleoenvironment reconstruction in extreme climates ranging from Early Cenozoic lignite deposits in India to modern day high elevation lakes of the Chilean Altiplano. Ross has recently accepted a Postdoctoral position through the Center for Research and Exploration in Space Science & Technology (CRESST) at NASA Goddard Space Flight Center in Maryland. There he will work on supporting the Sample Analysis at Mars (SAM) investigation on the Mars Science Laboratory (MSL). Ross has also recently welcomed a new family member into the world, his adorable son Hendrick Ross Williams. Ross, Hendrick, and his beautiful wife Christina are looking forward to the next chapter of their lives in Maryland. Ross has been a dedicated and valued colleague and friend, and he will be greatly missed by all!
Dr. Shane O’Reilly is a Postdoctoral Fellow who has been in Roger’s lab since 2014. Shane has received a competitive Marie Curie fellowship with a joint appointment with the University College in Dublin, where he will continue his research fellowship for an additional year after his tenure at MIT. Shane’s research involves the use of lipids and next generation sequencing approaches to study microbial communities associated with marine and terrestrial carbonate deposits and the fossil lipids that can be preserved within these carbonate over geologic time. These include ooids, tufa and pisoids. Shane has also been involved in a number of projects studying exceptional preservation of organic molecules in vertebrate fossils, including Messel birds and mammoth bones. He also contributed to astrobiology projects relating to the analog experiments to understand the Curiosity Rover’s detection of organic molecules on Mars. Shane has been an outstanding colleague and friend to all members of the Summons lab, and will be greatly missed!
Yongli Zhou is an undergraduate researcher from University of Science and Technology of China who has been in the Summons laboratory for a 3 month summer internship. Yongi has been a highly motivated and productive student, and his research has focused on characterizing fossilized plant lipids at an ancient site in Africa, and preserved functionalized lipids in mammoth bone fossils. Yongli will be considering graduate school opportunities in the future, and will have a bright and promising future in research. All members of the Summons lab have greatly enjoyed having Yongli in the lab during his visit, and he will be missed!
The Gordon Research Conference Organic Geochemistry meeting was held at Holderness School in Holderness, New Hampshire from July 24th – July 29th, 2016. The conference was chaired by Anne Pearson, and Lloyd Snowdon served as the vice chair. Many who attend this meeting will agree that the quality of science and unique “campy” experience in Holderness makes this GRC one of the most pleasurable to attend. The conference is held every two years, and since 1970 has traditionally been held in the same venue. Holderness is located in the heart of New Hampshire’s Lakes Regions, and includes 600 acres of woodlands, open fields, trails, and a river. The afternoons are open during the conference to encourage recreational activities. This year, the meeting topics were focused on using advanced technologies to address current and future societal challenges. The itinerary was packed with fascinating talks and poster sessions from scientists across a breadth of disciplines in the field of organic geochemistry. Representatives from the Summons lab who participated included Roger, Xialei, Ainara, Emily, and Heather.