14 November 2017

“Mummies” tummies to reveal digestive evolution


Dr. Ainara Sistiaga from 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  – 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 ,” 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  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

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 , 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  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.

Read more at: https://phys.org/news/2017-11-mummies-tummies-reveal-digestive-evolution.html#jCp

Provided by: Horizon: The EU Research & Innovation Magazine

14 November 2017

48-Million-Year-Old Wax Discovered in a Bird Fossil




(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


Adapted from EAPS News and the University of Bristol press release


18 September 2017

The Summons Lab bids farewell to a talented lab member and welcomes several new members


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.


23 June 2017

Latest Summons Lab Research


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 image

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.)

15 March 2017

Summons Lab Latest Research Highlights


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.


11 March 2017

Summons Lab 2017 Retreat


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.

15 September 2016

The Summons Lab bids farewell to several talented and valuable lab members!


RossPicpdfDr. 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!

12 August 2016

GRC Organic Geochemistry meeting 2016 in Holderness, NH


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.


13 July 2016

Latest Summons Lab Research


From the origin’s of complex life to the timing of oxygen’s first appearance in the atmosphere, the Summons lab has published a number of exciting and important papers in recent weeks.

David recently published his combined biomarker and genomic study in PNAS. Here, he presented conclusive evidence that sea sponges were indeed the source of the unusual biomarkers in 640 million year old rocks. This ‘sponge biomarker hypothesis’ was first proposed by Roger and co-workers, and this new work provides further evidence that sea sponges were one of the earliest animals on the scene on Earth. Read more about this in a number of media outlets such as The Independent, Newser, Boston CBS, TechTimes and MIT News.

In May in Scientific Advances, Genming published evidence for a rapid oxygenation of Earth’s atmosphere 2.33 billion years ago and a precise constraint on the timing of the Great Oxidation Event (known as the GOE). Media coverage for this include the Air & Space Magazine published by the Smithsonian, Phys.org, and MIT News.

Xiaolei recently published two papers providing significant advances in our knowledge of the diagenetic fate and structural diversity of glycerol dialkyl glycerol tetraether lipids. He published his work in the journals Geochimica et Cosmochimica Acta and Rapid Communications in Mass Spectrometry. Xiaolei’s work involved collaborations with members of the Bosak Lab in MIT and the Hinrich’s Lab in Bremen.

In June, Shane published a paper in Geobiology studying ooids from The Bahamas. Ooids are accretionary carbonate grains that occur in many Precambrian and Phanerozoic rocks, and provide an insight into the environmental/depositional conditions and seawater chemistry in marine environments through time. However, the formation of these enigmatic grains is actively debated. In this paper, Shane demonstrates that the major source of organic matter within ooids is from benthic microbial biofilms. Organic matter bound within ooid grains is old and altered, having been subject to microbial decomposition, likely under reducing conditions. The association of bacteria and these molecular signals with ooid carbonate crystals suggests that these biological processes may contribute to ooid formation.

10 April 2016

Cambridge Science Festival!



The Cambridge Science Festival is fast approaching us! Starting on Friday April 15th, the festival is an annual 10-day celebration of science, technology, engineering, art and math in Cambridge and beyond. Collaborators for the festival include MIT, Harvard University, the City of Cambridge and the Museum of Science. Every spring, the festival makes science accessible, engaging and fun for everyone through a host of exhibitions, activities and multicultural events. This year the festival is celebrating its 10th anniversary, and it promises to be a memorable one. The Summons Lab will be actively involved, together with other members of MIT EAPS department and the NAI Astrobiology Team Foundations for Complex Life.

The Science Carnival & Robot Zoo will happen on Saturday, April 16. This is an action-packed free carnival with science and technology exhibitors from around the globe. The Summons Lab and the NASA Astrobiology Institute Foundations for Complex Life time will have two stands side by side. We will be inviting everyone to come along and take their shot at the recently developed app game ‘Earth History in 60 Seconds’. This is an exciting, fast-paced, multiplayer game testing your knowledge of major events in Earth’s long history in 60 seconds! The app is available for download on iTunes here. We will also be providing an interactive demonstration and discussion of the amazing science of ‘molecular fossils’. Roll your sleeves up and join us for a molecular fossil hunt! The carnival will be on at the Cambridge Rindge & Latin Field House, Cambridge Public Library, Broadway and Ellery Street. It will run from 12:00-4:00pm.

Christy Grettenberger will be leading guided tours of ‘A Walk Through Geologic Time’. Earth’s history stretches back over 4.567 billion years—how are we supposed to grasp such a vast number? We’ve shrunken it down to a third of a mile along the Charles River, and invite you to join us on a walk through time to tour the many incredible events during Earth’s long and storied history. The tours will run on April 15th & 16th at 5:30 pm, and on April 17th at 11 am and 5:30 pm. All tours will meet at the intersection of Mass. Ave. and Memorial Drive (MIT side), lasts approximately 45 minutes and are totally FREE!

Shane will be given a science outreach talk for CafeSci Boston (presented by NOVA). His talk is titled ‘Hunting for fossil fat in Earth’s History’. The event will be held at Le Laboratoire (650 East Kendall Street) on Tuesday 19th April from 7 to 8pm. The talk is free, informal and open to the public. Here is a link to the event on Eventbrite and Boston Calendar.

Check out the full list of events for the Cambridge Science Festival on the festival website and the blog. A detailed calendar of events is available here.