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A comprehensive catalogue of human digestive tract bacteria

A comprehensive catalogue of human digestive tract bacteria

The human digestive tract is home to thousands of different strains of bacteria. Many of these are beneficial, while others contribute to health problems such as inflammatory bowel disease. Researchers from MIT and the Broad Institute have now isolated and preserved samples of nearly 8,000 of these strains, while also clarifying their genetic and metabolic context.

This data set (BIO-ML), which is available to other researchers who want to use it, should help to shed light on the dynamics of microbial populations in the human gut and may help scientists develop new treatments for a variety of diseases, says Eric Alm, director of MIT’s Center for Microbiome Informatics and Therapeutics and a professor of biological engineering and of civil and environmental engineering at MIT.

“There’s a lot of excitement in the microbiome field because there are associations between these bacteria and health and disease. But we’re lacking in being able to understand why that is, what’s the mechanism, and what are the functions of those bacteria that are causing them to associate with disease,” says Alm, who is the senior author of the study.

The researchers collected stool samples from about 90 people, for up to two years, allowing them to gain insight into how microbial populations change over time within individuals. This study focused on people living in the Boston area, but the research team is now gathering a larger diversity of samples from around the globe, in hopes of preserving microbial strains not found in people living in industrialized societies.

“More than ever before, modern techniques allow us to isolate previously uncultured human gut bacteria. Exploring this genetic and functional diversity is fascinating — everywhere we look, we discover new things. I’m convinced that enriching biobanks with a large diversity of strains from individuals living diverse lifestyles is essential for future advancements in human microbiome research,” says Mathilde Poyet, a senior postdoc at MIT and one of the lead authors of the study.

MIT research associate Mathieu Groussin and former postdoc Sean Gibbons are also lead authors of the study, which appears in the Sept. 2 issue of Nature Medicine. Ramnik Xavier, a professor of medicine at Harvard Medical School and member of the Broad Institute, is a senior author of the study along with Alm.

Microbiome dynamics

Humans have trillions of bacterial cells in their digestive tracts, and while scientists believe that these populations change and evolve over time, there has been little opportunity to observe this. Through the OpenBiome organization, which collects stool samples for research and therapeutic purposes, Alm and his colleagues at MIT and the Broad Institute had access to fecal samples from about 90 people.

For most of their analysis, the researchers focused on microbes found in about a dozen individuals who had provided samples over an extended period, up to two years.

“That was a unique opportunity, and we thought that would be a great set of individuals to really try to dig down and characterize the microbial populations more thoroughly,” Alm says. “To date there hadn’t been a ton of longitudinal studies, and we wanted to make that a key focus of our study, so we could understand what the variation is day-to-day.”

The researchers were able to isolate a total of 7,758 strains from the six major phyla of bacteria that dominate the human GI tract. For 3,632 of these strains, the researchers sequenced their full genomes, and they also sequenced partial genomes of the remaining strains.

Analyzing how microbial populations changed over time within single hosts allowed the researchers to discover some novel interactions between strains. In one case, the researchers found three related strains of Bacteroides vulgatus coexisting within a host, all of which appeared to have diverged from one ancestor strain within the host. In another case, one strain of Turicibacter sanguinis completely replaced a related strain of the same species nearly overnight.

“This is the first time we’re getting a glimpse of these really different dynamics,” Alm says.

Population variation

The researchers also measured the quantities of many metabolites found in the stool samples. This analysis revealed that variations in amino acid levels were closely linked with changes in microbial populations over time within a single person. However, differences between the composition of microbial populations in different people were more closely associated with varying levels of bile acids, which help with digestion.

The researchers don’t know exactly what produces these differences in amino acid and bile acid levels, but say they could be influenced by diet — a connection that they hope to investigate in future studies. They have also made all of their data available online and are offering samples of the strains of bacteria they isolated, allowing other scientists to study the functions of these strains and their potential roles in human health.

“Comprehensive and high-resolution collections of bacterial isolates open the possibility to mechanistically investigate how our lifestyle shapes our gut microbiome, metabolism, and inflammation. We aim to provide such a resource to the research community worldwide, including to lower-income research institutions,” Groussin says.

The researchers have also begun a larger-scale project to collect microbiome samples from a greater diversity of populations around the world. They are especially focusing on underrepresented populations who live in nonindustrialized societies, as their diet and microbiomes are expected to be very different from those of people living in industrialized societies.

“It may be that as populations that have been living traditional lifestyles start to switch to a more industrialized lifestyle, they may lose a lot of that biodiversity. So one of the main things we want to do is conserve it, and then later we can go back and characterize it as well,” Alm says.

Materials provided by Massachusetts Institute of Technology

graphene structure

Researchers demonstrate production of graphene using bacteria

Researchers have figured out a novel method to produce graphene, an amazing substance in a cheaper way with the help of bacteria. Graphene is a very useful material in filtering water, dyeing hair and great strengthening of substances. The study has been published in ChemistryOpen.

When the bacterium Shewanella oneidensis is mixed with oxidized graphite or graphene oxide (which is comparatively easy to produce but not conductive due to oxygen groups), the oxygen groups are withdrawn and conductive graphene is obtained as the product. It is inexpensive, quicker and more eco-friendly than the existing methods to produce the substance. It can also be stored for a long period of time making it appropriate for various applications. Using this method, we can produce graphene at a scale required for computing and medical devices of the next generation.

“For real applications, you need large amounts,” says biologist Anne Meyer from the University of Rochester in New York.

Using the new method, Meyer and her colleagues were able to make graphene that’s thinner, more stable, and longer-lasting than graphene that’s produced by chemical manufacturing. This will unlock all sort of opportunities for less costly bacteria-produced graphene and can be used in field-effect transistor (FET) biosensors.  It is a tool that identifies specific biological molecule such as glucose tracking for diabetics.

Bacteria production method leaves back specific oxygen group. It makes resulting graphene compatible to link with specific molecules. Graphene material obtained from this method can be used as conductive ink in circuit boards, computer keyboards or in small wires to unfreeze car windscreen or to produce one-sided conductive graphene by twisting the bacteria process. It can also lead to the creation of innovative computer technologies and medical equipment.

At present, graphene is produced by different chemical methods using graphite or graphene oxide compared to the past method where graphite was extracted by graphite blocks using sticky tape. The new method of production is the most favorable one to date without the use of unpleasant chemicals. Prior to scaling up and using it to develop next-generation devices, lots of research needs to be done to study the bacteria process. However, the future of this extraordinary material continues to look bright. Meyer said that bacterially produced graphene material will guide to much better applicability for product development and development of nanocomposite materials.

Journal: https://onlinelibrary.wiley.com/doi/full/10.1002/open.201900186

The newly described stone eating shipworm, known as Lithoredo abatanica.

Researchers discover stone eating creatures in Philippines

Researchers associated with numerous institutions across the U.S. have discovered a rare species of shipworms named Lithoredo abatanica that feeds on rocks and stones instead of woods. They published a paper in the Proceedings of the Royal Society B and described their study and the discovery.

The shipworms are water-dwelling mollusks which are known due to their ability to chew the wood and digest it. They are also popular for creating holes in wooden structures present in water and now, the researchers claim to have discovered a species of these shipworms that do not feed on wood at all but eats the limestone instead.

After breaking through the rocks to get a specimen of these worms, they reported their small size of 150mm and their close resemblance to worms than other mollusks. Unlike the wood-eating shipworms, these worms have large, flat teeth that could scrape away rocks unlike, sharp invisible teeth of the wood eater ship worms which could cover the shells and lacked the sac which was used to digest these woods. In addition to this, these shipworms were also found to excrete sand. Researchers, however, cannot determine any motive behind their rock eating nature but say that it does not impart any nutritional value.

These ship worms which eat rocks have the tendency to change the course of rivers as well. These shipworms have extremely shrunken shells, two in number which is modified into drill like heads.

The regular wood eating marine ship worms store the wood that they eat in a very special digestive sac which they ingest and scrape away to make a protective burrow for itself. The rock-eating ship worms do the same except that they differ from the usual ones in the fact that they lack the sac.

The rock-eating ship worms rely on the bacteria that reside in their gills to produce nutrients and food which is sucked in by this newly existing shipworms from the hind end for nourishment. The gills found in the stone-eating shipworms are quite larger than normal, which shows that they are important for their survival. Researchers are working on how their metabolism works.

E coli with synthetic DNA

Scientists successfully create first living organism with synthetic DNA

By the earnest effort of scientists, the world’s first ever living organism with completely synthetic DNA has been created. The ambitious project finally proved that life can exist in certain controlled conditions. This can be used to make drugs such as insulin for diabetes and other medical compounds for multiple sclerosis, heart attacks and eye diseases.

Since the inception of heredity and evolution, life on earth shares a common code of resemblance that’s called DNA. The four nucleic acid letters of adenine, cytosine, guanine and thymine– or A, C, G and T can be strung into 64 combinations of 3 letters called codons.

Nearly, in all life forms from jellyfish to humans, there are 64 codons. But many of them do the same job. In total, 20 amino acids which are natural are synthesised by 61 codons, which can be binded together like a necklace. Three more codons are in effect stop signs. They inform the cell when the protein is done like a full stop mark marking the ending of a sentence.

The Laboratory of Molecular Biology of Medical Research Council in Cambridge, read and redesigned the DNA of the bacterium E.Coli. Experts were in a fix whether it would be possible or not. The Cambridge team worked hard to redesign the E.coli genome by going through its DNA while working on a computer. Scientists made a whopping 18000 edits to the DNA, stitched the whole DNA together and exchanged it with the original DNA of the bacteria. The result was a microbe with a completely synthetic and radically altered DNA code known as SYN61. The bug was showing unusual characteristics such as a little longer than normal while showing slower growth.

This edited variation SYN61 isn’t quite a red alert for its ancestors as the cells were a touch longer and were virus resistant. Now, it can be thought that how it would act as a resistance to a virus. The answer is simple, as their DNA is different, invading viruses will struggle to spread inside them making them virus resistant.

Efforts were made earlier too like the bug Mycoplasma Mycoides but it has smaller genome than E Coli and was also not redesigned. But as “records are made to be broken” and in that sense, other researchers are persistently working on bacterial genomes with more coding changes.

Finally, scientists have taken the field of synthetic genomes to a new level by building the largest ever synthetic genome to date. It is a landmark step of completely novel life form. The invention of this remarkable life will be a milestone in the history of heredity and evolution.

Would you like to get your gene edited and get some changes in your body? Tell us what changes would you like to get with a quick and short comment.

Pseudomonas aeruginosa SEM

Scientists turn bacteria as an instrument for measuring fluid speeds

A group of researchers from Princeton University has detected bacteria which has the ability to find the speed of fluids in motion. There are many different types of cells which can sense flow similar to the skin cells in human beings. The research has been published in Nature journal.

Zemer Gitai, a biology professor and a senior author on the research paper of Princeton’s Edwin Grant Conklin University said that they have discovered that bacteria can also be used for detecting speed and also added that there’s an application where we can use the bacteria as a flow sensor and we can know the speed in real time. Pseudomonas aeruginosa is that bacteria which have a built-in speedometer.

Pseudomonas is the bacteria which is responsible for health issues and healthcare-related infections per year and this ubiquitous pathogen is found in and on the bodies, in the soil, in the streams of water and throughout the hospitals. This bacteria was found as a serious threat in the centre for disease control and prevention.

Gitai said that chemical disinfection is used instead of scrubbing in some hospitals since pseudomonas loves to grow in pipes. Pseudomonas is said to be surrounded by flowing fluids like the bloodstream, the urinary tract, the gastrointestinal tract as well as in the lungs or in plumbing systems or in medical equipment too like catheters which is one of the primary vectors used for post-surgical infections. Gitai also added that they have found something new about pseudomonas that they can also detect the flow and respond to it and they can change their attitude too.

A postdoctoral research associate in Gitai’s lab, Joseph Sanfilippo and a 2017 graduate alumnus Alexander Lorestani are the main authors on this paper. They together found out that the bacteria can detect the nearby flow of the genes too and those genes are known as fro which stands for flow-regulated operon. Sanfilippo said that fro is tuned as per the speed and it’s not just a switch to on and off but it’s more like a dimmer switch than a light switch.

The researchers created a link between the fro and gene so that they can see in the microscope and thus ended up creating visual speedometer and it is visualized using the light of the flow that is the brighter the glow the faster the flow and Gitai said that they found out something interesting that the speed range matched with the fluids present in the bloodstream of urinary tract.

The scientists found out that the rate of flow in average sized human veins are about 100 per second and they also found that the fro was not able to detect flows below 8 per second but it responded to the flow between 40 and 400 per-second and stay above that.

bacteriophage attack cell

Teenage girl saved from fatal infection by genetically engineered virus

In the 21st century, medical advancements have reached greater heights and continue to achieve new feats and higher levels of research has enabled scientists to scale greater heights in the field of medicine.

A recent medical case at the Great Ormond Street Hospital in London was a showcase of advances in medicinal science.  A pair of teenagers had cystic fibrosis, it is a disease where the lungs cannot clear mucus and disease-causing bacteria. They had undergone lung transplant and soon after which the infections that stayed in the body erupted from their sutures and soon these bacteria began to stain and spread over their skin through the skin tissues, doctors were giving antibiotics but they were of no use, as the body was not responding to them and the bacteria continued to spread. This is when phages came to rescue.

The history of phages dates back to the late 1990s where Graham Hatfull, a microbiologist of the University of Pittsburgh had the collection on bacteriophages which are viruses that prey solely on bacteria. These phages were stored at -80˚C in the university research lab. The boy, unfortunately, succumbed to his infection as it was too late however the girl was able to get the recovery and survived on the edge as her body parts were on the brink of organ failure. The infusion of the phage cocktail was first given to Isabelle in June 2018. Within 72 hours, her sores began to dry. After 6 weeks of intravenous treatment every 12 hours, the infection was all gone, soon she became back to her normal teenage life.

The two teenagers and their recovery became a case study which was published in the Journal Nature Medicine which represents the first ever use of engineered phages in a human patient. There is an emerging phase of synthetic biology which the disease researcher Eric Rubin of Harvard T.H School of Public Health commented that there is a need for rigorous testing of this before final implementation.

Phages typically kill a single bacterial strain which means if it works on one person it may not always work on the other person. Leading US universities have launched Phages research in their laboratories. There are claims that even if the treatment succeeds there are a lot of practical difficulties in the implementation. For further implementation, we also need to gauge the affordability factor of the treatment so people in all economic strata can afford this treatment.

 

Deepsea Challenger Pilot Sphere Interior

Researchers find oil-eating bacteria in Mariana Trench

A group of researchers from the University of East Anglia has found out a very unique bacteria which feeds on oil. They have observed this microorganism in the deepest portion of the oceans of Earth which is the Mariana Trench. Researchers from various parts of the world such as Russia and China also participated and they have made a very comprehensive analysis of the population of microbes on the ocean’s trench.

The Mariana Trench is situated in the western part of the Pacific Ocean and it is also the deepest natural trench on Earth. It appears as a crescent shaped moon on the Earth’s crust and the greatest depth is 10,994 metres which is also known as the Challenger Deep. On the other hand the height of Mount Everest is 8,848 metres.

Scientists believe that they know more about the conditions on Mars than the Mariana Trench. A reason is that till date very few expeditions have made a journey to the trench for studying the ecosystem and the inhabitant organisms. Perhaps the most famous of the expeditions is the one organised by famous marine explorer and Oscar winning film director James Cameron. He ordered a highly specialised submersible for collecting sample organisms from the trench.

Dr. Jonathan Todd who is in UEA’s School of Biological Sciences said that the research team collected various samples of the microbes at the deepest location in the Mariana Trench. After the analysis of the sample was done, the team identified a unique group of hydrocarbon degrading bacteria.

Hydrocarbons are basically organic compounds which are only composed of hydrogen and carbon atoms, as evident from the name. They are found in a wide variety of compounds all over the planet such as oil fields, manufacturing areas.

The microorganisms which were found mainly fed on the compounds which are similar to that of oil and then it was used for fuel. These similar microorganisms also played a role in decomposing the oil spills which occurred in the natural disasters such as the 2010 Oil Spill in Mexico Gulf. The bacteria has been found in a lot of abundance in the Mariana Trench or in other words, the proportion of hydrocarbon feeding bacteria on Earth is highest in the Mariana Trench.

A sample of the microbes was isolated for experimental purposes and it was found that if the similar conditions were simulated in the laboratories then they consumed the hydrocarbons even here. So, hydrocarbons are found even 6000 metres below the ocean surface level and even in the deepest places on Earth such as Mariana Trench. Hence this suggests that microbes are producing them even in such distinctive environments.

The results of the study have been published in the Microbiome journal.

Bacteria 3D Double Helix

Scientists able to create an entire genome set using programming algorithms

A team of researchers from ETH Zurich has reported about the creation of a bacterial genome entirely with the help of a computer algorithm. This report was published in the Proceedings of the National Academy of Sciences. The genome is named as Caulobacter ethensis-2.0. Although it is not yet a living microorganism it exists as a DNA bundle.

This new genome was created from the naturally occurring bacteria, Caulobacter Crescentus. It is usually found in spring waters, rivers, and several lakes. It is inherently harmless and thus used as a model creature in the laboratories. The bacteria’s genome has 4000 genes, but most of them are considered as “junk DNA” and around 680 are considered as essential to support its survival.

Apart from this, the gene set also contains several redundancies as many combinations of the amino acids and proteins which are assembled by the DNA often give the same result. As a result of this scientists created a program to find out the ideal DNA combination. The algorithm was able to fully rewrite the genome as a different DNA sequence which did not resemble the original one at all but was still able to perform the biological functions.

This research work is built on the work of Craig Venter, pioneer of American genetics. He was the first person to chemically synthesize the bacterial genome. This work took almost a decade to finish. The main difference between the work of Venter and the genome created by the algorithm is that the latest one contains a totally new set of genes whereas the former one was an exact copy.

Creating an entire set of bacteria genome totally from the beginning is a very complicated task to achieve. It requires very accurate calculations. The team started with a minimal gene set of the Caulobacter, and it created 236 genome segments from it. After this, the segments were tied together. This sounds like an easy task but it is very difficult to execute. It is very challenging as the DNA molecules can easily get stuck to each other and become twisted and messed up.

The natural world has inbuilt genetic redundancies because of which multiple genes can encode for a single protein. Because of this, the researchers used to rewrite the genome using absolutely unrelated genetic sequences and it still provided the same biological functions.

For testing the genome set, the team created several strains of bacteria using both the natural Caulobacter and the segments of the artificially created genome. When they removed the natural genes, it was found that 580 of the genes were still functional. Hence there is still some room for improvement before a fully functional artificial genome is produced.

international space station

Researchers find bacteria infested ISS to be as dirty as a gym

In a paper published in the Microbiome journal on Monday, researchers found that the International Space Station has become littered with microbes, namely Staphylococcus, Pantoea and Bacillus, that are found to carry numerous infectious diseases, and are very much capable of thriving in extreme conditions such as in a space station.

The ISS was built in 1998 and has been visited by approximately 222 astronauts with 6 re-supply missions nearly every year until August 2017. Every time an astronaut goes up to the station, they can potentially bring in bacteria allowing to thrive within the sealed space station. Though the capsules that astronauts travel are built in sterile environments before they are sent into orbit and routine monitoring takes place. On Earth, our immune system works against infections we have to fight on a day-to-day basis, however, in space, the odds are against us since, our immune systems don’t get along with the conditions of microgravity.

Aleksandra Checinska Sielaff, a post-doctoral researcher at Washington State University who collaborated with NASA’s JPL (Jet Propulsion Laboratory) on the study of this paper, says that they are not fully certain if these bacteria are harmful to the humans. Nonetheless, based on her observation she infers that whether the bacteria can cause diseases in astronauts on the ISS is yet unknown, however, it would depend on numerous factors, such as the health status of each individual and the function of these microbes in the space environment. Though these bacteria live in space, however, they didn’t come from space. They are passengers just like our astronauts who travelled to the International Space Station from Earth. Many of these bacteria are also found on the surface of our skin. For example Staph.


It’s very much important to monitor these bacteria in order to ensure that they don’t become infectious and antibiotic-resistant.

These bacteria are capable of forming biofilms which are the communities of tightly knitted bacteria, which are usually found accumulated in places like shower heads. Apart from health concerns, biofilms can cause mechanical blockages and corrosion.
If these microbes, one day become infectious or antibiotic-resistant, or both, we will have to deal with the first real space public health issue.

As of now, it looks as if the space hubs like ISS can be home for bacteria, only as long as the humans go there. Therefore, before we set out on missions to colonise space, we need to bring these bacteria under control!

electricity eating bacteria

Electricity-eating microbes use electrons and fix carbon dioxide to grow

We have often seen our metal products catching rust and we usually apply some grease over it in order to prevent the rust over it. According to the study carried out by the researchers at the Washington University in St. Louis, it explains that there are certain bacteria’s which eat the electricity and transfer electrons to fix carbon dioxide to fuel its growth.

The research was lead by Prof. Arpita Bose, assistant professor of biology in Arts & Sciences, and Michael Guzman, a PhD candidate in her laboratory. The team showed how a naturally occurring strain of Rhodopseudomonas palustris takes up electrons from conductive substances like metal oxides or rust.

This is a continuation of the previous research carried by Bose, which states that R. palustris TIE-1 can consume electrons from rust proxies like poised electrodes, a process called extracellular electron uptake. R. palustris being phototrophic, it uses energy from light to carry out certain metabolic processes.

The new research explains the cellular sinks where this microbe dumps the electrons it eats from electricity. “It clearly shows for the first time how this activity—the ability for the organism to eat electricity—is connected to carbon dioxide fixation,” said Bose.

physiology of R palustris bacteria

Overview of the physiology of R. palustris.( Credit: Nature journal)

This special ability clearly shows the microbe’s natural ability for sustainable energy storage or other bioenergy applications which have caught the attention of the Department of Energy and Department of Defense.

Explaining the origins of the bacteria Bose says “R. palustris strains can be found in wild and exotic places like a rusty bridge in Woods Hole, Massachusetts where TIE-1 was isolated from. You can find these organisms everywhere. This suggests that extracellular electron uptake might be very common.

Co-researcher Guzzam adds “The main challenge is that it’s an anaerobe, so you need to grow it in an environment that doesn’t have oxygen in order for it to harvest light energy. But the flip side to that is that those challenges are met with a lot of versatility in this organism that a lot of other organisms don’t have.”

The researchers in their newspaper showed that the electrons from electricity enter into proteins in the membrane that are important for photosynthesis. Surprisingly, when they deleted the microbe’s ability to fix carbon dioxide, they observed a 90 percent reduction in its ability to consume electricity which means that it really want to fix carbon. This process is similar to the recharging of the battery.

Bose adds “The microbe uses electricity to charge its redox pool, storing up the electrons and making it highly reduced. To discharge it, the cell reduces carbon dioxide. The energy for all this comes from sunlight. The whole process keeps repeating itself, allowing the cell to make biomolecules with nothing more than electricity, carbon dioxide and sunlight. We hope that this ability to combine electricity and light to reduce carbon dioxide might be used to help find sustainable solutions to the energy crisis.

The new research answers basic science questions and provides plenty of opportunity for future bioenergy applications.

Published Researchhttps://www.nature.com/articles/s41467-019-09377-6