Microbe dietary preferences influence the effectiveness of carbon sequestration in the deep ocean

The movement of carbon dioxide (CO2) from the surface of the ocean, where it is in active contact with the atmosphere, to the deep ocean, where it can be sequestered away for decades, centuries, or longer, depends on a number of seemingly small processes.

One of these key microscale processes is the dietary preferences of bacteria that feed on organic molecules called lipids, according to a journal article, "Microbial dietary preference and interactions affect the export of lipids to the deep ocean," published in Science.

"In our study, we found incredible variation in what the different microbes preferred to digest. Bacteria seem to have very distinct diet preferences for different lipid molecules. This has real implications for understanding carbon sequestration and the biological carbon pump," said journal article co-author Benjamin Van Mooy, a senior scientist in the Marine Chemistry and Geochemistry Department at the Woods Hole Oceanographic Institution (WHOI). "This study used state-of-the-art methods to link the molecular composition of the sinking biomass with its rates of degradation, which we were able to link to the dietary preferences of bacteria." The biological carbon pump is a process where biomass sinks from the ocean surface to the deep ocean.

About 5 to 30% of surface ocean particulate organic matter is composed of lipids, which are carbon-rich fatty acid biomolecules that microbes use for energy storage and cellular functions. As the organic matter sinks to the deep sea, diverse communities of resident microbes degrade and make use of the lipids, exerting an important control on global CO2 concentrations. Understanding this process is vital to improve our ability to forecast global carbon fluxes in changing ocean regimes. Geographic areas where more lipids reach the deep ocean undegraded could be hotspots for natural carbon sequestration.

"Bacteria isolated from marine particles exhibited distinct dietary preferences, ranging from selective to promiscuous degraders," the article states. "Using synthetic communities composed of isolates with distinct dietary preferences, we showed that lipid degradation is modulated by microbial interactions. A particle export model incorporating these dynamics indicates that metabolic specialization and community dynamics may influence lipid transport efficiency in the ocean's mesopelagic zone." The mesopelagic zone extends about 200-1000 meters below the ocean surface.

"I was thrilled to see how much there is to learn about the functioning of the ocean by combining two technologies- high-end chemical analysis and microscale imaging-that have historically never been used together," said co-author Roman Stocker, professor at the Institute of Environment Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Switzerland, "I believe that work at the interface between the exciting technologies we now have available in microbial oceanography will continue to yield important insights into how microbes shape our oceans, now and into the future."

"Scientists are starting to understand that lipids in the ocean can vary significantly depending on different environments, such as the coast versus the open ocean, and the season," said Van Mooy. "With this information, researchers can start to consider whether there are places in the ocean where lipids sink and are sequestered very efficiently, while there may be other locations where lipids are barely sequestered at all or are very inefficiently sequestered."

"What excites me about this paper is that it shows bacteria are not just eating any type of lipid, but are very specialized and, like us, have specific food preferences," said article co-author Lars Behrendt, associate professor and SciLifeLab fellow at the Science for Life Laboratory, Department of Organismal Biology, Uppsala University, Sweden. "This changes how we think about how microorganisms consume food in their natural environment and how they might help each other or compete for the same resource. It also supports the idea that combinations of bacteria better break down specific compounds, including lipids, or to achieve other desired functions."

In addition to studying specific bacteria species in isolation, the researchers also looked at how dietary preference affects degradation rates by multispecies communities of bacteria, which they stated is ecologically more relevant than species in isolation. The researchers found that simple synthetic co-cultures exhibited different degradation rates and delay times when compared to monocultures. The researchers also noted that the degradation of particulate organic matter in the natural environment is even more complex than what is described in the study.

"Phytoplankton are the main reason the ocean is one of the biggest carbon sinks. These microscopic organisms play a huge role in the world's carbon cycle -- absorbing about as much carbon as all the plants on land combined," said co-author Uria Alcolombri, senior lecturer, Alexander Silberman Institute of Life Sciences, Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Israel. "It's fascinating that we can study tiny microbial processes under the microscope while uncovering the biological factors that regulate this massive 'digestive system' of the ocean."

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Gut bacteria make neurotransmitters to shape the newborn immune system

Weill Cornell Medicine investigators discovered that unique bacteria colonize the gut shortly after birth and make the neurotransmitter serotonin to educate gut immune cells. This prevents allergic reactions to food and the bacteria themselves during early development.

The preclinical study, published in Science Immunology on Mar. 15, showed that bacteria abundant in the guts of newborns produce serotonin, which promotes the development of immune cells called T-regulatory cells or Tregs. These cells suppress inappropriate immune responses to help prevent autoimmune diseases and dangerous allergic reactions to harmless food items or beneficial gut microbes.

"The gut is now known as the second human brain as it makes over 90 percent of the neurotransmitters in the human body. While neurotransmitters such as serotonin are best known for their roles in brain health, receptors for neurotransmitters are located throughout the human body," explained the study's senior author, Dr. Melody Zeng, an assistant professor of immunology in the Gale and Ira Drukier Institute for Children's Research and the Department of Pediatrics at Weill Cornell Medicine.

Gut Bacteria in Babies Provide a Helping Hand

The researchers observed that the neonatal mouse gut had much higher levels of neurotransmitters, including serotonin, than the adult gut. "So far, almost all studies of gut neurotransmitters were conducted in adult animals or human subjects, where a specific gut cell type called enterochromaffin cells produce neurotransmitters," said Dr. Zeng. "However, we discovered that this isn't the case in the newborn gut where most of the serotonin is made by bacteria that are more abundant in the neonatal gut."

This was also confirmed in babies through a human infant stool biobank that the Zeng lab has established in collaboration with the Neonatal Intensive Care Unit in the NewYork-Presbyterian Alexandra Cohen Hospital for Women and Newborns. These samples were obtained with parental consent and deidentified.

The study results suggest that before the neonatal gut is mature enough to make its own neurotransmitters, unique gut bacteria may supply neurotransmitters that are needed for critical biological functions during early development.

"We found that gut bacteria in young mice not only directly produce serotonin but also decrease an enzyme called monoamine oxidase that normally breaks down serotonin, thus keeping gut serotonin levels high," said the study's lead author Dr. Katherine Sanidad, postdoctoral associate in pediatrics at Weill Cornell Medicine.

The high serotonin levels shift the balance of immune cells by increasing the number of Tregs, which helps prevent the immune system from overreacting and attacking gut bacteria or food antigens. "The neonatal gut needs these serotonin-producing bacteria to keep the immune system in check," Dr. Sanidad added.

Healthy Immune System Helps Later in Life

Dr. Zeng noted that this work underscores the importance of having the right types of beneficial bacteria soon after birth. Babies in developed countries have better access to antibiotics, less exposure to diverse microbes in their clean environments and potentially unhealthy diets that may significantly impact the abundance of serotonin-producing bacteria in their intestines.

As a result, these babies may have fewer Tregs and develop immune reactions to their own gut bacteria, or allergies to food. This may be one reason food allergies have become increasingly common in children, particularly in developed countries. "If educated properly, the immune system in babies would recognize that things like peanuts and eggs are okay, and it doesn't have to attack them," she said. This may also have an impact on developing autoimmune diseases -- when the immune system attacks the body's own healthy cells -- later in life.

The team next plans to look at bacteria in human infant stool samples to measure their production of serotonin, other neurotransmitters and molecules that may help train the immune system to prevent future immune-related diseases, such as allergies, infections and cancer.

"It's essential to understand how the immune system is trained during early life, but this is understudied in newborns and children. Further studies of these developmental periods may hopefully lead us to mitigation approaches to reduce the risk of inflammatory diseases like food allergies and inflammatory bowel disease later in life," Dr. Sanidad said.

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Blindness from some inherited eye diseases may be caused by gut bacteria

Sight loss in certain inherited eye diseases may be caused by gut bacteria, and is potentially treatable by antimicrobials, finds a new study in mice co-led by a UCL and Moorfields researcher.

The international study observed that in eyes with sight loss caused by a particular genetic mutation, known to cause eye diseases that lead to blindness, gut bacteria were found within the damaged areas of the eye.

The authors of the new paper, published in Cell and jointly led by researchers in China, say their findings suggest that the genetic mutation may relax the body's defences, thus allowing harmful bacteria to reach the eye and cause blindness.

The gut contains trillions of bacteria, many of which are key to healthy digestion. However, they can also be potentially harmful.

The researchers were investigating the impact of the Crumbs homolog 1 (CBR1) gene, which is known to be expressed in the retina (the thin layer of cells at the back of the eye) and is crucial to building the blood-retina barrier to regulate what flows in and out of the eye.

The CRB1 gene is associated with inherited eye disease, most commonly forms of Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP); the gene is the cause of 10% of LCA cases and 7% of RP cases worldwide.

Using mouse models, the research team discovered the CRB1 gene is key to controlling the integrity of the lower gastrointestinal tract, the first ever such observation. There, it combats pathogens and harmful bacteria by regulating what passes between the contents of the gut and the rest of the body.

The team found that when the gene has a particular mutation, dampening its expression (reducing its effect), these barriers in both the retina and the gut can be breached, enabling bacteria in the gut to move through the body and into the eye, leading to lesions in the retina that cause sight loss.

Crucially, treating these bacteria with antimicrobials, such as antibiotics, was able to prevent sight loss in the mice even though it did not rebuild the affected cell barriers in the eye.

Inherited eye diseases are the UK's leading cause of blindness in working-age people. Onset of disease may vary from very early childhood to adulthood, but deterioration is irreversible and has lifelong implications. To date, the development of treatments has largely focused on gene therapies.

The findings of this study suggest that simply using antimicrobials might help prevent deterioration in CRB1-associated inherited eye diseases. Future work will investigate whether this applies in humans.

Co-lead author Professor Richard Lee (UCL Institute of Ophthalmology and Moorfields Eye Hospital NHS Foundation Trust) said: "We found an unexpected link between the gut and the eye, which might be the cause of blindness in some patients.

"Our findings could have huge implications for transforming treatment for CRB1-associated eye diseases. We hope to continue this research in clinical studies to confirm if this mechanism is indeed the cause of blindness in people, and whether treatments targeting bacteria could prevent blindness.

"Additionally, as we have revealed an entirely novel mechanism linking retinal degeneration to the gut, our findings may have implications for a broader spectrum of eye conditions, which we hope to continue to explore with further studies."

Read more at Science Daily

Decline in microbial genetic richness in the western Arctic Ocean

The Arctic region is experiencing climate change at a much faster rate than the rest of the world. Melting ice sheets, runoff from thawing permafrost and other factors are rapidly changing the composition of the Arctic Ocean's water. And that change is being experienced all the way down to the microbial level.

In a Concordia-led study published in the journal ISME Communications, researchers analyzed archival samples of bacteria and archaea populations taken from the Beaufort Sea, bordering northwest Canada and Alaska.

The samples were collected between 2004 and 2012, a period that included two years -- 2007 and 2012 -- in which the sea ice coverage was historically low.

The researchers looked at samples taken from three levels of water: the summer mixed layer, the upper Arctic water below it and the Pacific-origin water at the deepest level.

The study examined the microbes' genetic composition using bioinformatics and statistical analysis across the nine-year time span.

Using this data, the researchers were able to see how changing environmental conditions were influencing the organisms' structure and function.

The researchers found subtle but statistically significant changes in the communities they studied.

"We observed a general overall loss in diversity of species across all the different water masses," says David Walsh, a professor in the Department of Biology and the paper's corresponding author.

"We also saw changes in the composition of the microbial community, meaning there were different species after the 2007 sea ice minimum than before."

However, the periods of population richness decline changed between the ocean's layers of water.

Sudden decline in the fresher summer mixed water level, between 3-9 meters deep, was observed in 2005-2007.

The upper Arctic water, between 16-78 metres, saw declines in 2010-2012, while the deeper Pacific water layer, between 49-154 meters, experienced a two-step decline -- once between 2005-2007 and again between 2010-2012.

Small beginnings

The researchers are taking care not to overemphasize the results of their findings, saying the changes, while significant, remain slight.

But with the summer Arctic ice cover shrinking steadily year over year, the data does hint at possible trends that may be visible in upcoming population studies in more recent years.

"With the warming and freshening of the Arctic Ocean comes a decrease of nutrients that are important for photosynthesis, which produces the organic matter that serves as energy and carbon sources for the marine food web," Walsh explains.

"This shift risks strengthening what is known as the microbial loop, in which the energy and carbon that would normally go into higher trophic levels -- meaning zooplankton and then fish -- is rapidly recycled by microorganisms. This ecosystem is already dominated by microbial processes, which will only get stronger as this system continues."

"This study provides us with a baseline idea of what is happening in the Arctic," says co-author Arthi Ramachandran, PhD 23. "The Arctic is warming four times faster than the rest of the world, which makes it a fascinating ecosystem to study. The oceans are all interconnected, and the physical barriers of these oceans are becoming much less defined."

Looking into the ocean's warmer, fresher future

The researchers are now planning a metagenomic study that extends the time series to cover periods of even more intense sea ice minima.

They hope to fully sequence the organisms' genomes to further understand the microbial communities' diversity and function in the environment.

Read more at Science Daily

Low-cost microbe can speed biological discovery

Cornell University researchers have created a new version of a microbe to compete economically with E. coli -- a bacteria commonly used as a research tool due to its ability to synthesize proteins -- to conduct low-cost and scalable synthetic biological experiments.

As an inexpensive multiplier -- much like having a photocopier in a test tube -- the bacteria Vibrio natriegens could help labs test protein variants for creation of pharmaceuticals, synthetic fuels and sustainable compounds that battle weeds or pests.

The microbe can work effectively without costly incubators, shakers or deep freezers and can be engineered within hours.

The research publishes Feb. 13 in PNAS Nexus.

"It's really easy to produce," said lead author David Specht, a postdoctoral researcher in the laboratory ofBuz Barstow, assistant professor of biological and environmental engineering.

To study proteins for creating medical cures or fashioning fuels, researchers use a plasmid (a small piece of DNA) that acts as the instruction manual to make the molecular machine -- a protein -- of interest.

Currently, when researchers place a plasmid into E. coli, they can create many copies to test several variants.

E. coli cells help molecular biologists multiply and manipulate plasmids for protein engineering, but the process is expensive since they often purchase the bacteria from manufacturers, must keep it cold and maintain rooms of expensive equipment to sustain it. A modified E. coli, used for this purpose, is also very fragile.

"As scientists, we don't often know precisely what those regulatory or molecular sequences should be to achieve our goals," said Barstow.

"So, we must test a lot of variants, and Vibrio natriegens allows researchers to scale up that process of testing."

The microbe V. natriegens is not complicated, Specht said. "It's so simple to make that someone with limited resources -- like high school labs, home inventors or startup biological businesses -- can do it," he said.

Researcher Timothy Sheppard compared the simplicity of V. natriegens in conducting synthetic and molecular experiments to using a simple writing instrument hundreds of years old: "We've found nature's pencil for cloning and conducting synthetic biology," he said.

The process is inexpensive with V. natriegens, as it requires no capital equipment purchases and it can work at room temperature.

The cells produced from V. natriegens grow quickly: According to the paper, a transformation started at 9 a.m. yields visible colonies by 5 p.m., each filled with masses of proteins.

Read more at Science Daily

Scientists develop artificial 'worm gut' to break down plastics

A team of scientists from Nanyang Technological University, Singapore (NTU Singapore) has developed an artificial 'worm gut' to break down plastics, offering hope for a nature-inspired method to tackle the global plastic pollution problem.

By feeding worms with plastics and cultivating microbes found in their guts, researchers from NTU's School of Civil and Environmental Engineering (CEE) and Singapore Centre for Environmental Life Sciences Engineering (SCELSE) have demonstrated a new method to accelerate plastic biodegradation.

Previous studies have shown that Zophobas atratus worms -- the larvae of the darkling beetle commonly sold as pet food and known as 'superworms' for their nutritional value -- can survive on a diet of plastic because its gut contains bacteria capable of breaking down common types of plastic.

However, their use in plastics processing has been impractical due to the slow rate of feeding and worm maintenance.

NTU scientists have now demonstrated a way to overcome these challenges by isolating the worm's gut bacteria and using them to do the job without the need for large scale worm breeding.

NTU Associate Professor Cao Bin at the School of CEE and Principal Investigator at SCELSE said, "A single worm can only consume about a couple of milligrams of plastic in its lifetime, so imagine the number of worms that would be needed if we were to rely on them to process our plastic waste. Our method eliminates this need by removing the worm from the equation. We focus on boosting the useful microbes in the worm gut and building an artificial 'worm gut' that can efficiently break down plastics."

The study, published in Environment International in January, is aligned with the University's commitment to fostering innovation and translating research into practical solutions that benefit society under its NTU2025 five-year strategic plan.

Developing an artificial worm gut

To develop their method, the NTU scientists fed three groups of superworms different plastic diets -- High-density polyethylene (HDPE), Polypropylene (PP) and Polystyrene (PS) -- over 30 days.

The control group was fed a diet of oatmeal.

The NTU scientists selected the plastics as they are among the most common plastics in the world, used in everyday items like food boxes and detergent bottles.

HDPE is a type of plastic known for its high-impact resistance, making it difficult to break down.

After feeding the worms plastic, scientists extracted the microbiomes from their gut and incubated them in flasks containing synthetic nutrients and different types of plastics, forming an artificial 'worm gut'. Over six weeks, the microbiomes were left to grow in the flasks at room temperature.

Increase in plastic-degrading bacteria

The scientists found that compared to the control group, the flasks which contained the gut microbiomes from the plastic-fed worms showed a significant increase in plastic-degrading bacteria.

Furthermore, the microbial communities colonising the plastics in the flasks were simpler and more tailored to the specific type of plastic than the microbes found on plastics that had been fed directly to the worms . When the microbial communities are simpler and targeted to a specific type of plastic, this translates to potential for more efficient plastic degradation when used in real-life applications.

First author of the study Dr Liu Yinan, Research Fellow at the School of CEE and SCELSE, said, "Our study represents the first reported successful attempt to develop plastic-associated bacterial communities from gut microbiomes of plastic-fed worms. Through exposing the gut microbiomes to specific conditions, we were able to boost the abundance of plastic-degrading bacteria present in our artificial 'worm gut,' suggesting that our method is stable and replicable at scale."

The researchers say their proof-of-concept lays the foundation for developing biotechnological approaches that use worms' gut microbiomes to process plastic waste.

Read more at Science Daily

Scientists engineer plant microbiome to protect crops against disease

Breakthrough could dramatically cut the use of pesticides and unlock other opportunities to bolster plant health

Scientists have engineered the microbiome of plants for the first time, boosting the prevalence of 'good' bacteria that protect the plant from disease.

The findings published in Nature Communications by researchers from the University of Southampton, China and Austria, could substantially reduce the need for environmentally destructive pesticides.

There is growing public awareness about the significance of our microbiome -- the myriad of microorganisms that live in and around our bodies, most notably in our guts.

Our gut microbiomes influence our metabolism, our likelihood of getting ill, our immune system, and even our mood.

Plants too host a huge variety of bacteria, fungi, viruses, and other microorganisms that live in their roots, stems, and leaves.

For the past decade, scientists have been intensively researching plant microbiomes to understand how they affect a plant's health and its vulnerability to disease.

"For the first time, we've been able to change the makeup of a plant's microbiome in a targeted way, boosting the numbers of beneficial bacteria that can protect the plant from other, harmful bacteria," says Dr Tomislav Cernava, co-author of the paper and Associate Professor in Plant-Microbe Interactions at the University of Southampton.

"This breakthrough could reduce reliance on pesticides, which are harmful to the environment. We've achieved this in rice crops, but the framework we've created could be applied to other plants and unlock other opportunities to improve their microbiome. For example, microbes that increase nutrient provision to crops could reduce the need for synthetic fertilisers."

The international research team discovered that one specific gene found in the lignin biosynthesis cluster of the rice plant is involved in shaping its microbiome.

Lignin is a complex polymer found in the cell walls of plants -- the biomass of some plant species consists of more than 30 per cent lignin.

First, the researchers observed that when this gene was deactivated, there was a decrease in the population of certain beneficial bacteria, confirming its importance in the makeup of the microbiome community.

The researchers then did the opposite, over-expressing the gene so it produced more of one specific type of metabolite -- a small molecule produced by the host plant during its metabolic processes.

This increased the proportion of beneficial bacteria in the plant microbiome.

When these engineered plants were exposed to Xanthomonas oryzae -- a pathogen that causes bacterial blight in rice crops, they were substantially more resistant to it than wild-type rice.

Bacterial blight is common in Asia and can lead to substantial loss of rice yields.

It's usually controlled by deploying polluting pesticides, so producing a crop with a protective microbiome could help bolster food security and help the environment.

Read more at Science Daily

Sophisticated swarming: Bacteria support each other across generations

When bacteria build communities, they cooperate and share nutrients across generations. Researchers at the University of Basel have been able to demonstrate this for the first time using a newly developed method. This innovative technique enables the tracking of gene expression during the development of bacterial communities over space and time.

In nature, bacteria usually live in communities. They collectively colonize our gut, also known as the gut microbiome, or form biofilms such as dental plaque.

Living in communities provides many advantages to the individual microbes.

They are more resilient against adverse environmental conditions, conquer new territories and benefit from each other.

Analyzing microbial communities in space and time

The development of bacterial communities is a highly complex process where bacteria form intricate three-dimensional structures.

In their latest study published in Nature Microbiology, the team led by Professor Knut Drescher from the Biozentrum of the University of Basel has investigated the development of bacterial swarm communities in detail.

They achieved a methodological breakthrough enabling them to simultaneously measure gene expression and image the behaviour of individual cells in microbial communities in space and time.

Bacteria provide resources for future generations

"We used Bacillus subtilis as a model organism. This ubiquitous bacterium is also found in our intestinal flora. We have revealed that these bacteria, which live in communities, cooperate and interact with each other across generations," explains Prof Knut Drescher, head of the study.

"Earlier generations deposit metabolites for later generations."

They also identified different subpopulations within a bacterial swarm, which produce and consume different metabolites.

Some of the metabolites secreted by one subpopulation become the food for other subpopulations that emerge later during swarm development.

Distribution of tasks within the community

The researchers combined state-of-the-art adaptive microscopy, gene expression analyses, metabolite analyses, and robotic sampling.

Using this innovative approach, the researchers have been able to simultaneously examine gene expression and bacterial behavior at precisely defined locations and specific times as well as to identify the metabolites secreted by the bacteria.

The bacterial swarm could thus be divided into three major regions: the swarm front, the intermediate region and the swarm center.

However, the three regions display gradual transitions.

"Depending on the region, the bacteria differ in appearance, characteristics and behavior. While they are mostly motile at the edges, the bacteria in the center form long non-motile threads, resulting in a 3D biofilm. One reason is the varying availability of space and resources," explains first author Hannah Jeckel.

"The spatial distribution of bacteria with distinct behavior enables the community to expand but also to hide in a protective biofilm." This process appears to be a widespread strategy in bacterial communities and is crucial for their survival.

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Microbiome development: Bacteria lay the foundations for their descendants

The microbiome (the symbiotic community of microbial organisms of a host) is of existential importance for the functioning of every plant and animal, including human beings. A research team from Düsseldorf and Kiel headed by Heinrich Heine University Düsseldorf (HHU) has now used the example of the sea anemone Nematostella vectenis to investigate how the microbiome develops together with the host. In the scientific journal Microbiome, the researchers describe that the bacterial community is primarily controlled by the host organism during the early stages of life, while bacteria-bacteria interactions play the lead role in subsequent development.

Every multicellular living creature -- from the simplest organisms to human beings -- lives in a community with a multitude of microorganisms, the so-called microbiome.

This microbiome comprises bacteria, fungi and viruses among other things and assumes various roles ranging from metabolism to immune defence.

For example, without the microbiome in the human intestine, many nutrients could not be absorbed from food and made available to the human body.

But how does the microbiome develop as the host develops? It is known that the composition and ratio of the microorganisms in the sea anemone Nematostella vectenis differ fundamentally between the different stages in its life cycle and only assume a stable form in the adult anemone.

But who and which factors decide how the microbiome changes as the host matures -- does the host control colonisation with the right microbes or do the microbes regulate themselves?

A team from HHU, Kiel University (CAU) and the GEOMAR Helmholtz Centre for Ocean Research Kiel addressed this question.

The study was headed by Professor Dr Sebastian Fraune from the Institute of Zoology and Organismic Interactions at HHU.

The research was conducted within the framework of the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms," which is headed by CAU.

Dr Hanna Domin, lead author of a study that has now been published in Microbiome: "We took adult Nematostella polyps, which had no microbiome following intensive antibiotic treatment, and then recolonised them in a targeted way. To do this, we used bacterial communities that corresponded to those of firstly a Nematostella larva, secondly a juvenile animal and thirdly an adult polyp."

In all three cases, the researchers examined how the microbiome developed over the course of time.

They discovered that only the initial colonisers -- i.e. the bacteria forming the microbiome of the youngest animals -- became really well-established in the adult polyps.

By contrast, it was difficult for the bacteria from older animals to become established.

Professor Fraune, corresponding author of the study: "Following recolonisation, the microbiome then undergoes a development process that is very similar to the normal development of host and microbiome. It takes around four weeks to reach the same status as adult animals that have undergone a normal growth process."

The researchers conclude from this that the host -- presumably through its innate immune system -- controls the composition of the original colony.

Domin: "However, the host no longer has a significant influence over the further development of the microbiome after this point. The bacteria control this themselves and lay suitable foundations for their descendants."

One important aspect of the project, which was driven forward by the research group headed by Professor Dr Christoph Kaleta in Kiel, was the examination of so-called metabolic networks.

This involved investigating how the different bacteria are linked via their metabolism and influence each other.

"We were able to identify metabolic pathways, which are specific to the initial colonisers as well as pathways that only play a role at a later stage," says Dr Johannes Zimmermann from CAU.

The research team established that the degradation of the polysaccharide chitin plays a central role for the initial colonisers in particular.

It was only recently discovered that Nematostella can produce chitin.

Why the animals do this was however unknown as they for example -- by contrast with insects -- do not need chitin for their structural development.

Fraune: "Our results provide clear indications that chitin plays a role for the microbiome."

The sea anemone only has an innate immune system. Nevertheless, the results are also relevant for medical research.

Newborn babies come into contact with numerous bacteria immediately after birth, whereby they also only have an innate immune system at that phase in their lives.

Consequently, initial colonisation with the right microbes is also key to establishing a functioning microbiome and training the adaptive immune system in humans.

Read more at Science Daily

Plants that survived dinosaur extinction pulled nitrogen from air

Once a favored food of grazing dinosaurs, an ancient lineage of plants called cycads helped sustain these and other prehistoric animals during the Mesozoic Era, starting 252 million years ago, by being plentiful in the forest understory. Today, just a few species of the palm-like plants survive in tropical and subtropical habitats.

Like their lumbering grazers, most cycads have gone extinct. Their disappearance from their prior habitats began during the late Mesozoic and continued into the early Cenozoic Era, punctuated by the cataclysmic asteroid impact and volcanic activity that mark the K-Pg boundary 66 million years ago. However, unlike the dinosaurs, somehow a few groups of cycads survived to the present.

A new study appearing Nov. 16 in the journal Nature Ecology & Evolution has concluded that the cycad species that survived relied on symbiotic bacteria in their roots, which provide them with nitrogen to grow. Just like modern legumes and other plants that use nitrogen fixation, these cycads trade their sugars with bacteria in their roots in exchange for nitrogen plucked from the atmosphere.

What originally interested lead author Michael Kipp is that the tissues of nitrogen-fixing plants can provide a record of the composition of the atmosphere they grew up in. He combines geochemistry with the fossil record to try to understand the Earth's climate history.

Knowing already that modern cycads are nitrogen-fixers, Kipp began analyzing some very old plant fossils during his Ph.D. work at the University of Washington to see if he could get a different look at ancient atmospheres. Most of the old cycads revealed that they weren't nitrogen-fixers, but these also turned out to be the extinct lineages.

"Instead of being a story about the atmosphere, we realized this was a story about the ecology of these plants that changed through time," said Kipp, who spent nearly a decade on this finding, first at UW and then as a postdoctoral researcher at CalTech.

Kipp is joining the Duke faculty this year as an assistant professor of Earth and Climate Sciences in the Nicholas School of the Environment to continue using the fossil record to understand Earth's climate history so that we can understand its possible future.

Much of what we know about ancient atmospheres comes from chemical studies of ancient sea life and sediments, Kipp said. Applying some of those methods to terrestrial plants is a new wrinkle.

"Going into the project, there were no published nitrogen isotope data from fossilized plant foliage," Kipp said. It took a while for him to fine-tune the method and to secure samples of precious plant fossils that museum curators were reluctant to see vaporized to get the data.

"In the few fossil samples that are of surviving (cycad) lineages, and that are not so old -- 20, 30 million years -- we see the same nitrogen signature as we see today," Kipp said. That means their nitrogen came from symbiotic bacteria. But in the older and extinct cycad fossils, that nitrogen signature was absent.

What is less clear is how nitrogen fixation helped the surviving cycads. It may have helped them weather the dramatic shift in climate or it may have allowed them to compete better with the faster-growing angiosperm plants that flourished after the extinction, "or it could be both."

Read more at Science Daily

Plastic-eating bacteria turn waste into useful starting materials for other products

Mountains of used plastic bottles get thrown away every day, but microbes could potentially tackle this problem. Now, researchers in ACS Central Science report that they've developed a plastic-eating E. coli that can efficiently turn polyethylene terephthalate (PET) waste into adipic acid, which is used to make nylon materials, drugs and fragrances.

Previously, a team of researchers including Stephen Wallace engineered a strain of E. coli to transform the main component in old PET bottles, terephthalic acid, into something tastier and more valuable: the vanilla flavor compound vanillin. At the same time, other researchers engineered microbes to metabolize terephthalic acid into a variety of small molecules, including short acids. So, Wallace and a new team from the University of Edinburgh wanted to expand E. coli's biosynthetic pathways to include the metabolism of terephthalic acid into adipic acid, a feedstock for many everyday products that's typically generated from fossil fuels using energy-intensive processes.

The team developed a new E. coli strain that produced enzymes that could transform terephthalic acid into compounds such as muconic acid and adipic acid. Then, to transform the muconic acid into adipic acid, they used a second type of E. coli, which produced hydrogen gas, and a palladium catalyst. In experiments, the team found that attaching the engineered microbial cells to alginate hydrogel beads improved their efficiency, and up to 79% of the terephthalic acid was converted into adipic acid. Using real-world samples of terephthalic acid from a discarded bottle and a coating taken from waste packaging labels, the engineered E. coli system efficiently produced adipic acid. In the future, the researchers say they will look for pathways to biosynthesize additional higher-value products.

From Science Daily

Genetically modified bacteria break down plastics in saltwater

Researchers have genetically engineered a marine microorganism to break down plastic in salt water. Specifically, the modified organism can break down polyethylene terephthalate (PET), a plastic used in everything from water bottles to clothing that is a significant contributor to microplastic pollution in oceans.

"This is exciting because we need to address plastic pollution in marine environments," says Nathan Crook, corresponding author of a paper on the work and an assistant professor of chemical and biomolecular engineering at North Carolina State University.

"One option is to pull the plastic out of the water and put it in a landfill, but that poses challenges of its own. It would be better if we could break these plastics down into products that can be re-used. For that to work, you need an inexpensive way to break the plastic down. Our work here is a big step in that direction."

To address this challenge, the researchers worked with two species of bacteria. The first bacterium, Vibrio natriegens, thrives in saltwater and is remarkable -- in part -- because it reproduces very quickly. The second bacterium, Ideonella sakaiensis, is remarkable because it produces enzymes that allow it to break down PET and eat it.

The researchers took the DNA from I. sakaiensis that is responsible for producing the enzymes that break down plastic, and incorporated that genetic sequence into a plasmid. Plasmids are genetic sequences that can replicate in a cell, independent of the cell's own chromosome. In other words, you can sneak a plasmid into a foreign cell, and that cell will carry out the instructions in the plasmid's DNA. And that's exactly what the researchers did here.

By introducing the plasmid containing the I. sakaiensis genes into V. natriegens bacteria, the researchers were able to get V. natriegens to produce the desired enzymes on the surface of their cells. The researchers then demonstrated that V. natriegens was able to break down PET in a saltwater environment at room temperature.

"This is scientifically exciting because this is the first time anyone has reported successfully getting V. natriegens to express foreign enzymes on the surface of its cells," Crook says.

"From a practical standpoint, this is also the first genetically engineered organism that we know of that is capable of breaking down PET microplastics in saltwater," says Tianyu Li, first author of the paper and a Ph.D. student at NC State. "That's important, because it is not economically feasible to remove plastics from the ocean and rinse high concentration salts off before beginning any processes related to breaking the plastic down."

"However, while this is an important first step, there are still three significant hurdles," Crook says. "First, we'd like to incorporate the DNA from I. sakaiensis directly into the genome of V. natriegens, which would make the production of plastic-degrading enzymes a more stable feature of the modified organisms. Second, we need to further modify V. natriegens so that it is capable of feeding on the byproducts it produces when it breaks down the PET. Lastly, we need to modify the V. natriegens to produce a desirable end product from the PET -- such as a molecule that is a useful feedstock for the chemical industry.

"Honestly, that third challenge is the easiest of the three," says Crook. "Breaking down the PET in saltwater was the most challenging part.

"We are also open to talking with industry groups to learn more about which molecules would be most desirable for us to engineer the V. natriegens into producing," Crook says. "Given the range of molecules we can induce the bacteria to produce, and the potentially vast scale of production, which molecules could industry provide a market for?"

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Bit by bit, microplastics from tires are polluting our waterways

Urban stormwater particles from tyre wear were the most prevalent microplastic a new Griffith-led study has found.

Published in Environmental Science & Technology, the study showed that in stormwater runoff during rain approximately 19 out of every 20 microplastics collected were tyre wear particles with anywhere from 2 to 59 particles per litre of water.

"Pollution of our waterways by microplastics is an emerging environmental concern due to their persistence and accumulation in aquatic organisms and ecosystems," said lead author Dr Shima Ziajahromi, a research fellow at the Australian Rivers Institute.

"Stormwater runoff which contains a mixture of sediment, chemical, organic and physical pollutants, is a critical pathway for microplastics to washed off from urban environments during rain and into local aquatic habitats.

"But to date, our knowledge of the amount of microplastics in urban stormwater, particularly tyre wear particles, is limited, as is the potential strategies we can use to minimise this source."

Tyre rubber contains up to 2500 chemicals with the contaminants that leach from tyres considered more toxic to bacteria and microalgae than other plastic polymers.

"Due to the analytical challenges in measuring this source of microplastics in stormwater, research to date often lacks information about the actual number of tyre wear particles water samples," said Dr Ziajahromi.

Quantitative information of this type is crucial to improve our understanding of the amount of tyre wear particles in stormwater, assess the risk to the environment, and to develop management strategies.

"Our study quantified and characterize microplastics and tyre wear particles in both stormwater runoff and sediment of stormwater drainage systems in Queensland," said co-author Professor Fred Leusch, who leads the Australian Rivers Institute's Toxicology Research Program.

"We also assessed the effectiveness of a stormwater treatment device to capture and remove these contaminants from stormwater and evaluated the role of a constructed stormwater wetland for capturing microplastics in the sediment, removing it from stormwater runoff.

"The device is a bag made of 0.2 millimetre mesh which can be retrofitted to stormwater drains. Although originally designed to capture gross pollutants, sediment, litter and oil and grease, it significantly reduced microplastics from raw runoff, with up to 88% less microplastics in treated water which had passed through the device."

Sediment samples collected from the inlet and outlet of a constructed stormwater wetland contained between 1450 to 4740 particles in every kilogram of sediment, with more microplastics in the sediment at the inlet than the outlet, indicating the wetland's ability to remove them from stormwater.

"Microplastics that enter constructed wetlands for stormwater drainage systems settle in the sediment and form a biofilm, leading to their accumulation over time, removing them from stormwater runoff," said Dr Ziajahromi.

"Urban stormwater runoff typically requires treatment for the removal of suspended solids and nutrients such as nitrogen and phosphorus in many jurisdictions in Australia, with some also requiring the removal of gross pollutants. However, regulations are lagging behind when it comes to microplastics and tyre wear particles."

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Common origin behind major childhood allergies

Several major childhood allergies may all stem from the community of bacteria living in our gut, according to a new study led by researchers at the University of British Columbia and BC Children's Hospital.

The research, published in Nature Communications, identifies gut microbiome features and early life influences that are associated with children developing any of four common allergies -- eczema, asthma, food allergy and/or hay fever. The findings could lead to methods of predicting whether a child will develop allergies, and ways to prevent them from developing at all.

"We're seeing more and more children and families seeking help at the emergency department due to allergies," said Dr. Stuart Turvey, professor in the department of pediatrics at UBC and an investigator at BC Children's Hospital Research Institute, and co-senior author on the study. "Hundreds of millions of children worldwide suffer from allergies, including one in three children in Canada, and it's important to understand why this is happening and how it can be prevented."

The study is one of the first to examine four distinct school-aged pediatric allergies at once. While these allergic diseases each have unique symptoms, the Turvey lab was curious whether they might have a common origin linked to the infant gut microbiota composition.

"These are technically different diagnoses, each with their own list of symptoms, so most researchers tend to study them individually," says Dr. Charisse Petersen, co-senior author on the paper and postdoctoral fellow in the Turvey lab. "But when you look at what is going wrong at a cellular level, they actually have a lot in common."

For the study, researchers examined clinical assessments from 1,115 children who were tracked from birth to age five. Roughly half of the children (523) had no evidence of allergies at any time, while more than half (592) were diagnosed with one or more allergic disorders by an expert physician. The researchers evaluated the children's microbiomes from stool samples collected at clinical visits at three months and one year of age.

The stool samples revealed a bacterial signature that was associated with the children developing any of the four allergies by five years of age. The bacterial signature is a hallmark of dysbiosis, or an imbalanced gut microbiota, that likely resulted in a compromised intestinal lining and an elevated inflammatory response within the gut.

"Typically, our bodies tolerate the millions of bacteria living in our guts because they do so many good things for our health. Some of the ways we tolerate them are by keeping a strong barrier between them and our immune cells and by limiting inflammatory signals that would call those immune cells into action," says Courtney Hoskinson, a PhD candidate at UBC and first author on the paper. "We found a common breakdown in these mechanisms in babies prior to the development of allergies."

Many factors can shape the infant gut microbiota, including diet, how we are born, where we live, and our exposure to antibiotics. For example, antibiotics may wipe out sensitive bacteria, while breastfeeding tends to replenish and provide necessary food for bacteria in the infant gut. The researchers examined how these types of influences affected the balance of gut microbiota and the development of allergies.

"There are a lot of potential insights from this robust analysis," says Dr. Turvey. "From these data we can see that factors such as antibiotic usage in the first year of life are more likely to result in later allergic disorders, while breastfeeding for the first six months is protective. This was universal to all the allergic disorders we studied."

Now the researchers hope to leverage the findings to inform treatments that correct an imbalanced gut microbiota and could potentially prevent allergies from developing.

"Developing therapies that change these interactions during infancy may therefore prevent the development of all sorts of allergic diseases in childhood, which often last a lifetime," says Dr. Turvey.

The research is part of the Canadian Healthy Infant Longitudinal Development (CHILD) Cohort Study that recruited families through BC Children's Hospital and BC Women's Hospital + Health Centre and other pediatric hospitals across Canada. Since launching in 2008, the team of Canadian researchers has tracked the health, growth and environments of kids from birth and made important discoveries about how asthma and allergies develop.

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Bacteria as Blacksmiths

A hot bath is a place to relax. For scientists, it is also where molecules or tiny building blocks meet to form materials. Researchers at the Institute of Science and Technology Austria (ISTA) take it to the next level and use the energy of swimming bacteria to forge materials. A recent study in Nature Physics shows us how this works and the potential sustainability benefits that may arise from this innovative approach.

You never know when dazzling ideas will strike you. Sometimes they emerge from the most unexpected places, like a boulder gym in Vienna. Such was the case for ISTA's Daniel Grober, a graduate student in the research group of physicist Jérémie Palacci, who had been working on how to assemble materials leveraging the energy of swimming bacteria, and Mehmet Can Uçar, a postdoc in Edouard Hannezo's group. Fueled by their shared passion for science and climbing, discussions at the gym turned into a paper-pen model of Grober's experiment. Their concept captivated Ivan Palaia, a postdoc in Anđela Šarić's group, who decided to join the task force.

Together, this dynamic all-ISTA trio embarked on a collaborative effort that now reaches its pinnacle with a paper published today in Nature Physics. The study shows a novel experimental strategy to fabricate materials from small building blocks. It translates ideas from metallurgy -- the fine art of blacksmithing, where cycles of high temperature and slow cooling set a material's structure -- into soft materials, using the activity from a bath of swimming bacteria.

What are active baths?

In Jérémie Palacci's research group at the Institute of Science and Technology Austria, it is all about microscopic particles. "Our work revolves around tiny 'Lego'-like building blocks that are a hundred times smaller than a hair. We try to understand how these components come together and form larger structures," he explains. Typically, when these building blocks are suspended in water, they jiggle due to temperature, which provides the energy for the particles to hop back and forth randomly. A phenomenon first rationalized by Einstein in 1905 and known as Brownian motion.

To introduce order amidst the chaos, adding an "active agent" to the water is beneficial. This results in what is known as an "active bath," where the agent acts like a small fire. In principle, with this extra energy, you can hope to control the assembly and properties of materials -- the way the blacksmith forges. However, until now, an approach where for instance bacteria is used to forge, had never been explored.

Bacteria -- the fire

Palacci's student, Daniel Grober, took on this challenge and started to construct such an active bath with characteristics inspired by metallurgy. Grober says, "We used E. coli bacteria as an active agent, as their swimming movement provided energy and some kind of agitation -- 'temperature' for a physicist, equivalent to 2000 °C, similar to the one needed to craft metals. But because it is made by bacteria, and it is not a real oven, it remains gentle enough to be used with gels and soft materials without burning them." The building blocks were microscopic particles in the form of sticky colloids -- round beads that stick together when in contact.

This idea proved to be successful. The swimming bacteria effectively amplified the motion of the beads, resulting in the formation of aggregations and gel-like structures.

Dance to the beat of bacteria

Moreover, the observation of these newly formed clusters showed an intriguing singularity. At all times, the aggregates were spinning clockwise, but very slowly. To shed light on this observation, Grober conducted a statistical analysis of the system's motion. He confirmed a slow and persistent rotation of the aggregates that originates in the clockwise spin (chirality) of the E. coli flagella -- the minuscule appendages that propel the bacteria in their movement. The scientist suspected that the rotational motion played a pivotal role in forming the unconventional structures he observed.

Presenting his work in a weekly lab meeting intrigued his colleague Ivan Palaia, which led to the understanding of the phenomenon. Palaia proposed a minimal computational model, to capture the chirality of the bacterial bath without simulating the swimming bacteria. The computer simulations were first validated by quantitatively reproducing the experimental results before providing a deeper understanding of the mechanism. The model confirmed the salient role of the rotation in shaping gels, by forming remarkable structures with exotic mechanical properties that cannot be achieved conventionally.

More to come in the future

This utilization of bacterial baths to assemble unconventional materials holds great promise. For instance, although the study was limited to 2D structures at the micron scale, the approach was designed for its potential in upscaling. "With this innovative approach, it could theoretically be possible to construct 3D samples, large enough to be held in the palm of my hand!" Palacci adds. This advancement could also enhance the sustainability of material production by harnessing energy from bacteria rather than relying on external energy sources.

Read more at Science Daily

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

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

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

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

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

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

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

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

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

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

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

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

Optimising intestinal bacteria

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

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

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

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

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4,000-year-old plague DNA found -- the oldest cases to date in Britain

Researchers at the Francis Crick Institute have identified three 4,000-year-old British cases of Yersinia pestis, the bacteria causing the plague -- the oldest evidence of the plague in Britain to date, reported in a paper published today in Nature Communications.

Working with the University of Oxford, the Levens Local History Group and the Wells and Mendip Museum, the team identified two cases of Yersinia pestis in human remains found in a mass burial in Charterhouse Warren in Somerset and one in a ring cairn monument in Levens in Cumbria.

They took small skeletal samples from 34 individuals across the two sites, screening for the presence of Yersinia pestis in teeth. This technique is performed in a specialist clean room facility where they drill into the tooth and extract dental pulp, which can trap DNA remnants of infectious diseases.

They then analysed the DNA and identified three cases of Yersinia pestis in two children estimated to be aged between 10-12 years old when they died, and one woman aged between 35-45. Radiocarbon dating was used to show it's likely the three people lived at roughly the same time.

The plague has previously been identified in several individuals from Eurasia between 5,000 and 2,500 years before present (BP), a period spanning the Late Neolithic and Bronze Age (termed LNBA), but hadn't been seen before in Britain at this point in time. The wide geographic spread suggests that this strain of the plague may have been easily transmitted.

This strain of the plague -- the LNBA lineage -- was likely brought into Central and Western Europe around 4,800 BP by humans expanding into Eurasia, and now this research suggests that it extended to Britain.

Using genome sequencing, the researchers showed that this strain of the Yersinia pestis looks very similar to the strain identified in Eurasia at the same time.

The individuals identified all lacked the yapC and ymt genes, which are seen in later strains of plague, the latter of which is known to play an important role in plague transmission via fleas. This information has previously suggested that this strain of the plague was not transmitted via fleas, unlike later plague strains such as the one that caused the Black Death.

Because pathogenic DNA -- DNA from bacteria, protozoa, or viruses which cause disease -- degrades very quickly in samples which might be incomplete or eroded, it's also possible that other individuals at these burial sites may have been infected with the same strain of plague.

The Charterhouse Warren site is rare as it doesn't match other funeral sites from the time period -- the individuals buried there appear to have died from trauma. The researchers speculate that the mass burial wasn't due to an outbreak of plague but individuals may have been infected at the time they died.

Pooja Swali, first author and PhD student at the Crick, said, "The ability to detect ancient pathogens from degraded samples, from thousands of years ago, is incredible. These genomes can inform us of the spread and evolutionary changes of pathogens in the past, and hopefully help us understand which genes may be important in the spread of infectious diseases. We see that this Yersinia pestis lineage, including genomes from this study, loses genes over time, a pattern that has emerged with later epidemics caused by the same pathogen."

Pontus Skoglund, group leader of the Ancient Genomics Laboratory at the Crick, said, "This research is a new piece of the puzzle in our understanding of the ancient genomic record of pathogens and humans, and how we co-evolved.

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Tiny microbes could brew big benefits for green biomanufacturing

A research team led by Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley has engineered bacteria to produce new-to-nature carbon products that could provide a powerful route to sustainable biochemicals.

The advance -- which was recently announced in the journal Nature -- uses bacteria to combine natural enzymatic reactions with a new-to-nature reaction called the "carbene transfer reaction." This work could also one day help reduce industrial emissions because it offers sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels.

"What we showed in this paper is that we can synthesize everything in this reaction -- from natural enzymes to carbenes -- inside the bacterial cell. All you need to add is sugar and the cells do the rest," said Jay Keasling, a principal investigator of the study and CEO of the Department of Energy's Joint BioEnergy Institute (JBEI).

Carbenes are highly reactive carbon-based chemicals that can be used in many different types of reactions. For decades, scientists have wanted to use carbene reactions in the manufacturing of fuels and chemicals, and in drug discovery and synthesis.

But these carbene processes could only be carried out in small batches via test tubes and required expensive chemical substances to drive the reaction.

In the new study, the researchers replaced expensive chemical reactants with natural products that can be produced by an engineered strain of the bacteria Streptomyces. Because the bacteria use sugar to produce chemical products through cellular metabolism, "this work enables us to perform the carbene chemistry without toxic solvents or toxic gases typically used in chemical synthesis," said first author Jing Huang, a Berkeley Lab postdoctoral researcher in the Keasling Lab. "This biological process is much more environmentally friendly than the way chemicals are synthesized today," Huang said.

During experiments at JBEI, the researchers observed the engineered bacterium as it metabolized and converted sugars into the carbene precursor and the alkene substrate. The bacterium also expressed an evolved P450 enzyme that used those chemicals to produce cyclopropanes, high-energy molecules that could potentially be used in the sustainable production of novel bioactive compounds and advanced biofuels. "We can now perform these interesting reactions inside the bacterial cell. The cells produce all of the reagents and the cofactors, which means that you can scale this reaction to very large scales" for mass manufacturing, Keasling said.

Recruiting bacteria to synthesize chemicals could also play an integral role in reducing carbon emissions, Huang said. According to other Berkeley Lab researchers, close to 50% of greenhouse gas emissions come from the production of chemicals, iron and steel, and cement. Limiting global warming to 1.5 degrees Celsius above pre-industrial levels will require severely cutting greenhouse gas emissions in half by 2030, says a recent report by the Intergovernmental Panel on Climate Change.

Huang said that while this fully integrated system can be envisioned for a large number of carbene donor molecules and alkene substrates, it is not yet ready for commercialization.

"For every new advance, someone needs to take the first step. And in science, it can take years before you succeed. But you have to keep trying -- we can't afford to give up. I hope our work will inspire others to continue searching for greener, sustainable biomanufacturing solutions," Huang said.

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Scientist uncovers roots of antibiotic resistance

Bacteria naturally adapt to various environmental stimuli and as they mutate, these changes can make them resistant to drugs that would kill or slow their growth.

In a recent article published in PLoS Genetics, UCF College of Medicine microbiologist Dr. Salvador Almagro-Moreno uncovers the evolutionary origins of antimicrobial resistance (AMR) in bacteria. His studies on the bacterium that causes cholera, Vibrio cholerae, provide insight into deciphering what conditions must occur for infectious agents to become resistant.

"How AMR occurs in bacterial populations and the pathways leading to these new traits are still poorly understood," he said. "This poses a major public health threat as antimicrobial resistance is on the rise."

Dr. Almagro-Moreno studied genetic variants of a protein found in bacterial membranes called OmpU. Using computational and molecular approaches, his team found that several OmpU mutations in the cholera bacteria led to resistance to numerous antimicrobial agents. This resistance included antimicrobial peptides that act as defenses in the human gut. The researchers found that other OmpU variants did not provide these properties, making the protein an ideal system for deciphering the specific processes that occur to make some bacteria resistant to antimicrobials.

By comparing resistant and antibiotic sensitive variants, the researchers were able to identify specific parts of OmpU associated with the emergence of antibiotic resistance. They also discovered that the genetic material encoding these variants, along with associated traits, can be passed between bacterial cells, increasing therisk of spreading AMR in populations under antibiotic pressure.

By understanding how mutations occur, researchers can better understand and develop therapeutics to combat resistant infections. Dr. Almagro-Moreno is also looking at environmental factors such as pollution and warming of the oceans, as possible causes of resistant bacteria. "We are studying the genetic diversity ofenvironmental populations, including coastal Florida isolates, to develop a new approach to understandinghow antimicrobial resistance evolves," he explained.

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Your baby's gut is crawling with unknown viruses

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

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

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

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

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

Bacterial viruses are our allies

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

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

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

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

Shiraz Shah adds:

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

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

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

Could play an important role in inflammatory diseases

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

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

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

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

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

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