A team of researchers have conducted a study on the human microbiome — the trillions of microbial organisms found on and within the human body. They studied microbial communities originating from the gut, skin, mouth, and other parts of the body, revealing new information detailing how these microbes benefit the body and its health.
Researchers from the University of Maryland School of Medicine (UM SOM), Harvard T.H. Chan School of Public Health, the Broad Institute of MIT and Harvard, and the University of California San Diego collaborated on the study, making it the largest study on human microbial communities to ever take place — it’s the continuation of work started by the National Institutes of Health Human Microbiome Project, which initially launched in 2007.
According to Curtis Huttenhower, associate professor of computational biology and bioinformatics at Harvard Chan School, and senior author on the project, the findings provide “the most detailed information to date about exactly which microbes and molecular processes help to maintain health in the human microbiome.”
1,631 new microbial samples were taken from 265 individuals of various ages. DNA sequence analysis tools were used to identify which organisms were present at different body sites, and if their functions or stability changed over time.
At its conclusion, the team was able to identify microbes belonging to specific strains, observe the biochemical activity that allows microbes to maintain the human body’s health, and compile one of the largest profiles of viruses and fungi residing within microbiomes.
Despite the team’s progress, there are still many things about microbial communities that remain unclear — their complexity, while fascinating, requires more time and research.
“In one sense, this study is a great advancement for the research community,” said Anup Mahurkar, executive director of software engineering & information technology at University of Maryland’s Institute for Genome Sciences. “On the other hand, it still just moves the needle. There will always be more we can learn.”
Creating a huge global network connecting billions of individuals might be one of humanity’s greatest achievements to date, but microbes beat us to it by more than three billion years. These tiny single-celled organisms aren’t just responsible for all life on Earth. They also have their own versions of the World Wide Web and the Internet of Things. Here’s how they work.
Much like our own cells, microbes treat pieces of DNA as coded messages. These messages contain information for assembling proteins into molecular machines that can solve specific problems, such as repairing the cell. But microbes don’t just get these messages from their own DNA. They also swallow pieces of DNA from their dead relatives or exchange them with living mates.
These DNA pieces are then incorporated into their genomes, which are like computers overseeing the work of the entire protein machinery. In this way, the tiny microbe is a flexible learning machine that intelligently searches for resources in its environment. If one protein machine doesn’t work, the microbe tries another one. Trial and error solve all the problems.
But microbes are too small to act on their own. Instead, they form societies. Microbes have been living as giant colonies, containing trillions of members, from the dawn of life. These colonies have even left behind mineral structures known as stromatolites. These are microbial metropolises, frozen in time like Pompeii, that provide evidence of life from billions of years ago.
Microbial colonies are constantly learning and adapting. They emerged in the oceans and gradually conquered the land – and at the heart of their exploration strategy was information exchange. As we’ve seen, individual members communicate by exchanging chemical messages in a highly coordinated fashion. In this way, microbial society effectively constructs a collective “mind”.
This collective mind directs pieces of software, written in DNA code, back and forth between trillions of microbes with a single aim: to fully explore the local environment for resources using protein machines.
When resources are exhausted in one place, microbial expedition forces advance to find new lands of plenty. They transmit their discoveries back to base using different kinds of chemical signals, calling for microbial society to transform from settlers to colonisers.
In this way, microbes eventually conquered the entire planet, creating a global microbial network that resembles our own World Wide Web but using biocehmical signals instead of electronic digital ones. In theory, a signal emitted in waters around the South Pole could effectively travel fast to waters around the North Pole.
Internet of Living Things
The similarities with human technology don’t stop there. Scientists and engineers are now working on expanding our own information network into the Internet of Things, integrating all manner of devices by equipping them with microchips to sense and communicate. Your fridge will be able to alert you when it is out of milk. Your house will be able to tell you when it is being burgled.
Microbes built their version of the Internet of Things a long time ago. We can call it the “Internet of Living Things”, although it’s more often known as the biosphere. Every organism on the planet is linked in this complex network that depends on microbes for its survival.
More than a billion years ago, one microbe found its way inside another microbe that became its host. These two microbes became a symbiotic hybrid known as the eukaryotic cell, the basis for most of the lifeforms we are commonly familiar with today. All plants and animals are descended from this microbial merger and so they contain the biological “plug-in” software that connects them to the Internet of Living Things.
For example, humans are designed in a way that means we cannot function without the trillions of microbes inside our bodies (our microbiome) that help us do things like digest foodand develop immunity to germs. We are so overwhelmed by microbes that we imprint personal microbial signatures on every surface we touch.
The Internet of Living Things is a neat and beautifully functioning system. Plants and animals live on the ecological waste created by microbes. While to microbes, all plants and animals are, as author Howard Bloom puts it, “mere cattle on whose flesh they dine”, whose bodies will be digested and recycled one day.
Microbes are even potential cosmic tourists. If humans travel into deep space, our microbes will travel with us. The Internet of Living Things may have a long cosmic reach.
The paradox is that we still perceive microbes as inferior organisms. The reality is that microbes are the invisible and intelligent rulers of the biosphere. Their global biomass exceeds our own. They are the original inventors of the information-based society. Our internet is merely a by-product of the microbial information game initiated three billion years ago.
While the average depth of the ocean is just 2.2 miles, you’d have to travel another four or so to reach the bottom of the massive underwater canyon known as the Mariana Trench. This underwater world is the deepest known place on Earth today, and now, scientists are reporting that the mysterious canyon may also tell the story of how some of the earliest lifeforms on our planet survived in the past.
The Mariana Trench is part of a subduction zone where the sea floor is cluttered with mud volcanoes and hydrothermal vents — evidence of our planet’s molten core. The entire region is located directly over the friction point between the Philippine Sea and Pacific tectonic plates.
Approximately four billion years ago, nascent life on a much younger Earth was hard-pressed to survive the hostile surroundings. The planet endured frequent asteroid strikes and was pock-marked with craters and molten rock. Livable spaces and food were scarce, even for microbes, so researchers think some early lifeforms managed to survive despite these challenges by going deep and calling the Mariana Trench home.
A new study published in the Proceedings of the National Academy of Sciences reports that researchers found traces of organic materials in samples of mineral-rich mud from a mud volcano near the Mariana Trench. Although they did not find actual microbes intact, the organic material could indicate that even the most extreme environments may be able to support life. If these samples do prove to be evidence of life, it would be the deepest form of life ever found on our planet.
“This is another hint at a great, deep biosphere on our planet,” study leader Oliver Plümpertold National Geographic. “It could be huge or very small, but there is definitely something going on that we don’t understand yet.”
Other Life, Other Worlds
Subduction zones like the one in which the samples were discovered are relatively cool — what we understand to be the temperature limit for life, 121 degrees Celsius (250 degrees Fahrenheit), wouldn’t be reached until six or more miles below the floor of the ocean. Furthermore, the minerals in which the organic materials were found are formed through a process known as serpentinization, which produces both methane and hydrogen gases that microbes can then consume as food.
Since they started to look for it in the 1960s, scientists have found serpentinization all over the planet: where continents meet and form, inside mountain ranges that were once at the bottom of the ocean, and near hydrothermal vents.
Because serpentinization is fairly common and can support life in extreme conditions, scientists think it might be the key to finding life on other worlds. Both Saturn’s moon Enceladus and Jupiter’s moon Europa likely have deep liquid oceans underneath their icy exteriors, and Enceladus appears to have some tectonic activity, the source of subduction zones like those of the Mariana Trench.
However, scientists in search of microbial life deep within the trenches of other worlds would need to conquer the same challenges as scientists studying the Mariana Trench here on Earth. Reaching deep enough for direct study isn’t possible, so you’re limited to interpreting evidence spewed from geysers and extracted from rock. “I think of it kind of like a message in the bottle,” explained Plümper. “We have this container coming up, and we are opening it up and trying to figure out what’s going on.”
Evidence of a link between various cognitive and developmental disorders and bacteria living in the gut is growing. Studies have shown a difference in the microbiomes of children living with autism and children not on the spectrum of autism disorders. Now, research is emerging that suggests a link between gut bacteria and Parkinson’s disease.
According to Haydeh Payami, Ph.D., professor in the Department of Neurology, at the University of Alabama (UAB) School of Medicine, “Our study showed major disruption of the normal microbiome — the organisms in the gut — in individuals with Parkinson’s.” Researchers are unsure which comes first, the microbial disruption or the disease. They will have to continue studying to see if having Parkinson’s causes changes in the bacteria or if abnormalities in the microbiome contribute to the development of the disease.
The study consisted of 197 Parkinson’s sufferers and 130 control subjects. The research has been published in Movement Disorders, the journal of the International Parkinson and Movement Disorder Society.
The implications of these study results mean are immense. It could now be possible to find ways to better and faster diagnose Parkinson’s disease and maybe one day even find more effective treatment options.
The study found that some species of bacteria were found in greater numbers in non-Parkinson’s subjects, while other species were found in significantly fewer numbers. Current Parkinson’s medications could partially be to blame for these disparities.
“It could be that, in some people, a drug alters the microbiome so that it causes additional health problems in the form of side effects,” Payami said. “Another consideration is that the natural variability in the microbiome could be a reason some people benefit from a given drug and others are unresponsive. The growing field of pharmacogenomics — tailoring drugs based on an individual’s genetic makeup — may need to take the microbiome into consideration.”
The study is currently being repeated in Alabama to replicate and confirm the results. Payami says, “This opens up new horizons, a totally new frontier.”
Penelope Boston, head of NASA’s Astrobiology Institute, recently made some fascinating discoveries deep in an abandoned zinc and lead mine in Mexico. This abandoned mine, the Naica caves, run 800 meters (2,625 feet) deep and are home to some punishing conditions. These unwelcoming qualities make the discovery of microbes
deep below the Earth’s surface even more remarkable. Boston found 40 different strains of microbes and even some viruses in the depths of these caves.
The team was only able to work for twenty minutes at a time as the caves are extremely hot. They had to wear spacesuit knockoffs and be strapped with ice packs to endure the high temperatures, even for such a short period of time. To put it in perspective, the section of cave designated as the “cool” room was about 38C (100F).
The lifeforms found were unlike anything seen before on Earth. In fact, the nearest genetic relatives to this microscopic organisms still retain a 10% genetic difference. As The Guardianreports, that’s about the same as the difference between humans and mushrooms.
Tough Lil’ Buggers
The lifeforms have been evaluated and determined to be about 50,000 years old. This is a far leap from previous discoveries of life forms that were potentially a half a million years old, but surviving unforgiving conditions in rock or crystal, differing them from the organisms enduring from within ice and salt.
University of South Florida biologist, Norine Noonan stated, “Why are we surprised? As a biologist, I would say life on Earth is extremely tough and extremely versatile.” Such versatility allows for scientists to get a clearer view of the origins of life on planet Earth. Seeing how life endures such harsh conditions can clue us into how the earliest life on Earth survived when the entire planet was inhospitable to most lifeforms that we are familiar with.
Boston’s research has yet to be peer reviewed but she continues to do testing on the microbes. Data from living creatures combined with existing knowledge and what we can learn from ancient lifeforms in the form of fossils can give us a clearer view of Earth’s earliest life, as well as life on other seemingly inhospitable planets.
“Among many flexible and integrative paper-based batteries with a large upside, paper-based microbial fuel cell technology is arguably the most underdeveloped,” says Seokheun “Sean” Choi, lead researcher of the study. His team’s latest research is based on a previous matchbook-styled prototype they developed back in 2015, which evolved into a more powerful version that took the shape of a ninja throwing star.
In the latest version of their technology, a cathode is created using a sliver of silver nitrate placed under a very thin layer of wax on a single sheet of chromatography paper. A reservoir created out of conductive polymer is made on the opposite half of the paper to form the anode. Once a bit of bacteria-laden liquid is dropped onto the paper and the two sides come in contact with one another through folding, the microbes’ cellular respiration is used to generate electricity.
Because this battery can be folded into various configurations, it is both easily portable and capable of generating differing amounts of energy depending on the needs of the user. A configuration of six batteries in three parallel series produced 31.51 microwatts at 125.53 microamps, while a six-by-six configuration generated 44.85 microwatts at 105.89 microamps, according to Newswise.
While this amount of energy wouldn’t be enough to illuminate a light bulb, let alone power a smartphone, it’s more than enough to power things like biosensors that can perform life-saving functions. Combine that energy output with the device’s portability and low cost, and you have a technology that could prove remarkably useful in remote areas or in emergency and disaster situations.
“We are excited about this because microorganisms can harvest electrical power from any type of biodegradable source, like wastewater, that is readily available,” Choi adds. “I believe this type of paper biobattery can be a future power source for papertronics.”