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Tag: archaea

Published on Leave a comment on Archaea May Be Living In Your Sinuses

Everyone has millions of microbes living in complex communities in their sinuses. All these hundreds of species of bacteria, fungi, and viruses are the sinus microbiome or sinus microbiota. In addition, some (many?) people also have tiny organisms called archaea living in their sinuses.

What are archaea? Archaea are single-celled organisms that lack cell nuclei, and have a unique cell wall membrane. Very little is known about them, what their role is in the sinuses (that is, what are they doing there?), how do they interact with the host (the person), and whether their presence is beneficial or not.

There are only a few studies looking at archaea in humans, and while very little is known, the current view is that there are no known harmful archaea ("archaeal pathogens or parasites").

In a 2019 study, French researchers found archaea in the sinuses of 9 of their patients with chronic sinusitis - and therefore thought they were linked to disease. But unfortunately they didn't look to see if archaea are also found in the sinuses of healthy persons, thus there wasn't a comparison group. They found methanogenic archaea (the only microorganisms able to produce methane) in these nine patients, and they thought that the archaea were contributing to or causing the chronic sinusitis.

The Methanobrevibacter species they found were  M. smithii, M. oralis, and M. massiliense, of which 2 have been found in dental plaque and periodontitis lesions, and one is a gut methanogen. [Note: This means it is found in the gut and is methane producing - but that doesn't mean it is harmful.]

Finally, a more recent and comprehensive study looked at archaea and bacteria in the sinuses of both healthy persons and those with chronic sinusitis. University of Auckland researchers found that only 6 out of 70 persons (both healthy and with sinusitis) had archaea in the sinuses, and they were very low in numbers and in diversity. In those with archaea, there was a lot of variation between people. They did not see any archaea associated with chronic sinusitis.

Archaea found were from Euryarchaeota, Thaumarchaeota, and Methanobrevibacteriaceae phyla.

One can only wonder what the archaea are doing in the sinuses in those with them. Especially, as the researchers point out that archaea are characterized by a unique cell wall membrane that "assists survival in extreme conditions such as hydrothermal vents, salt lakes, anoxic and highly acidic or alkaline environments". Also, that recent studies suggest that the human immune system recognizes and can be "activated" by archaea.

Archaea. Credit: Wikipedia

Finally, studies also mention that archaea are resistant to many antibiotics (because of lack of peptidoglycan in their cell wall). It is unknown how this influences their role (if any) in human health and disease.

As you can see, much is unknown right now. Even how many people have archaea in their sinuses, and what kinds of archaea. Stay tuned.

Article by B.W. Mackenzie et al in Frontiers in Cellular Infection and Microbiology: A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis

Published on Leave a comment on It Is Normal to Have Archaea On Our Skin

Something new to add to the list of what is in our skin microbiome - the community of microbes (bacteria, fungi, viruses) living on our skin. It turns out we also have archaea, which are single-celled microorganisms that are thought to be beneficial. (Earlier post on archaea found in our bodies.)

The human skin microbiome acts as a barrier protecting our body from pathogens and other environmental influences. The most common archaea found in the samples (from the chest area of 51 volunteers between the ages of 1 to 75 years) is called Thaumarchaeota. The results reveal that archaea are more abundant in people older than 60 years or younger than 12 years (as compared to middle-aged persons). But there were no differences between males and females. From Science Daily:

What's on your skin? Archaea, that's what

It turns out your skin is crawling with single-celled microorganisms -- and they're not just bacteria. A study by the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and the Medical University of Graz has found that the skin microbiome also contains archaea, a type of extreme-loving microbe, and that the amount of it varies with age. The researchers conducted both genetic and chemical analyses of samples collected from human volunteers ranging in age from 1 to 75. They found that archaea (pronounced ar-KEY-uh) were most abundant in subjects younger than 12 and older than 60. 

In addition to the influence of age, they found that gender was not a factor but that people with dry skin have more archaea. "Archaea might be important for the cleanup process under dry skin conditions," said Moissl-Eichinger. "The results of our genetic analysis (DNA-based quantitative PCR and next-generation sequencing), together with results obtained from infrared spectroscopy imaging, allowed us to link lower levels of sebum [the oily secretion of sebaceous glands] and thus reduced skin moisture with an increase of archaeal signatures."

It was not until the 1970s that scientists realized how different archaea were from bacteria, and they became a separate branch on the tree of life -- the three branches being Bacteria, Archaea, and Eukarya (which includes all plants and animals). Archaea are commonly found in extreme environments, such as hot springs and Antarctic ice. Nowadays it is known that archaea exist in sediments and in Earth's subsurface as well, but they have only recently been found in the human gut and linked with the human microbiome.

Their study focused on Thaumarchaeota, one of the many phyla of archaea, as little evidence of the others was found in the pilot study. "We know that Thaumarchaeota are supposed to be an ammonia-oxidizing microorganism, and ammonia is a major component of sweat, which means they might play a role in nitrogen turnover and skin health," Holman said. .... the team also correlated archaeal abundance with skin dryness, as middle-aged persons have higher sebum levels and thus moister skin than the elderly. So far, most archaea are known to be beneficial rather than harmful to human health. They may be important for reducing skin pH or keeping it at low levels, and lower pH is associated with lower susceptibility to infections.  [Original study.]

Thaumarchaeota archaea. These single-celled organisms have just one membrane sac that encloses their bodies. Credit: Univ. of Washington

 

Published on Leave a comment on A New Tree of Life That’s Mainly Bacteria

In 1837, Charles Darwin sketched a simple tree of life (shown left) to illustrate the idea that all living things share a common ancestor. Ever since then, scientists have been adding names to the tree of life, including a massive effort of 2.3 million named species of animals, plants, fungi and microbes in 2015. A tree of life is a visual hypothesis of how scientists think species are related to one another, so it has been evolving over the years as more information is learned and species discovered.

Now a group of 17 researchers have sketched out a radically different tree of life. It has two main trunks—one full of bacteria and another comprised of archaea, a group of single-celled microbes that run on very different biochemistry. The eukaryotes—the domain that includes all animals, fungi, and plants—are crowded on a thin branch coming off the archaeal trunk. About half of these bacterial branches belong to a supergroup, which was discovered very recently and is currently known as the candidate phyla radiation. Within these branches are numerous species that we’re almost completely ignorant about, and they’ve never been isolated or grown in a lab (with one exception called TM7). In fact, this supergroup of bacteria and “other lineages that lack isolated representatives clearly comprise the majority of life’s current diversity,” write researchers Hug and Banfield. Wow. From Science Daily:

Wealth of unsuspected new microbes expands tree of life

Scientists have dramatically expanded the tree of life, which depicts the variety and evolution of life on Earth, to account for over a thousand new microscopic life forms discovered over the past 15 years. The expanded view finally gives bacteria and Archaea their due, showing that about two-thirds of all diversity on Earth is bacterial -- half bacteria that cannot be isolated and grown in the lab -- while nearly one-third is Archaeal.

Much of this microbial diversity remained hidden until the genome revolution allowed researchers like Banfield to search directly for their genomes in the environment, rather than trying to culture them in a lab dish. Many of the microbes cannot be isolated and cultured because they cannot live on their own: they must beg, borrow or steal stuff from other animals or microbes, either as parasites, symbiotic organisms or scavengers.

The new tree, to be published online April 11 in the new journal Nature Microbiology, reinforces once again that the life we see around us -- plants, animals, humans and other so-called eukaryotes -- represent a tiny percentage of the world's biodiversity.

"Bacteria and Archaea from major lineages completely lacking isolated representatives comprise the majority of life's diversity," said Banfield.....According to first author Laura Hug,... the more than 1,000 newly reported organisms appearing on the revised tree are from a range of environments, including a hot spring in Yellowstone National Park, a salt flat in Chile's Atacama desert, terrestrial and wetland sediments, a sparkling water geyser, meadow soil and the inside of a dolphin's mouth. All of these newly recognized organisms are known only from their genomes.

One striking aspect of the new tree of life is that a group of bacteria described as the "candidate phyla radiation" forms a very major branch. Only recognized recently, and seemingly comprised only of bacteria with symbiotic lifestyles, the candidate phyla radiation now appears to contain around half of all bacterial evolutionary diversity.

Charles Darwin first sketched a tree of life in 1837 as he sought ways of showing how plants, animals and bacteria are related to one another. The idea took root in the 19th century, with the tips of the twigs representing life on Earth today, while the branches connecting them to the trunk implied evolutionary relationships among these creatures.....Archaea were first added in 1977 after work showing that they are distinctly different from bacteria, though they are single-celled like bacteria. A tree published in 1990 by microbiologist Carl Woese was "a transformative visualization of the tree," Banfield said. With its three domains, it remains the most recognizable today.

With the increasing ease of DNA sequencing in the 2000s, Banfield and others began sequencing whole communities of organisms at once and picking out the individual groups based on their genes alone. This metagenomic sequencing revealed whole new groups of bacteria and Archaea, many of them from extreme environments, such as the toxic puddles in abandoned mines, the dirt under toxic waste sites and the human gut. Some of these had been detected before, but nothing was known about them because they wouldn't survive when isolated in a lab dish.

For the new paper, Banfield and Hug teamed up with more than a dozen other researchers who have sequenced new microbial species, gathering 1,011 previously unpublished genomes to add to already known genome sequences of organisms representing the major families of life on Earth.....The analysis, representing the total diversity among all sequenced genomes, produced a tree with branches dominated by bacteria, especially by uncultivated bacteria. A second view of the tree grouped organisms by their evolutionary distance from one another rather than current taxonomic definitions, making clear that about one-third of all biodiversity comes from bacteria, one-third from uncultivable bacteria and a bit less than one-third from Archaea and eukaryotes. (Original article and diagrams.)

This is a new and expanded view of the tree of life, with clusters of bacteria (left), uncultivable bacteria called 'candidate phyla radiation' (center, purple) and, at lower right, the Archaea and eukaryotes (green), including humans.
Credit: Graphic by Zosia Rostomian, Lawrence Berkeley National Laboratory

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It turns out that we also have microbes called archaea living in and on our bodies. They are part of our microbiome (community of microbes living in and on us, which also includes bacteria, viruses, and fungi). Archaea constitute a domain or kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells. Archaeal cells have unique properties that separate them from bacteria and eukaryotes. Archaea were initially classified as bacteria and thought to only exist in extreme environments (such as hot springs and salt lakes), and given the name archaebacteria, but this classification is now outdated. We now know that archaea live in less extreme places, including oceans, marshlands, animals, and humans.

So little is known about archaea that not even medical schools discuss this topic. This may be due to the fact that we currently don't know of any archaea that are human pathogens (that is, that cause illness) or parasitic. They are generally viewed as mutuals (the relationship is beneficial to both organisms) or commensals (they benefit, but don't help or harm the other organism). Humans appear to have low levels of archaea, and so far they have  been found in the human gut (part of digestion and metabolism), on the skin, and in subgingival dental plaque (and perhaps involved with periodontal disease). But studies rarely look for them. We don't know the importance or roles that they play in our bodies (but there are suspicions), but it turns out that drugs such as statins and the antibiotic metronidazole  are eliminating them.

Note that methanogens are archaea that excrete or produce methane as a metabolic byproduct in anoxic (no oxygen) conditions such as the gut. They help digest our food. The species Methanobrevibacter smithii  has been shown to be present in up to 95.7% of humans studied, and found to be the most abundant methanogen in the human gut, comprising up to as much as 10% of all anaerobes found in a healthy individual's colon. Anaerobes are organisms that require oxygen-free conditions to live. Some of the June 2015 article (by M. N. Lurie-Weinberger and U. Goph) excerpts from PLOS:

Archaea in and on the Human Body: Health Implications and Future Directions

Although they are abundant and even dominant members of animal microbiomes (microbiotas), from sponges and termites to mice and cattle, archaea in our own microbiomes have received much less attention than their bacterial counterparts. The fact that human-associated archaea have been relatively little-studied may be at least partially attributed to the lack of any established archaeal human pathogens. Clinically oriented microbiology courses often do not mention archaea at all, and most medical school and biology students are only aware of archaea as exotic extremophiles that have strange and eukaryotic-like molecular machinery. Since archaea have been known to be associated with the human gut for several decades, one would think that human microbiome studies may unravel new facets of archaea–human interactions...  ...continue reading "We Have Archaea In and On Our Bodies"

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Excerpts from an interesting article about microbes and some findings from 2014. From Wired:

9 Amazing and Gross Things Scientists Discovered About Microbes This Year

We can’t see them, but they are all around us. On us. In us. Our personal microbes—not to mention those in the environment around us—have us outnumbered by orders of magnitude, but scientists are only beginning to understand how they influence our health and other aspects of our lives. It’s an increasingly hot area of science, though, and this past year saw lots of interesting developments. Here are some of the highlights.

When you move, your microbes move with you

In a study published in Science in August, scientists cataloged the microbes of seven families, swabbing the hands, feet, and noses of each family member—including pets—for six weeks. They also collected samples from doorknobs, light switches, and other household surfaces. Each home had a distinct microbial community that came mostly from its human inhabitants, and the scientists could tell which home a person lived in just by matching microbial profiles. Three of the families moved during the study period, and it only took about a day for their microbes to settle in to the new place. As the journal’s editors put it: “When families moved, their microbiological ‘aura’ followed.”

Microbes could help solve crimes

Scientists made several findings this year that could potentially show up in court one day. One study found that the microbiome of human cadavers evolves in a predictable way, hinting at a new way to determine time of death. And earlier this month, researchers suggested that bacteria on pubic hair could be used to identify the perpetrators of sex crimes—especially useful when a rapist uses a condom to avoid leaving behind DNA evidence.

Your gut bacteria may be inherited

Exactly which bacteria choose to take up residence in your gut is determined, in part, by your genes, scientists reported this year after examining more than 1,000 fecal samples from 416 pairs of twins... One of the most heritable types was a family of bacteria called Christensenellaceae, which are more abundant in lean people than in obese people. 

Forget fecal transplants, poo pills may be just as effective

Clostridium difficile (pictured) is a nasty bacteria that wreaks havoc on the guts and kills 14,000 people a year in the US alone. Normally, other intestinal bacteria keep C. diff in check, but in the worst infections it starts to dominate. One effective but off putting treatment is a fecal transplant: taking a stool sample from a healthy person and transplanting it into the patient (in through the out door, so to speak). This year researchers developed a less cringe-inducing alternative. They created odorless frozen capsules that contained bacteria isolated from healthy stool samples. The poo pills successfully treated 18 of 20 patients with antibiotic-resistant C. diff infections, the team reported in JAMA in October.

Yeast evolved to lure fruit flies (not to make delicious beer)

There is crazy microbial diversity in cheese rinds

A tiny crumb of cheese rind contains about 10 billion microbial cells: bacteria and fungi that turn boring milk into something funky and delicious. Although cheesemakers have been manipulating them for centuries, not much is known about these microbes. This year scientists conducted the largest study yet on the microbial diversity of cheese, examining 137 cheeses from 10 countries.They found that microbial communities vary according to the style of cheese, but not so much according to where the cheese is made.

The microbiome could be a source of novel drugs

The bacteria that live on and in our bodies make countless molecules. Some of those molecules might make good drugs. 

We may need new branches on the tree of life for all the microbes

Life on Earth has traditionally been divided into three domains: Eukaryotes (plants, animals, and all other organisms that stash their DNA in a special compartment—the nucleus—inside their cells), Bacteria (our familiar one-celled friends and foes), and Archaea (single-celled organisms that are biochemically and genetically distinct from the other two groups). But do we really know that’s all there is? We do not, two scientists argued last month in Science. There may be entire domains of life that have eluded our methods of detection.

Without microbes, life as we know it would end

In December, two scientists posed a thought question in the journal PLOS Biology: What would happen in a world without microbes? ...Without nitrogen-fixing soil bacteria, crops would begin to fail. Decomposition would stop, waste would pile up, and the nutrient recycling that supports life as we know it would grind to a halt. “We predict complete societal collapse only within a year or so, linked to catastrophic failure of the food supply chain,” the researchers write. “Annihilation of most humans and nonmicroscopic life on the planet would follow a prolonged period of starvation, disease, unrest, civil war, anarchy, and global biogeochemical asphyxiation.”

 Clostridium difficile. Credit: CDC

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Flatulence is good, and up to 18 a day is totally normal! From NPR:

Got Gas? It Could Mean You've Got Healthy Gut Microbes

We know that air often comes after eating nutrient-packed vegetables, such as cabbage, kale and broccoli. And researchers have found that fiber-rich foods, like beans and lentils, boost the levels of beneficial gut bacteria after only a few days, as we reported in December.

So all this got us wondering: Could passing gas, in some instances, be a sign that our gut microbes are busy keeping us healthy? Absolutely, says Purna Kashyap, a gastroenterologist at the Mayo Clinic in Rochester, Minn. "Eating foods that cause gas is the only way for the microbes in the gut to get nutrients," he says. "If we didn't feed them carbohydrates, it would be harder for them to live in our gut."

And we need to keep these colon-dwelling critters content, Kashyap says. When they gobble up food — and create gas — they also make molecules that boost the immune system, protect the lining of the intestine and prevent infections.

"A healthy individual can have up to 18 flatulences per day and be perfectly normal," he adds.

Gas gets into the digestive tract primarily through  two routes: Swallowing air (which we all do when we eat and chew gum) and your microbiome. That's the collection of organisms in the GI tract that scientists and doctors are currently all fired up about. (Check our colleague Rob Stein's recent series on it.) That microbiome includes hundreds of different bacteria. But there are also organisms from another kingdom shacking up with them: the archaea.

All these microbes are gas-making fools. They eat up unused food in your large intestine, like fiber and other carbohydrates we don't digest, and churn out a bunch of gases as waste. But that's not all they make. They also produce a slew of molecules (called short chain fatty acids) that may promote the growth of other beneficial bacteria and archaea.

And the more fiber you feed these friendly inhabitants, the more types of species appear, studies have found. "Undigested carbohydrates allow the whole ecosystem to thrive and flourish," Kashyap says. Most gas made by the microbiome is odorless. It's simply carbon dioxide, hydrogen or methane. But sometimes a little sulfur slips in there."That's when it gets smelly," Kashyap says.

But here's the hitch: Many of the smelly sulfur compounds in vegetables have healthful properties. Take for instance, the broccoli, mustard and cabbage family. These Brassica vegetables are packed with a sulfur compound, called sulforaphane, that is strongly associated with a reduced risk of cancer. Another possible benefit of a little smelly gas? It may reduce the total volume of air in the gut, Kashyap says.