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We are Not Us Without The Microbes Within Us

Posted on April 16, 2017  Comments (1)

I Contain Multitudes is a wonderful book by Ed Young on the microbes within us.

Time and again, bacteria and other microbes have allowed animals to transcend their basic animalness and wheedle their way into ecological nooks and crannies that would be otherwise inaccessible; to settle into lifestyles that would be otherwise intolerable; to eat what they could not otherwise stomach; to succeed against their fundamental nature. And the most extreme examples of this mutual assured success can be found in the deep oceans, where some microbes supplement their hosts to such a degree that the animals can eat the most impoverished diets of all – nothing.

This is another book exploring the wonders of biology and the complexity of the interaction between animals and microbes.

For hundreds of years, doctors have used dioxin to treat people whose hearts are failing. The drug – a modified version of a chemical from foxglove plants – makes the heart beat more strongly, slowly, and regularly. Or, at least, that’s what it usually does. In one patient out of every ten, digoxin doesnt’ work. Its downfall is a gut bacterium called Eggerthella lenta, which converts the drug to an inactive and medically useless form. Only some strains of E. lenta do this.

The complex interactions within us are constantly at work helping us and occasionally causing problems. This obviously creates enormous challenges in health care and research on human health. See related posts: Introduction to Fractional Factorial Designed Experiments, “Grapefruit Juice Bugs” – A New Term for a Surprisingly Common Type of Surprising Bugs and 200,000 People Die Every Year in Europe from Adverse Drug Effects – How Can We Improve?.

Every person aerosolized around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment.

Avoiding bacteria is not feasible. Our bodies have evolved with this constant interaction with bacteria for millions of years. When we are healthy bacteria have footholds that make it difficult for other bacteria to gain a foothold (as does our immune system fighting off those bacteria it doesn’t recognize or that it recognized as something to fight).

A few pages later he discusses the problem of hospital rooms that were constantly cleaned to kill bacteria and largely sealed to reduce airflow. What happened is those bacteria the sick people had in them were the bacteria that were flourishing (the number of other bacteria to compete for space was small). Opening the windows to welcome the outside air resulted in better results.

Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world

Human health is a fascinating topic. It is true antibiotics have provided us great tools in the service of human health. But we have resorted to that “hammer” far too often. And the consequences of doing so is not understood. We need those scientists exploring the complex interactions we contain to continue their great work.

Related: People are Superorganisms With Microbiomes of Thousands of Species (2013) – Bacteria are Always Living in Our Bodies (2014) – Gut Bacteria Explored as Medical Treatment – even for Cancer

Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

Posted on February 17, 2013  Comments (3)

The percent of human genes that emerged in various stages of evolution: 37% bacterial, 28% eukaryotic, 16% animal, 13% vertebrate, 6% primate. The history that brought us to where we are is amazing. Eukaryotes include animals, plants, amoebae, flagellates, amoeboflagellates, fungi and plastids (including algae). So eukaryotic genes are those common to us and other non-animal eukaryotes while those classified as animal genes are shared by animals but not non-animal eukaryotes.

We are living in a bacterial world, and it’s impacting us more than previously thought by Lisa Zyga

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal’s immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have “hijacked” these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.
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Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.
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We want badly for the message in ‘Animals in a bacterial world,’ to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper.”

Very cool stuff. This amazing facts scientists discover provide an amazing view of the world we live in and how interconnected we are to other life forms in ways we don’t normally think of.

Related: People’s Bodies Carry More Bacterial Cells than Human Cells – Microbes Flourish In Healthy People – Tracking the Ecosystem Within Us – Foreign Cells Outnumber Human Cells in Our Bodies – Bacteria Beneficial to Human Health

Sex and Development of Life in the Ocean

Posted on June 16, 2012  Comments (0)

TED education is providing access to really interesting education material. In this webcast learn about fertilization, development and growth in the ocean depths.

Related: Hydromedusae, Siphonophora, Cnidarians, Ctenophores – Darwin’s Jellyfish – The Secret Life of Plankton – Researchers Explain How Rotifers Thrive Despite Forgoing Sex

Evidence of Extraterrestrial Life Discovered?

Posted on March 5, 2011  Comments (1)

Has evidence of extraterrestrial life been discovered? In Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites , Richard B. Hoover, Ph.D. NASA/Marshall Space Flight Center, puts forth his evidence on the discovery of evidence of cyanobacteria in meteorites.

Dr. Hoover has discovered evidence of microfossils similar to Cyanobacteria, in freshly fractured slices of the interior surfaces of the Alais, Ivuna, and Orgueil CI1 carbonaceous meteorites. Based on Field Emission Scanning Electron Microscopy (FESEM) and other measures, Dr. Hoover has concluded they are indigenous to these meteors and are similar to trichomic cyanobacteria and other trichomic prokaryotes such as filamentous sulfur bacteria. He concludes these fossilized bacteria are not Earthly contaminants but are the fossilized remains of living organisms which lived in the parent bodies of these meteors, e.g. comets, moons, and other astral bodies. The implications are that life is everywhere, and that life on Earth may have come from other planets.

The importance of this claim is hard to ignore. The journal includes a statement from Dr. Rudy Schild, Center for Astrophysics, Harvard-Smithsonian, Editor-in-Chief, Journal of Cosmology:

Dr. Richard Hoover is a highly respected scientist and astrobiologist with a prestigious record of accomplishment at NASA. Given the controversial nature of his discovery, we have invited 100 experts and have issued a general invitation to over 5000 scientists from the scientific community to review the paper and to offer their critical analysis. Our intention is to publish the commentaries, both pro and con, alongside Dr. Hoover’s paper. In this way, the paper will have received a thorough vetting, and all points of view can be presented. No other paper in the history of science has undergone such a thorough analysis, and no other scientific journal in the history of science has made such a profoundly important paper available to the scientific community, for comment, before it is published. We believe the best way to advance science, is to promote debate and discussion.

Read the full paper.

The filaments have been observed to be embedded in freshly fractured internal surfaces of the stones. They exhibit features (e.g., the size and size ranges of the internal cells and their location and arrangement within sheaths) that are diagnostic of known genera and species of trichomic cyanobacteria and other trichomic prokaryotes such as the filamentous sulfur bacteria. ESEM and FESEM studies of living and fossil cyanobacteria show similar features in uniseriate and multiseriate, branched or unbranched, isodiametric or tapered, polarized or unpolarized filaments with trichomes encased within thin or thick external sheaths. Filaments found in the CI1 meteorites have also been detected that exhibit structures consistent with the specialized cells and structures used by cyanobacteria for reproduction (baeocytes, akinetes and hormogonia), nitrogen fixation (basal, intercalary or apical heterocysts) and attachment or motility (fimbriae).
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These studies have led to the conclusion that the filaments found in the CI1 carbonaceous meteorites are indigenous fossils rather than modern terrestrial biological contaminants that entered the meteorites after arrival on Earth. The δ13C and D/H content of amino acids and other organics found in these stones are shown to be consistent with the interpretation that comets represent the parent bodies of the CI1 carbonaceous meteorites. The implications of the detection of fossils of cyanobacteria in the CI1 meteorites to the possibility of life on comets, Europa and Enceladus are discussed.

Has life been found in a meteorite? by Phil Plait
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Changing Life as We Know It

Posted on December 2, 2010  Comments (1)

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

photo of Felisa Wolfe-Simon

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
Continue reading →

All present-day Life on Earth Has A Single Ancestor

Posted on June 21, 2010  Comments (3)

All present-day life arose from a single ancestor

All life on Earth shares a single common ancestor, a new statistical analysis confirms.
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Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.
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A universal common ancestor is at least 102,860 times more probable than having multiple ancestors, Theobald calculates.
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For his analysis, Theobald selected 23 proteins that are found across the taxonomic spectrum but have structures that differ from one species to another. He looked at those proteins in 12 species – four each from the bacterial, archaeal and eukaryotic domains of life.

Then he performed computer simulations to evaluate how likely various evolutionary scenarios were to produce the observed array of proteins. Theobald found that scenarios featuring a universal common ancestor won hands down against even the best-performing multi-ancestor models.

Very interesting. Surprising too. As the article points out this doesn’t mean all life ever on Earth evolved from the single ancestor – life that has gone extinct could be from outside this single “tree.”

Related: Viruses and What is Life – Evolution is Fundamental to Science – Bacteria “Feed” on Earth’s Ocean-Bottom Crust

A single Liter of Seawater Can Hold More Than One Billion Microorganisms

Posted on April 20, 2010  Comments (0)

Mat of microbes the size of Greece discovered on seafloor

mighty microbes, which constitute 50 to 90 percent of the oceans’ total biomass, according to newly released data.

These tiny creatures can join together to create some of the largest masses of life on the planet, and researchers working on the decade-long Census of Marine Life project found one such seafloor mat off the Pacific coast of South America that is roughly the size of Greece.

A single liter of seawater, once thought to contain about 100,000 microbes, can actually hold more than one billion microorganisms, the census scientists reported. But these small creatures don’t just live in the water column or on the seafloor. Large communities of microscopic animals have even been discovered more than one thousand meters beneath the seafloor. Some of these deep burrowers, such as loriciferans, are only a quarter of a millimeter long.

“Far from being a lifeless desert, the deep sea rivals such highly diverse ecosystems as tropical rainforests and coral reefs,”
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Microbes help to turn atmospheric carbon dioxide into usable carbon, completing about 95 percent of all respiration in the Earth’s oceans…

Related: Iron-breathing Species Isolated in Antarctic for Millions of Years – Life Far Beneath the Ocean – Life Untouched by the Sun

Surprise Shrimp Under Antarctic Ice

Posted on March 27, 2010  Comments (0)

A three-inch long Lyssianasid amphipod found 600 feet beneath the Ross Ice Shelf stars in a recent popular webcast (see below). NASA scientists were using a borehole camera to look back up towards the ice surface when they spotted this pinkish-orange creature swimming beneath the ice.

Stacy Kim of Moss Landing Marine Laboratory was the first biologist to see the video and immediately recognized it as a Lyssianasid amphipod. It was about 3 inches long and Stacy concluded that this meant there was quite an extensive biological community under the ice here – even 20 miles from open water.

Related: Iron-breathing Species Isolated in Antarctic for Millions of Years – Pine Island Glacier (PIG) Ice Shelf – The Brine Lake Beneath the Sea – Lake Under 2 Miles of Ice
Continue reading →

Microcosm by Carl Zimmer

Posted on December 26, 2009  Comments (0)

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on Earth – Foreign Cells Outnumber Human Cells in Our Bodies – Amazing Designs of Life – Amazing Science: Retroviruses – One Species’ Genome Discovered Inside Another’s

Ant mega-colony

Posted on July 2, 2009  Comments (0)

Ant mega-colony takes over world

Argentine ants living in vast numbers across Europe, the US and Japan belong to the same interrelated colony, and will refuse to fight one another. The colony may be the largest of its type ever known for any insect species, and could rival humans in the scale of its world domination.
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In Europe, one vast colony of Argentine ants is thought to stretch for 6,000km (3,700 miles) along the Mediterranean coast, while another in the US, known as the ‘Californian large’, extends over 900km (560 miles) along the coast of California. A third huge colony exists on the west coast of Japan.
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While ants are usually highly territorial, those living within each super-colony are tolerant of one another, even if they live tens or hundreds of kilometres apart. Each super-colony, however, was thought to be quite distinct. But it now appears that billions of Argentine ants around the world all actually belong to one single global mega-colony.
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The team selected wild ants from the main European super-colony, from another smaller one called the Catalonian super-colony which lives on the Iberian coast, the Californian super-colony and from the super-colony in west Japan, as well as another in Kobe, Japan.

Ants from the smaller super-colonies were always aggressive to one another. So ants from the west coast of Japan fought their rivals from Kobe, while ants from the European super-colony didn’t get on with those from the Iberian colony.
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But whenever ants from the main European and Californian super-colonies and those from the largest colony in Japan came into contact, they acted as if they were old friends.

Related: posts on ants – E.O. Wilson: Lord of the Ants – Huge Ant Nest

2,000 Species New to Science from One Island

Posted on December 4, 2008  Comments (1)

photo of squat lobster

Photograph by Dr Tin-Yam Chan, University of Keelung

153 scientists from 20 countries fanned out across the remote South Pacific island of Espiritu Santo, examining mountains, forests, caves, reefs, and water for all living organisms. In five months, they collected 10,000 species. Some 2,000 of these may be new to science.

This squat lobster, found in waters 150 meters (492 feet) deep, is one of the new species. Eighty percent of the world’s species remain to be discovered, notes French scientist Philippe Bouchet, one of the expedition’s leaders.

A World of Crabs from One Tiny Island

About 600 of these were crab species. The two-horn box crab is able to crack and peel open snails’ shells using a sharp “tooth” on its right claw to cut open shells and long, slender “fingers” on the left claw to yank out its prey.

Related: Most Dinosaurs Remain Undiscovered – Ocean Life – Huge Gorilla Population Found in Congo – Still Just a Lizard – 50 Species of Diatoms