A Home for the Microbiome

 Biologists Identify How Beneficial Bacteria Reside and Thrive in Gastrointestinal Tract

A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel. (Credit: Caltech / Mazmanian Lab)

The human body is full of tiny microorganisms -- hundreds to thousands of species of bacteria collectively called the microbiome, which are believed to contribute to a healthy existence. The gastrointestinal (GI) tract -- and the colon in particular -- is home to the largest concentration and highest diversity of bacterial species. But how do these organisms persist and thrive in a system that is constantly in flux due to foods and fluids moving through it? A team led by California Institute of Technology (Caltech) biologist Sarkis Mazmanian believes it has found the answer, at least in one common group of bacteria: a set of genes that promotes stable microbial colonization of the gut.

A study describing the researchers' findings was published as an advance online publication of the journal Natureon August 18.

"By understanding how these microbes colonize, we may someday be able to devise ways to correct for abnormal changes in bacterial communities -- changes that are thought to be connected to disorders like obesity, inflammatory bowel disease and autism," says Mazmanian, a professor of biology at Caltech whose work explores the link between human gut bacteria and health.

The researchers began their study by running a series of experiments to introduce a genus of microbes called Bacteriodesto sterile, or germ-free, mice. Bacteriodes, a group of bacteria that has several dozen species, was chosen because it is one of the most abundant genuses in the human microbiome, can be cultured in the lab (unlike most gut bacteria), and can be genetically modified to introduce specific mutations.

"Bacteriodes are the only genus in the microbiome that fit these three criteria," Mazmanian says.

Lead author S. Melanie Lee (PhD '13), who was an MD/PhD student in Mazmanian's lab at the time of the research, first added a few different species of the bacteria to one mouse to see if they would compete with each other to colonize the gut. They appeared to peacefully coexist. Then, Lee colonized a mouse with one particular species, Bacteroides fragilis, and inoculated the mouse with the same exact species, to see if they would co-colonize the same host. To the researchers' surprise, the newly introduced bacteria could not maintain residence in the mouse's gut, despite the fact that the animal was already populated by the identical species.

"We know that this environment can house hundreds of species, so why the competition within the same species?" Lee says. "There certainly isn't a lack of space or nutrients, but this was an extremely robust and consistent finding when we tried to essentially 'super-colonize' the mice with one species."

To explain the results, Lee and the team developed what they called the "saturable niche hypothesis." The idea is that by saturating a specific habitat, the organism will effectively exclude others of the same species from occupying that niche. It will not, however, prevent other closely related species from colonizing the gut, because they have their own particular niches. A genetic screen revealed a set of previously uncharacterized genes -- a system that the researchers dubbed commensal colonization factors (CCF) -- that were both required and sufficient for species-specific colonization by B. fragilis.

But what exactly is the saturable niche? The colon, after all, is filled with a flowing mass of food, fecal matter and bacteria, which doesn't offer much for organisms to grab onto and occupy.

"Melanie hypothesized that this saturable niche was part of the host tissue" -- that is, of the gut itself -- Mazmanian says. "When she postulated this three to four years ago, it was absolute heresy, because other researchers in the field believed that all bacteria in our intestines lived in the lumen -- the center of the gut -- and made zero contact with the host…our bodies. The rationale behind this thinking was if bacteria did make contact, it would cause some sort of immune response."

Nonetheless, when the researchers used advanced imaging approaches to survey colonic tissue in mice colonized with B. fragilis, they found a small population of microbes living in miniscule pockets -- or crypts -- in the colon. Nestled within the crypts, the bacteria are protected from the constant flow of material that passes through the GI tract. To test whether or not the CCF system regulated bacterial colonization within the crypts, the team injected mutant bacteria -- without the CCF system -- into the colons of sterile mice. Those bacteria were unable to colonize the crypts.

"There is something in that crypt -- and we don't know what it is yet -- that normal B. fragilis can use to get a foothold via the CCF system," Mazmanian explains. "Finding the crypts is a huge advance in the field because it shows that bacteria do physically contact the host. And during all of the experiments that Melanie did, homeostasis, or a steady state, was maintained. So, contrary to popular belief, there was no evidence of inflammation as a result of the bacteria contacting the host. In fact, we believe these crypts are the permanent home ofBacteroides, and perhaps other classes of microbes."

He says that by pinpointing the CCF system as a mechanism for bacterial colonization and resilience, in addition to the discovery of crypts in the colon that are species specific, the current paper has solved longstanding mysteries in the field about how microbes establish and maintain long-term colonization.

"We've studied only a handful of organisms, and though they are numerically abundant, they are clearly not representative of all the organisms in the gut," Lee says. "A lot of those other bacteria don't have CCF genes, so the question now is: Do those organisms somehow rely on interactions with Bacteroides for their own colonization, or their replication rates, or their localization?"

Suspecting that Bacteroides are keystone species -- a necessary factor for building the gut ecosystem -- the researchers next plan to investigate whether or not functional abnormalities, such as the inability to adhere to crypts, could affect the entire microbiome and potentially lead to a diseased state in the body.

"This research highlights the notion that we are not alone. We knew that bacteria are in our gut, but this study shows that specific microbes are very intimately associated with our bodies," Mazmanian says. "They are living in very close proximity to our tissues, and we can't ignore microbial contributions to our biology or our health. They are a part of us."

Funding for the research outlined in the Nature paper, titled "Bacterial colonization factors control specificity and stability of the gut microbiota," was provided by the National Institutes of Health and the Crohn's and Colitis Foundation of America. Additional coauthors were Gregory Donaldson and Silva Boyajian from Caltech and Zbigniew Mikulski and Klaus Ley from the La Jolla Institute for Allergy and Immunology in La Jolla, California.

Source : California Institute of Technology.

By Science and Universe

Fresh Analysis of Dinosaur Skulls Shows Three 'Species' Are Actually One

Landmark locations. The locations of the 3D landmarks are presented here in (A) dorsal and (B) lateral views on ZMNH M8137. Since the landmarks were not reflected on either side of the skull, the left lateral landmarks have different landmark numbers than the right lateral landmarks. A 3D model of the skull of ZMNH M8137 is included in Multimedia S1 for reference. Scale = 50 mm. (Credit: Brandon P. Hedrick, Peter Dodson. Lujiatun Psittacosaurids: Understanding Individual and Taphonomic Variation Using 3D Geometric Morphometrics. PLoS ONE, 2013; 8 (8): e69265 DOI: 10.1371/journal.pone.0069265)

A new analysis of dinosaur fossils by University of Pennsylvania researchers has revealed that a number of specimens of the genus Psittacosaurus — once believed to represent three different species — are all members of a single species. The differences among the fossil remains that led other scientists to label them as separate species in fact arose from how the animals were buried and compressed, the study found.

"Because of the vagaries of fossilization, no two fossils are the same," said senior author Peter Dodson, professor of anatomy in Penn's School of Veterinary Medicine and professor of paleontology in the School of Arts and Sciences' Department of Earth and Environmental Science. "Animals are alive and they die, but what's crucial in paleontology is what happens to the animals after they die."

The research involved a cutting-edge technique, known as three-dimensional geometric morphometrics, which uses lasers to generate data about the shape of different specimens. This is the first time the approach has been used to study dinosaur fossils and could lead to a re-examination of the taxonomic classifications of additional dinosaur species as well as other long-extinct fossil organisms.

Brandon Hedrick, a doctoral student in the Department of Earth and Environmental Science, led the study in collaboration with Dodson. Their research will be reported in the journal PLOS ONE.

The investigation focused on dinosaurs in the genus Psittacosaurus, a word that comes from the Greek for "parrot lizard." The group was named for the animal's beaked face, not unlike that of a turtle. Originally discovered in 1923, 15 species have been classified as Psittacosaurus, though a recent analysis confirmed only nine of these as definite members of the genus. These animals were small plant-eaters that lived 120 to 125 million years ago. Paleontologists have discovered Psittacosaurus fossils in Mongolia, China and Russia and possibly in Thailand.

"Meat-eaters are sexy; plant-eaters are not," Dodson said. "This isn't a flashy dinosaur. But it has an interesting feature in that it's one of the most abundant dinosaurs known to science."

Indeed, many hundreds of Psittacosaurus specimens have been found. This abundance made the genus ideal for Hedrick and Dodson's comparative study, as it is easier to determine relationships within and between species when there are more individuals to compare.

"For example, if you have a single dachshund and a single beagle, they may appear to be different species until you found 40 dachshund-beagle mixes of various grades to examine," Hedrick said.

The scientists examined Psittacosaurus skulls discovered in the fossilized ashes of the Lujiatun beds of northeastern China's Yixian Formation. Paleontologists had previously identified the skulls as belonging to three different species, Psittacosaurus lujiatunensis, P. major or Hongshanosaurus houi.

To compare and contrast the specimens, the researchers used two techniques. First they conducted a traditional study in which they examined every skull that had been classified as one of those three species — a total of 74 specimens — for a variety of characteristics that had been used in prior studies to distinguish the species. The Penn team also compared these fossils to skulls that had been classified as belonging to eight other Psittacosaurus species.

Next they completed a more high-tech analysis of 30 skulls from the three named species. Using a hand-held stylus that captures a point in space relative to a transmitter, they pinpointed 56 "landmarks," or particular anatomical locations, on each fossil and compared the relative position of those marks between specimens. They also used a hand-held, laser-emitting scanner to make a three-dimensional image of each specimen, similar to a CT scan, from which they also collected landmark data.

Based on the "old-fashioned" method of examining the physical skulls, the researchers concluded that the three purported species were in fact one. They propose that all three can be considered members of the species P. lujiatunensis.

Results from the geometric morphometric analysis, though not sufficient on its own to classify species, supported this conclusion and suggested that how an animal's body was crushed as it fossilized — from the top, from the side or twisted — could lead to inaccurate species determinations.

"Our study found all of these false 'species' that are not biological species but are apparent species caused by the process of fossilization," Dodson said.

The Penn team said their investigation shows the value of traditional taxonomic analysis, while also revealing the potential of a new approach to analyzing fossils.

"Hopefully this will open up the paleontological community to using three-dimensional geometrics morphometrics in a variety of ways," Hedrick said. "This technique has limitless applications to understanding dinosaurs."

Article Source : University of Pennsylvania
By Science and Universe