Study something in a test tube, and scientists say that the research was performed in vitro. That’s Latin meaning “in glass.” Study it in a living body, and it’s in vivo (“in a living thing”). But what if your research has you poking around in poop? Scientists haven’t had a word for that — until recently.
Introducing in fimo. This new scientific term describes experiments done on feces. The term, based on the Latin word fimus, meaning “dung,” was introduced this past April in the journal Gastroenterology (GAS-troh-en-tur-OL-oh-gee).
For most of us, poop is gross stuff. We deal with it only grudgingly. But for some scientists, it can be a gold mine of useful data. Feces can provide clues to someone’s health, an animal’s diet or the environment in which an organism lives. That’s what drove these three scientists to in fimo research. They use it to learn about the bacteria in our gut, dinosaur diets and just how poop gets its variety of shapes.
Investigating square scat
Patricia Yang studies fluid mechanics — the science of moving fluids — in animals at the Georgia Institute of Technology in Atlanta. Coming from a family of scientists, "I knew what it was like to have a lab coat and work in a clean lab,” she says. But she was looking for a different way to do science. The answer came on a trip to the zoo. She accompanied her advisor, who was studying how animals urinate. "I thought, 'This is a fluid mechanics problem that I can solve,' At the same time,” she notes, “I saw animals pooping and thought there were probably some similarities there, as well."
Yang has since studied many info-packed bodily substances, including urine, blood and, of course, feces. And after spending a lot of time with poop, she thought she knew it well. It comes in two main shapes. People, dogs and cats are in the group that poop cylinders. Deer and bunnies are among those whose droppings resemble pellets.
But, it turns out, there’s a third shape: square.
“I gave a talk at a conference, and a professor told me, ‘You missed one. There’s a square poop. Wombat poop is square.’” she recalls. That one was new to her.
Wombats are squat marsupials from Australia. They look a bit like small bears. Yang was curious — and suspicious. Square poop? It didn’t make sense. “It’s not right for body design,” she says. “I didn’t think a human or animal could really make a square.” In fact, she observes, square shapes are extremely rare in nature. Other than the bones of some sea horses, Yang couldn’t think of many examples of naturally occurring squares. She says, “We decided we had to see it before we claim that it’s true.”
Yang found pictures of wombat droppings online. Still, she wasn’t convinced. Someone could have shaped the droppings into cubes after the fact. So she contacted zoos with wombats and asked for samples of poop. They refused.
Finally, Yang got in touch with Scott Carver. He’s a wildlife ecologist at the University of Tasmania in Hobart, Australia. And because he was interested in the same topic, he was happy to help.
He confirmed firsthand that out of four wombat species, Vombatus ursinus — also known as the common or bare-nosed wombat — indeed makes square feces. Then, to help Yang figure how they do it, he sent her the intestines of two such wombats that had died after being hit by cars.
Opening up the intestines, Yang was excited by what she found.
“There are squares inside,” she notes, “even before the feces come out.” The wombat’s anus doesn’t produce the square shape, she realized. “It’s happening in their gut.”
On to ballooning research
Yang also noticed that, while the intestine was 6 meters (19 feet) long, only the last 1.5 meters (5 feet) had the unusually shaped feces. Before that, the wastes were soft and unformed. “In the final length, they are all square, with the same dimensions,” she says. Well, at 2 by 2 by 4 centimeters (0.8 by 0.8 by 1.6 inches), they’re actually rectangles.
Yang and her colleagues thought about how their squared shape might form. An animal’s intestine squeezes waste into solid pieces and then pushes it through the body by contracting. What if the wombat intestine was not contracting uniformly?
The researchers got a long balloon, the type used to make balloon animals. They made tick marks along the now-empty intestine and then inflated the balloon inside it. The marks allowed the researchers to see how different parts of the intestine moved as it expanded. These marks don’t expand evenly, Yang notes.
That revealed the tissue of the intestine was not uniform. Some areas were soft. Others were stiff. So when the intestine contracted, it did not do so evenly. It pushed down harder in some areas than others. This created edges and angles. The result: rectangles with slightly rounded edges.
“This is an extreme case of how the property of intestines changes the shape of feces,” Yang concludes.
Her discovery is more than just an interesting factoid. Says Yang, it could help shape items in a poop-free venue: manufacturing. “Right now, we only have two ways of making cubes: We either mold them with solid molds, or we cut them,” she says. These wombat data point to “a third way of making cubes.”
Digging into dino droppings
Ancient poop gives a different type of information. Most manure breaks down and becomes compost — a good thing, since a poop-covered planet would be disgusting. But under special conditions, feces may get preserved as fossils for millions of years. They also get a special name: coprolites. And to Karen Chin, they’re a great tool for studying how dinosaurs ate and interacted with their environment.
Chin works at the University of Colorado at Boulder. As a paleoecologist, she studies the ancient environment. Chin first became interested in feces while working as a seasonal interpreter at national parks such as Yellowstone and Glacier. When she led people on hikes, the groups rarely saw animals. They instead encountered scat. That poop offers a window into “what’s happening in the natural world when you’re not there,” she says.
Later, as a paleontologist, one of her early jobs was writing descriptions for a museum's dinosaur collection. When she was asked to write about its dinosaur coprolites, she got hooked. Chin wanted to know how soft material like feces might become fossilized. She was also curious about what that poop could tell her about what dinosaurs eat and the environment in which they lived.
Unlike deer pellets or bear scat, “dinosaur coprolites are very rare,” she notes. To be preserved, feces had to land in a place where they would be quickly buried. One sample she’s studied, for instance, came from a tidal flat. “The dinosaur walked across and defecated, then the tide rose and helped bury the feces,” she explains.
Smaller coprolites are a bit easier to find. “They’re sausage-shaped and look like dog feces,” she says. But bigger dinosaur poops can be hard to identify. “If you go to the zoo — which I have — and watch elephants defecate, [the poop balls] drop from a considerable height,” she says. “They can be deformed when they fall, or trampled.”
Chin studies these larger coprolites from dinosaurs. To make sure they’re not just “ugly misshapen rocks,” she checks what chemicals they’re made from. She also looks for pieces of chopped-up organic matter, such as leaves, shell or bone. If she sees signs of tiny tunnels or burrowing by dung beetles or other invertebrates, that’s even more evidence that she’s got genuine dinosaur poop on her hands.
If she has permission from the coprolite’s owner (usually a museum), she can cut a thin section from the sample and place it under a microscope. She’ll be looking for bits of what the dinosaur ate, such as cells from animal muscle or bone, plant tissues or pieces of fungi.
In one recent study, Chin examined coprolites that probably came from one or more types of hadrosaurs. These duck-billed dinos lived some 75 million years ago in what is now southern Utah. Their coprolites contained evidence that the dinosaurs had been eating rotting wood. Even more surprising, mixed in with the wood was crunched up pieces of crustacean. That was odd since these dinosaurs were thought to be strictly plant-eaters.
The crustaceans were big enough that the dinosaurs could have spit them out if they didn’t want to eat them. What’s more, the crustaceans were found in seven out of every 10 coprolites she studied. This led Chin to think this carnivorous snack was no accident. But this isn’t necessarily weird behavior for plant-eaters. Some modern herbivorous birds eat insects or other animals to increase their protein intake when they are getting ready to lay eggs. Maybe these dinos — the ancestors of birds — were doing the same thing.
“Whether or not the dinosaurs actually hunted the crustaceans, we don’t know. But if they were feeding on rotting wood and happened to ingest crustaceans, I think they ate them readily,” she says. “That changes our traditional view of these lumbering herbivorous dinosaurs.” They weren’t just standing there feeding on leaves.
Developing stool standards
Poop can give a different view of much smaller critters, too. Over the past 10 years, scientists have learned that the community of microbes living in the gut is hugely important to human health. This collection of microbes is known as our microbiome. Scientists can learn about the gut microbiome by studying what comes out of the gut: poop. Now researchers and drug companies are racing to learn more about how this microbiome works, how it can be used to diagnose diseases and how it might lead to new treatments.
But there’s a catch. There is no standard, agreed-upon way to analyze the genetics of the human microbiome. So every lab uses slightly different tools and methods to extract and analyze the DNA from a bacterial sample. No surprise, then, that different studies get different results.
Scott Jackson wants to change that. As a microbial genomicist (Juh-NOAM-ih-sizt), he studies the genes of microbes. He works at the National Institute of Standards and Technology in Gaithersburg, Md. He leads its Complex Microbial Systems group.
Figuring out the DNA of a member of a microbiome is far harder than sequencing the DNA of a single animal or plant. (Sequencing involves figuring out the order of nucleotides — chemicals that make of the rungs in the ladder-like structure — in an organism’s DNA.)
A scientist looking at the DNA of a single organism often already knows who or what it is. When delving into a bit of poop or other microbiome sample, scientists will be starting with something that contains hundreds of different species of microbes. What’s more, half of those microbes might still be unknown to science. Researchers have to sort out the DNA to see which species are in the sample, and roughly how many of each are present.
Since each lab can come up with slightly different results as they do these analyses, Jackson’s group came up with a plan to compare results from a big group of labs. That might prove helpful for future research in this field.
The researchers started by collecting stool from five generous people. Each donor’s feces were blended to homogenize the samples, or make them uniformly mixed. Researchers from another group, the BioCollective, prepared the samples using a household Ninja blender. The resulting product had “the consistency of a smoothie," Jackson says.
That poop smoothie was then divided up into 700 tubes. Each held about one milliliter (one-fifth of a teaspoon) of poop. The tubes were then divvied up into 700 kits, with each kit containing one tube from each of the five people. “That’s 3,500 tubes of poop,” Jackson notes.
Jackson’s team recruited labs around the world to participate in the tests. Each was asked to sequence the DNA from the microbes in a kit, then upload their results to a website. That would let Jackson’s group compare the findings from lab to lab.
His group has sent out about 100 kits since they launched the project last year. “We have 700 kits, and we’re not going to stop until that 700th kit is shipped,” he says. “What we want to see is how much variability you get when you measure one sample using 100 different [methods].”
Jackson has some theories about what the study will reveal. For one, he expects that not all 700 labs will get the same results.
Besides getting more data how widely the labs’ findings differ, Jackson hopes the project will help identify the tools and methods that work the best. And that’s info that can help guide the next generation of poop scientists.
To most of us, feces are just smelly wastes. But a select group of scientists is finding new meaning in “waste not, want not.”
academic Relating to school, classes or things taught by teachers in formal institutes of learning (such as a college).
anus The opening at the end of an animal's digestive system through which solid waste leaves the body.
bacteria (singular: bacterium) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals). Bacteria are one of the three domains of life on Earth.
beetle An order of insects known as Coleoptera, containing at least 350,000 different species. Adults tend to have hard and/or horn-like “forewings” which covers the wings used for flight.
behavior The way something, often a person or other organism, acts towards others, or conducts itself.
cell The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.
chemical A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.
colleague Someone who works with another; a co-worker or team member.
compost The end product in the breakdown, or decomposition, of leaves, plants, vegetables, manure and other once-living material. Compost is used to enrich garden soil, and earthworms sometimes aid this process.
coprolite Fossilized feces. The word coprolite, in Greek, means “dung stones.” Coprolites are very important because they can provide direct evidence of what ancient creatures ate.
crustaceans Hard-shelled water-dwelling animals including lobsters, crabs and shrimp.
defecate To discharge solid waste from the body.
diagnose To analyze clues or symptoms in the search for their cause. The conclusion usually results in a diagnosis — identification of the causal problem or disease.
diet The foods and liquids ingested by an animal to provide the nutrition it needs to grow and maintain health.
dinosaur A term that means terrible lizard. These ancient reptiles lived from about 250 million years ago to roughly 65 million years ago. All descended from egg-laying reptiles known as archosaurs. Their descendants eventually split into two lines.
DNA (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.
dung The feces of animals, also known as manure.
dung beetle A type of insect found on all continents except for Antarctica. They feed on a soupy liquid that they extract from animal feces (or dung). Able to fly long distances, these beetles use specialized antennae to sniff out the dung and home in on this food source.
ecology A branch of biology that deals with the relations of organisms to one another and to their physical surroundings. A scientist who works in this field is called an ecologist.
environment The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of things in the vicinity of an item of interest).
feces A body's solid waste, made up of undigested food, bacteria and water. The feces of larger animals are sometimes also called dung.
field An area of study, as in: Her field of research was biology. Also a term to describe a real-world environment in which some research is conducted, such as at sea, in a forest, on a mountaintop or on a city street. It is the opposite of an artificial setting, such as a research laboratory.
fluid mechanics The study of the properties of fluids (liquids and gases) and their reactions to the forces acting upon them under various conditions.
fossil Any preserved remains or traces of ancient life. There are many different types of fossils: The bones and other body parts of dinosaurs are called “body fossils.” Things like footprints are called “trace fossils.” Even specimens of dinosaur poop are fossils. The process of forming fossils is called fossilization.
gastroenterology A branch of medicine that deals with the tissues and diseases of the gut — those food-processing organs that include the stomach and intestines. Doctors who specialize in this field are known as gastroenterologists.
gene (adj. genetic) A segment of DNA that codes, or holds instructions, for a cell’s production of a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.
genetic Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.
genomic Having to do with an organism’s genome, which is the complete set of genes or genetic material in a cell or an organism.
gut An informal term for the gastrointestinal tract, especially the intestines.
hadrosaur A duck-billed, plant-eating dinosaur that lived during the late Cretaceous Era.
herbivore (adj. herbivorous) A creature that either exclusively or primarily eats plants.
information (as opposed to data) Facts provided or trends learned about something or someone, often as a result of studying data.
ingest (n. ingestion) To eat or deliberately bring nutrients into the body by mouth for digestion in the gut.
insect A type of arthropod that as an adult will have six segmented legs and three body parts: a head, thorax and abdomen. There are hundreds of thousands of insects, which include bees, beetles, flies and moths.
invertebrate An animal lacking a backbone. About 90 percent of animal species are invertebrates.
journal (in science) A publication in which scientists share their research findings with experts (and sometimes even the public). Some journals publish papers from all fields of science, technology, engineering and math, while others are specific to a single subject.
manufacturing The making of things, usually on a large scale.
manure Feces, or dung, from farm animals. Manure can be used to fertilize land.
marsupial A type of mammal that carries its young for a period after birth in external pouches. There the developing babies have access to their mother’s nipples — and milk. Most of these species evolved in Australian and have especially long hind-legs. Examples of marsupials include kangaroos, opossums and koalas.
microbe Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.
microbiome The scientific term for the entirety of the microorganisms — bacteria, viruses, fungi and more — that take up permanent residence within the body of a human or other animal.
microscope An instrument used to view objects, like bacteria, or the single cells of plants or animals, that are too small to be visible to the unaided eye.
muscle A type of tissue used to produce movement by contracting its cells, known as muscle fibers. Muscle is rich in protein, which is why predatory species seek prey containing lots of this tissue.
nucleotides The four chemicals that, like rungs on a ladder, link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA. In RNA, uracil takes the place of thymine.
organic (in chemistry) An adjective that indicates something is carbon-containing; also a term that relates to the basic chemicals that make up living organisms.
organism Any living thing, from elephants and plants to bacteria and other types of single-celled life.
paleontologist A scientist who specializes in studying fossils, the remains of ancient organisms.
protein A compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. Among the better-known, stand-alone proteins are the hemoglobin (in blood) and the antibodies (also in blood) that attempt to fight infections. Medicines frequently work by latching onto proteins.
range The full extent or distribution of something. For instance, a plant or animal’s range is the area over which it naturally exists. (in math or for measurements) The extent to which variation in values is possible. Also, the distance within which something can be reached or perceived.
scat The feces shed by a wild animal, usually a mammal.
sea An ocean (or region that is part of an ocean). Unlike lakes and streams, seawater — or ocean water — is salty.
sequence The precise order of related things within some series. (in genetics) n. The precise order of the nucleotides within a gene. (v.) To figure out the precise order of the nucleotides making up a gene.
sequencing Technologies that determine the order of nucleotides or letters in a DNA molecule that spell out an organism’s traits.
species A group of similar organisms capable of producing offspring that can survive and reproduce.
stool (in medicine) Another name for feces.
Tasmania A major, mountainous island of Australia, south of the eastern part of the mainland across the Bass Strait. Until 1856, Tasmania had been known as Van Diemen's Land. Home to nearly 500,000 people, it’s capital city is Hobart. The name also refers to a state in Australia that comprises this island and several smaller ones.
technology The application of scientific knowledge for practical purposes, especially in industry — or the devices, processes and systems that result from those efforts.
tidal flat A broad and flat area that usually has a muddy or rocky bottom. It gets its name from the fact that it becomes covered by sea water every time the tide comes in — then drains again when the tide goes out.
tissue Made of cells, it is any of the distinct types of materials that make up animals, plants or fungi. Cells within a tissue work as a unit to perform a particular function in living organisms. Different organs of the human body, for instance, often are made from many different types of tissues.
waste Any materials that are left over from biological or other systems that have no value, so they can be disposed of as trash or recycled for some new use.
wood A porous and fibrous structural tissue found in the stems and roots of trees, shrubs and other woody plants.
Journal: A.P. Bhatt et al. In fimo: A term proposed for excrement examined experimentally. Gastroenterology. Vol. 156, April 2019, p.1232. doi: 10.1053/j.gastro.2018.11.070
Meeting: P.J. Yang et al. How do wombats make cubed poo? American Physical Society Division of Fluid Dynamics meeting, November 18, 2018. Atlanta, Georgia.
Journal: K. Chin et al. Consumption of crustaceans by megaherbivorous dinosaurs: dietary flexibility and dinosaur life history strategies. Scientific Reports. Vol. 7, Sept. 21, 2017. doi: 10.1038/s41598-017-11538-w.