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This interrupted case study for the flipped classroom introduces the human microbiome from the perspective of one of its occupants, Heidi Helicobacter (Helicobacter pylori).  Heidi lives in the gut of Kristen, a college student, and discusses her fellow microbial inhabitants, functions of these various microbes, and alludes to factors that can disrupt the healthy human microbiome. Students prepare for class by viewing several brief videos and then discuss in class whether Kristen should undergo a fecal microbiota transplant to treat her Clostridium difficile infection.  A lab component has students model, using colored beads, how antibiotics can act as a selective agent for drug-resistant microbes such as C. difficile. The case concludes with Kristen about to give birth to a new baby several years later.  Students listen in as Kristen's microbes discuss the formation of the new baby's microbiome. The case has been used successfully in a general biology class and could easily be adapted for a microbiology, human physiology, ecology, or evolution course.

The bacteria in our guts can break down food the body can't digest, produce important nutrients, regulate the immune system, and protect against harmful germs. And while we can't control all the factors that go into maintaining a healthy gut microbiome, we can manipulate the balance of our microbes by paying attention to what we eat. Shilpa Ravella shares the best foods for a healthy gut.

Sonnenburg, his wife Erica, and the graduate student Samuel Smits confirmed this idea in a recent experiment. The researchers started with mice that had been raised in sterile bubbles and then loaded with identical collections of gut microbes. They then fed these mice a high-fiber diet, before randomly switching half of them to low-fiber chow for seven weeks. Predictably, the fall in fiber caused upheavals in the rodents' guts. In the low-fiber group, the numbers of 60 percent of the local microbe species fell dramatically, and some remained low even after the mice returned to high-fiber meals. Those seven low-fiber weeks left lingering scars on the animals' microbiomes.

Researchers at the University of Pennsylvania performed "stress tests" on pregnant mice using a predator's odor, restraint, or unfamiliar noises. After the mice gave birth, the scientists analyzed the bacterial communities in their vaginas and in their pups' colons. The researchers found that stress during pregnancy altered the expression levels of several proteins involved in vaginal immunity and the frequency of Lactobacillus bacteria, which, expectedly, correlated to lower frequencies of Lactobacillus within their pups' gut microbiomes. Male pups of stressed mothers also displayed an increase in anaerobic bacteria like Clostridium and Bacteroidesin.

Research has revealed striking differences in the trillions of bacteria - a.k.a., the microbiome - in the intestines of children with and without autism. But the gut bacteria in individuals with autism aren't just different. Researchers at the California Institute of Technology have shown for the first time that they may actually contribute to the disorder. They reported in the journal Cell in December 2013 that an experimental probiotic therapy alleviated autism-like behaviors in mice and are already planning a clinical trial.

HIV is a disease of the gut, a concept that's easy to lose sight of with all the attention paid to sexual transmission and blood measurements of the virus and the CD4+ T cells it infects and kills. But the bottom line is that about two thirds of all T cells reside in the lymphoid tissue of the gut, where the virus spreads after exposure, even before it shows up in blood.

Hilary Brown is a PhD student, working in the infection genomics group at the Wellcome Trust Sanger Institute. In this film he describes how to work safely in the lab with bacteria from the human gut including culturing them on agar plates and extracting the DNA for genome sequencing. The infection genomics programme uses a variety of different research approaches to study the biology and evolution of disease-causing organisms such as viruses, bacteria and parasites and understand how they cause disease in humans and other animals.

But when Sokol did a comparative DNA analysis of diseased sections of intestine surgically removed from the patients, he observed a relative depletion of just one common bacterium, Faecalibacterium prausnitzii. Rather than "bad" microbes prompting disease, he wondered, could a single "good" microbe prevent disease?

Your mother's DNA may have determined your eye color, but some traits that you thought came from her may instead have come from the DNA of bacteria she passed on to you soon after birth, a new study finds. The study found that a mother mouse can pass along to her offspring a susceptibility to intestinal disorders, such as inflammatory bowel disease, by way of a gut-residing bacterium called Sutterella, the researchers reported in the journal Nature on Feb. 16.

Life on Earth is intimately connected to the natural cycles of light and dark that make up a 24-hour day. For plants, animals, and even bacteria, these circadian rhythms control many biological functions. Humans can overrule their body clocks, but at a price: People whose circadian rhythms are regularly disrupted-by frequent jet lag or shift work, for example-are more vulnerable to diabetes, obesity, cardiovascular disease, and cancer. There are various theories to explain these associations, and researchers now have a new player to consider: the bacteria that live in the digestive tract. According to a study in mice and a small group of human volunteers, the internal clocks of these gut microbes sync up with the clocks of their hosts. When our circadian rhythms get out of whack, so do those of our bacteria.

When scientists first made contact with an isolated village of Yanomami hunter-gatherers in the remote mountains of the Amazon jungle of Venezuela in 2009, they marveled at the chance to study the health of people who had never been exposed to Western medicine or diets. But much to their surprise, these Yanomami's gut bacteria have already evolved a diverse array of antibiotic-resistance genes, according to a new study, even though these mountain people had never ingested antibiotics or animals raised with drugs. The find suggests that microbes have long evolved the capability to fight toxins, including antibiotics, and that preventing drug resistance may be harder than scientists thought.

UCLA researchers now have the first evidence that bacteria ingested in food can affect brain function in humans. In an early proof-of-concept study of healthy women, they found that women who regularly consumed beneficial bacteria known as probiotics through yogurt showed altered brain function, both while in a resting state and in response to an emotion-recognition task.

Some 20 percent of cancer-related deaths in the U.S. can be attributed to obesity, making it the number-one preventable cause of cancer death in the country. But with myriad metabolic and inflammatory changes associated with obesity, determining the mechanisms that underlie the obesity-cancer link has proven challenging.

The human large intestine (colon), in healthy individuals, has extremely low oxygen concentrations, and over 90% of its microbiota are strict anaerobes. Researchers taking metagenomic fecal microbiota surveys of adult Europeans could assign about 0.8% of the genes in their dataset to archaea [9], and similar numbers (0.2%-0.3%) were reported for Amerindians and Malwaians [10], while North Americans had much lower fractions (<0.05%).