Proton pump inhibitors affect the microbiome

Proton pump inhibitors (PPI) are used to reduce gastric acid production in individuals’ guts and are prescribed to treat ulcers, gastroesophogeal reflux disease (GERD), and other conditions associated with acid production. It is one of the most commonly used drugs in the world. We know (and have written about) that PPIs are associated with increased intestinal infections, specifically Clostridium difficile, and the gut microbiome plays an important role in infections of the intestine. A recent study looked at the influence that PPIs had on the gut microbiome.

The team of researchers studied the gut microbiome of 1815 individuals. They looked at PPI users vs non-users. Of those sampled, 215 of them were taking a PPI at the time that a sample was taken. It was found that those taking the PPIs had lower microbial diversity compared to those not taking PPIs. They also found that bacteria usually found in the mouth was over-represented in the fecal samples of those taking PPIs, including those in the Rothia genus. They also observed an increase in Enterococcus, Streptococcus, Staphylococcus, and Escherichia coli, a potentially pathogenic bacterium.

PPI usage effects are more prominent than those of most other drugs, including antibiotics. The results of this study are consistent with a less healthy microbiome and allow us to better understand why PPIs may lead to an increase of susceptibility to intestinal infections like C. diff.

Variation exists in microbiome sequencing and analysis

Microbiome sequencing and analysis is at the heart of microbiome science.  While established protocols do exist in order to identify the bacteria in samples, there is still a lot of variability between labs, individuals, reagents, analytics techniques, and instruments.  This makes comparing data across groups difficult.  The microbiome quality control project (MBQC) was carried out in order to determine the sources of variability that exist.  During the project identical samples were sequenced by various labs, and the results were compared.  The project’s conclusions were published this past week in the journal Genome Biology.

There was a lot of variation from many of the sources during experimentation.  Overall, DNA extraction technique proved to be a major source of error.  On the other hand, sample storage protocols, such as length of time the sample spent in the freezer, appeared to only play a small role in variability. Another encouraging result was that the the bioinformatics pipelines, i.e. the software programs used to determine the bacteria from the raw data, displayed consistent results.  The project also included negative controls that should have contained no bacterial DNA at all, however many labs reported seeing non-trivial sequences.  In addition, the samples with known compositions often times had spurious DNA from bacteria that should not have been there.  Sometimes the results showed upwards of 7x more bacteria organizational taxonomic units (OTUs) than expected.

This initial MBQC project accomplished two of its major goals, and therefore should be considered a success.  First, it demonstrated a need for quality control within microbiome scientists.  Second, it helped narrow down the variables that need to be studied more robustly in future MBQC projects.  For now though, we must just acknowledge that error does exist in microbiome studies, and to keep that in mind when interpreting results.

Exposure to the cold affects our microbiome and modulates our energy homeostasis

When exposed to cold temperatures, you begin shivering to compensate for the sudden temperature decrease.  Biologically, exposure to cold environment can induce brown adipose tissue differentiation and catabolism of lipids to produce heat.  The gastrointestinal tract is an important site for the regulation of our energy metabolism, and as we know, harbors a diverse population of gut bacteria.  A team of researchers sought to investigate what role the microbiome of mice plays in induction of physiological changes to cold exposure.

The researchers exposed different groups of mice to cold temperatures for 31 days, and the initial observation was attenuation of energy expenditure and white fat.  Importantly, food intake was consistent throughout the trial, pointing to a temperature-driven effect.  Fecal collection and post-mortem intestinal analysis revealed marked shifts in microbiota compositions of cold-exposed mice as compared to those kept at room temperature.  Notably, families within Actinobacteria, Verrucomicrobia, and Tenericutes were less abundant in the cold sample mice, and Akkermansia muciniphila species were observed to be significantly decreased in the cold mice.  The researchers also transplanted microbiota from cold-group mice to naïve, germ-free mice.  Upon cold temperature exposure, germ-free mice demonstrated heightened insulin sensitivity, browning of white fat, increased energy expenditure, and white fat loss, indicative of a tolerance to the cold.  Prolonged cold exposure in both cold-exposed and cold-transplanted mice also induced adaptive biological mechanisms in intestinal villi and microvilli to maximize caloric uptake, ultimately attenuating weight loss.  This increase in intestinal absorption was observed concomitant to altered intestinal gene expression, as genes that promote tissue remodeling where upregulated while apoptotic genes were suppressed.  In a final experiment, the aforementioned effect was reduced when Akkermansia muciniphila (which were originally observed to decrease in cold-induced mice) were transplanted to cold-exposed mice, supporting a microbiota-driven relationship.

This was a very interesting study that sheds lights on organismal adaptive mechanisms during energy scarcity brought on by factors such as cold temperatures.  Again we observe heavy involvement of the microbiome in these processes, a finding that calls for more investigation.  

Type 2 diabetes drug, metformin, impacts gut bacteria

Patients with type 2 diabetes have what is called insulin resistance, an inability to properly use insulin. The pancreas will make more insulin to keep blood glucose levels normal however, eventually, the pancreas can’t keep up and drugs may need to be taken. The most common drug to treat type 2 diabetes is metformin. A large team of scientists throughout Europe and China published a study in Nature showing that metformin affected gut bacteria in type 2 diabetics.

The researchers analyzed stool samples from 784 individuals with and without type 2 diabetes and looked at the effects that metformin had on gut bacteria. Metformin is usually prescribed in high doses and because it is a chronic disease, patients end up taking the drug often for many years. Based just on stool samples, they were not able to identify which sample was from a diabetic patient or control unless they took metformin. Type 2 diabetics who were on metformin had higher levels of E. coli and lower levels of I. bartletti than the controls or type 2 diabetics not taking metformin.

Studying the bacteria that changed in abundance in the gut suggested to the scientists that butyrate and propionate had elevated production. These two short chain fatty acids are associated with lowering blood glucose levels.

Importantly, this study helps explain some existing studies with conflicting results comparing gut bacteria of people with and without type 2 diabetes. This was most likely due to the fact that there were more individuals taking metformin in one study than another and this was not controlled for.

This study not only informs us on what is happening with gut microbes after taking metformin but also shines a light onto the importance of controlling for all external factors in microbiome studies, including treatments that could have confounding effects.  

Operating room bacteria colonize infants’ guts after C-sections

Newborns are a great study subject in the field of microbiology, because scientists are still discovering how the microbiome develops and what factors affect it. In human infants, it has been proven that vaginal birth exposes infants to bacteria that are different from those received by the mother through C-section. Babies born by vaginal delivery have gut bacteria correlated with vaginal bacteria, while babies born by C-section have gut bacteria correlated with human skin bacteria. For babies born by C-section, the sources of the human skin microbes that are acquired are still unknown.  In a study published by Microbiome, a group of scientists tested the hypothesis that the operating room environment contains human skin bacteria that could be seeding the gut microbiome of C-section born babies.

To test their hypothesis, the researchers collected samples from 11 sites in four operating rooms from three hospitals in New York City, NY and San Juan, PR. Of the 44 operating room samples that were collected, 68% of the samples contained a sufficient number of bacterial DNA samples for sequence analysis. After analyzing the bacteria collected, it was found that all samples contained human skin bacteria, with Staphylococcus and Corynebacterium being the greatest in quantity. Lamps on the operating bed and baby crib showed higher abundances of these bacteria relative to the other sampling sites. The scientists confirmed that the samples collected were more similar to human skin microbiota than other body sites, by comparing the samples to oral, fecal, and vaginal database samples.       

Even though operating rooms are supposed to be spotlessly clean and germ-free, this study shows that there are still dust particles containing human skin, and therefore human skin microbiota, samples. These samples could be from people moving in and out of the operating room during a C-section, or it could come from the people cleaning the OR. Either way, the human skin bacteria in the operating room most-likely are what influences the infant’s developing gut microbiome. 

Prevotella in the gut appears to improve glucose tolerance

Last week we wrote about a study that showed that the glycemic response from foods was a function of the microbiome, and alluded to the fact that the microbiome likely affects many aspects of metabolism.  Another paper was published this week, in the journal Cell Metabolism, that describes which bacteria are responsible for some of these effects.  The authors describe how Prevotella improve glucose metabolism in healthy human subjects.

The scientists gave 39 subjects white bread and barley bread for three consecutive days and measured their glucose and insulin responses to the diets.  For the most part, the barley bread was associated with an improved response over white bread, but some of the individuals’ responded with a much more stark improvement than others.  The scientists then measured the gut microbiomes of each individual and noted that the microbiome changed in the most responsive individuals, and this change was characterized by an increase in Prevotella (specifically Prevotella copri) and methanogenic archaea.  The opposite effect was seen in the individuals that responded least to the barley bread intervention.  The scientists then confirmed these results in mice.  Mice that were given fecal microbiota transplants from human responders, or P. copri probiotics had improved glycemic responses to high fiber diets than control mice.

Prevotella comes up in a lot of microbiome literature as a bug seen in ‘traditional’ societies that eat a lot of fiber.  This paper demonstrates that many of the genes from Prevotella are crucial to digest the complex fibers and that this may stimulate an improved glycemic response.  Collectively, many papers now support the idea that Prevotella is a critical bacterium to a ‘healthy’ microbiome.