The giant panda’s microbiome isn’t doing it any favors

Panda bears are quite unique in the animal kingdom because they are nearly strictly herbivores yet they are descended from omnivores.  In fact, scientists aren’t quite sure why panda’s made the transition to eating bamboo, because it is a relatively inefficient energy source.  Making matters worse for the panda, its gastrointestinal tract is rather short, and resembles other carnivores, whereas most herbivores have very long gastrointestinal tracts that allow for long retention times for the microbiome to do its work.  This microbiome, of course, breaks down plant material into usable sources of energy for the host and it is critical in all herbivores.  Scientists from China recently investigated the panda’s microbiome, and to their surprise discovered that it too, resembled carnivores’ microbiomes, rather than herbivores’ as one might expect.  They published their results last week in MBio.

The scientists measured the fecal microbiomes of 45 captive pandas over the course of one year, including cubs, juveniles, and adults.  They then compared these microbiome samples with previously reported microbiomes of 54 other species, and wild, rather than captive pandas.  Their first discovery was that the panda’s microbiome was not as diverse as many of these other species, and as our regular readers know, low diversity has been implicated in many diseases in humans.  Next, they found that the panda’s microbiome was actually much more similar to other carnivorous species, especially other bears and tigers, than herbivorous species, and was dominated in Escherichia/Shigella, and Streptococcus, rather than bacteria that are known to degrade cellulose from plant matter, such as Ruminococcaceae, and Bacteroides.  Finally, of particular interest in light of the recent research on the importance of diurnal changes in the microbiome, the scientists noted that the panda microbiome undergoes huge shifts in accordance with the seasons, although they do not speculate as to the effects these shifts may be having.

These discoveries are quite surprising, but they help explain why pandas must eat around 25 lbs. of bamboo every day.  Their microbiomes are just not well equipped to digest this food.  In fact, the lack of cellulose degrading bacteria in pandas’ guts has led some scientists to speculate that pandas are merely living off the cellular contents of each plant cell, rather than the energy dense cellulytic plant cell wall.  Whichever the case, their inefficient digestion certainly is not helping them thrive as a species.

The maturation of the microbiome during the first year of life

Dr. Jeffrey Gordon recently published a review article describing the importance of the proper development of the microbiome in the early stages of life.  One paper that certainly would have made it into the review if it was published in time is a new paper published last week out of Sweden and China that studied the developing microbiome of children over the course of their first year of life.

The team of scientists studied 98 women and their newborn babies. They sequenced the mother’s stool, the newborns stool, and again the child’s stool at 4 and 12 months. Throughout the study, because they used a technique called shotgun sequencing, they identified 4,000 new microbial genomes.

The infants in the study were breastfed for varying amounts of time with some never being breastfed at all. The researchers found that breastfeeding and the timeline of cessation of breastfeeding was critical to driving microbiome development. Many had previously hypothesized that it was the time at which solid foods were introduced was most important for microbiome development, however this study found that it was the time at which breastfeeding was stopped. Children that stopped breastfeeding earlier had microbiomes more similar to adults at 12 months while children who were breastfed for the duration of the study continued to have microbiomes dominated by Bifidobacterium and Lactobacillus.

The scientists also found that the 15 babies born via C-section had different microbiomes than the other 83 babies studied.  The infants born via C-section had microbiomes that more closely resembled skin and mouth microbial communities while the babies born vaginally had microbiomes more closely resembling the bacteria in their mother’s stool.

We still don’t know exactly what a “healthy” microbiome looks like and which microbial profile is best for the child. This study provides a very solid experimental design to study the development of the microbiome and allows for the continued monitoring of these children’s microbial development over the course of their lives. 

Using microbiome bacteria for cosmetics

Topical cosmetics are widely used for skin care, maintenance, and beauty.  There are entire industries dedicated to providing skin care products to a wide range of consumers, because for the most part, everyone desires healthy skin.  Scientifically speaking, skin is considered healthy if it effectively retains moisture, has a low surface acidity, and has good texture.  Many topical cosmetics act to augment or support these features.  Interestingly, researchers in Japan demonstrated that a microbiome bacterium can also provide these benefits to the skin, introducing the possibility of developing novel skin care therapy.

Staphylococcus epidermis has recently gained attention as a beneficial topical agent due its demonstrated skin care benefits.  Specifically, its metabolic products have been shown to enhance moisture retention and reduce surface acid levels.  Researchers investigated this by creating their own S. epidermidis topic gel and testing it on human subjects in a double-blind randomized study.  Skin was collected from the foreheads of 21 patients enrolled in this clinical trial.  Genetic analysis confirmed that S. epidermidis was removed from the skin.  Once isolated from other cells and bacteria, the S. epidermidis bacteria were cultured and lyophilized – or freeze dried – to preserve bacterial integrity.  The lyophilized S. epidermidis was then mixed in with a gel and continuously applied to patients’ faces in a double blind randomized clinical trial study that included a control population just receiving the gel, no bacteria. 

Patients who received the S. epidermidis had 1.4 times the amount of water in their skin after the trial was completed compared to before they started.  Additionally, a suppression of water evaporation on the skin surface was shown, concomitant to an increase in lipid content.  The increased lipid content was hypothesized to be a direct result of S. epidermidis metabolism, as the lipid metabolites provided an ample surface coat to keep moisture trapped on the skin surface.  Moreover, the S. epidermidis regiment also maintained a low acidic environment on the skin surface.

This study demonstrates S. epidermidis’s efficacy to support healthy skin.  Using certain microbiota as a topical agent is already being seen in practice, as Cambridge-based AOBiome are developing skin therapies using bacteria.  This unique approach has a lot of potential, and it will be interesting to see how bacteria can be used in this health arena.

The oral microbiome may harbor harmful bacteria in CF patients

P. aureginosa (green line) is the most common cause of infection for CF patients older than 18 years old.

By Ninjatacoshell (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons

Cystic fibrosis is a hereditary disease characterized by thick mucus secretions that obstruct the lungs and harbor harmful bacteria in a person’s airways. A common cause of death among CF patients is bacterial infection, usually by Pseudomonas aeruginosa, that subsequently leads to inflammation and respiratory failure. Scientists at the CF Reference Center in Roscoff, France were interested in a possible link between oral bacteria and lung bacteria of CF patients.  Specifically, they wondered if the mouth could harbor P. aeruginosa, which could then go on and inflame the lungs.  The results of their study were published in the Journal of Clinical Microbiology.

The researchers in France focused their study on detecting and measuring the genetic relatedness of P. aeruginosa in saliva and sputum (mucous) samples in 10 CF patients.  Of the 10 patients, 5 were chronically colonized (CC) by P. aeruginosa, with an average age of 23.8 years, and 5 were not colonized (NC), with an average age of 16.6 years. None of the patients had gingivitis or periodontitis.

No P. aeruginosa was detected in oral or sputum samples of NC patients, while 16 samples from the CC patients contained P. aeruginosa. Of the 16 sampled, six were salivary and ten were sputum. From these samples, the researchers discovered that the genetic make-up of the strain samples within each CC patient was more similar to other samples from the same patient than to those of other patients.

Overall, this study suggests that the oral cavity is a possible reservoir of P. aeruginosa and other bacteria that can infect the lungs. While this possibility is suggested by the discovery of similar P. aeruginosa strains in both saliva and sputum, it is not clear if the oral strains can actually descend and infect the lungs. As the article mentions, a longitudinal study that could follow the changes in bacterial colonization in CF patients would be beneficial. 

Your microbiome could be used to identify you

Scientists have long speculated that each individual’s microbiome may be unique and static enough so that it could be used for identification.  This becomes very important for forensic investigations, which we have written about before, and also raises many ethical concerns regarding privacy during microbiome sampling and donation.  Previously, most of the studies on this topic were not exhaustive enough to provide any firm conclusions.  Last week though, Curtis Huttenhower’s group from the Harvard School of public health published a powerful, and statistically robust method for tracing the a microbiome back to its host.  The study was published in the Proceedings of the National Academy of Sciences.

Using the Human Microbiome Project (HMP) database, the scientists used machine learning to construct a test for the most important conserved metagenomics traits after comparing individuals’ microbiomes over time.  The algorithm depended on both 16s rRNA sequences, as well as whole genome sequencing (in addition to derivatives of the whole genome sequencing).  The researchers note that the algorithm is not just looking for microbiome genes that are conserved over time, but rather microbiome genes that are conserved over time and unique amongst the population.  Overall, they found that after a year, their algorithm could accurately identify 86% of people based on their stool samples, with very few false positives.  Other sites on the body, like the skin, were less effective for identification, but it was feasible to use them.

This team definitively proved that a microbiome can be used to identify its host.  They admit that full sequencing if the microbiome is necessary, but regardless, it is possible.  This has all sorts of ethical and privacy concerns associated with it.  For example, microbiome data that is made publically available, though anonymized, could be traced back to its donors.  This could include information like STDs or other diseases.  Another obvious application of this would be in forensics, and it probably wont be long before a case hinges on microbiome evidence.

Episode 7 of The Microbiome Podcast: Gut bacteria and circadian clocks with Drs. Eugene Chang and Vanessa Leone

On the seventh episode of The Microbiome Podcast we had a great conversation with Drs. Eugene Chang and Vanessa Leone from the University of Chicago. Drs. Chang and Leone found that bacteria in the gut influence the circadian clock in mice.  They discovered that altering the diet of the mouse by introducing a high-fat diet caused conventionally raised mice to have a disrupted circadian clock and became obese. They looked at what genes were expressed in the liver and found that the genes expressed varied widely from mice that were germ-free and those that were normal and conventionally raised.  We talked with them about this work and what influence this could have on humans and on our eating and sleeping patterns.

Listen to the podcast here on our website, here on iTunes, and here on Stitcher.

Below are more detailed show notes:

• Two scientific talks that David saw in New York City. First (0:37), a talk by AMI Scientific Advisory Board member Marty Blaser about antibiotics and obesity. We then (1:23) discussed a talk by Chris Mason about the microbiome and his study on the microbes in the NYC transit system. Dr. Mason published his slides on twitter so if you’re interested in seeing his slides, you can see them here.
• (2:26) Dr. Tim Spector from Kings College London had his son eat only McDonalds for 10 days straight. His son lost approximately 40% of the bacterial diversity in his gut. Read more about it here.
• (3:40) The British Gut Project that Dr. Tim Spector leads, a partner of The American Gut Project. Check out the British Gut Project.
• (5:37) A company called Biomecite Diagnostics that licensed technology from The University of Maryland School of Medicine to develop molecular diagnostics to detect inflammatory bowel diseases like Crohn's disease and ulcerative colitis. Read more here. 
• (6:10) We gave an overview of diurnal changes, circadian clock, and the microbiome.
• (9:21) We began the interview with Drs. Chang and Vanessa Leone and discussed their paper that found that cirdcadian clocks were influenced by gut microbes. Read the paper in Cell Host and Microbe. Read our blog post about this work.     
• (11:47) Dr. Leone discussed a few seminal papers from 2014 about diurnal changes. Read this paper about jet-lag and the microbiome. 
• (34:15) After the interview with Drs. Chang and Leone we talked about our own sleep patterns.
• (37:18) We gave our own opinions on Deflategate and Bill goes on a little rant about the Patriots, Tom Brady, and deflated footballs.