The placental microbiome

Microbiome populations have been well-characterized in many distinct body-sites.  Interestingly, there is a lack of knowledge in the microbiome of the placenta, an environment that was long thought to be sterile.  Investigating the placenta is important toward understanding the microbiome in human development, especially in light of previous evidence demonstrating that human microbiota populations fluctuate extensively in the first year(s) of life.  The placenta is the cradle of life for fetal development, leading researchers from Baylor School of Medicine to study the microbiome of this tissue.  Placenta samples were collected and analyzed to characterize the placenta microbiome, and explore links to fetal development and microbiome compositions. 

320 placenta specimens were collected, and PCR was used to characterize bacterial populations.  The Meta genome sequencing revealed that the placenta microbiome harbored unique abundances in specific bacteria compared to other body sites.  E. coli in particular had the highest species abundance.  Interestingly, the microbiota populations were most similar to the oral microbiome.  Species such as Prevotella tannerae and Neisseria, known to populate the mouth, were also abundantly present in the placenta.  Further analysis confirmed that the placenta bacteria were indeed most similar to bacteria specifically found in the tongue, tonsils, and gingival plaques. 

The researchers also demonstrated an association between placental microbiome composition and healthy births or births with complications.  Specifically, a significant association was shown between distinct placental microbiome populations and pre-term birth.  Taxa such as Durkholderia were shown to be enriched in the placentas of those who delivered their infants preterm, whereas Paenibacillus was abundant in normal terms placental specimens. 

This study reveals a couple very interesting associations between cross-site microbiome similarities and disruptions in compositions that appeared to be linked to preterm birth.  Although not definitive evidence, these findings could lead to some important research in the future.  There were a few confounding elements to this study, such as other body site samples occurred in non-pregnant subjects, or the fact that the mass of the placental microbiota was particularly low.  However, these findings certainly raise awareness of the uniqueness of the placental microbiome, and what this means in terms of the microbiome entering the developing fetus.  It will be interesting to see what further research can reveal about this relationship. 

The oral microbiome of children, and its relation to dental caries

The oral microbiome is a popular area of exploration because bacteria are a prominent part of dental health, and because it is one of the most heavily colonized and easily accessible niches in the body. Many studies have been discussed on this blog concerning adult oral microbiomes, and its relations to bodily issues such as cystic fibrosis and periodontitis. It is also very useful to investigate children and the ways that their bacterial communities first inhabit and develop. A study done in Sweden at the Umeå University, and published by Plos One, takes a look at the maturation of the oral microbiome from infants at 3 months old to children at 3 years old.

The Swedish researchers performed a longitudinal study that followed children from 3 months to 3 years of age, looking for microbial characteristics of children with dental caries (i.e. cavities) compared to those without. There were 207 original participating 3 month olds that were consented by their parents to be in the study. The parents provided information on mode of feeding, mode of delivery, use of antibiotics or probiotics, health issues like allergies, and presence of teeth. At 3 months and later at 3 years samples were taken from the buccal mucosa, tongue, and alveolar ridges. Teeth were also scraped for plaque and saliva was collected. Of the original 207 participants, 155 returned for sampling at 3 years of age, and 13 of those children had dental caries.

After sequencing the bacterial DNA samples, it was found that Escherichia coli, Staphylococcus epidermidis, and various Pseudomonas species were significantly more prevalent in 3 month olds. However, there were 23 genera that were more significantly prevalent at 3 years of age than at 3 months.

By comparing the children with and without caries, the scientists were able to make several conclusions.  The researchers identified seven taxa that appear to be associated with healthy teeth.  On the other hand, Streptococcus mutans seemed to be more prevalent in the children with caries, than in those without caries. Additionally, the colonization of this species was most prevalent in girls. This is possibly because girls develop faster, so earlier tooth eruption allows for a longer time for the colonization of these bacteria.

The results of this study show us that during the first three years of life, species richness and diversity seems to increase significantly in the mouth. While there is an increase in the type of the bacteria, there are also some taxa that are lost with age. The researchers also concluded that the oral microbial composition of the mouth at 3 months does not appear related to the development of dental caries. With this information, it might be smart to perform a related study that collects oral microbiome samples in children within the time frame of 3 months to 3 years, because it could show a clearer picture of the changes that take place in bacterial composition.

The oral microbiome of periodontitis patients has distinct profiles dependent on disease severity

A few weeks ago we discussed periodontitis, a bacterial infection of the gums that leads to inflammation and deep pockets to develop in which harmful bacteria can colonize. Periodontitis develops in association with dramatic changes in the makeup of the oral microbiome. Smokers and diabetics are more frequently victims of the disease. The study we discussed previously was one performed by researchers in Istanbul, Turkey in which they tested whether a probiotic lozenge could improve the patients’ condition. In a different, more recently published study concerning periodontitis, researchers in Connecticut and Massachusetts looked not to change the oral microbiome of patients suffering from periodontitis, but to organize and identify the microbial characteristics of the disease.

In the study published in Plos One, seventeen subjects, 8 of whom were diabetic, with Chronic Kidney Disease (CKD) and seventeen subjects without CKD, 3 of whom were diabetic, were studied.  All 34 subjects suffered from periodontitis. Samples were taken from each participant, from the deepest pockets in two different areas of the mouth. DNA was then isolated and sequenced to identify microbial communities in each individual. After much statistical analysis, the researchers found that the microbial communities tended toward two clusters, A and B, with type B communities correlating with more severe periodontitis. Group A subjects had communities with greater health-associated bacteria and cluster B communities were dominated by Porphyromonas gingivalis and Tannerella forsythia. Additionally, the analysis showed that diabetes and CKD are not correlated with a certain periodontitis microbial makeup.

A set-back of this experiment is the low sample size, which makes for less meaningful statistical analysis. Greater sample sizes of each cluster could give stronger claim to the findings of this study. However, this study does begin to clarify the bacterial community characterization of healthy, unhealthy, and severely unhealthy oral microbiomes. In addition, the results from this study could be used to ask further questions about the disease, including questions such as: what environmental factors cause the difference in clusters A and B? Do inflammatory diseases such as CKD and diabetes have anything to do with the severity of inflammatory response of periodontitis? Further analysis may allow us to answer these tough questions.

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. 

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. 

Microbiome bacteria help cancer cells evade the immune system

Optical microscope image of bacteria from the genus Fusobacteria.

A few weeks ago Kris Campbell wrote about the microbiome’s association with colorectal cancer.  This association is complex, but perhaps critically important, and last week a new study reinforced this connection.  Researchers, primarily from Israel, published results in Cell Immunity that showed common microbiome bacteria are protecting cancer cells by helping the cancer cells evade the immune system.

The researchers noticed that a type of bacteria, Fusobacterium nucleatum, which is normally found in the oral microbiome and is a cause of periodontal disease, can be found in high concentrations around colorectal tumors.  In addition, these same bacteria had been linked to various microbiome associated diseases, such as preterm birth and rheumatoid arthritis.  They suspected that these bacteria may somehow be protecting the cancer cells from the immune system, so they performed a series of experiments to find out.

The scientists grew cancer cells in the presence and absence of the F. nucleatum and then exposed these cancers to immune system cells that are designed to attack cancers.  They noticed that those cancer cells that had been grown with the bacteria were naturally protected from these immune cells.  Through a series of tests they discovered that the bacteria produce a protein called Fap2 that naturally bound with the immune cells and essentially deactivated them (technically speaking, Fap2 bound to the Natural Killer cells’ TIGIT inhibitory receptors).  Interestingly, this TIGIT receptor is nearly ubiquitous across many types of immune system cells, which means that this bacteria, and others like it, may be especially good at protecting themselves and other cancer cells from our bodies’ natural defenses.

It may be surprising for our readers to hear that bacteria are sometimes used to destroy cancer cells, like in the case of bladder cancer, but this paper shows a more dichotomous relationship between the microbiome and cancer.  While some bacteria may be helpful in killing cancers others may be helping them grow.  Either way, one thing is clear, the microbiome and cancers are intimately related, and learning about the microbiome should lead to advanced therapies for treating cancers.