Breastmilk contains many prebiotics to support the growth of beneficial bacteria in the infant’s gut.  It also contains bacteria that seed the infant’s gut.  Previous research has shown that the bacteria in breast milk do indeed take hold and colonize the gut, and so it is imperative to infant microbiome development.  An article published last week sought to discover if the breastmilk microbiome changes depending on mode of delivery, especially since we have seen that C-section infant’s have much different microbiomes than their vaginally delivered counterparts.  The scientists published their results in the journal Microbiome.

The scientists tested the breastmilk of 39 Canadian women.  Despite various backgrounds, each woman’s milk was dominated by Staphylococcus, Enterobacteriaceae, and Pseudomonas.  Moreover, there were not major differences in the breast milk microbiomes between modes of delivery, showing that it is not effected by C-section of vaginal birth.  In addition, the gender of the baby did not change the microbiome either.  Interestingly, the microbiomes were very different between mothers, meaning that babies are being exposed to highly diverse bacteria from milk.  In one case 80% of the bacteria were staphylococci, and in another case more than 50% was Pseudomonas.

There is little evidence that shows how differences in breast milk microbiomes are affecting children.  That said, we know the microbiome is critical to immune system development, and therefore it reasons that these differences may be important.  In any event, it is useful to see that mode of delivery itself is unlikely to change the breastmilk microbiome.

What bacteria live in the gym?

A lot of research goes into understanding the complexity and dynamics of the human microbiome in the GI tract or the mouth, to name a few locations. In an article published by Microbiome, researchers at Northwestern University took a different perspective in that they looked at how the human microbiome affects the environments around us. A very interesting point raised by the article is that Americans spend most of their time in so-called “built environments,” which are indoors. The microbes of these indoor environments are mainly affected by the humans that interact with them, so the scientists at Northwestern University took to studying how the bacterial composition of indoor athletic equipment and facilities are affected. This specific environment was chosen mainly because of the numerous different human encounters it experiences.

For 2 days, the researchers collected swab samples in 3 athletic facilities. Samples were collected every 2 hours from the floor, mats, elliptical handles, free weights, and benches from 8 am to 6 pm, and a total of 356 samples were collected.  After sequencing and analysis, the researchers concluded that, consistent with all three facilities, the bacteria found on the equipment was most likely to be from the human skin, with Pseudomonas and Acinetobacter showing up in the most samples. Besides microbiota from the skin, other bacteria were found to be abundant such as Bacteroides from the human intestinal tract on elliptical handles and Finegoldia, also from the GI tract, on benches.

As for which sampled location had the most stable bacterial community, it was found that the floor and mats showed the least change in structure. This is most likely because elliptical handles, free weights, and benches come in more direct contact with human skin. Across the board, the only genera which were found in all samples from every surface type were Staphylococcus and Pseudomonas. It is important to remember that none of this means athletic facilities are blooming with harmful bacteria, and we should stay far away. In fact, the environment is not very conducive to the thriving of bacteria, because it lacks a lot of resources. What we should take away from this study is that any surface that comes in contact with human skin is likely to reflect the microbiome of that person. 

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 lung microbiome changes during cystic fibrosis flare-ups

Cystic fibrosis is a genetically inherited disease characterized in part by thick mucus secretion that can obstruct the lungs and aid in the harboring of bacteria in airways. A leading cause of death within persons with cystic fibrosis (CF) is infection of the lungs and inflammation that leads to respiratory failure. In a study performed by members of the Department of Pediatrics and Communicable Diseases at the University of Michigan Medical School, and published by Microbiome, sputum (mucus) samples were taken from four CF patients over a period of a days leading up to pulmonary exacerbation, a period of worsening lung infection. The hope was to identify possible bacterial changes that lead to exacerbation.

 The samples collected from individuals with cystic fibrosis – referred to as subjects A, B, C, and D – were sequenced to identify bacterial and viral content during the period leading up to and including exacerbation. At baseline, the most abundant bacteria in subject A was Staphlyococcus, in subject C Streptococcus, and in subjects B and D Burkholeria. Subject A showed to most change in bacterial communities during the week prior to exacerbation symptoms, subject B showed bacterial community change just after onset of exacerbation, and subjects C and D remained relatively stable with the onset of exacerbation. After the changes that occurred in subject A’s bacterial community it never bounced back to its pre-exacerbation population, and stabilized to one with reduced Staphylococcus and increased Pseudomonas and Prevotella. Different from subject A, subject B’s bacterial community shifted one week after the onset of exacerbation from one dominated by Burkholderia  to Pseudomonas.

 While there were many differences among the four subjects sampled in the study, there was one similarity in that the dominant taxa of subjects A, B, and C all decreased in relative abundance around the period of exacerbation. The study’s findings also suggest that rather than changes in total bacterial density, it is more likely that shifts in relative abundance of a member of a bacterial community is associated with changes in CF symptoms. Additionally, none of the respiratory viruses tested for were found present during time of exacerbation, which was surprising to the researchers.

 The results of this study do not give us any solid rules for the characteristics of bacterial communities in the lungs during time of exacerbation in cystic fibrosis patients; however it is a step in the right direction toward identifying such characteristics. Perhaps with a larger sample size we can better understand the changes in community composition that lead to changes in CF symptoms.  

What exactly are antibiotics doing to our bodies?

We’ve talked a lot about antibiotics in the past as well as antibiotic resistant bacteria but it is still unknown exactly what all the effects of antibiotics are on the body and specifically our microbiome.  The increase in antibiotic resistance is a rising concern and this week President Obama and the White House announced that in their 2016 budget they would be doubling their investment in fighting antibiotic resistant bacteria to $1.2B this year. Antibiotics are essential for the treatment of bacterial infection; however, many individuals have adverse effects due to alterations of the microbiome and the increase of antibiotic resistance. These are very real concerns that are causing increasing public health issues and we are glad to see that this administration is continuing to make fighting antibiotic resistant bacteria a priority.

A study recently published in the journal Gut sought to further our understanding of the effects of antibiotics on the host. To look at the physiological effects of antibiotics, the scientists studied three groups of mice: regular germ-free mice; germ-free mice treated with antibiotics; and germ-free mice that were colonized with microbiota from antibiotic-treated normal mice. They found that the use of antibiotics influenced the host in three major ways: depletion of the overall microbiota; having a direct toxic effect on tissues in the host; and the increase of antibiotic resistant bacteria in the microbiota. The researchers also found that the antibiotic-resistant bacteria Pseudomonas aeruginosa were involved in mitochondrial damage, leading to mitochondria-dependent apoptosis (or programmed cell death) in the epithelial tissue of the intestines.

While antibiotics save lives and are incredibly important in fighting bacterial infection, they can also have very unpleasant effects such as local immunodeficiency and cell death. This study took an important, in depth look at the effects of antibiotics on the physiology of the host the effects on the microbiome.        

Asthma, COPD, and the Microbiome

Asthma and chronic obstructive pulmonary disease (COPD) are both illnesses that are caused by chronic inflammation of the respiratory tract, and recent research suggests that the microbiota of the lower respiratory tract may influence the development of these two diseases.  The upper respiratory tract, though, remained unstudied, until a new article was recently published in PLoS ONE.  This article characterized the microbiome of the oropharynx (in the upper respiratory tract) to discover the association between these problems and the microbiome.

Samples were swabbed from the oropharynx of patients who were recently diagnosed with asthma and COPD, as well as from a healthy control group.  Researchers performed 16S rRNA gene sequencing of the bacteria collected from the patients, in order to determine which bacteria were present. They found that there are few differences in microbiome diversity between asthma and COPD patients, however there was a prevalent presence of the bacteria Lactobacillus (phylum Firmicutes) and Pseudomonas (phylum Proteobacteria) in both, which were identified in only very small amounts in healthy patients. On the contrary, the upper respiratory tract of healthy individuals was found to be dominated by Streptococcus, Veillonella, Prevotella, and Neisseria, from the phylum Bacteroidetes, compared to individuals with asthma and COPD.

This study showed distinct differences in the microbiomes of diseased and healthy individuals.  The researchers also note that the low abundance of Neisseria they observed in this study has also been seen in studies of smokers, meaning that this bacteria may be important to respiratory health.  Further work is still needed, though, to determine if the bacteria identified in this study are contributing to the diseased individuals.  Even if they are not, they could still potentially be used in diagnosis.