The microbiome’s response to the flu and its treatment

In 2013 there was an avian flu (H7N9) outbreak in China that affected 140 people, killing 46 of them.  During the outbreak doctors from one of the major hospitals in China treated 40 of these patients by giving them antivirals and antibiotics, amongst other first line treatments.  In addition, they gave probiotics along with the antibiotics to restore the gut microbiome.  All the while, they measured the patients’ microbiomes to track how they changed throughout the course of treatment.  The results of this study were published last week in the journal Nature Scientific Reports.

Twenty six patients were enrolled in the study, and each of them was given antibiotics within 6 hours of admission to the hospital.  In addition, each one was given Clostridia probiotic capsules along with the antibiotics.  Thirty one healthy control stool samples that represented the demographics of those undergoing flu treatment were also measured as a part of the study.  Before the antibiotics were taken, the patients with the flu already had altered microbiomes that were low in diversity and had lower abundances of Bacteroidetes and higher levels of Proteobacteria.  After antibiotics were given there was a dramatic shift in the microbiomes, that was characterized by a relative increase in the abundance of Escherichia coli.  In addition, the scientists noted that the probiotics were in fact increasing the amounts of Clostridia in the guts of patients who took them, and that the probiotics may have led to better clinical outcomes.  In their hospital only 20% of patients died of the flu, whereas 40% died in the rest of China.

The major takeaway from this study is the changes that the flu has on the microbiome, decreasing diversity and altering the levels of certain phyla.  The fact that the probiotics did appear to take hold and improve clinical outcomes is interesting, but the study was extremely small and limited in its scope to reach any statistically significant conclusions.  Overall though, this study suggests that if you come down with a flu that it may be wise to feed and nourish your microbiome because it is ‘getting sick’ right alongside you.

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.

How does the gut microbiome recover after diarrhea?

Scanning electron microscope image of Vibrio cholerae, the cause of cholera and a major cause of diarrhea-associated deaths each year.

Diarrhea is an important global health challenge that kills nearly two million people each year.  Even when it is not lethal it can have important detrimental impacts, especially on children.  For example, frequent diarrhea is associated with decreases in height, IQ, and heart health.  Diarrhea is frequently a microbiome – based disorder, and gut pathogens like enterotoxin producing Escherichia coli and Vibrio cholerae are often the culprits.  Using diarrhea caused by these pathogens as their model, scientists from Harvard University recently studied how the gut microbiome rebounds after diarrhea.  They published their results in Mbio.

The scientists measured the stools of 41 people (both children and adults) in Bangladesh that had diarrhea caused by E. coli or V. cholerae (the cause of cholera).  They measured the patients’ stools before, during, and after their diarrhea episodes and tracked the changes that occurred in all patients’ stools.  Interestingly, they identified a consistent succession of the gut microbiome that occurred in nearly all cases, regardless of the cause of diarrhea.  First, the diarrhea (or antibiotic treatment for the diarrhea) clears out much of the microbiome, and leaves both carbohydrates and oxygen to accumulate in the gut.  (Carbohydrates and oxygen would normally be metabolized by the microbiome, but in the absence of many bacteria, these things accumulate.)  Next, oxygen respiring and carbohydrate utilizing bacteria (especially those using simple carbs) colonize the gut and decrease the abundance of both of these substrates.  After, the lack of simple sugars and oxygen leads to a decline in the population of bacteria that use these, and the succession to anaerobic (i.e. do not respire oxygen), complex carb fermenting bacteria begins.  Finally, the gut microbiome resembles the complex community that existed prior to infection and the onset of diarrhea.  The entire process takes about 30 days to complete, but depends on a variety of factors such as diet, antibiotic use, and duration of diarrhea.

Studies like this one are important to combatting diarrhea, and shortening recovery time.  For example, it is now known that oxygen accumulates after diarrhea, and that while it exists at high levels the microbiome is not fully recovered.  Perhaps introducing an agent after diarrhea that rapidly decreases the amount of oxygen in the terminal gut could hasten the microbiome recovery time and improve the patient’s wellbeing.  Next time you have diarrhea, remember that it takes almost a month for your microbiome to recover, so nurture during that time.

Our immune system selectively chooses which gut bacteria to keep, and which to eliminate

We have come a long way in our understanding how exactly pathogenic bacteria can invade and populate the gut.  Yet, there still remains uncertainty as to how exactly our immune system responds to and eliminates these infectious bacteria.  A recent study addressed this by investigating the immune response to pathogenic bacteria in mice guts. 

Some Escherichia coli can be pathogenic and infect the human gastrointestinal tract.  In these instances, these Gram-negative bacteria attach to and populate the gut and cause lesions to the epithelium through a well-characterized attaching-and-effacing behavior.   It is currently understood that IgG antibodies are produced in response to E. coli infection, but the exact cellular underpinnings as to how the bacteria are eliminated are unknown. 

To model this, researchers infected germ free mice with Citrobacter rodentium, a bacterial strain known to carry genes that exhibits effacement pathology in mice.  The specific genes of interest that induce enterocyte effacement (LEE) are referred to as a pathogenicity island, loci responsible for virulent behavior, and they are present in both E. Coli and C. rodentium.   The researchers measured adaptive immunity reaction in response to C. rodentium infection, and specifically looked to see if LEE - the virulent bacterial signature - was down-regulated. 

It was found that the LEE virulent strain was down-regulated concomitant to an increase in release of IgG antibodies.  These IgG antibodies were found to be specific to the LEE virulent expression, as supported by significant IgG binding affinity to the virulent strain.  The IgG antibodies eliminated the specific C. rodentium phenotype that expressed the LEE loci, and upon binding to the bacteria, they were removed by neutrophils.

Interestingly, the C. rodentium avirulent phenotype that lacked the LEE was not eliminated by IgG antibodies.  However, these bacteria were subsequently outcompeted by other microbiota populations.  Together, this information suggests that IgG could selectively eliminate the C. rodentium virulent phenotype, and innate immunity could eventually remove the non-virulent populations. 

This study provides excellent insight into how our immune system can distinguish between good and bad bacteria in addition to describing the underlying cellular mechanism.  Defining the molecular underpinnings of antibody action will allow us to make significant advancements in therapeutic approach.  Understanding the molecular pathways is a critical first step toward pharmacotherapeutic intervention, and this study could potentially lead to the development of some exciting advancements in the future.  

Significant bacterial diversity found in the microbiomes of remote Amerindians

A group of Yanomami people in Demini, Brazil © Fiona Watson/Survival

The Yanomami Indians are a native people that reside in remote areas of the Amazon jungle in South America, where they live in a society devoid of westernization and modernization.  They were first contacted in the 1960s, and the Venezuelan government has since preserved isolation among these societies by preventing modern development from expanding into their lands.  From an anthropologic perspective, these people therefore represent a glimpse into the past of a hunter-gatherer subsistence living human society.  Capitalizing on this unique characteristic, researchers from several institutions led by AMI Scientific Advisory Board member Maria Gloria Dominguez Bello, set out to investigate the human microbiomes of these remote communities in a twofold manner.  Bacterial diversity of the Yanomami microbiota was characterized, concomitant to exploring bacterial and gene responses to antibiotics commonly utilized in clinics in Western societies. 

Thirty four Yanomami subjects between 4 and 50 years old were selected for analysis.  Forearm skin, oral mucosa, and fecal samples were collected for bacterial analysis and compared to subjects from the U.S., Guahibo Amerindian, and Malawian tribes (the latter two were selected for comparison, as their cultures are in transition to modernization).  E. coli cultures were examined and genomic libraries were created for further analysis of bacterial expression, functional diversity, and resistome (the collection of antibiotic resistant genes) gene expression in response to antibiotic treatment. 

The Yanomami people displayed extraordinary levels of bacterial diversity as compared to the U.S. subjects, Guahibo Amerindians, and Malawians.  Specifically, the Yanomami fecal samples were characterized by high expression of Prevotella and low expression of Bacteroide bacteria.  With respect to functional bacterial diversity, the Yanomami displayed higher fecal and skin functional diversity among the other Amerindian and U.S. subjects.  Furthermore, over-enrichment in bacteria that interact with pathways involved with protein and carbohydrate metabolism was observed in the Yanomami. 

23 antibiotics were tested on 131 E. coli strains isolated from 11 fecal samples, and sensitivity to all antibiotics was observed.  Interestingly, functional libraries created from these E. coli isolates displayed antibiotic resistant genes targeted against 8 of the 23 antibiotics.  This suggests that antibiotic resistance genes have been maintained despite the lack of apparent antibiotic selection pressure that is characteristic among Western societies. 

Results from this study indicate a greater scope of bacterial diversity in a defined group of people than ever reported before.  Furthermore, the investigation illuminated an important characteristic of the bacterial resistome, as the results indicated that resistant genes were present in a population that had not been exposed to any Westernization.  This suggests that some antibiotic resistant genes are archaic, dating back to pre-westernization times and also that westernization affects microbiome diversity.  Ultimately, this study employed a fascinating approach to investigating human microbiome divergence and evolution, in addition to providing more insight to host-species relationships with respect to pharmacologic therapies.