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.

Microbiome metabolite in urine predicts severity of graft versus host disease

Molecular structure of indoxyl-sulfate

People that suffer from blood cancers, such as acute myeloid leukemia, often times receive hematopoietic stem cell transplants (HSCT) as part of their therapy.  This procedure typically replaces the sick person’s white blood cells with those of a healthy donor.  While this is a life-saving procedure it does carry a type of transplant ‘rejection’ risk.  While in a normal organ transplant a person’s own white blood cells will attack the foreign organ, in this case the new, donor white blood cells begin attacking parts of the recipient’s body.  This is called graft versus host disease (GvHD), and can often times be fatal.  One of the primary areas that are attacked by the new blood cells is the gut microbiome.  This is not surprising because the ‘replacement’ immune system is not programmed to tolerate and accept the bacteria in the gut, because they are so different from the bacteria it was originally adapted for.  Therefore, GvHD, is often considered a microbiome disease, and there have even been studies to investigate whether matching microbiomes decreases risk for the disease. 

An important area of research is focused on detecting GvHD before it begins so that it can be treated early.  While normally GvHD is diagnosed by symptoms, it may be possible to use the microbiome itself for early detection of the disease.  A group out of Germany recently showed that by monitoring a specific metabolite produced in the gut, indoxyl sulfate, one could predict the severity of GvHD.  This molecule is only produced by bacteria, mostly in the gut, by breaking down the amino acid tryptophan.  Moreover, indoxyl sulfate is an important signaling molecule that is thought to modulate the gut epithelial function, and may cause inflammation.  They published the results of their study in the journal Blood last week. 

The scientists measured the indoxyl sulfate concentration in the urine of 131 individuals undergoing HSCT over the course of 28 days following the treatment.  After, the ranked the patients in terms of indoxyl sulfate level during the first ten days after transplant, and compared their outcomes.  Remarkably, the people that had the lowest levels of indoxyl sulfate had a statistically significant higher risk of dying of GvHD after 12 months.  Next, the scientists attempted to relate the gut microbiome composition of the patients with the indoxyl sulfate levels.  They realized higher diversity microbiomes were related to higher indoxyl sulfate levels, and healthier outcomes.  In addition, higher levels of Clostridia and lower levels of Bacilli led to higher indoxyl sulfate.

This study may go a long way in informing clinicians about GvHD risk in their patients.  Not only does it show that monitoring indoxyl sulfate may predict GvHD severity, but it also points to specific bacteria that may be important in controlling its levels.  HSCTs are a highly effective treatment for blood cancer, that often times have a higher efficacy/safety profile compared with traditional cancer therapies.  Understanding the microbiome’s role in GvHD, one of the most important risks of HSCT, will hopefully lead to improved therapies and better overall cancer outcomes.

The anorexia nervosa gut microbiome differs from healthy controls and is related to mental health

Two photographs, before and after treatment for anorexia

Anorexia nervosa is devastating condition in which an individual purposely starves themselves leading to severely low weight.  In addition, most patients with anorexia have depression, and there is a definitely mental aspect to this disease.  The disease then, has both dietary and mental components, making it extremely interesting to microbiome scientists, because the microbiome is implicated with both of these facets.  Scientists from UNC recently conducted a preliminary study on both of these aspects of the disease by comparing the microbiomes and mental state of anorexic patients before and after treatment, along with healthy controls.  They published there results last week in the journal Psychosomatic Medicine.

Sixteen patients with anorexia nervosa who sought treatment for their disease had stool samples collected at admission to the hospital as well as their mental health assessed.  Ten of these individuals that made partial recoveries (improved body mass index) were discharged from the hospital and donated stool samples and had their mental health assessed upon leaving.  The researchers discovered that the patients’ microbiomes severely lacked diversity compared to aged matched controls, and that was true for both admission and discharge from the hospital.  The scientists noted though, that the patients that left the hospital had microbiomes that more resembled the control individuals than when they entered.  For example, the anorexic patients had very little Clostridia when they entered the hospital, but these populations rebounded during treatment.  In terms of the mental health aspect of anorexia and the microbiome, the researchers found a direct association between eating disorder psychopathology and microbiome diversity, with lower diversity corresponding to worse eating disorder psychopathology.  The same was true for depression, as the degree of depression was inversely correlated with bacterial diversity.  In terms of individual families of bacteria, a lack of Ruminococcaceae had the strongest association negative mental state.

This study shows that a lack of eating decreases gut flora diversity and negatively impacts the microbiome.  While not surprising, this lack of diversity will almost certainly cause a dysbiosis that detriments many other aspects of health.  One of these, in the case of anorexia, may be mental health, but of course it is not clear which causes which, or if there is any causation or merely just correlation.  In any event, disorders that have both mental and dietary components are extremely fascinating to investigate, as it is possible the microbiome is of primary importance to these diseases.

New research helps determine what is healthy and unhealthy in the vaginal microbiome

Editor’s note: This blog about the vaginal microbiome is a good primer for this coming Monday’s Microbiome Podcast with Jacques Ravel, where we will discuss the vaginal microbiome and women’s health at length.  There will also be a special announcement during this podcast, so anyone interested should be sure to download it Monday, June 1.

The typical ‘healthy’ vaginal microbiome is dominated by a Lactobacillus.  However many women, especially those of African descent, are not dominated by this genus, and instead have a high diversity of bacteria in their vaginal tract.  This low lactobacilli, high diversity phenotype has been associated with many disease states, such as bacterial vaginosis (BV), preterm birth, and higher rates of sexually transmitted disease (STD) transmission.  (We have written about some of these diseases before, and encourage any interested reader to click the ‘vaginal microbiome’ below this story to learn more.)  Vaginal microbiome research is still in its early days though, and it is not clear why vaginal microbiome not dominated by Lactobacillus should lead to these diseases, and if this phenotype, if asymptomatic, should even be considered unhealthy.  New research though, out of Harvard University, shows that this phenotype does lead to inflammation, and that these inflammatory response can affect reproductive health and STD transmission.  They published their study in the journal Immunity last week.

The scientists studied the vaginal microbiomes of a cohort of 146 HIV negative, asymptomatic, black, South African women.  They discovered that 63% of them were not dominated by Lactobacillus, an extremely high percentage, especially compared to their counterparts in developed countries (38% of black women and 10% of white women).  Nearly half of those women were dominated by Gardneralla vaginalis, which is most commonly associated with BV, and a large percentage of the other half were diagnosed with BV after investigation.  This is especially interesting because, as stated before, all of the women in the cohort claimed to be asymptomatic, but as we are learning, many women are unaware that there is anything wrong.  Overall, the women were able to be grouped into 4 specific phenotypes, those dominated by Lactobacillus iners, those dominated by other Lactobacillus crispatus, those dominated by Gardnerella vaginalis, and those with a high diversity including Gardnerella vaginalis, Fusobacterium gonidiaformans, Prevotella bivia, and Atopobium vaginae (note the lack of Lacotbacillus in this high diversity group). 

The scientists discovered that there were no associations between each vaginal microbiome group and the rate of STDs, contraceptive use, or sexual behavior.  This is important in showing that, at least on first pass, these bacterial communities were not the result of these exogenous factors (nor did they cause them, for that matter).  They also discovered that there was only a loose association between inflammatory cells in the vaginas of these women, and whether or not they had an STD.  The loose association was only observed in women with Chlamydia, and the women with the highest levels of inflammation had no apparent STDs.

The fact that STDs were not strongly associated with inflammation led the researchers to hypothesize that the vaginal microbiome community, rather than STDs, were responsible for vaginal inflammation.  Indeed, when they compared the amount of inflammatory cells in each vagina with the different microbiome groups described earlier, they found a strong association between inflammation and the highly diverse microbiome group.   Moreover, when they tracked individual women over time, those women whose vaginal microbiomes shifted to the high diversity group also increased inflammatory responses.  The researchers then took this work a step further, and identified specific bacteria that were associated with the inflammatory response:  Prevotella amnii, Mobiluncus mulieris, Sneathia amnii, and Sneathia sanguinegens.

Finally, the researchers measured genes for specific receptors in the vagina that are known to trigger an immune response.  They discovered that those women with the high diversity vaginal microbiomes upregulated genes for these receptors, which are known to be activated by bacteria.  Making matters worse, specific immune cells that are triggered by these receptors, which are thought to be critically important to HIV transmission, were found in higher abundances in women in the high diversity vaginal microbiome group.

This paper did a really great job showing that a vaginal microbiome that lacks Lactobacillus is indeed an unhealthy state, because it creates a highly inflammatory vaginal microbiome which likely causes or contributes to many other ailments, beyond just the higher rates of HIV transmission that was demonstrated.  Unfortunately, at the moment, there are no easy ways for women to check which vaginal microbiome they have, but that should be changing soon, and we recommend that all of our readers tune into the Microbiome Podcast this coming Monday to hear a big announcement in this area. 

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.  

Specific bacteria and overall diversity linked to severity of necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is an inflammation of the gut that occurs due to bacterial infection in premature infants.  It has long been considered that a ‘healthy’ microbiome is important to preventing NEC in low birth weight infants, and, as we have written about before, there is a lot of science that supports this.  Still though, it is not known which bacteria are most responsible for causing NEC, and how overall diversity is associated with the disease.  Many studies have tried to nail this down, but there has been conflicting results.  Scientists at Louisiana State University thought that perhaps these conflicting results were from neglecting to consider the severity of the NEC as a variable in each study.  They hypothesized that the infants’ microbiomes would vary depending on the severity of the NEC, and that the most severe cases would show a characteristic microbiome that may be important to understanding the disease.  They published their results in the Journal Microbiome last week.  

The scientists studied the microbiomes of 74 healthy infants and 21 infants suffering from NEC.  They then categorized the NEC infants into three groups based on the severity of the disease.  The scientists learned that two bacterial genera, Veillonella and Streptococcus, were more abundant in all the NEC microbiomes compared to non-NEC controls.  They also discovered that overall microbiome diversity was decreased in NEC versus controls.  When the researchers looked microbiome differences that were a function of NEC severity they discovered that Clostridia were completely absent from the microbiomes of infants suffering from the most severe NEC and its increased with decreasing severity of NEC (15% in controls, 12% in mild NEC, 3% in moderate NEC, and 0% in severe NEC).  In addition, a similar trend was seen with diversity, it decreased with severity of NEC.

Many Clostridia species have been associated with a healthy microbiome, and they may be critically important to maintaining a homeostasis in the gut.  According to this study, their abundance appears to be of upmost importance in premature infants, and this should be considered moving forward.  Many countries administer probiotics to low birthweight infants who are at risk for NEC, but this is not yet down in the United States.  Fortunately, there are a number of clinical trials that are trying to nail down the science so that the FDA has enough evidence to make a recommendation.