There are important differences in the gut mucus of germ free and conventionally raised mice

Mucus is not just produced by snails.

The mucus lining of our intestines are the critical interface between the microbiome and the epithelial cells that make up the intestines.  It provides many essential roles in its interaction with the microbiome, but perhaps most importantly it is a physical barrier that separates microbiome bacteria from the vasculature.  Without it, bacteria can elicit an immune response which results in inflammation that is characteristic of IBDs.  New research out of Sweden shows how mucus changes over time as the result of microbiome colonization.  The results were published in the journal Cell Host and Microbe last week.

The researchers undertook a number of experiments whereby they measured the mucus in germ free and conventionally raised mice.  In general, the conventionally raised mice had thinner, more easily shed mucus in their small intestines that allow for diffusion of nutrients.  This mucus contained antimicrobial peptides that prevented bacteria from passing across it.  The conventional mice’s large intestines’ mucus was thick and stiff and impenetrable to bacteria.  This mucus maintained most of its properties even after the conventionally raised mic were treated with antibiotics.  On the other hand, the germ free mice had thin and stiff mucus in their small intestines, as well as thick, but easily penetrable mucus in their large intestines.  This shows that the conditions under which the mucus develops is important to its eventual structure and function.  After, the scientists inoculated some of the germ free mice with the microbiome of the conventional mice and monitored the mucus over time.  It took an entire 6 weeks for the mucus to finally resemble the mucus of a conventionally raised mice.  In addition, the scientists looked that the glycans that were being formed in the mucus, and also noticed differences between the germ free and conventional mice.  As discussed on this blog previously, these glycans can be important in determining which bacteria colonize the gut.  To that end, the researchers measured the microbiome in the mice and discovered that conventional mice had a higher Firmicutes to Bacteroidetes ratio compared to germ free mice.  In addition, even after the germ free mice had been inoculated with the new bacteria, their microbiomes never truly matched the conventionally raised mice’s.

More than anything, this paper shows us the critical importance that mucus plays in microbiome health, science and research.  It demonstrates the importance of an early life microbiome to the maturation of a healthy mucus that can properly regulate the microbiome.  It also shows a possible negative consequence of antibiotics or dietary compounds can have on the mucus, and by extension the microbiome.  Finally, among many other things, it shows that microbiome research should consider the effect of the mucus on their experiments, especially ones involving germ free mice. 

Atopic dermatitis associated gut microbe identified

A moderate case of hand dermatitis

Atopic dermatitis, otherwise known as eczema, is an inflammatory autoimmune response of the skin.  Today in the United States it affects around 25% of children, and as many as 3% of adults, with its incidences increasing each year.  Like many other allergies, the microbiome is now being implicated in the cause of this disease.  A few months back evidence was published linking atopic dermatitis to the skin bacteria Staphylococcus aureus.  Other work, however, has shown that the gut microbiome may be critically important to this disease as well, especially because gut bacteria are more likely to control and elicit certain inflammatory responses seen in dermatitis, such as the release of specific cytokines.  A group of Korea recently compared the gut bacteria in atopic dermatitis patients and healthy controls and identified a specific organism that may be important to the disease.  They published their results last week in the Journal of Allergy and Clinical Immunology.

The researchers measured the gut microbiomes of 132 people, including 90 of which had atopic dermatitis and were seeking medical treatment.  They also measured gene expression by bacteria in the gut, and short chained fatty acids (SCFAs) in the guts of all the individuals.  They discovered that one particular bacterial species was much more abundant in dermatitis patients compared to controls, Faecalibacterium prausnitzii.  After, they measured SCFA production, and noted that a decrease in butyrate and propionate was directly linked with the presence of F. prausnitzii, suggesting an important link between this bug, SCFAs, and the disease state. In addition, they noted that the overall diversity of bacteria was similar in all microbiomes measured.  Finally, the scientists investigated the gene expression, and observed an increase in bacteria that are capable of breaking down gut mucins, or mucous, in the guts of atopic dermatitis individuals.  For example, these bugs were expressing proteins that break down fucose and N-acetylgalactosamine (GalNAc), two monosaccharides that are normally derived from mucins rather than food.

This study presents a number of differences in the gut microbiomes of individuals with an without atopic dermatitis.  The scientists suggest that an important species associated with this disease may be F. prausnitzii, and perhaps it may even be influencing the disease through a lack of SCFA production, and the breakdown of gut mucins.  Atopic dermatitis is a complex disease, and certainly cannot be explained by the presence of an individual bug.  However, this paper does support the notion that diseased individuals, who present rashes on their skin, may have disruptions to gut, and that changes in the gut microenvironment create a niche for specific bacteria to grow.  This, in turn, may inform new therapeutic strategies that target the gut microbiome, rather than topical treatments.

New study shows how E. coli and B. theta grow in the gut mucus

The mucosal membrane continues to be one of the most intriguing and vexing components of the gut microbiome.  It is the interface between the body and the environment, it is inhabited many bacteria, and it is a nutritional source that shapes the populations in the gut.  There is still very little known about the specific interactions between gut mucous and bacteria, but this critical system is rapidly being studied.  In the most recent advance, scientists from Switzerland and Germany examined two very different gut bacteria that fill different mucosal niches. They published their results in the journal Nature Communications.  The two bacteria they studied were Bacteroides thetaiotaomicron (B. theta) and Escherichia coli.  B. theta is a slow growing bacteria that has high metabolic flexibility that is capable of directly using gut mucins as an energy source.  E. coli is a fast growing bacteria that is much more limited in its metabolism and can’t directly use the carbohydrates in the gut, but can take hold and rapidly proliferate after a course of antibiotics. 

The researchers meticulously researched gnotobiotic mice and made many discoveries about bacteria in their mucous.  First, they discovered that the mucosal microbiome varies across its thickness, and is sterile closest to the intestines, but rich in life closest to the lumen.  In addition, they noted that the luminal microbiome is distinct from the mucosal microbiome, even though the mucous is constantly being shed into the lumen.  To this end, they confirmed that with regards to E. coli, these bugs replicate faster than they are shed (in about 3 hours in the mucous but 8 hours in the lumen), and that their persistence is due to replication rather than uptake from the lumen.  How though, can E. coli thrive with their limited ability to break down mucins?  The scientists learned that they likely metabolize iron, in addition to atypical carbon sources such as fatty acids and glycerol.  B. theta, on the other hand, has a huge repertoire of genes to break down mucins.  They do, though, have the ability to leave the mucins and form biofilms on bits of food, such as fiber, that pass through the lumen, and this is one way they travel through the gut.  Regardless of whether they are in the lumen or the mucins they proliferate at the same rate.

Each of these bacteria occupy different niches in the gut, and each is important to our health.  The discovery that E. coli can use iron for metabolism is particularly interesting, as chemotrophy is not normally considered as important in the body, and may be important to iron regulation.  As more research is published the mucous appears to be ‘where the rubber meets the road’ in the microbiome, and new discoveries in this area will be crucial to our overall understanding of the microbiome’s interaction with the body.

Bacteria from infants’ microbiome metabolize breast milk differently.

Human milk oligosaccharides (HMOs) are a diverse group of carbohydrates found in breastmilk.  Because the HMOs can’t be used by the infant directly for energy, scientists believe their purpose is to stimulate the development of a healthy gut microbiome.  During the first year of life, an infant’s gut is dominated by Bifidobacteria, in particular B. infantis, and B. bifidum.  In a recent publication scientists measured the difference in HMO utilization between these bugs, and discovered they have very different and important strategies for HMO utilization. The results were published in Nature Scientific Reports.

The scientists first isolated multiple strains of each species, B. infantis and B. bifidum, from the feces of newborn infants.  They then attempted to culture each strain alone in a mixture of HMOs from breastmilk, as well as the individual HMOs alone.  They learned that the each B. infantum strain could grow on pooled HMOs, but interestingly some of the B. bifidum strains could not grow alone on HMOs.  When the bacteria were cultured with mucins (containing sialic acid or fucose, as previously discussed on this blog) none of the B. infantis could grow, whereas most of the B. bifidum could.  This implies that B. infantis alone cannot utilize fucose or sialic acid, but rather needs the help of other bugs to break these down to utilize them.  After, the scientists looked at the regulation of different genes during the culturing experiments.  From these results they determined that B. infantum transports the HMOs inside the cell before breaking them down for energy.  B. bifidum, on the other hand, breaks the oligosaccharides down extracellularly before taking up smaller, simpler sugars. 

All together we see that there is a complex assemblage of bugs in the guts of infants that all rely on one another for energy and metabolism.  The breastmilk cocktail of HMOs itself is so complicated that it almost necessitates the interdependent communities to grow.  Overall, this creates a robust and resilient microbiome that prevents pathogens from taking hold and protects the infant during his or her most vulnerable years.

Sialic acid may be key carbohydrate responsible for inflammation and dysbiosis in the gut

A surface mucous cell bordering on the stomach lumen secretes mucus (pink stain).

Our diet is full of various carbohydrates, composed of different monosaccharides and polysaccharides.  Many of these survive our own digestion and make it all the way to the colon where they modulate our microbiome.  Another source of saccharides for our gut bacteria is the mucous that we produce, which can be a rich source of fucose or sialic acid.  Sialic acid has been implicated in many inflammatory diseases, such as bacterial vaginosis.  Last week, researchers from Switzerland showed that sialic acid may play a critical role in colitis, at least in one colitis model commonly used in mice.  They published their results in Nature Communications.

One way to induce intestinal inflammation in mice is to feed them dextran sodium sulfate (DSS).  The reason this molecule causes colitis in this mice is unknown, but it is used in many models of the disease.  In order to understand the possible role of sialic acid in the colitis, scientists created mice that could not produce mucous with sialic acid.  They quickly realized that these mice were not as susceptible to the DSS-induced colitis as their normal counterparts.  After, they tested how various antibiotics affected colitis in the DSS—colitis mice and discovered that Escherichia coli abundance was directly associated with the severity of the disease. Putting these ideas together, they tested and discovered that E. coli used sialic acid as their main carbohydrate source in vitro.

Interestingly, the E. coli cannot actually access the sialic acid from mucins, but instead need other bacteria, such as Bacteroides vulgatus to cleave and release the sialic acid from the mucins in order to access it.  If sialic acid is indeed important to the human form of the disease there may be multiple approaches to combatting the disease.  First, by eliminating E. coli, and second by eliminating the free sialic acid.

A new way in which some gut bacteria rely on their hosts’ mucous for energy

It is often understood that our gut bacteria live off of the foods we eat.  However, many gut bacteria can actually metabolize the mucous that protects the lining of our gut.  In fact, many bugs have the ability to digest a specific sugar that is attached to our mucins, called sialic acid.  Interestingly, some bacteria have the ability to cleave this sugar from the mucins, others have the ability to consume this sugar once it is released, and others have the ability to perform both of these tasks.  Last week, a new method for how gut bacteria can transform sialic acid was discovered, that some bacteria can actually transform sialic acid before cleaving it, and that this may be clinically relevant for Crohn’s disease and colitis.  The authors published their results in Nature Communications.

The authors were testing a common commensal bacteria, Ruminococcus gnavus, and noted that it had the ability to both cleave and consume sialic acid from gut mucins.  When they identified the metabolites from this process they discovered that the sialic acid was actually being converted to a different form by these bugs.  After further experimentation they realized that a type of enzyme, called an intramolecular trans sialidase, which had never before been observed in gut bacteria, was responsible.  The researchers then compared the genes from R. gnavus to other bugs common in the gut and noted that a full 11% of human gut commensals had this enzyme, and that these bacteria were overrepresented in people with IBD.  The authors think that the bugs who code for this enzyme have an inherent advantage over other gut microbiota because after they transform the sialic acid they can still use it for energy, whereas other bugs cannot, leaving the sugar all to themselves. 

The paper did not discuss specific mechanisms as to why these bugs may be overrepresented in Crohn’s and colitis.  They did however test a few molecules that inhibited the activity of the enzymes.  Perhaps if these enzymes or the responsible bugs are the cause of IBD, than these inhibitors could be used as therapeutics to combat the disease.