Foul Mouthed Sweet Tooth

Happy 2010 from guest blogger Holly... Here's my New Year wish for everyone.

If you’re like me then you frequently find yourself reading articles about things that you know nothing about (which, unfortunately, describes the content of probably 99.99% of the things that I read). There are many explanations for such behavior. And why I clicked on, “The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity,” needs a little bit of back story.

The last week of November I was hit with hemorrhagic E. coli.* I think my body pretty well expelled the bug on its own, but a strong dose of two different antibiotics made sure it was real dead.

Many people who’ve taken Cipro have experienced that notoriously unpleasant taste in their mouths. The flavor is difficult to describe, but ever since I finished taking the medicine, I’ve continued to have a foul tasting mouth and a foul mouth (ba dum bum bum). My dogs love the makeover (which was amusing for about five seconds), but I can’t bear to ask my husband if he’s noticed a difference. (Ego, 1: Scientific rigor, 0.)

Is this new taste a signal that my mouth’s ecosystem is different? My mind (I take no credit for this) imagines that the antibiotics killed off more micro-critters than just the E. coli and those that better survived are now more prevalent compared to their ancestors. Maybe the species that currently dominates my mouth, or its products, tastes different from the bacterial composition that I had before.

Since this shift in balance would have happened abruptly during the Cipro killing spree, it makes sense that my taste receptors are detecting it now – my brain would have ignorantly ignored a slow bacterial change just like it couldn’t detect my transformation from 2 cells to 32-year-old.

I’ve been popping mints, gargling, and flossing like a lumberjack, for a month now and this whole oral fiasco is why I was naturally drawn to this recent article,“The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity.”

Bacteria. Adaptation. Oral Cavity. This is totally going to be about me! See, first I happened to watch Food Inc., in which they discuss hemorrhagic E. coli while I was recovering from hemorrhagic E. coli, and now just as there’s a bacterial coup in my oral cavity, I stumble upon new research on oral bacteria!** Is it going to identify the species that differentially survived antibiotics, ran rampant in my mouth, and ruined my breath?***

Well, it turns out that this article is not at all about me or my dilemma - despite the common themes which you'll read about below, I can't solve my bad breath mystery by simply reading about oral bacteria. But it’s still a good read for people with oral cavities, people with cavities in their oral cavities, people who are afraid of getting cavities, and people who are fascinated with evolution. It’s especially poignant if you’ve got a sweet tooth that has taken command of your life for the past few weeks like mine has.****

We’ve all got like 900 species of microbiota in our “oral biofilm.” Some of those species are more similar to what’s down the hatch than others. The genus Bifidobacterium is one group that has species living from the lips all the way down to the colon, and also in the vagina (although the article doesn't mention the vaginal species, only my brief internet search said so). You may recognize the genus Bifidobacterium because many of its species are considered “probiotics” and they are included in foods and food supplements to help with digestion, sometimes under the term “Bifidus.”

Most species in this genus are your friends. They’ve teamed up with your body so that they get what they want out of the food that you eat while at the same time they're helping you get what you need out of the food that you eat. It’s a win-win situation and all these microbiotic critters running around inside you (well, more like clinging desperately to your epithelial linings) are why you are more cells of them than you are cells of you.

Like many microbiota in your mouth, B. dentium (the focal species of the paper we're talking about here) is great at metabolizing carbohydrates and approximately 14% of the genes in its entire genome code for proteins that are involved in this process. How does this compare to human genes for metabolizing carbohydrates? I don’t know, but I’m guessing we have relatively fewer genes that are involved in carbohydrate metabolism and that by teaming up with other species which are essentially born to do this, our own system can afford to slack, functionally speaking. It’s a beautiful relationship. But it comes with some costs.

For example, although B. dentium helps with our digestive functions, it has evolved in such a way that it’s no longer just a friend. It’s also a pathogen!

B. dentium is by far the most popular Bifidobacterium to be associated with cavities on tooth crowns in both children and adults and those on the roots of adult teeth. By producing acid, it lowers the pH enough to cause teeth to demineralize. And it’s so good at surviving in this highly acidic environment that it that it can make a living like this, on our rotting holiday cookie-smothered teeth.

The whole genome sequence revealed that the intergenic regions of the B. dentium genome have more nucleotide differences than the protein-coding regions. Sound familiar? (Everything boils down to human vs. chimp, doesn’t it?)

The results of these differences found in the genome of B. dentium are (1) it can withstand low pH conditions (as mentioned above), (2) it can metabolize a wider range of stuff that we eat compared to what its cousins in the colon can metabolize (which makes sense considering the smorgasbord presented to B. dentium vs. what metaphorical crumbs make it down to the colon) and it can even live off our own saliva, and (3) it seems to be able to resist biocide better than its relatives (which was tested by growing B. dentium in mouthwash which sounds completely unethical).

Regarding that third point, B. dentium has a relative abundance of what are called “two-component systems (2CSs)” which are instances where protein-coding genes are essentially flanked by regulator genes, and this seems to be a surprise to the authors based on what is known about other bifidobacterial genomes. The implications of these numerous 2CSs are that they may be indicative of B. dentium’s “ability to sense dynamic environmental cues and to modulate appropriate physiological responses.” Perhaps this is what enables them to differentially survive despite our attempts to murder them with mouthwash (or, heh heh, during E. coli-cide? Hmmm?). Or at least, perhaps this is what enables them to not just tolerate but thrive in fluctuating habitat acidity. And what's even more exciting is that these adaptations may be linked.

Naturally we’re left to wonder: How long ago or recently did B. dentium originate? Did our behavior induce B. dentium to adapt this way through our diet and/or through our dental hygiene? Is it smart to ingest commercially sold probiotics if they contain species that can evolve to be opportunistic pathogens like B. dentium did or, worse, if they actually contain the pathogenic B. dentium and we just don’t know it?

Because it's the holidays, should we just forget about it and eat all the cookies and sweets that we want because we can't stop the evolution of our oral microbiota?

I like that idea. More cookies, please, and pass the biocide and the floss, thanks.

Starred Footnotes:

*No, hemorrhagic E. coli is not why I’ve been gone since mid November (apart from dropping comments on Anne and Ken’s posts). University life has kept me sufficiently busy and generally abloggish. But getting hemorrhagic E. coli certainly didn’t help. No, I don’t know where it came from. And no, I didn’t go to this doctor for treatment (amicably sarcastic emoticon).

** I believe this is what Oprah calls “The Secret.”

***Please do not take this opportunity to tell me that my breath was already ruined.

**** I used to think that a gold tooth was a sweet tooth and that it could actually taste sweets better than enamel teeth. This is because my uncle has a gold tooth and a sweet tooth, so naturally a 5-year-old me who had never seen or heard of either of those things thought that they were one in the same, and thought that a sweet tooth was a pretty neat trait to have. For much of my childhood I was incredibly jealous of every person I saw sporting a gold tooth.

Gutting it out

Only a small fraction of bacteria can be grown in laboratories; apparently nobody understands what they need in their environment well enough. This can be a problem for microbiologists trying to identify the bacterium causing a new infectious disease, but it also means that it has not been possible to know all of the little bugs to which we our bodies are willing or unwilling hosts. The same would be true for other animals, wild ones as well as our pets and farm species. We say 'willing or unwilling' because, of these pathogens, some are presumed to be harmless commensals, and others are necessary to our survival (such as the E. coli in our intestine, that we depend on for digestion, and similarly for other mammals such as grazers like cows and goats who need bacteria in their rumens to digest cellulose).

One of the characteristics of bacteria is that they can exchange structures (e.g., plasmids) that contain some actively used genes. This is where many if not all of the genes are that lead the bacteria to resist nasty things in their environments such as antibiotics that bacterial targets have evolved to protect themselves. A vulnerable strain of bacteria can acquire a gene that makes them antibiotic resistant. This is of course a very important current problem in farm animals and humans, driven by the amount of antibiotics we ingest. And farm animals are reservoirs of pathogens that can affect humans, so humans and the animals they live with are part of large bacterial-host ecosystems.

Since we can't culture most bacteria, our knowledge of who's where, and the characteristics of many bacterial species, has been quite limited. But DNA sequencing technology has opened the way to identifying our visitors. By extracting all the DNA from a sample of some tissue, fragmenting the DNA and sequencing the fragments, their owners can be identified, and their genetic makeup and function characterized. This is done by comparing the sequence fragments against all sequences currently known (in Genbank). Even if we don't identify an exact match, we can find a known species that is close enough to our tissue-sampled sequence to identify its place in the bacterial tree of life. Antibiotic resistance genes can be identified in the same way, too, since many are already known.

A new paper in Science (Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, Sommer et al., Aug 28, 2009, 1128-1131) reports on a detailed analysis of the antibiotic resistance genes found in the microbiome, the resident bacteria, of healthy individuals. The study was done in an effort to learn more about how antibiotic resistance genes are acquired by pathogens that infect humans.

This study found that, indeed, many of the resistance genes in multidrug resistant bacteria were acquired by lateral gene transfer--that is, the gene hopped into the pathogen on a plasmid from a different bacterium. Bacteria in the wild usually live in large communities of many different species, where they can promiscuously exchange plasmids, thus antibiotic resistance can spread rapidly.

The authors wondered if the extensive history of antibiotic use in humans might mean that microflora in the human gut might be a reservoir of resistance genes readily transferable to pathogens. They isolated DNA from saliva and fecal samples from two healthy individuals who had not taken antibiotics for at least a year, and sequenced fragments of bacterial DNA that were resistant to all the antibiotics they tested.

They found that there was some, but by no means complete overlap between the two people who were sampled, and that nearly half the resistance genes they identified in this way were identical to resistance genes in human pathogens. This doesn't tell them whether gene transfer went from the commensal microflora to the pathogen or vice versa, but Sommer et al. suggest that it's quite plausible that our gut microflora are a reservoir of resistance genes just waiting to jump into pathogens which are now controllable with drugs. The remaining genes, although not yet found in pathogens, were functional when transferred to E. coli, suggesting that if they do eventually find their way into pathogens, they will be active, although there seems to currently be a barrier to lateral gene transfer which isn't yet understood.

The authors conclude:

Many commensal bacterial species, which were once considered relatively harmless residents of the human microbiome, have recently emerged as multidrug-resistant disease-causing organisms. In the absence of in-depth characterization of the resistance reservoir of the human microbiome, the process by which antibiotic resistance emerges in human pathogens will remain unclear.

This study provides interesting ecological information about bacterial dynamics, and of course warns us that antibiotic resistance may be more complex, challenging, and difficult to predict than we have thought. It's evolution in action.