In the past half-millennium, we’ve learned a lot about our friends in the bacterial kingdom. Early microscopes allowed us to see single-celled organisms, like bacteria, in the 1600s. The 1800s solidified the germ theory of disease – that most diseases are caused by microorganisms (bacteria, viruses, and other tiny things). Today we’ve learned that not all bacteria are harmful. In fact, our bodies contain trillions of bacteria and we suspect that many of the bacteria that live inside us are actually beneficial! The Han lab at CU Boulder shows us one such relationship where bacteria help their host absorb iron using a molecule called enterobactin.
The community of microorganisms that live within our bodies is called the microbiome. With trillions of bacteria in our microbiome, it can seem like an outsized task to determine what role they play in our health. Much of the bacteria in our digestive system is commensal, meaning that they derive nutrients from us but don’t harm or benefit us. However, a portion of the human gut microbiome is predicted to play a role in breaking down hard-to-digest substances and producing hormones, such as those that help us feel full. One goal of scientists studying the microbiome is to understand what bacteria are producing to help us out.
Using tiny worms and the common laboratory bacteria E. coli, Bin Qi and Min Han, authors of a new paper in the journal Cell, asked which genes in bacteria are important to worm survival. To understand their experiment, we need a bit of background information about the worms called C. elegans.
These tiny transparent worms – beloved in laboratories all over the world – have simple digestive tracts but are a good model for our own gut because both contain lots of E. coli. The worms eat E. coli as their main food source in the lab, but if you “cook” their food, i.e. kill the E. coli using heat, the worms won’t be able to grow very well. If you give the worms a small amount of live food along with the cooked food, the worms can get most of their nutrients from the cooked food and will be able to grow because they are also getting necessary nutrients from the few living microbes they eat. This suggests that the living bacteria contain or produce necessary nutrients for the worms’ survival.
“We put a little bit of live bacteria here,” explained Han as he pointed to one side of a petri dish, “and that alone cannot support worm growth. They still don’t grow because there’s not enough food, but if you put them together [with dead bacteria] the worm can grab a little bit of [live] bacteria and colonize [the gut], and then come down and eat the cooked food. And yes [they] can grow!”
The worms don’t need to eat very much live bacteria to produce important nutrients for the worms’ digestive system. Then they can eat the heat-killed bacteria for food and grow normally.
To find important bacterial pathways for worm survival, Qi created multiple different strains of live bacteria, each of which was missing an E. coli protein. If a gene that is important for host growth or digestion is knocked out in the tiny patch of live bacteria, the worms won’t be able to grow normally. Using this method, Qi and Han found 36 genes that, when knocked out in E. coli, slowed worm growth. They concluded that those genes are important for the mutually beneficial relationship between E. coli and C. elegans.
Among these 36 mutants, five of the knocked-out genes are in the pathway that makes the molecule enterobactin. “If you don’t have the ability to make enterobactin,” Han explained, “the worms don’t grow. But you can have the pure chemical added to the food and [the worms] just recover. That clearly indicates that it is functional.”
So, what is enterobactin? It is a small molecule that binds iron, an essential metal nutrient. Bacteria use enterobactin to fetch iron from their environment that they use to survive and reproduce. Usually we think of molecules like this when we think of “bad” bacteria entering our bodies and stealing our nutrients. But E. coli live inside of us peacefully, so they wouldn’t want to cause us harm every day. Somehow the enterobactin must be fetching iron for the host as well as for the bacteria.
Han revealed that the iron that enterobactin binds actually ends up in the host mitochondria, where it is essential for producing energy for worm growth. Han’s lab is also doing studies in mice to see if the same trend holds—are bacteria unable to produce enterobactin good or bad for the host? So far the mice that are fed bacteria without enterobactin grow slower than mice fed normal bacteria, suggesting that the findings in worms may translate to mammals.
This research has implications to human health because iron deficiency – anemia – is a huge global problem. Unfortunately, iron supplements are not very good at treating iron deficiency because our bodies don’t absorb them very well. Also, a large percentage of anemia patients have plenty of iron in their bodies but have problems with iron uptake into cells. Enterobactin is a pro at bringing iron into cells! To test the possibility of using enterobactin to treat anemia, the Han lab is now moving to mouse studies where they remove most of the iron in the mouse food and add enterobactin to see if the chemical alone can help the animal grow and survive better, leading to potential pharmaceuticals.
Thanks to the Han lab, now we know one important role that bacteria can play in our guts. But as scientists begin to understand the microbiome better and better, we might learn new ways that bacteria are helping us out with our diet needs. The future might bring us more effective, more tailored probiotics. After all, a happy gut is a colonized gut—provided the colonists are helping us out, too.
By Kelsie Anson