Did you know, as a patient, you present more organisms to your doctor for treatment than there are humans on earth? It’s okay if you didn’t, even Alexander Fleming probably didn’t realize when he discovered penicillin that the effects of this xenobiotic (foreign chemical substance found within an organism that is not naturally produced by or expected to be present within) depended on trillions (over ten trillion to be exact) of bacteria’s metabolic pathways. These bacteria account for the microbial world known as the gut microbiome, and their effects on xenobiotics can have beneficial, or sometimes deadly, effects.
When you think back to the age of dinosaurs, you probably picture a world of giant, ferocious animals roaming around humid and densely green environments. As such, it’s hard to imagine modern humans coexisting with anything from that time period. Yet, according to research published recently in Cell, we are living amongst creatures today that thrived not only in the era of dinosaurs but also as early as animals first adapted to living on land. Those creatures are antibiotic-resistant bacteria.
It was roughly six years ago – back in 2011 – that a magnitude-9 earthquake triggered a catastrophic tsunami, which devastated areas of northeastern Japan. You may recall the subsequent headlines, many of which focused on the resulting Fukushima Daiichi Nuclear Power Plant meltdown. It’s scary to think that this disaster was neither the largest nor deadliest earthquake-tsunami combo in history. And that grim point is one reason a team from the Japan Agency for Marine-Earth Science and Technology Kochi Institute is looking for ways to mitigate the size of tsunamis. What's possibly most interesting about the institute’s recent tsunami research, though, is that they’ve been investigating how to use bacteria to stifle tsunami size.
If you aren’t a dendrologist (an expert on woody plants, like trees), you’re probably not up-to-date on the latest news in the world of trees. Fortunately, we at CosmosID are obsessed with unlocking the world of microbes, which are everywhere, including in and on trees and soil, so we’ve got you covered with this post.
This week, we came across a fascinating finding, published in Nature Ecology & Evolution, about how soil microbes could be critical to the migration of certain tree species in the Rocky Mountains. The trees in focus are retreating, as trees do, to higher elevations in the mountains to survive increasing environmental temperatures. And as the University of Tennessee researchers who undertook this study discovered, the soil microbiome plays a role in this remarkable migration, and may even encourage it. Specifically, it appears soil microbes construct what the researchers call “soil highways”, which they believe may determine whether and how quickly young trees are able to spread to higher elevations.
While many questions about the ocean remain unanswered, researchers have been able to understand the journey algae take when they die, namely floating to the ocean floor and settling with the rest of the deep-sea sludge. Given that this process is happening constantly in oceans all around the world, lots of algal remains accumulate on top of the bacteria living on the seafloor. Over time, this kills many of those bacteria. However, a peculiar bunch of these bacteria have been able to survive. To learn more about these mysterious organisms, biologists and geochemists collected drilled-out samples of seabed that represent hundreds of thousands of years of organic matter accumulation. As reported recently in a Proceedings of the National Academy of Sciences publication, researchers have made some remarkable observations about the microbial communities surviving beneath the seafloor sediment.
As the PNAS publication details, contrary to what you might expect, the bacteria surviving beneath thousands of years of algae do not seem to be evolving at all. This finding stems from the fact that the bacteria living in such an energy-deprived environment are reproducing at a glacial pace – incredibly slowly. In fact, researcher calculations estimate that it takes these bacteria hundreds of years to double in number, in contrast to the doubling in minutes that most bacteria we’re familiar with undergo. Logic suggests that because the seabed bacteria are reproducing so slowly, any adaptations that they may be pressured to experience do not have much of an opportunity to be expressed.
One hurdle to studying the fascinating organisms that live in one of the most challenging environments on the planet is their inability to grow in a Petri dish. This has forced researchers to get creative by analyzing bacterial DNA present in seafloor samples. By using carbon dating on seabed mud samples pulled from different depths, researchers can get a good idea of how the bacteria, living at these various depths, have changed over time. However, as this analysis showed, the DNA of the microbes that have been buried for thousands of years has not really changed. In other words, there were minimal genetic differences within a population of bacteria over time. Researchers suggest that these results mean that the microbes on the surface of the seafloor are very similar to those buried under thousands of years of sediment. Further, it means that the microbes that are surviving were primed for this existence from the beginning, so it is not likely that they adapted to it.
Another interesting question the scientists sought to answer is how active these bacteria’s metabolisms are. From analyzing the sediment that is about 400 years old, the scientists found that the bacteria would likely be capable of one replication per year. Digging even deeper, to the 5,000-year-old sediment, researchers estimated one replication would take about 100 years!
As is often the case with scientific research, these findings have generated more questions than researchers started with but that’s just science at its best.
As the CosmosID blog illustrates regularly, microbes are remarkable for their ability to shape and affect just about every aspect of the world we live in. Yet, each week we are newly awed by publications that highlight discoveries of microbial feats and applications. This week was no different, as we were captivated by a story about a researcher who aims to cure cancer using salmonella. The idea of treating cancer with bacteria is not new. In fact, research on this particular topic dates back to at least the 1890s. However, up until now, research efforts have been inhibited by the toxicity of salmonella.
The person behind this more recent effort is the research director for the Cancer Research Center in Columbia, Missouri, Abe Eisenstark, who has a background in salmonella research. It was this experience that drove him to direct Alison Dino, a scientist at the University of Missouri, to start experimenting with using old salmonella samples as weapons against cancer. Entertaining this wild notion, Dino began by putting these bacterial samples into the same petri dishes occupied by tumor cells. As she combined the two biological warriors for a showdown, she wanted to see if the salmonella would be drawn to the tumor cells, and if the bacteria would also leave healthy cells alone. A win would mean the bacteria attacked the cancer cells while leaving the healthy cells unharmed. To her amazement, she found a promising candidate in a strain labeled CRC 1674.
It helps to first understand that research had already shown that salmonella is drawn to tumor cells. But the novel idea behind this research story is Dr. Eisenstark’s insight to use aged salmonella. He predicted that the bacteria samples, having survived in isolated vials for decades, would have adapted to low energy environments by inhibiting their own toxicity, as that characteristic demands energy that the bacteria could not have spared.
When placed in a petri dish with cancerous tissue, the scientists found that the bacteria moved straight to the tumor cells but showed no attraction to healthy cells. Working from this validation, the Mizzou researchers have since genetically altered the CRC 1674 strain to make it even less toxic and more troublesome to cancer cells. As a publication from 2016 shows, this altered strain was able to target prostate cancer tumors in mice and even shrink the tumors but could not stop their spread. The team is continuing to work on modifying the promising strain, and is looking to begin clinical trials in larger animals as early as 2018.
As with the greater story of oncology efforts, this research has great promise but also much progress to be made. Regardless, it’s worth marveling at the ingenuity required to successfully modify one of the world’s most common food-borne diseases to target cancer.
While biomanufacturing processes have improved in performance and complexity since the mid ‘70s, and the early days of companies like Genentech, scientists have remained diligent students of natural cellular processes, which efficiently produce all sorts of beneficial compounds for products like drugs and fuels. It was in this line of research that Princeton University scientists discovered recently a global genetic regulator that can activate many otherwise silent gene clusters in a bacterium. As described in a Proceedings of the National Academy of Sciences (PNAS) publication, this finding could enable scientists to supercharge these microbes’ natural compound production capabilities.
You may or may not be a beer drinker or know much about the brewing industry as a whole but regardless of where you fall on those spectrums of familiarity, you’ll likely be surprised by the role bacteria were found to play in hurting the quality of beer in the United Kingdom, as reported in the Beer Quality Report 2017. Published by Cask Marque, a beer quality watchdog in the UK, the Beer Quality Report shares the results of research done in 22,000 pubs across the United Kingdom. Perhaps of note to the microbiology community is the report’s section on line cleaning.
As mundane as line cleaning sounds, the report projects that the economic value lost for a typical pub due to bacteria and yeast-laden draught beer lines is around $40,000 – no small sum for your average pub. What may be more disturbing to most beer drinkers is the finding that one in three pints served in the UK is drawn through unclean beer lines. That means that a third of the lines were found to have yeast and bacterial buildup to the extent that it hurt beer quality. Besides being unnerving, it’s worth noting that bacteria tend to spoil the aroma and flavor of beer, which ruins the experience for consumers, and is just bad for business.
Another interesting finding from the report is the breakdown of unclean beer lines by type of beer. For instance, cider lines were found to be the dirtiest in the UK on average, with 44 percent of inspected lines determined to be unclean. When beer type was combined with location, it was found that 53 percent of cider lines in Wales were determined to be unclean. The next most likely beer type to be drawn through dirty lines were stout beers, as the report found that 36 percent of those lines were found to be unclean. Premium and standard lagers were the next most likely lines to be unclean, with 35 percent and 36 percent of those lines found to be dirty, respectively.
Fortunately, beer is generally considered inhospitable to the majority of the microorganisms, as the low pH and ethanol concentration effectively limit bacterial growth. As a result, there are only a few known bacterial strains that are able to grow under these conditions. Nonetheless, these types of reports illustrate the importance of understanding microbes and their potential to affect every aspect of daily life. As the Beer Quality Report 2017 shows, microbes even play a significant role in economic success and consumer satisfaction. Not bad for being microscopic.
Fertilizer is a staple of industrial farming, as it primes the soil for optimal plant growth. The industrial process for making fertilizer was dreamt up more than 100 years ago by two chemists, named Haber and Bosch, and it’s the same intensive process that allows fertilizer to be produced at commercial quantities that also puts it out of reach for the world’s poorest farmers. Specifically, the production process, which requires huge chemical plants to transform nitrogen and methane into ammonia, and considerable resources to distribute the fertilizer, leaves many impoverished farmers with no way to access this critical agricultural tool. However, Harvard University chemist Daniel Nocera and a team of researchers have engineered microbes that make their own fertilizer, and have thus found a potential solution to this significant problem.