Loss of life and serious illness from contamination of manufactured products that are consumed as food or used in medical procedures illustrate the need to prevent contamination events rather than merely detect them after the fact. High-profile news stories have described contamination events in compounding pharmacies (1), food processing and packaging plants (2) and medical device manufacturers (3). Although contamination in manufacturing settings can be physical, chemical, or biological, this article will focus environmental monitoring to determine the quality of a manufacturing facility with respect to microbial contamination.
To ensure that the products they produce and package are manufactured in a high-quality, contaminant-free environment, many industries are required to establish routine environmental monitoring programs. Samples are collected from all potential sources of contamination in the production environment including air, surfaces, water supplies and people. Routine monitoring is essential to detect trends such as increases in potential pathogens over time or the appearance of new species that have not been seen before so that contamination events can be prevented.
Because environmental monitoring requires identification to the level of the species, most environmental monitoring programs will collect samples and then send them off to a facility to be sequenced for genomic identification of any microbial species. Such genotypic analysis involves DNA sequencing of ribosomal RNA (rRNA) genes to determine the taxonomic classification of bacteria and fungi. In this method, informative sections of the rRNA genes are amplified by PCR; the PCR products sequenced; the sequence is compared to reference libraries; and the results interpreted to make a species-level identification for a given microbial isolate.
Yellowstone National Park —located partially in Idaho, Montana and Wyoming—puts modern volcanic activity on full display. Near boiling, ominous pools of water in the form of geysers, mud pots, fumaroles (vents that release steam) and hot springs are all present and active in the park and visitors flock to the park to view a handful of thermal features every year during the peak summer visitor season. Coincidentally, this is when a large portion of scientific research also takes place at the park. Combining both the boardwalk paths that are open to all who visit the park and the expansive backcountry, Yellowstone is host to over 10,000 thermal features. These thermal features are fed by superheated water that travels through a complex groundwater system—think the pipes under your kitchen sink—where subsurface water collects gases and chemical compounds en route to the surface. As a result, near-boiling water that bubbles through to the surface is often rife with chemicals like sulfur, iron or magnesium. Early scientists thought of hot springs as uninhabitable, but as it turns out, these conditions are just the right environment for thermophilic (or “heat-loving”) bacteria to thrive.
Oral vaccines are a great strategy and are especially beneficial in areas with poor sanitation. This form of vaccine distribution could help control the acute diarrheal disease caused by Vibrio cholera. There are an estimated 1.3 to 4 million cases and 21,000 to 143,000 deaths from cholera each year. A recent study from The Lancet Microbe finds new hope in a rice-based cholera vaccine that will fight against the diarrheal toxin without severe adverse events.
Over the last few years, human microbiome studies have revealed fascinating connections between our colonizing microorganisms and ourselves—including associations between gut bacterial populations and obesity, disease susceptibility, and even mood. The relationship between us and our microbial colonists—once considered completely benign, is now being revealed as an intricate, complicated partnership with the potential to redefine who “we” are in fundamental ways.
Two papers published back-to-back in the November 27 issue of Science add further to this growing body of knowledge—reporting a new and unexpected connection between gut bacterial species and the effectiveness of cancer immunotherapies in mice. The work suggests one reason why such treatments are effective in some circumstances, but not others. Both papers report that the presence of specific bacterial populations may be required for the efficacy of certain treatments, and raise the intriguing question “Could the composition of bacteria in the gut be manipulated to enhance the effectiveness of cancer treatments?” Continue reading “Unexpected connections: Gut bacteria influence immunotherapy outcomes”
While looking through some “Top Ten” lists of the various science stories and discoveries of 2014, I came across a paper, published in Cell in September, describing a new approach to the search for antimicrobials. The paper’s authors screened the vast amount of genomic data from the human microbiome project against known sequences to find genes with homology to existing small molecule drug candidates.
The authors reasoned that any genes that were common across many species would be more likely to affect conserved microbe:host or microbe:microbe interactions. Having identified a large group of these gene clusters, they then homed in on a subset that was commonly found in the microbiome of healthy individuals. As a proof-of-concept, they then identified and characterized a thiopeptide molecule produced by the bacterium Lactobacillus gasseri and showed that it had the expected antimicrobial activity. The Cell paper was the first report of the characterization of any small molecule drug candidate isolated from the human microbiome. Continue reading “Mining Genomes for Antimicrobials”
A study published in the Nov 6 issue of Cell outlined results suggesting that an obscure family of bacteria colonizing the human gut may be inherited and may also have a direct influence on body weight. The paper is the first to identify such an association and to link a particular microbial colonist with lower BMI. Continue reading “Christensenellaceae—A Natural Way to Stay Thin?”
If battlegrounds could speak they would have many stories to tell. In some cases the microbes found in those soils have lived on to separate fact from fiction. One such story has its origins in the Battle of Shiloh, which went down in history as one of the bloodiest battles fought during the American Civil War. As the soldiers lay mortally wounded on the cold, hard grounds of Shiloh waiting for medical aid, they noticed a very strange phenomenon. Some of the wounds actually appeared to be glowing in the dark casting a faint light into the darkness of the battlefield. And the legend goes that soldiers with the glowing wounds had a better chance at survival and recovery from infections than their fellow brothers-in-arms whose wounds were not similarly luminescent. The seemingly protective effect of the mysterious light earned it the moniker “Angel’s Glow.”
The availability of next-generation sequencing, and the accompanying capability to process and analyze large amounts of data, has made many previously unthinkable projects possible. Examples include the sequencing of entire microbial genomes to track the spread of antibiotic-resistant infections in a hospital setting, sequencing all the contents of a particular foodstuff to identify meat sources and contaminants, and the microbiome project—a multi-national research effort to characterize the microrganisms colonizing the human body to look for associations with health and disease.
The ability to both get and process data on this large a scale has led to numerous advances in our understanding of the complex relationships between ourselves and our microbial colonizers. Over the last couple of years the microbiome project has generated data suggesting previously unimagined connections between bacteria colonizing our bodies and obesity, cardiac disease, and even personal identification.
Do you count colonies on agar plates? Do you often need to average counts over a series of plates? The Promega Colony Counter app for iPhone® (3GS, 4S, and 5) and iPod® Touch (4th and 5th generation) allows you to take a picture of your plate, obtain a good first-guess count and refine it quickly by marking additional colonies and masking areas where the app may have over-counted.
The app is available for purchase for 3.99 USD from the iTunes store in North America and Europe.
When I was in school I learned that there were two different kinds of bacteria, the nasty ones (pathogens) that could make you sick and the nice ones (commensals), which simply colonized you and did nothing much except occupy a spot that could otherwise be taken up by a pathogen. Any role for those commensal bacteria in health and disease was assumed to be no more than that of a harmless squatter. In recent years, studies of this benign microbial population (microbiome studies) have begun to reveal many more intriguing details about how they affect our health and wellbeing. Maybe it’s not so surprising that “good” bacteria could be good for our health—but could they actually affect how we behave? This month, a review in Science summarized new findings that indicate that this is indeed the case—at least for certain animal populations. Could it be true for humans as well? Could our colonizing organisms actually influence how we feel and what we do? Continue reading “My Microbiome Made Me Do It”
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