While it is understandable that the majority of research on bacteriophages involve human illness and food spoilage, there is an enormous amount of viruses that prey on bacteria in the environment that are still undiscovered. These environmental bacteriophages are very important since they can direct many significant changes in conditions of the natural world such as the flux of carbon and oxygen levels.
For many years, scientists have defined speciation as an evolutionary event by which a new species arises due to genetic drift. However, a new study suggests that species may diverge because of the microbes in their gut, not their DNA. Biologists Seth Bordenstein and Robert Brucker of Vanderbilt University studied this phenomenon in three different species of parasitic jewel wasps, tiny insects that drill into fly pupae and allow their eggs to feed on the host.
Antibiotic resistant bacteria emerge from improper and over usage of antibiotics. However, antibiotic resistant bacteria have some disadvantages of their own. When not exposed to antibiotics, non-resistant bacteria are often selected for due to the fact that there is an energetic cost associated with being immune to antibiotics. Because of this, it is now desired to reduce antibiotic use in proper situations with the hope of decreasing resistance among bacteria. This is often successful. However, due to the vast complexity of these studies, the results are not easily interpreted. Patients are often taking a cocktail of antibiotics to fight disease and it is possible for there to be contact between hospitals and the community, resulting in the exchange of resistant bacteria. This makes the process increasingly difficult. Additionally, depending on which antibiotics are reduced in usage, the results can vary. For instance, in the case of Staphylococcus aureus, otherwise known as MRSA, a reduction in the use of penicillins does not result in decreased resistance because many strains of S. aureus are already resistant to penicillin. On the other hand, a reduction in the use of clindamycin and methicillin lead to lessened antibiotic resistance.
Unculturable bacteria are not necessarily uncharacterizable. Microbiological techniques, like PCR and DNA sequencing of "housekeeping" genes, has allowed scientists to continue to gain understand about microbes, whether or not they are culturable. However, the ability to fight human infections and develop cures requires these unculturables to become cultured, so the microorganisms can be grown and studied in laboratory settings.
The question remains, why are these organisms 'unculturable' ?
Dictyostelium discoideum is a eukaryotic microbe that lives a unique lifestyle that involves changing from a unicellular to multicellular organism. Recent studies have shown that not only is it unique in this aspect, but it is unique in that it actually cultivates its own food supply, being dubbed the world’s “smallest farmer” amongst microbiologists. This article is based on a recent study led by Debra Brock at the Washington Universty of St. Louis.
Dictyostelium discoideum is a heterotrophic, soil-living amoeba, and it’s unique in the fact that is starts out as a unicellular organism, but becomes a multicellular organism later in life. This occurs when its unicellular pieces come together to from a slug that can move around in the soil. But it’s not just unique in this aspect. It is also a rare species because it has been proven to carry its bacterial prey around with it and essentially “farm” it for a larger food supply
The world is surrounded by microbes that interact with one another competitively or symbiotically, creating a dynamic environment. These interactions occur everywhere, even in our own digestive system. Microbes swarm around the digestive tracts and a myriad of viruses modify key characteristics in bacteria, molding the bacterial population and metabolism. A study led by Fredric D. Bushman, a microbiology professor at University of Pennsylvania, looked at interactions between virus and bacteria in our digestive systems that can ultimately affect humans.
A recent study led by biologists from Indian University and Montana State University has found a connection between viruses that infect eukaryotes and viruses that infect archaea growing in volcanic springs (article). Viruses like HIV and Ebola that infect eukaryotic cells and the virus Sulfolobus turreted icosahedral virus (STIV) that infects Sulfolobus sofataricus, an archaea found in volcanic springs, share a common feature; they both must hijack the same set of proteins found in their hosts' cells to be able to complete their life cycles.
Cholera is a deadly disease that is present in many third world countries, including Bangladesh and India. The disease has been infecting people for thousands of years, meaning it is more likely to be causing evolutionary changes in humans, compared to newly emerged diseases.
Sure enough, researchers from Massachusetts and Bangladesh have found that the human genome has evolved in people who are more likely to contract cholera. Regina LaRocque, an infectious disease specialist from Massachusetts General Hospital and Elinor Karisson, a computational geneticist from Harvard, along with collaborators in Bangladesh, have determined that 305 regions of the human genome were altered by natural selection in individuals in Bangladesh. DNA from 36 Bangladeshi families was compared to that of people from northwestern Europe, West Africa, and eastern Asia. The researchers utilized a new statistical technique that finds regions of the genome that are being affected by natural selection.
At the UT Southwestern Medical Center, researchers are investigating a seafood contaminant that thrives in the summer. This contaminant, Vibrio paraphaemolyticus, is a bacterium that causes a stomach flu and has a novel mechanism by which it infects cells. The bacterium inject proteins, known as effectors which regulator biological activity, into the cell. VopQ is an important effector and is the focus of this research. Once into the cell, VopQ disrupts autophagy. Autophagy is the process of recycling nutrients to be reused as metabolites for the cell. The mechanism by which VopQ disrupts autophagy is novel. VopQ creates gated ion channels in the cell membrane. These channels are pores that only permit regulated ions and/or small molecules to pass through the cell membrane. They also have an open and close mechanism for the particles, similar to a gate.
The immune system of animals is extremely complex and helps defend against a plethora of diseases. Plants, on the other hand, are not as lucky when it comes to defense. Plants have a few systems to stop chemicals and diseases from moving in, but overall are very susceptible to infection. Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory have found that many plants are relying on microbes in the soil to defend themselves against diseases and pathogens.
Clostridium difficile is the leading cause of hospital infections in England and Wales, and treating these infections is becoming more difficult as the causative organism becomes more resistant to antibiotics. Microbiologists are experimenting with the use of bacteriophages, viruses that infect bacteria, as a way to help control these bacterial infections despite antibiotic resistance.
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
The depths of the Oceans on this world are unexplored territory by humans. Until recently. Scientists have created equipment that can withstand the pressure of the depth of the sea to begin exploring the world unseen by many land-bound eyes. Little did we know there was an underwater land teeming with life, especially microbial life. This article discusses the microbial communities that may be contributors to the methane levels found in our ocean sediments.
The Prokaryotic biomass found in the deep sea sediments are greater than 105 microbial cells/cm3; this holds true for roughly 1000 meters below the seafloor. These microbes just might represent one-tenth to one-third of the living biomass on Earth. But the relationship between the microbial community and the conditions of the sub-seafloor environments are largely unknown to us. The scientists in this article explain that their interest lies in the Archaeal and Bacterial communities of the sub-seafloor sediments and how they can distinguish the community based on the presence or absence of methane hydrate (essentially methane trapped within a crystal water structure forming something like ice).
For decades, we have known that proper nutrition is essential for human health, but recent studies have demonstrated that variations in composition and operations of the human gut microbiome can influence the host energy metabolic function, host energy expenditure, and ultimately the nutritional value of food. Knowing this, it would be logical to ask how we may be able to further promote our health by improving ecological health of the microbial communities in our gut. Turnbaugh PJ, et al. set out to examine how variations in diet, nutrition, and environmental exposures can impact the human microbial communities in the gut.
In a new study conducted by researchers at the Woods Hole Oceanographic Institution (WHOI) and King Abdullah University of Science and Technology (KAUST), there is new evidence of a complex symbiotic relationship between certain species of reef building coral and bacteria that wasn't previously understood. It has been known that many coral form symbiotic relationships with many other organisms, such as algae. Researchers have already understood that a species of reef building coral, Stylophora pistillata, hosts a group of bacteria called Endozoicomonas. However, where these bacteria live and what they do for the coral isn't well known.
Microbes are all around us. Scientists have been trying to find and sequence each microbe's DNA for a long time now, but because many of the microbes will not grow in the lab, many of their DNA sequences are unknown. These un-sequenced organisms are known as “microbial dark matter.” Three years ago, microbiologist Tonja Woyke developed a new technique to sequence the genome of one cell. Before this new technique was developed, determining a cell's DNA sequence required many copies of the sample DNA. Using Woyke’s technique, only one cell’s DNA is needed, which is a huge break through in the creation of a family tree for microbes.
Woyke’s team collected samples from nine habitats, which included an ocean hydrothermal vent and the inside of a reactor used to degrade plastic byproducts. The research team was able to single out and sequence 201 cells. What the microbes ate and how they were able to survive in their unique environments were discovered using the sequenced genomes. Many microbes utilized hydrogen as a food source, while a few others used sulfur to create energy. The genomic information was used to name 18 phyla and a few superphyla.
Most folks would typically consider bacteria to be either good or bad. The bad such as those that cause infectious disease or the good like the normal flora that aid in digestion, but none would think of viruses having a dual nature as well. A group of scientists led by Jeremy Barr discovered that mucus, a viscid gel-like secretion rich in mucins that act as a protective lubricant from infectious agents, is more than just a barrier. Surprisingly, the active layer of mucus consists of bacteriophages that attack and kill infectious bacteria; such that, Barr later called them “friendly viruses”. The group also found out that there are more phages in mucus than in mucus-free areas. For example, human saliva harbors about five phages for every bacterium, but mucus directly on the gums host nearly eight times more phages.
Microbial life is important to human and animal health, as they help with important functions of the body. Looking specifically at the gut, gut bacteria (gastrointestinal bacteria), help the body with digestion, immune functions, and general health. There is little knowledge about how the many different bacterial communities change in animal bodies. To have a better understanding about this change, Wouter van Dongen and his colleagues at the Vetmeduni Vienna have scrutinized the cloaca of black-legged kittiwakes at different ages. The cloaca of a vertebrae is a passage for feces, urine, and other body fluids to exit the body. Since the cloaca has similar bacteria to the gastrointestinal tract, Wouter van Dongen and his colleagues have examined the bacteria samples from there.
In the article “ Using Gut Bacteria to Fight Diarrhea”, microbiologist Trevor Lawley of the Wellcome Trust Sanger Institute and his colleagues examined Clostridium difficile infection in mice. In humans, C. difficile is a significant pathogen in hostpitals and nursing homes, causing nearly 336,000 infections and 14,000 deaths a year in the United States. Clostridium difficile is an anaerobic, gram-positive bacterium that is the major cause of antibiotic-associated diarrhea.
Typically we think of biomes as large communities of organisms covering vast areas; but a new idea of microbiome is becoming popularized as our understanding of microorganisms grows. The human body is just such a microbiome. For every one human cell in the body there are 10 microbial cells! If that sounds like disportionate amount and you find yourself wondering how it is possible to have more microbial cells than human cells, consider the fact that a typical microbe cell is much smaller than a human cell and can fit in between the spaces of human cells. In a 200 pound adult, it roughly amounts to 2-6 pounds.
These microbes are mostly bacterial, many of which are critical to the body’s healthy growth and function. Bacteria live inside our digestive system and help our bodies digest nutrients and synthesize vitamins. Many also help our immune systems fight disease or even other harmful bacteria. In return these bacteria receive their own small share of nutrients. Like it or not, our bodies are ecosystems complete with niches that other organisms compete for.
In recent years, researches have been looking for alternative energy sources that can replace fossil fuels. One of them is biofuel, a fuel produced from living organisms. A recent study, conducted by University of Wisconsin-Madison on the communities of leaf-cutter ants, has led to a discovery of potential model for better biofuel production.
Microorganisms, though individually capable of significant metabolic feats, often cooperate with other organisms to perform population-wide tasks. One example is the emission of light by biological organisms, termed bioluminescence, a phenomenon in which a population of bacteria must all express their genes encoding for luciferase, a light-producing protein, at the same time. This process is regulated by quorum sensing, the central focus of a 2012 study relating the expression of bioluminescence in Vibrio harveyi to the concentrations of extracellular signaling compounds.
The biochemical role of the protein, TonB, was relatively unknown for decades, but recent research has helped clear that up. TonB was noted to be especially important, as it is a pivotal factor in the membrane protein of Gram-negative bacteria—specifically aiding in the uptake of iron into the microorganism. The key in this discovery is finding it within the parameters of Gram-negative bacteria. Gram-negative bacteria, as opposed to Gram-positive bacteria, are typically considered the more virulent of the two types of bacteria because of a cell wall found only in Gram-negative bacteria that act as a physical barrier against antibiotics. Gram-negative bacteria cause a significant number of serious diseases and clinical conditions. In the spectrum of the medicinal aspect of microorganisms, Gram-negative bacteria are perceived as posing a threat to the progression of anti-biotics.
A new APT binding cassette, multi-resistant gene (ABC MDR) was discovered in 3 strains of bacteria unknown for housing this gene. Bacillus, Paenibacillus and Staphylococcus strains are new vehicles for this horA gene relative. These strains are usually found in the environment and are not known for spoiling beer. ABC MDR is homologous to the horA gene which has been linked with its ability to grow in beer and is already present in Lactobacillus and Pediococcus, which are bacteria that have been known to cause beer spoilage nationwide. In fact, 90% of all batches of spoiled beer tested have one or more strains of these bacteria.
Upon discovery of this homologous gene cassette a multitude of tests were done to make sure this gene was not induced by the new beer environment or other contaminating factors. Two home brewed light and dark beer batches were made and contaminated. This helped obtain four isolates of the newly discovered bacteria vehicles for ABC MDR; Bacillus cereus, Bacillus licheniformis, Paenibacillus humicus and Staphylococcus epidermidis. 16S rRNA PCR was used to identify the strains. Along with the home brews, commercially brewed beer was also tested for bacterial growth of all four strains. Each beer had different alcohol percentages, pH levels and amount of bitterness units. Both beers allowed growth of all 4 bacteria.
One ancient and potentially overlooked application is microbiology’s relevance to brewing beer. Brewing has been going on for thousands of years and the process has changed drastically over time, especially recently. A recent review compiled hundreds of relevant studies on microbiology’s importance on beer quality from barley field to your glass.
Brewing is a process of fermentation, thus yeast does most of the heavy lifting when producing beer. However, not any yeast will do. Beers can be split into two categories: lagers and ales. Lagers use strains of Saccharomyces pastorianus whereas ales use strains of Saccharomyces cerevisiae. The reason for this is due to the process in which these beers are made. Lagers are fermented at cooler temperatures whereas ales are fermented at warmer temperatures. S. pastorianus is a more complex organism and not isolatable in nature, suggesting that it’s a hybrid of two types of yeast. Studies suggest S. cerevisiae hybridized with S. bayanus to generate S. pastorianus. S. cerevisiae and S. pastorianus both have many strains (S. cerevisiae is much more diverse), which leads to lager breweries keeping their own specific strains of yeast. During the brewing process, some breweries recollect the yeast after fermentation and reuse it to ferment a new batch. Each batch may be slightly different, which may lead to selective pressures favoring a variant in the population, which could lead to a population of yeast that differs from the brewery’s own special strain. In order to combat this, many breweries keep master cultures of their particular strains in order to help reduce the number of variants and maintain a consistent product.
Influenza viruses are a great threat to humans and have very well proven their pandemic nature such as the H1N1 pandemic in 2009. They contain the protein haemagglutinin (HA) which determines the host range by identifying specific receptors such as sialic acid linked to galactose by α2,6-linkages in humans. Recent studies at UW-Madison and University of Tokyo by Yoshihiro Kawaoka have identified a reassortant H5 HA/H1N1 virus that can be transferred through droplet transmission in a ferret model and is capable of identifying Siaα2,6Gal linkages.