MicrobiologyBytes

We all live in an information rich, highly interconnected world, and the success of evolution can be measured in terms of how living organisms make sense of and respond to information. Past posts on quorum sensing are some of the most popular out of all the subjects I have covered on MicrobiologyBytes. Quorum sensing is the use of small molecules by bacteria to coordinate behavior by groups of individual cells and carry out decision-making processes.

Bacteria have evolved a number of communication systems which can be broadly described as contact-independent and contact-dependent signaling mechanisms. Quorum sensing is a contact-independent process since it involves transfer of secreted molecules called autoinducers. As autoinducer levels increase throughout a growing bacterial population, changes in gene transcription are triggered resulting in altered growth rates and group dynamics. There is an energy cost in producing these compounds and throwing them out of the cell, and in some conditions, the secretion of autoinducers may attract unwanted attention from competitors (Bacterial landlines: contact-dependent signaling in bacterial populations. Curr Opin Microbiol. Feb 24 2009). Contact-dependent signaling methods allow bacteria to carry out more direct, and possibly less costly, communication between cells – it’s the landline alternative to expensive cellphone bills.

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Known methods of contact-dependent signaling include C-signaling in Myxococcus xanthus which allows groups of cells to coordinate motile behavior. The process is mediated by a non-diffusable 17 kDa surface protein encoded by the csgA gene. Contact between neighboring myxobacteria initiates a p17-dependent signaling cascade resulting in expression of genes required for control of motility or for sporulation.

The Gram-positive soil bacterium Bacillus subtilis also undergoes a contact-dependent differentiation process as a means to produce dormant spores when faced with starvation. Under nutrient poor conditions, vegetative B. subtilis cells divide asymmetrically, forming a large mother cell and a smaller daughter cell called a forespore. Despite their intimate association, the mother cell and the forespore remain separated by two membranes and maintain distinct gene expression profiles. Endospore formation is an energy intensive process that is coordinated by multiple signaling pathways. Contact-dependent signaling plays an important role in allowing the cells to coordinate this process.

Contact-dependent inhibition also occurs in E. coli, where a single E. coli cell in the logarithmic phase of growth can use a CDI system to inhibit the growth of hundreds of susceptible target cells in mixed cultures, forcing them to enter a viable but non-replicating state. However, one of the first recognized instances of contact-dependent communication between bacteria was, arguably, conjugation mediated by sex (F) pili. Bacteria encode a large variety of other pilus types and adhesive molecules, many of which have been studied primarily with respect to their abilities to modulate bacteria–host cell interactions. However, it is feasible that some of these organelles also function in inter-bacterial communication. For example, recent studies indicate that several types of soil bacteria can express complex networks of electrically conductive pili known as nanowires.

Although quorum sensing has been getting all the attention recently, we have known about contact-dependent communication mechanisms in bacteria for far longer. Perhaps only now are we realizing how these complimentary systems might fit together and how they could shed light on the development of true multicellularity during evolution.

Related:

• Quorum Sensing in Bacteria: We Two Are One
• Pneumococcus: the quorum-sensing killer
• Quorum sensing in Serratia
• Cracking the cholera code

BBC News

BBC News

Larval therapy for leg ulcers (VenUS II): randomised controlled trial. BMJ 2009;338:b773
Objective: To compare the clinical effectiveness of larval therapy with a standard debridement technique (hydrogel) for sloughy or necrotic leg ulcers.
Design: Pragmatic, three armed randomised controlled trial.
Setting: Community nurse led services, hospital wards, and hospital outpatient leg ulcer clinics in urban and rural settings, United Kingdom.
Participants: 267 patients with at least one venous or mixed venous and arterial ulcer with at least 25% coverage of slough or necrotic tissue, and an ankle brachial pressure index of 0.6 or more.
Interventions: Loose larvae, bagged larvae, and hydrogel.
Main outcome measures: The primary outcome was time to healing of the largest eligible ulcer. Secondary outcomes were time to debridement, health related quality of life (SF-12), bacterial load, presence of meticillin resistant Staphylococcus aureus, adverse events, and ulcer related pain (visual analogue scale, from 0 mm for no pain to 150 mm for worst pain imaginable).
Results: Time to healing was not significantly different between the loose or bagged larvae group and the hydrogel group (hazard ratio for healing using larvae v hydrogel 1.13, 95% confidence interval 0.76 to 1.68; P=0.54). Larval therapy significantly reduced the time to debridement (2.31, 1.65 to 3.2; P<0.001). Health related quality of life and change in bacterial load over time were not significantly different between the groups. 6.7% of participants had MRSA at baseline. No difference was found between larval therapy and hydrogel in their ability to eradicate MRSA by the end of the debridement phase (75% (9/12) v 50% (3/6); P=0.34), although this comparison was underpowered. Mean ulcer related pain scores were higher in either larvae group compared with hydrogel (mean difference in pain score: loose larvae v hydrogel 46.74 (95% confidence interval 32.44 to 61.04), P<0.001; bagged larvae v hydrogel 38.58 (23.46 to 53.70), P<0.001).
Conclusions: Larval therapy did not improve the rate of healing of sloughy or necrotic leg ulcers or reduce bacterial load compared with hydrogel but did significantly reduce the time to debridement and increase ulcer pain.

Related:

• MRSA: Methicillin-resistant Staphylococcus aureus
• Novel treatments for MRSA
• Evolution and pathogenesis of Staphylococcus aureus

Related:

• LabWork: Bacterial growth
• Saturday Cinema: Logarithmic growth of bacteria

Many bacteria are facultative anaerobes, that is, they can grow in the presence or absence of O₂. In contrast to anaerobic respiration or fermentation, O₂ and aerobic respiration confer enormous energetic benefits on facultative bacteria by allowing the complete oxidation of a growth substrate and the concomitant conservation of much larger amounts of energy. Moreover, some energetically expensive processes such as nitrogen fixation are inhibited by O₂. Furthermore, hypoxic conditions are a signal to adopt a different “lifestyle” for some bacteria such as the dormant state of Mycobacterium tuberculosis associated with latent TB infections. The ability to adapt to changes in O₂ availability by expressing different groups of genes is controlled at the level of transcription by O₂-sensing regulatory proteins.

Bacterial sensors of oxygen. Curr Opin Microbiol. Feb 24 2009
The concentration of molecular oxygen (O₂) began to increase in the Earth’s atmosphere approximately two billion years ago. Its presence posed a threat to anaerobes but also offered opportunities for improved energy conservation via aerobic respiration. The ability to sense environmental O₂ thus became, and remains, important for many bacteria, both for protection and switching between anaerobic and aerobic respiration. Utilizing an iron–sulfur cluster as the sensor of O₂ exploits the ability of O₂ to oxidize the iron–sulfur cluster, ultimately resulting in cluster disassembly. When utilizing heme as the sensor, the capacity of O₂ to form a reversible Fe–O₂ bond or alternatively the oxidation of the heme iron atom itself is used to detect O₂ and switch regulators between active and inactive forms.

Related:

• Microbes and Oxygen
• The first appearance of eukaryotes and cyanobacteria

Alternative methods to antimicrobial chemotherapy for combating infectious disease do exist. In this article in Microbiology Today, Roy Sleator describes the role of probiotics in keeping pathogens at bay:

With life-cycles measured in minutes as opposed to years, bacteria have an extraordinary ability to evolve and adapt rapidly to changes in their environment. Thus, in a world where only the fittest survive, those bacteria which have developed resistance to antibiotics will predominate. This is particularly apparent in hospital environments where bacteria are in constant contact with many different antibiotics; such repeated exposure has facilitated the development of resistance to multiple antibiotics and what we now refer to as hospital acquired or nosocomial infections.

Read more

Related:

• Probiotics – friendly bacteria?
• Probiotics – weapons in the war against gut pathogens
• Antibiotics, your gut, and you
• Gut Feeling

Obesity is an enormous public health problem, arising as a consequence of alterations in eating behavior and how the body regulates energy intake, expenditure, and storage. Although an increased intake of energy-dense foods, especially when combined with reduced physical activity, contributes to the high prevalence of obesity, the existence of complex systems that regulate energy balance requires that this paradigm be considered in a larger context. In particular, recent evidence suggests that the gut microbiota may play a role in obesity by increasing the host’s energy-harvesting efficiency.

The treatment of obesity is challenging. Various surgical procedures designed to interfere with the ingestion and/or absorption of foods have been developed over the last 60 years. The Roux-en-Y gastric bypass (RYGB), currently the most commonly performed operation, involves creating a small gastric pouch from the stomach. This surgery leads to changes in acid exposure to the gastric remnant and proximal small bowel, restricts the amount and types of food that can be comfortably ingested, promotes a modest degree of nutrient malabsorption by shortening the length of the small bowel, and may result in intestinal dysmotility, all of which might be expected to alter the gut microbiota. Presently, very little is known about the changes in the gut microbiota that occur after RYGB, and no information has been published on changes in microbial diversity after RYGB in humans.

A recent study used the traditional Sanger and high-throughput 454 pyrosequencing methods to analyze the human gut microbiota in 9 individuals, 3 in each of the categories of normal weight, morbidly obese, and post-gastric bypass surgery. The goals were to identify specific microbial lineages that may play important roles in the development of obesity and also to determine whether the presence or abundance of these microorganisms changes after RYGB.

Human gut microbiota in obesity and after gastric bypass. PNAS USA January 21, 2009
Recent evidence suggests that the microbial community in the human intestine may play an important role in the pathogenesis of obesity. We examined 184,094 sequences of microbial 16S rRNA genes from PCR amplicons by using the 454 pyrosequencing technology to compare the microbial community structures of 9 individuals, 3 in each of the categories of normal weight, morbidly obese, and post-gastric-bypass surgery. Phylogenetic analysis demonstrated that although the Bacteria in the human intestinal community were highly diverse, they fell mainly into 6 bacterial divisions that had distinct differences in the 3 study groups. Specifically, Firmicutes were dominant in normal-weight and obese individuals but significantly decreased in post-gastric-bypass individuals, who had a proportional increase of Gammaproteobacteria. Numbers of the H2-producing Prevotellaceae were highly enriched in the obese individuals. Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H2-oxidizing methanogens. Using real-time PCR, we detected significantly higher numbers of H2-utilizing methanogenic Archaea in obese individuals than in normal-weight or post-gastric-bypass individuals. The coexistence of H2-producing bacteria with relatively high numbers of H2-utilizing methanogenic Archaea in the gastrointestinal tract of obese individuals leads to the hypothesis that interspecies H2 transfer between bacterial and archaeal species is an important mechanism for increasing energy uptake by the human large intestine in obese persons. The large bacterial population shift seen in the post-gastric-bypass individuals may reflect the double impact of the gut alteration caused by the surgical procedure and the consequent changes in food ingestion and digestion.

Related:

• Infectobesity: the bugs that make you fat
• Gut Feeling
• Antibiotics, your gut, and you
• Probiotics – weapons in the war against gut pathogens

There are many options still available for new antibiotics. While the search for new drugs seems to be declining, in this article in Microbiology Today, Flavia Marinelli takes a look at the need for new antimicrobials:

Novel classes of antibiotics are constantly required due to the expanding population of patients at risk and the growing prevalence of resistant pathogens in hospital- or community-acquired infections. Despite this need, major pharmaceutical players seem to be reducing their efforts to discover new antibiotics. This is due to a combination of factors such as the maturity, great competition and increased genericization of the antibiotic market. Unrealized expectations from high-throughput screening, combinatorial chemistry and pathogen-genome-derived targets have also had a negative effect. The perception prevails that the discovery of novel antibiotics is a very rare event. On the other hand, past and present successes speak for a return to microbial product screening.

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Related:

• Streptomyces
• Antibiotics, your gut, and you
• Towards The Next 80 Years of Penicillin Production

A recent paper in Trends in Microbiology examined the possibilities for using bacteriophages in controlling biofilms which might result in healthcare-associated infections (Preventing biofilms of clinically relevant organisms using bacteriophage. 2009 Trends in Microbiology 17: 66-72). Biofilms are firmly attached microbial communities in which the organisms produce an extracellular polymeric matrix. Biofilm organisms might cause disease by detachment of individual cells or clumps of cells, by production of endotoxin, or by providing a niche for the development of antibiotic-resistant organisms. Biofilm organisms are usually tolerant to antimicrobial agents and the treatment of indwelling medical device-associated infections with systemic antimicrobial agents is usually ineffective.

Bacteriophages have been used for the treatment of infectious diseases in plants and animals, although few clinical trials with stringent negative controls have been carried out. There is a renewed interest in phage therapy in light of growing concerns with antimicrobial resistance in healthcare institutions worldwide. The use of phages for the treatment of device-associated infections could reduce the use of antibiotics and might limit the spread of resistant organisms.

There is some evidence for the potential of phages in biofilm control. Bacteriophage T4 phage was effective against E. coli biofilms in a glucose-limited chemostat, although the rate of phage synthesis and assembly were directly proportional to the amount of protein synthesis in the host cell. Some phages produce polysaccharide depolymerases that have the potential to degrade the biofilm matrix.

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However, there are several important characteristics of phage that should be considered when evaluating the potential of phages to control clinically relevant biofilms. The specificity of receptors for a single phage strain will determine its host range; some phage have specificity at the strain level, such as strain typing phages, whereas some are more broad-spectrum and can infect multiple strains or related species. This high degree of specificity could be a drawback, especially in the case of polymicrobial biofilms.

Few studies have explored the role of biofilms in the development of phage-resistance. Phage cocktails developed via the isolation of host range mutants and broad spectrum phage could be advantageous. Another important question is how a patient’s immune system will respond to the therapeutic introduction of phage. Phages are antigenic and elicit a response by serum antibodies and the cellular immune system. Repeated exposure to the phage results in increasing antibody titers and studies in animal models have shown that phage is cleared from the bloodstream by the cellular immune system. In a short-lived treatment, the antibody response to phage is weak except in cases were serum antibody titers are present before phage treatment. It is possible, although unproven, that phage might associate with biofilms and thereby be protected from inactivation. It might also be possible to design mutant phages with enhanced ability to resist clearance by the cellular immune system.

Related:

• Biofilms
• Saturday Cimema: Bacteriophage Therapy
• Bacteriophages for plant disease control
• Coevolution with viruses drives bacterial mutations