MicrobiologyBytes

I publish MicrobiologyBytes as an easy way for you to stay up to date with the latest news from the field of microbiology. The concept has always been to publish bitesize microbiology chunks on easy to consume sticks for today’s busy lifestyle. The devious part is that over a period of time, this mosaic is intended to build up into a comprehensive overview of contemporary microbiology. Clever, huh?

In spite of that, I don’t expect you to have to schlep all the way over here to read my daily words of wisdom (although if you do, you get the extra goodies such as all the sidebar treats). We’ve always published an RSS feed which you can read in any feed reader of your choice (check out the link for lots of suggestions), but we’re also on Twitter, Friendfeed and even on your cell phone. If you want, you can read the content without leaving the comfort of Facebook.

We’ve been going for nearly three years, but in November 2009, something interesting happened. For the first time, more people learned about the lastest news in microbiology through these other routes than by visiting the site. Do I care? No, I’m delighted that more people than ever are reading about microbiology. Spread the word!

Best wishes for 2010, and keep reading – wherever you chose to do it.

Bifidobacteria are relatively abundant inhabitants of the gastrointestinal tract of humans and animals. Many bifidobacterial species, in conjunction with other members of the intestinal microbiota are believed to contribute to host nutrition, while also impacting on intestinal pH, cell proliferation and differentiation, development and activity of the immune system, and innate and acquired responses to pathogens. These perceived beneficial health effects have driven commercial exploitation of bifidobacteria as live components of many functional foods and therapeutic adjuncts. However, bifidobacteria have also been isolated from the human oral cavity, where their presence is linked to the progression of tooth decay: bifidobacteria have been detected in high numbers in infected dentine from carious lesions in children and have been associated with childhood dental caries. can be found as part of the microbiota implicated in human dental caries. In recent surveys of oral bifidobacteria associated with caries in adults and children and root caries in adults, Bifidobacterium dentium was the most frequently isolated Bifidobacterium species, representing approximately eight percent of the culturable bacteria isolated from active lesions. This species is capable of acidogenesis to produce a final pH in glucose-containing media below pH 4.2, sufficient to cause extensive demineralisation of tooth tissues. B. dentium may therefore significantly contribute to the pathogenesis of dental caries which is one of the most common chronic diseases, remaining untreated in many underdeveloped countries where dental pain is often alleviated only by the loss or extraction of the affected tooth.

Researchers have now uncovered the complete genetic make-up of the cavity-causing bacterium B. dentium Bd1, revealing the genetic adaptations that allow this microorganism to live and cause decay in the human oral cavity. Bifidobacteria, largely known as long-term beneficial gut bacteria, are often included as probiotic components of food to aid digestion and boost the immune system. However, not all species within the genus Bifidobacterium provide beneficial effects to the host’s health. In fact, B. dentium is an opportunistic pathogen since it has been linked to the development of tooth decay. The genome sequence of B. dentium Bd1 reveals how this microorganism has adapted to the oral environment through specialized nutrient acquisition features, acid tolerance, defences against antimicrobial substances and other gene products that increase fitness and competitiveness within the oral niche. This report identifies, through various genomic approaches, specific adaptations of a Bifidobacterium taxon to a lifestyle as a tooth decay-causing bacterium. The data in this study indicate that the genome of this opportunistic pathogen has evolved through only a small number of horizontal gene acquisition events, highlighting the narrow boundary that separates bacteria that are long-term residents on or in the human body from opportunistic pathogens.

The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity. 2009 PLoS Genet 5(12): e1000785. doi:10.1371/journal.pgen.1000785
Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota, are considered one of the key groups of beneficial intestinal bacteria (probiotic bacteria). However, in addition to health-promoting taxa, the genus Bifidobacterium also includes Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic basis for the ability of B. dentium to survive in the oral cavity and contribute to caries development is not understood. The genome of B. dentium Bd1, a strain isolated from dental caries, was sequenced to completion to uncover a single circular 2,636,368 base pair chromosome with 2,143 predicted open reading frames. Annotation of the genome sequence revealed multiple ways in which B. dentium has adapted to the oral environment through specialized nutrient acquisition, defences against antimicrobials, and gene products that increase fitness and competitiveness within the oral niche. B. dentium Bd1 was shown to metabolize a wide variety of carbohydrates, consistent with genome-based predictions, while colonization and persistence factors implicated in tissue adhesion, acid tolerance, and the metabolism of human saliva-derived compounds were also identified. Global transcriptome analysis demonstrated that many of the genes encoding these predicted traits are highly expressed under relevant physiological conditions. This is the first report to identify, through various genomic approaches, specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral cavity. In silico analysis and comparative genomic hybridization experiments clearly reveal a high level of genome conservation among various B. dentium strains. The data indicate that the genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events.

Anopheles gambiae mosquitoes are the principal vectors of human malaria, a disease with devastating consequences for public health and the economic development of disease-endemic countries. The creation of new tools to control vector populations is a focal point of intensive efforts to eradicate the burden of malaria. As mosquitoes generally copulate only once during their lives, interfering with the mating process is a promising avenue for research into vector control. Unfortunately, very little is known about the molecular or physiological basis of mating and insemination in malaria vectors. Of particular concern is our lack of knowledge about factors and pathways ensuring male reproductive success, such as those that result in sperm storage, oviposition, and the inhibition of remating in females. Improving our understanding of mating biology might not only inform currently proposed strategies for vector control, but could potentially allow the development of entirely novel tools for combating malaria.

Stopping male mosquitoes from sealing their sperm inside females with a ‘mating plug’ could prevent mosquitoes from reproducing, and offer a potential new way to combat malaria. The new study focuses on An. gambiae, the species of mosquito primarily responsible for the transmission of malaria in Africa. These mosquitoes mate only once in their lives, which means that disrupting the reproductive process offers a good way of dramatically reducing their populations. When these mosquitos mate, the male transfers sperm to the female and then afterwards transfers a coagulating mass of proteins and seminal fluids known as a mating plug. This plug is not found in any other species of mosquito and until now, very little was known about the role it plays in An. gambiae reproduction. The authors show that the mating plug is essential for ensuring that sperm is correctly retained in the female’s sperm storage organ, from where she can fertilise eggs over the course of her lifetime. Without the mating plug, sperm is not stored correctly, and fertilisation cannot occur.

The researchers analysed the composition of the protein-rich mating plug and discovered that it is formed when an enzyme called transglutaminase interacts with other proteins in the male mosquito’s seminal fluid. This interaction causes the seminal fluids to coagulate into a gelatinous solid mass. When the research team removed this enzyme in male mosquitoes in the lab, the fluids failed to coagulate and form the plug. Furthermore, when these males, lacking the key protein and therefore the plug, mated with females, reproduction was not successful. The male mating plug is not a simple barrier to insemination from rival males, as has been previously suggested. Instead, the plug plays an important role in allowing the female to successfully store sperm in the correct way inside her, and as such is vital for successful reproduction. If in the future we can develop an inhibitor that prevents the coagulating enzyme doing its job inside male An. gambiae mosquitoes in such a way that can be deployed easily in the field – for example in the form of a spray as it is done with insecticides – then we could effectively induce sterility in female mosquitoes in the wild. This could provide a new way of limiting the population of this species of mosquito, and could be one more weapon in the arsenal against malaria.

Transglutaminase-Mediated Semen Coagulation Controls Sperm Storage in the Malaria Mosquito. 2009 PLoS Biol 7(12): e1000272. doi:10.1371/journal.pbio.1000272
Insect seminal fluid proteins are powerful modulators of many aspects of female physiology and behaviour including longevity, egg production, sperm storage, and remating. The crucial role of these proteins in reproduction makes them promising targets for developing tools aimed at reducing the population sizes of vectors of disease. In the malaria mosquito Anopheles gambiae, seminal secretions produced by the male accessory glands (MAGs) are transferred to females in the form of a coagulated mass called the mating plug. The potential of seminal fluid proteins as tools for mosquito control demands that we improve our limited understanding of the composition and function of the plug. Here, we show that the plug is a key determinant of An. gambiae reproductive success. We uncover the composition of the plug and demonstrate it is formed through the cross-linking of seminal proteins mediated by a MAG-specific transglutaminase (TGase), a mechanism remarkably similar to mammalian semen coagulation. Interfering with TGase expression in males inhibits plug formation and transfer, and prevents females from storing sperm with obvious consequences for fertility. Moreover, we show that the MAG-specific TGase is restricted to the anopheline lineage, where it functions to promote sperm storage rather than as a mechanical barrier to re-insemination. Taken together, these data represent a major advance in our understanding of the factors shaping Anopheles reproductive biology.

Related:

• New methods of biocontrol for malaria
• Evolution-proof insecticides against malaria
• Malaria, mosquitoes and the legacy of Ronald Ross

• Gender: biological and behavioral differences determining “the state of being male or female”)
• Sex: biological differences in males and females

In most countries, tuberculosis (TB) notification is twice as high in men as in women. Although there is clear evidence that socioeconomic and cultural factors leading to barriers in accessing health care may cause undernotification in women, particularly in developing countries, biological mechanisms may actually account for a significant part of this difference between male and female susceptibility to TB. The role of biological gender has been determined in a number of infectious and noninfectious diseases. However, there is an absence of information on the role of biological gender in TB. Thus, investigations should be conducted to clearly understand the role of sexual hormones, sex-related genetic background and genetic regulations, and metabolism, among other factors, in susceptibility differences between men and women. This research may help not only to fully understand the obviously biased gender distribution among TB cases, but also to better adapt future intervention strategies at the community level. In this review, we expand on the various issues relating to TB notification and gender bias.

Large prevalence surveys have suggested that the sex bias observed in pulmonary TB cases may result partly from genuine biological differences in male and female susceptibility to M. tuberculosis infection or the development of TB disease. This finding would not be particularly surprising, as many studies in humans and experimentally infected animals have established clear links between sex-specific factors, including steroid hormones and genetic variants, and the differential susceptibility of males and females to a number of other infectious and noninfectious diseases. In particular, gender bias among pulmonary microbial diseases is not restricted to TB, and important sex differences in the incidence and severity of a number of respiratory tract bacterial infections have been reported in the literature. As a selected example, it has been shown that men have a four-times higher risk of developing nosocomial Legionella pneumophila infection than women. Only 5% to 10% of individuals exposed to M. tuberculosis develop TB, and up to 70% of those who do develop the disease are male. In other words, the human population as a whole is remarkably resistant to M. tuberculosis, but women seem to be even more resistant to the bacillus than men. So, why do only a minority of individuals, other than patients with HIV/AIDS, fail to control infection? Why are women less likely to develop TB than men? Why are some women more resistant to TB than other women exposed to a similar extent? Field research consortia including not only microbiologists, immunologists, and human geneticists, but also epidemiologists and sociologists, should be established to unravel the many faces of sexual inequality in TB, and to decipher the delicate mechanisms involved in natural and sex-associated resistance to TB. Such work would facilitate the design of future intervention strategies for combating the disease and the development of useful tools for evaluating prognosis and protection in future clinical trials.

Sexual Inequality in Tuberculosis. PLoS Med 6(12): e1000199. doi:10.1371/journal.pmed.1000199

Related:

• Tuberculosis – is the white plague winning?
• Tuberculosis diagnostic tools
• Tuberculosis and the mystery of the missing genes

Over the past two decades, the study of marine viruses using electron and fluorescent microscopy revealed an unexpected abundance of virus particles. At 10⁶ to 10⁹ particles per milliliter of sea water, viruses are the most abundant microbes in the sea and, most likely, in the entire biosphere. Furthermore, they have emerged as crucial geochemical and ecological factors in marine ecosystems. More recently, extensive data on the metagenomics of marine viruses have been reported. Viral metagenomics is either pursued specifically by deep sequencing of environmental samples enriched for virus particles or emerge serendipitously through detection of virus-specific sequences in databases yielded by other metagenomic projects. The latter type of study is mostly limited to known classes of viruses but the former has the potential to discover completely unknown viruses.

The gene repertoires of the putative marine viromes that were derived by sequencing double-stranded DNA (dsDNA) isolated from the fractions enriched for virus-like particles brought several major surprises and potential concerns. In particular, the estimates of the number of unique viral genotypes yielded breathtaking numbers of >10³⁰, making the marine viromes the most genetically diverse biological communities on earth. The main and highly unexpected findings were that a substantial majority of the putative viral sequences were not significantly similar to any sequences in the current databases, and that those sequences that did have detectable homologs represented, primarily, various bacterial genes often having specific roles in central metabolism rather than distinct classes of genes commonly found in known bacteriophages or other viruses. These remarkable findings suggest two possibilities that are not mutually exclusive. First, known viruses might not be representative of actual viromes, with the implication that marine viruses are the principal reservoir of new genes in the ocean. Second, the samples deemed to represent viromes might be, largely, not of viral origin and reflect contamination of the samples with non-viral DNA, which would indicate a serious shortcoming of the current metagenomic protocols.

This paper applies computational approaches to analyze the marine dsDNA viromes and shows that, despite non-negligible contamination with bacterial genes, these sequences represent a collection that is markedly different in its statistical features from both prokaryotic and known viral genomes. Thus, there seems to be a realistic possibility that the actual marine viromes consist predominantly of virus-like particles that are different from well-characterized phages and might resemble gene transfer agents (GTAs). Although still a young field, metagenomics is already revealing unexpected yet fundamental features of the virus world.

New dimensions of the virus world discovered through metagenomics. Trends Microbiol. Nov 24 2009
Metagenomic analysis of viruses suggests novel patterns of evolution, changes the existing ideas of the composition of the virus world and reveals novel groups of viruses and virus-like agents. The gene composition of the marine DNA virome is dramatically different from that of known bacteriophages. The virome is dominated by rare genes, many of which might be contained within virus-like entities such as gene transfer agents. Analysis of marine metagenomes thought to consist mostly of bacterial genes revealed a variety of sequences homologous to conserved genes of eukaryotic nucleocytoplasmic large DNA viruses, resulting in the discovery of diverse members of previously undersampled groups and suggesting the existence of new classes of virus-like agents. Unexpectedly, metagenomics of marine RNA viruses showed that representatives of only one superfamily of eukaryotic viruses, the picorna-like viruses, dominate the RNA virome.

Related:

• A Glimpse Into the World of Metagenomics
• Genomes of unknown marine viruses

Bdellovibrio species are naturally predatory, small, motile, Deltaproteobacteria that invade the periplasm of other larger gram-negative bacteria, killing and digesting them. Bdellovibrio grows and divides inside the prey cell, in a structure called a bdelloplast, which then lyses, releasing the Bdellovibrio to prey upon more bacteria. This capability makes Bdellovibrio a potential therapeutic agent, but since its discovery in the 1960s it has not been applied in this way.

This review considers what is known about Bdellovibrio and its predatory lifestyle, drawing also from what was learned by the excellent microbial physiology work of the early Bdellovibrio researchers. Recent work on the diversity and evolution of predatory bdellovibrios, the role of surface structures in predation, and the ongoing questions about how Bdellovibrio switches between axenic and predatory growth and how its predatory activities may be tempered in the wild, as well as suggestions for future research priorities, are discussed.

Predatory lifestyle of Bdellovibrio bacteriovorus. Ann Rev Microbiol. 2009 63: 523-539

Related:

• Bdellovibrio bacteriovorus – an inside job
• Microbial Mitopathogens

A new article in the open-access journal PLoS ONE presents scientific research conducted on “The Tomb of the Shroud” – a tomb found in Jerusalem dating back to the time of Jesus. This rock-hewn burial cave belongs to a cemetery known as Akeldama or “Field of Blood” as described in the Bible (Matthew 27:3-8; Acts 1:19), and located in the lower Hinnom Valley in Jerusalem. In comparison to more than 70 other tombs in the Akeldama area, this particular tomb is unique as it contains remnants of a burial shroud and evidence of leprosy (Hansen’s disease) and tuberculosis in the shrouded male remains therein. This is the oldest known case of leprosy with confirmed dates and molecular evidence. Some of the other individuals in this multi-chambered tomb showed signs of tuberculosis, and ancient human DNA was detected to piece together the family relationships.

No other first century tomb from Jerusalem had ever been examined by molecular methods. The discovery of the presence of Mycobacterium tuberculosis and Mycobacterium leprae in the individuals buried within the “Tomb of the Shroud” is significant in understanding the geographical and temporal distribution of tuberculosis and leprosy in antiquity. This research has evidenced that molecular pathology clearly adds a new dimension to the archaeological exploration of disease in ancient times. The successful genetic analyses of unique archaeological sites such as “Tomb of the Shroud” pose great promise for future investigations into host-pathogen relationships and evolution, geographic distribution, and epidemiology of disease and social health in antiquity.

Molecular Exploration of the First-Century Tomb of the Shroud in Akeldama, Jerusalem. 2009 PLoS ONE 4(12): e8319. doi:10.1371/journal.pone.0008319
The Tomb of the Shroud is a first-century C.E. tomb discovered in Akeldama, Jerusalem, Israel that had been illegally entered and looted. The investigation of this tomb by an interdisciplinary team of researchers began in 2000. More than twenty stone ossuaries for collecting human bones were found, along with textiles from a burial shroud, hair and skeletal remains. The research presented here focuses on genetic analysis of the bioarchaeological remains from the tomb using mitochondrial DNA to examine familial relationships of the individuals within the tomb and molecular screening for the presence of disease. There are three mitochondrial haplotypes shared between a number of the remains analyzed suggesting a possible family tomb. There were two pathogens genetically detected within the collection of osteological samples, these were Mycobacterium tuberculosis and Mycobacterium leprae. The Tomb of the Shroud is one of very few examples of a preserved shrouded human burial and the only example of a plaster sealed loculus with remains genetically confirmed to have belonged to a shrouded male individual that suffered from tuberculosis and leprosy dating to the firstcentury C.E. This is the earliest case of leprosy with a confirmed date in which M. leprae DNA was detected.

Related:

• Oldest Evidence of Leprosy Found in India
• Origin and spread of Mycobacterium tuberculosis
• New hope for leprosy?

Influenza is circulating in Africa, but virtually no information or attention is evident, says a new essay in this week’s PLoS Medicine. Maria Yazdanbakhsh and Peter Kremsner argue that the lack of adequate surveillance means that the burden of influenza in Africa is incorrectly believed to be negligible. But sporadic reports from various regions in Africa indicate that influenza is circulating and may be regularly causing epidemics. Whereas in temperate areas influenza activity displays a seasonal pattern with marked peaks in the winter, influenza is present all year round throughout the tropics. The authors say that the well-established surveillance network WHO Flu Net in place in Europe and North America, provides continuous data on influenza burden and the spread of viral types and subtypes. Recent threats of pandemic influenza have prompted similar active monitoring in parts of Southeast Asia and Latin America. But the prevalence and incidence of influenza in most tropical countries especially in Africa are largely unknown, say the authors, and improved surveillance is needed. For example, the authors state, the WHO H1N1 swine flu update of May 2009 contained reports of infected patients in many countries, but none in Africa, whereas two reports in October 2009 confirmed swine flu cases from South Africa and Kenya. This indicates that that the virus was circulating in Africa, but because of the lack of a rigorous surveillance system, it was not reported as readily.

Influenza in Africa. 2009 PLoS Med 6(12): e1000182. doi:10.1371/journal.pmed.1000182

Related:

• Global migration of influenza viruses
• Spotting pandemic influenza viruses
• The Biology of Influenza

Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments. The halophilic archea are a group of microorganisms that grow best in highly salted lakes (with KCl concentrations between 2 and 6 molar). To avoid osmotic shock, halophilic archea have the same ionic strength inside their cells as outside. All their macromolecules, including the proteins, have therefore adapted to remain folded and functional under such ionic strength conditions. As a result, the amino acid composition of proteins adapted to a hypersaline environment is very characteristic: they have an abundance of negatively charged residues combined with a low frequency of lysines.

A new study provides an explanation at the molecular level for the adaptation of these salt-loving microorganisms to their extreme environments. The findings reveal that the peculiar amino acid composition found in the proteins of halophilic archea results in a reduction in the contact surface with the solvent, and that this is the key mechanism by which they are adapted to life in high-salt environments. Bacteria can thrive even in the harshest conditions. In salt flats and salt lakes, halophilic archea survive the osmotic shock induced by a high salt concentration outside their cells by accumulating salt in the interior of their cytoplasm. However, such a high intracellular salt concentration can seriously alter the normal functioning of the cellular machinery. The proteins from these organisms have therefore evolved with a very biased amino acid composition: some amino acids, like aspartic acid, prevail, whereas others, like lysine, are almost absent. The study makes apparent that the reason the short aspartate side chain is preferred to the long lysine residue is because it minimizes interactions with the surrounding water molecules.

Three different protein domains were included in the study: a domain from a halophilic enzyme, its mesophilic counterpart (preferring moderate conditions), and a totally unrelated model protein. Site-directed mutagenesis was used to modify the surfaces of the proteins and progressively to transform the mesophilic domains into halophilic ones, and vice versa. After measuring the stability for all of the mutant proteins, nuclear magnetic resonance spectroscopy (NMR) was used to obtain high resolution structures for several of the modified proteins. The NMR structures are key to accurately determining the contacts with the solvent. This study provides insight into how high salt concentrations modulate protein stability, and paves the way for understanding the effect of salt on the catalytic activity of certain enzymes. A medium with high salt concentration is somewhat similar to the conditions found in bioreactors, and the biased amino acid composition found in halophilic archea could perhaps be helpful in redesigning enzymes for use in industrial biocatalysis.

Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea. 2009 PLoS Biol 7(12): e1000257. doi:10.1371/journal.pbio.1000257
Proteins from halophilic organisms, which live in extreme saline conditions, have evolved to remain folded at very high ionic strengths. The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids, a low frequency of lysine, and a high occurrence of amino acids with a low hydrophobic character. Using extensive mutational studies on the protein surfaces, we show that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form. NMR studies demonstrate complete preservation of the three-dimensional structure of extreme mutants and confirm that salt dependency is conferred exclusively by surface residues. In spite of the statistically established fact that most halophilic proteins are strongly acidic, analysis of a very large number of mutants showed that the effect of salt on protein stability is largely independent of the total protein charge. Conversely, we quantitatively demonstrate that halophilicity is directly related to a decrease in the accessible surface area.

Related:

• Unique cell division machinery in the Archaea
• Life on (well, under) earth