Microbiology Blog: The weblog for microbiologists.

Metagenomics, which can be defined as the science of biological diversity, consists of the genomic analysis of a microbial population with similar but not identical members, by the use of genetic and molecular analysis. A comprehensive metagenomic study provides understanding of the dynamics of a microbial population and includes analysis of nucleotide sequence, structure, regulation and function. Metagenomics has applications in a broad range of areas. For example the metagenomics approach has been used to study the intestinal microflora (Norin et al 2009 in Lactobacillus Molecular Biology), in studies of bioremediation and biodegradation (Díaz 2008 Microbial Biodegradation), and in the study of bacteriophage in the environment (Weinbauer et al 2007 in Bacteriophage: Genetics and Molecular Biology).

Labels: metagenomics

Bacteria have developed numerous systems to secrete proteins or DNA in order to modify their immediate surroundings or to obtain an advantage in a competitive and hostile environment. Since Gram-negative bacteria possess two membranes, the inner (cytoplasmic) membrane and the outer membrane, transport machines for protein secretion have the challenging task of circumventing two barriers to reach the exterior. A rather simple transport apparatus, the Type I secretion machinery, composed of only three proteins residing in the inner and outer membrane of Gram-negative bacteria achieve this objective in a single step. The Type I secretion pathway although also present in Gram-positive bacteria, has been analysed in greatest detail in Gram-negative bacteria. Almost all Type I transport substrates are polypeptides, varying from the small Escherichia coli peptide colicin V, (10 kDa) to the large Pseudomonas fluorescens cell adhesion protein LapA of 900 kDa. While these two examples reflect the range of the size of Type I transport substrates, the best characterized are the RTX toxins and the lipases. Type I secretion is also involved in export of non-proteinaceous substrates like cyclic β-glucans or polysaccharides.

from Jenewein et al in Bacterial Secreted Proteins

Further reading:

1. Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis
2. Pseudomonas: Genomics and Molecular Biology
3. Microbial Toxins: Current Research and Future Trends

Labels: bacteria, protein, protein secretion, proteins, Pseudomonas, toxin

A description of the twin-arginine translocation (Tat) pathway continues our series on protein secretion in microorganisms.

The twin-arginine translocation (Tat) pathway is a protein transport system in bacteria, archaea and chloroplasts with the ability to export proteins in a fully folded conformation. Proteins are targeted to the Tat pathway by an N-terminal signal peptide containing an almost invariant twin-arginine sequence motif. Pretranslocational folding is necessitated by the incorporation of metallo-cofactors, assembly into oligomeric complexes, and presumably rapid folding kinetics. Many Tat systems comprise three functionally individual membrane proteins, termed TatA, TatB, and TatC, whereas especially Gram-positive bacteria possess minimal TatAC translocases, in which TatA functionally replaces TatB. TatC and TatB form a complex that is involved in recognition of Tat signal sequences and their insertion into the membrane. TatA mediates the actual translocation event, but it is unclear whether it does so by forming the pore-like structures that it displays when purified to homogeneity. Energy is derived from either component of the proton-motive force, ΔpH or ΔΨ, and is required only for late steps following signal sequence cleavage. Substrates that either lack the twin-arginine pair or are in a malfolded conformation in general are not translocated. The mechanisms by which non-functional substrates are rejected are not understood. For cofactor-containing substrates, proof-reading seems to depend on the activity of specific cytosolic chaperones.

from Panahandeh et al in Bacterial Secreted Proteins

Further reading: Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis

Labels: archaea, bacteria, protein, protein secretion, proteins

Protein secretion is an important process for bacteria and is particularly important to bacterial pathogens. Secreted proteins have a range of biological functions.

The majority of proteins destined for export across the microbial cytoplasmic membrane or integration into the membrane are handled by the evolutionarily conserved Sec system. The Sec substrates have specific topogenic signals and are targeted to the membrane-embedded SecYEG translocon that serves as a polypeptide-conducting channel either co-translationally by SRP for lipid-phase integration or post-translationally by SecB for complete translocation. The plug helix of SecY that clogs the unused channel and the central constriction that seals around the translocating chain make the translocon function compatible with the permeability barrier of the membrane. The translocon also contains a lateral gate, through which it not only accepts a newly synthesized client protein but also allows its hydrophobic segment, if any, to partition into the lipid phase. The post-translational mode of translocation, characteristic of the bacterial systems, is driven by the SecA ATPase, which interacts with SecY and a preprotein and accordingly undergoes conformational transitions coupled with the ATPase cycles.

from Ito and Mori in Bacterial Secreted Proteins

Further reading: Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis

Labels: pathogen, pathogenic, protein, protein secretion, proteins

Acanthamoeba is an opportunistic protozoan that is widely distributed in the environment. Acanthamoeba has two stages in its life cycle, an active trophozoite stage during which Acanthamoeba reproduces, and a dormant cyst stage during which Acanthamoeba remains inactive with little metabolic activity, but viable, for years. During the last few decades, Acanthamoeba has become increasingly appreciated as an important microbe and now well-recognized to produce serious human infections, including a vision-threatening keratitis (called Acanthamoeba keratitis) and a rare but fatal encephalitis, known as granulomatous amoebic encephalitis. Initially the term "granulomatous amoebic encephalitis" was coined specifically to describe brain infection due to Acanthamoeba. However, with the discovery of a number of amoebae that can produce granulomatous encephalitis, including Acanthamoeba, Balamuthia mandrillaris, Sappinia diploidea, and perhaps other unidentified amoebae, it is necessary to differentiate the disease according to its causative agent. "Granulomatous amoebic encephalitis due to Acanthamoeba" can be referred to as "Acanthamoeba granulomatous encephalitis".

The true burden of keratitis and encephalitis due to Acanthamoeba on the human health is not known. Furthermore, the pathogenesis and pathophysiology associated with Acanthamoeba infections, as well as the molecular identification of virulence traits of Acanthamoeba, which may be potential targets for therapeutic interventions and/or the development of preventative measures remain incompletely understood. In recent years, there has been a tremendous interest in this pathogen by the scientific and the medical community. This is due to (i) an increasing number of Acanthamoeba infections, associated with a rise in the number of immunocompromised individuals and contact lens wearers, (ii) the potential role in ecosystems, and (iii) the ability to act as a host or reservoir for microbial pathogens, including viruses, prokaryotes, other protozoa and fungi.

from Naveed Khan in Acanthamoeba: Biology and Pathogenesis

See also: Acanthamoeba pictures, illustrations and figures

Labels: Acanthamoeba, amoeba, protozoa

Lactobacilli are members of the Lactic Acid Bacteria group and constitute an ecologically and phylogenetically very diverse group. Some strains are of industrial importance since they are applied in a range of fermentation processes, whereas other strains are exploited for their probiotic properties. Ten Lactobacillus genomes encompassing nine species have been sequenced, and their genome content broadly reflects the diversity of this genus. With the exception of members of the "acidophilus- complex", there is no long range synteny based on whole-genome alignments. The species are diverse in their metabolic capacity, and some species appear to be in an ongoing phase of specialization, largely determined by preferred ecological niches. Each of these species produces proteins which enable them to compete or survive within their preferred habitat. A repertoire of diverse adhesins has been functionally characterized in several gastrointestine-associated lactobacilli. The comparative genomics of different Lactobacillus strains has revealed novel insights in the complexity of this diverse genus.

from Van Pijkeren and O'Toole in Lactobacillus Molecular Biology (Chapter 3)

Labels: genomics, lactic acid bacteria, lactobacillus

Six further conferences have been added to our list at Microbiology Conferences

• December 1 - 5, 2008. International Research Conference on Huanglongbing
  Orlando, USA
  The disease of citrus fruit caused by the bacterium Candidatus spp.


• February 24 - 28, 2009. Conference on Amoebiasis
  Guanajuato, Mexico
  Amebiasis: Molecular approaches in an important but neglected disease.


• March 17 - 22, 2009. 25th Fungal Genetics Conference
  Asilomar, California, USA
  Billed as the biggest worldwide conference on genetics of filamentous fungi.


• May 3 - 6, 2009. 31st Symposium on Biotechnology for Fuels and Chemicals
  San Francisco, CA
  General and concurrent sessions, as well as two poster sessions, tabletop exhibits and social events are planned.


• June 15 - 17. SPORE2009 - Spore forming bacteria in food
  Quimper, France
  Despite investments of the food and feed industry to control contaminants in the food chain, the achievement of commercial sterility requirements has been hampered by the presence of unintended heat-resistant spores in food. Sporulated bacteria are involved in food spoilage, but also in toxin-mediated food poisoning, two phenomena that lead to high economic losses. Different evolution trends have been observed over the past two decades highlighting the urge to focus on the (re)emergence of sporeformers in food and discuss whether an adaptation or selection of sporeformers by food processes is occurring. The SPORE2009 meeting aims at presenting and discussing state of the art research and the very latest scientific developments on the theme of sporeformers in food.


• July 12 - 17, 2009. 1st International Conference on Nitrification (ICoN1)
  Louisville, Kentucky, USA
  The first International Conference on Nitrification (ICoN1) is meant to be the start of a tradition of bringing together investigators and students at all levels to discuss the most recent concepts in nitrification research. The meeting will present and discuss reports on the ecology, physiology, biochemistry, molecular genetics, genomics, metagenomics, transcriptomics and evolution of ammonia- and nitrite-oxidizing bacteria and archaea, and their roles in the nitrogen cycle.

For further details of these conferences please visit Microbiology Conferences

Labels: Amoebiasis, conference, fungi, Huanglongbing, microbiology conference, microbiology meeting, Nitrification, spore

Foot-and-mouth disease (FMD) virus is still the most feared in animal farming. The re-emergence of old viruses and emergence of new sero- and genotypes of the virus is a constant threat to agriculture, resulting in dramatic losses either due to direct harm to the infected host, to trade restrictions or to the necessity of slaughtering animals on a large scale to contain disease outbreaks. Molecular analyses of FMD virus (the type member of the genus Apthovirus within the Picornaviridae) has yielded important insight into the role that different viral proteins play for replication in cell culture and in the infected animal. Viral factors relevant for FMD pathogenesis have been identified, and new diagnostic assays have been developed that allow the differentiation between vaccinated and infected animals. Moreover, work on FMD virus has also contributed to the revolutionary concept of the quasispecies of RNA viruses, which stands at the basis of their impressive evolutionary potential. The concept of quasispecies, which results from the error-prone genome replication by RNA-dependent RNA polymerase, leads straight to the new finding that, besides increasing the fitness, i.e. the extent of virus adaptation to the environment, it can also lead to extinction.

from Martinez-Salas, Saiz and Sobrino in Chapter 1: Foot-and-Mouth Disease Virus from Animal Viruses: Molecular Biology

Further reading: Animal Viruses: Molecular Biology

Labels: virology, virus

Legionella: Perspectives and Practice Workshop
October 16 - 17, 2008.
Hetzel Lecture Theatre, State Library of South Australia Further information
A 2-day workshop covering both technical and practical aspects of the environmental control of Legionella and Legionnaires' disease.

Further reading: Legionella: Molecular Microbiology

Labels: conference, legionella, microbiology conference

14th International Symposium on Biodeterioration and Biodegradation
October 6 - 11, 2008. Messina, Italy Further information
The IBBS-14 Symposium is dedicated to different topics dealing with biodeterioration and biodegradation of organic and inorganic materials including cultural heritage objects, medical devices, corrosion of metals and other applied aspects such as hydrocarbons and pollutants biodegradation and techniques applied to the study of microorganisms involved in these processes.

Suggested further reading: Microbial Biodegradation: Genomics and Molecular Biology

Labels: biodegradation

Clostridia: from old diseases to new threats
October 5 - 9, 2008. Villars-sur-Ollon, Switzerland
Basic science meets infectious diseases. The fourth Conference on New Frontiers in Microbiology and Infection jointly organized by the Federation of European Microbiological Societies (FEMS) and ESCMID.

Lectures include:
* The discovery of Clostridium and its clinical impact. An insight in the history of medicine
* Basis of the mode of action of clostridial toxins
* Insights into the mechanism of botulinum neurotoxin (BoNT) receptor binding and substrate cleavage from a structural perspective
* C. perfringens epsilon-toxin
* Comparative genomics of clostridia and pathogenic properties
* Clostridium difficile: an overview of the changes in our understanding the organism over the last 30 years
* C. difficile: the wider perspective (humans, animals, environment)
* Clostridium difficile: an overview of the disease, host defences, risk factors and changing host susceptibility
* Clinical spectrum of Clostridium difficile Infection (CDI) and the emergence of hypervirulent strains
* Clostridial infections in the immunocompromised host
* Emerging clostridial infections in USA
* Clostridia in cancer therapy
* Toll-like receptors and intestinal inflammation

Suggested further reading: Clostridia: Molecular Biology in the Post-genomic Era

Labels: clostridia, clostridium, conference, microbiology conference