Hot off the presses! Jan 01 Nat Rev Micro

The Jan 01 issue of the Nat Rev Micro is now up on Pubget (About Nat Rev Micro): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

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  - Nat Rev Micro 9(1):1 (2011)
  
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  - Nat Rev Micro 9(1):2 (2011)
  
• Bacterial toxins: The touch of death | PDF (164 KB)
  - Nat Rev Micro 9(1):3 (2011)
  On direct cell-to-cell contact, Escherichia coli str. EC93 inhibits the growth of other E. coli
• Bacterial pathogenicity: Pneumolysin: stimulating protection | PDF (168 KB)
  - Nat Rev Micro 9(1):4 (2011)
  Pneumolysin, a key Streptococcus pneumoniae virulence factor, is a cholesterol-dependent cytolysin that creates pores in cholesterol-containing membranes, thus causing host cell lysis. Pneumolysin has been proposed as a potential pneumococcal vaccine candidate, but although its cytolytic effects are well understood, less is known about the interactions between this potent toxin and the host immune system.
• Pathogenesis: The SWEET life of pathogens | PDF (121 KB)
  - Nat Rev Micro 9(1):4 (2011)
  Sugar efflux is important for the development of plants, feeding developing seeds and pollen, for example. Despite having important roles in such basic physiological processes, the mechanisms underlying sugar efflux have remained unclear.
• Viral evolution: Pandemic flu can go from bad to worse | PDF (119 KB)
  - Nat Rev Micro 9(1):4 (2011)
  Despite the rapid worldwide spread of the current pandemic influenza virus, no variants of increased pathogenicity have so far been identified from patients, which suggests a stable viral phenotype. However, it is not clear whether this situation may change in the near future.
• Microbial ecology | Symbiosis | Bacterial physiology | PDF (130 KB)
  - Nat Rev Micro 9(1):5 (2011)
  High local substrate availability stabilizes a cooperative trait Bachmann, H.et al. ISME J.9 Dec 2010 (doi:10.1038/ ISMEJ.2010.179)
• Bacterial secretion: Vibrio cholerae beats the competition | PDF (187 KB)
  - Nat Rev Micro 9(1):6 (2011)
  Several bacterial systems have been described that secrete effector proteins into the extracellular milieu or directly into host cells. The type VI secretion system (T6SS) was recently discovered, and its main role is still unclear, as only some T6SSs seem to contribute to pathogenesis.
• Symbiosis: Soil fungi helped ancient plants to make land | PDF (226 KB)
  - Nat Rev Micro 9(1):6 (2011)
  The suggestion that symbiotic soil fungi assisted in the colonization of the land by early terrestrial plants in the Palaeozoic era is now widely accepted. However, evidence to support this scenario is based mainly on phylogenetic information and the fossil record.
• A 'clap' for in silico studies | PDF (175 KB)
  - Nat Rev Micro 9(1):7 (2011)
  This month, Genome Watch discusses the importance of in silico studies for the investigation of Treponema pallidum and Neisseria gonorrhoeae, two sexually transmitted pathogens for which few genetic tools are available.
• In the news | PDF (204 KB)
  - Nat Rev Micro 9(1):8 (2011)
  The cholera outbreak in Haiti has developed more quickly than expected. By the end of November 2010, the disease had claimed more than 1,600 lives and infected about 70,000 people, 30,000 of whom had been hospitalized.
• Chronic and acute infection of the gall bladder by Salmonella Typhi: understanding the carrier state
  - Nat Rev Micro 9(1):9 (2011)
  Despite major treatment and prevention efforts, millions of new typhoid infections occur worldwide each year. For a subset of infected individuals, Salmonella enterica subsp. enterica serovar Typhi colonizes the gall bladder and remains there long after symptoms subside, serving as a reservoir for the further spread of the disease. In this Progress article, we explore recent advances in our understanding of the mechanisms by which Salmonella spp. — predominantly S. Typhi — colonize and persist in the human gall bladder.
• DNA motifs that sculpt the bacterial chromosome
  - Nat Rev Micro 9(1):15 (2011)
  During the bacterial cell cycle, the processes of chromosome replication, DNA segregation, DNA repair and cell division are coordinated by precisely defined events. Tremendous progress has been made in recent years in identifying the mechanisms that underlie these processes. A striking feature common to these processes is that non-coding DNA motifs play a central part, thus 'sculpting' the bacterial chromosome. Here, we review the roles of these motifs in the mechanisms that ensure faithful transmission of genetic information to daughter cells. We show how their chromosomal distribution is crucial for their function and how it can be analysed quantitatively. Finally, the potential roles of these motifs in bacterial chromosome evolution are discussed.
• Microbiota restoration: natural and supplemented recovery of human microbial communities
  - Nat Rev Micro 9(1):27 (2011)
  In a healthy host, a balance exists between members of the microbiota, such that potential pathogenic and non-pathogenic organisms can be found in apparent harmony. During infection, this balance can become disturbed, leading to often dramatic changes in the composition of the microbiota. For most bacterial infections, nonspecific antibiotics are used, killing the non-pathogenic members of the microbiota as well as the pathogens and leading to a substantial delay in the restoration of a healthy microbiota. However, in some cases, infections can self-resolve without the intervention of antibiotics. In this Review, we explore the mechanisms underlying microbiota restoration following insult (antibiotic or otherwise) to the skin, oral cavity, and gastrointestinal and urogenital tracts, highlighting recovery by natural processes and after probiotic administration.
• In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
  - Nat Rev Micro 9(1):39 (2011)
  There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.
• Archaea — timeline of the third domain
  - Nat Rev Micro 9(1):51 (2011)
  The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea — their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.
• Targeting bacterial membrane function: an underexploited mechanism for treating persistent infections
  - Nat Rev Micro 9(1):62 (2011)
  Persistent infections involving slow-growing or non-growing bacteria are hard to treat with antibiotics that target biosynthetic processes in growing cells. Consequently, there is a need for antimicrobials that can treat infections containing dormant bacteria. In this Review, we discuss the emerging concept that disrupting the bacterial membrane bilayer or proteins that are integral to membrane function (including membrane potential and energy metabolism) in dormant bacteria is a strategy for treating persistent infections. The clinical applicability of these approaches is exemplified by the efficacy of lipoglycopeptides that damage bacterial membranes and of the diarylquinoline TMC207, which inhibits membrane-bound ATP synthase. Despite some drawbacks, membrane-active agents form an important new means of eradicating recalcitrant, non-growing bacteria.
• Correspondence: Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy
  - Nat Rev Micro 9(1):75 (2011)
  In their recent article (Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nature Rev. Microbiol.8, 593–599 (2010)