Where Next for Microbiome Research?

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002050

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of “van Leeuwenhoek”–like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what’s next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.

Calorie Restriction-Mediated Replicative Lifespan Extension in Yeast Is Non-Cell Autonomous

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002048

In laboratory yeast strains with Sir2 and Fob1 function, wild-type NAD+ salvage is required for calorie restriction (CR) to extend replicative lifespan. CR does not significantly alter steady state levels of intracellular NAD+ metabolites. However, levels of Sir2 and Pnc1, two enzymes that sequentially convert NAD+ to nicotinic acid (NA), are up-regulated during CR. To test whether factors such as NA might be exported by glucose-restricted mother cells to survive later generations, we developed a replicative longevity paradigm in which mother cells are moved after 15 generations on defined media. The experiment reveals that CR mother cells lose the longevity benefit of CR when evacuated from their local environment to fresh CR media. Addition of NA or nicotinamide riboside (NR) allows a moved mother to maintain replicative longevity despite the move. Moreover, conditioned medium from CR-treated cells transmits the longevity benefit of CR to moved mother cells. Evidence suggests the existence of a longevity factor that is dialyzable but is neither NA nor NR, and indicates that Sir2 is not required for the longevity factor to be produced or to act. Data indicate that the benefit of glucose-restriction is transmitted from cell to cell in budding yeast, suggesting that glucose restriction may benefit neighboring cells and not only an individual cell.

A rapid antimicrobial susceptibility test based on single-cell morphological analysis

A rapid antibiotic susceptibility test (AST) is desperately needed in clinical settings for fast and appropriate antibiotic administration. Traditional ASTs, which rely on cell culture, are not suitable for urgent cases of bacterial infection and antibiotic resistance owing to their relatively long test times. We describe a novel AST called single-cell morphological analysis (SCMA) that can determine antimicrobial susceptibility by automatically analyzing and categorizing morphological changes in single bacterial cells under various antimicrobial conditions. The SCMA was tested with four Clinical and Laboratory Standards Institute standard bacterial strains and 189 clinical samples, including extended-spectrum b-lactamase–positive Escherichia coli and Klebsiella pneumoniae, imipenem-resistant Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci from hospitals. The results were compared with the gold standard broth microdilution test. The SCMA results were obtained in less than 4 hours, with 91.5% categorical agreement and 6.51% minor, 2.56% major, and 1.49% very major discrepancies. Thus, SCMA provides rapid and accurate antimicrobial susceptibility data that satisfy the recommended performance of the U.S. Food and Drug Administration.

http://stm.sciencemag.org/content/6/267/267ra174

Another good one from ASCB: Two component systems in Caulobacter

Fiebig 2014 - A Cell Cycle and Nutritional Checkpoint Controlling Bacterial Surface Adhesion

Went to a sweet talk by Petra Schwille at ASCB the other day and made a reading list about self-organization of the Min and Fts proteins.  Enjoy.


Loose 2008 - Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro

Zieske 2012 - Reconstitution of Pole-to-Pole Oscillations of Min Proteins in Microengineered Polydimethylsiloxane Compartments

Arumugam 2012 - Surface Topology Engineering of Membranes for the Mechanical Investigation of the Tubulin Homologue FtsZ

Loose 2013 - The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns

Zieske 2014 - Surface topology assisted alignment of Min protein waves

Zieske 2014 - Reconstitution of self-organizing protein gradients as spatial cues in cell-free systems

Arumugam 2014 - MinCDE exploits the dynamic nature of FtsZ filaments for its spatial regulation

Oldies but goodies

These are courtesy of Tristan and Ethan:

1) Everyone likes star-shaped bacteria, but not everyone has read the original paper!

Prosthecomicrobium and Ancalomicrobiutm: New Prosthecate Freshwater Bacteria

2) Amazing EM images of the type VI secretion system, from 1967:

A "MICROTUBULE" IN A BACTERIUM 

Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB

 

Kathrin Schirner, Ye-Jin Eun, Mike Dion, Yun Luo, John D Helmann, Ethan C Garner &
Suzanne Walker

Abstract:
The bacterial actin homolog MreB, which is crucial for rod shape determination, forms filaments that rotate around the cell width on the inner surface of the cytoplasmic membrane. What determines filament association with the membranes or with other cell wall elongation proteins is not known. Using specific chemical and genetic perturbations while following MreB filament motion, we find that MreB membrane association is an actively regulated process that depends on the presence of lipid-linked peptidoglycan precursors. When precursors are depleted, MreB filaments disassemble into the cytoplasm, and peptidoglycan synthesis becomes disorganized. In cells that lack wall teichoic acids but continue to make peptidoglycan, dynamic MreB filaments are observed, although their presence is not sufficient to establish a rod shape. We propose that the cell regulates MreB filament association with the membrane, allowing rapid and reversible inactivation of cell wall enzyme complexes in response to the inhibition of cell wall synthesis.

http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1689.html