You are currently browsing the monthly archive for May 2012.

From the genome of ancient organisms we now move on to ancient therapies for the next #Microtwjc meeting.  This week’s paper (5th June 2012) goes “back to basics” reporting the ability of manuka honey to inhibit Streptococcus pyogenes biofilms and reduce binding to human tissue proteins.

A big thanks needs to go to The Society for General Microbiology (@SocGenMicro) and the journal Microbiology for making this week’s journal open access (until the 7th June 2012).  They have been and will continue to be very supportive of #Microtwjc.

If you have any problems accessing the paper then please let me know!


Streptococcus pyogenes is a problematic organism of clinical significance, whereby infection of skin trauma sites can result in increased patient morbidity and mortality.  The authors first identified the antibacterial effects of manuka honey on both planktonic and biofilm cultures of Group A Streptococcus progenies by growing cells in the presence/absence of manuka honey.  The minimum inhibitory concentration (MIC) was  found to be 20% w/v and the minimum bactericidal concentration (MBC) was found to be 45% w/v with growth analysis showing a dose dependent inhibitory effect.

Having established a bactericidal mode of action, they went on to investigate the effects of manuka honey on biofilms, aggregation, and micro-colony formation.  Manuka honey was effective at permeating established biofilms, killing bacterial cells (reduction in CFU/ml), and reducing the overall biomass of the biofilm (reduction in crystal violet staining).  Microscopy looking at micro-colony formation showed the inability of S. pyogenes to form micro-colonies when grown in sub-lethal concentrations of manuka honey.  Binding of S. pyogenes to human tissue proteins was observed for fibronectin but not fibrinogen at sub-lethal concentrations which were confirmed by end point RT-PCR.

Based on the evidence provided by the authors they conclude that “manuka honey is effective at inhibiting the development of biofilms and disrupting established biofilms of S. pyogenes”.  They go on state that this most likely “mediated by the specific interruption of binding to host tissue ligands” and that manuka honey has potential as a “preventative measure against and treatment for wounds infected with S. pyogenes”.

Discussion Points:

  • Was the paper written clearly and logically with a natural progression of thoughts and ideas through the article?
  • Were the methods robust enough to draw conclusions from?
  • Would you have liked to see any other experiments, maybe some other host tissue proteins tested?
  • Do you agree with the authors closing statements?
  • Finally, is there place for this ancient remedy in modern health care practices?
Relavent Links:
I’ll add new links to the list below so be sure to check back regularly!

The transcript for last night’s journal club is now up and can be found here: or hopefully if you scroll up it should be embedded in a later entry…

Hope you will join us all for the next session Tuesday 5th June 8pm BST!

Edited in an attempt to embed storify

The paper for 22nd May journal club presents the genome of a Yersinia pestis strain isolated from a victim of the Black Death from the 14th century.

The authors developed a novel capture array to fish out bacterial DNA from the dental pulp of a plague victim buried in London’s East Smithfield cemetery.  The captured sequences were then sequenced and mapped to a contemporary Y. pestis strain. Differences in gene content and synteny, as well as polymorphic sites, were investigated through a combination of BLAST searches and reference-guided assembly of sequence reads.  The study concludes that the 14th century strain does not contain any unique polymorphisms, or significant genetic changes, that would make it more virulent than modern strains.

The authors go on to place the 14th century strain in the phylogenetic context of other Yersinia strains, and show that it sits “close to the ancestral node of all extant human pathogenic Y. pestis strains”.  Using a Bayesian coalescent method, they estimate a date for the emergence of human-associated Y. pestis to between 1282–1343 AD, calling into question the commonly accepted hypothesis that the earlier Justinian Plague was caused by the same pathogen.

The authors feel that the study of ancient pathogens can inform the study of mechanisms of host adaptation and pandemic spread of modern pathogens.  The authors close by stating “At our current resolution, we posit that molecular changes in pathogens are but one component of a constellation of factors contributing to changing infectious disease prevalence and severity, where genetics of the host population, climate, vector dynamics, social conditions and synergistic interactions with concurrent diseases should be foremost in discussions of population susceptibility to infectious disease and host–pathogen relationships with reference to Y. pestis infections.”

Discussion points

  • What are the drawbacks of the capture array/sequencing method used?
  • Is the method used sufficient to support the conclusions the authors have drawn?
  • Do you feel that the study of ancient pathogens is useful for informing the study of contemporary strains?
  • Is the conclusion that the causative agent of the Black Death is distinct from earlier supposed plagues convincing?

Links to other relevant discussions

The paper received quite a bit of coverage when it was published, thought I’d link to the NY Times article and the TWiM podcast that discussed a bit about the previous work done.

Storify transcript of last nights #microtwjc

The storify’d version of last nights first Microbiology Twitter Journal Club is now live. We are treating this a transcript of the event so take a look and hopefully learn something about bacteria, microbiology and how to critique a paper.

Look forward to seeing you all again in two weeks time on Tuesday 22nd May at 20:00 BST.

This week’s paper reports on the characterisation of a gene, pgp1, that is important for the helical shape of the bacterium Campylobacter jejuni.

The authors first identified the gene by screening for hypofluorescent C. jejuni mutants  with calcofluor white (which reacts with certain carbohydrate linkages and fluoresces under UV light).  (The researchers in previous work had shown that hypofluorescent mutants “exhibit changes in pathogenesis, virulence, fundamental and/or stress survival phenotypes”).  They then investigated the functional consequences of loss of this gene for C. jejuni by creating a non-polar pgp1 targeted deletion strain .

Having identified that the pgp1 gene is required for the helical shape of C. jejuni and having identified that it plays a role in motility and biofilm formation they went on to characterise the muropeptide content of the C. jejuni strain and determine how this is altered by loss of pgp1 function.

Then they looked at the effect the pgp1 gene had on how C. jejuni interacts with host cells, finding that the deletion strain showed a decreased ability to colonise one day old chicks but that in vitro there was little difference between the deletion strain and the wild type strain when it came to invasion and intracellular survival in epithelial and macrophage cell line.  Finally, they showed that the deletion strain did produce an increased epithelial cell Nod1  response compared to the wild type and increased IL-8 production by epithelial cells.

In the discussion the authors state that “identification and characterisation of pgp1 provides a critical first step in understanding how shape and PG modifications impact C. jejuni pathogenesis“.  They conclude by saying that the deletion strain “will be a valuable tool to continue to study the effects of the loss of C. jejuni helical shape on its biology and pathogenesis“.

Discussion points

These are points/questions that occurred to me as I read the paper.  If you have anything else you think would be interesting to discuss please post in the comments below.

  • Was the paper written clearly and logically with the results informing the discussion?
  • Much of this paper is by necessity descriptive, as the authors discuss how they characterised the gene.  Once they identified its role in C. jejuni biology was there a clear hypothesis for its role in C. jejuni pathogenesis?
  • Have the authors shown sufficiently that it is pgp1‘s role in helical shape formation that is directly affecting C. jejuni‘s pathogenesis?
  • Are there any other experiments you would like to have seen done?