Archive for category Literature review

Disclaimer

The following review is my own interpretation of the linked-to article. Please do not use my review as a complete reference for the article as I will most likely skip important information that you feel is relevant. If I do miss something, please feel free to comment about it in the comments section below. Please read the article before reading my review and remember, this is my notebook, which means these are my notes on the article and they will more-than-likely hold no relevance to you or your research.

Paper

van Loosdrecht MCM, Heijnen JJ, Eberl H, Kreft J, Picioreanu C (2002) Mathematical modelling of biofilm structures. Antonie van Leeuwenhoek 81: 245-256. doi:10.1023/A:1020527020464.

Review

In this paper, the authors did both experiments and calculations on biofilms. They used an interesting device called a Biofilm Airlift Suspension device which, is used to study wastewater treatment.

 

  • The authors confirmed my suspicion that the structures of biofilms are highly dependent on the flow of the medium that they are in. This paper does not go into that analysis rather they reference a paper that did.
    • Gjaltema A, Tijhuis L, van Loosdrecht MCM & Heijnen JJ (1995) Detachment of biomass from suspended nongrowing spherical biofilms in airlift reactors. Biotechnol. Bioeng. 46: 258–269.
  • The authors stipulate that the dominant factor governing biofilm morphology is a ratio of the detachment rate to the the biofilm surface loading rate.
    • While I agree with this statement, I do not believe it is the root reason why biofilms obtain a certain morphology. I still think is is dependent on flow rates of the environment the biofilm is in. So, I think Navier-Stokes has to come into play at some point.
  • They reference an article that states that shear rates govern the thickness of biofilms as do lower surface loading rates.
    • Kwok WK, Picioreanu C, Ong SL, van Loosdrecht MCM, Ng WJ & Heijnen JJ (1998) Influence of biomass production and detach- ment forces on biofilm structures in a biofilm airlift suspension reactor. Biotechnol. Bioeng. 58: 400–407.
  • They define the biofilm density as the amount of biomass per volume excluding the pores in the biofilm. They state that this is a measure for the number of cells in the biofilm.
  • They reference another paper that investigated biofilm density. This paper showed that biofilm density increased when the substrate used selected for slower growing bacteria. This paper also showed that fast growing bacteria in a low shear rate and a high loading rate led to more porous biofilms.
    • Villaseñor JC, van Loosdrecht MCM, Picioreanu C & Heijnen JJ (2000) Influence of different substrates on the formation of biofilms in a biofilm airlift suspension reactor. Water Sci. Techn. 41(4–5): 323–330.
  • They reference another attempt at mathematically modeling biofilms in one dimension.
    • Wanner O & Gujer W (1986) A multispecies biofilm model. Biotechnol. Bioeng. 28: 314–328.
  • They also discuss other references where more advanced studies were done modeling biofilms.
  • They are apparently using the model defined by Picioreanu. This model incorporates several parameters:
    • Convection
    • Diffusion
    • Reaction
    • Biofilm growth
    • Detachment
  • The authors note that at the time of the writing, proper measurements of the gel properties of biofilms still have not been accomplished. This is interesting and now gives me a better search term “biofilm properties”. They do give several references.
  • The author’s final thought is to obtain experimental data in the following areas in order to improve computational reliability.
    • EPS formation kinetics and stoichiometry.
    • Biofilm mechanical strength.
    • Kinetics of production and decay of quorum sensing signals.
    • Biomass spreading in the biofilm.
    • Movement of biofilm filaments.
    • Movement of the biofilm itself.

 

I think the take-home from this paper is that they were able to model biofilms. This was definitely a review paper even though it didn’t state that it was. The important things I learned were:

  • Fast flow rates give a denser less porous biofilm.
  • Low flow rates give a more porous biofilm.

Also, I completely agree with the author’s desire to get more experimental data in their closing remarks. Actually, everything they suggested are questions that I have about biofilms and I need to search for every term above.

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Literature review

Disclaimer

The following review is my own interpretation of the linked-to article. Please do not use my review as a complete reference for the article as I will most likely skip important information that you feel is relevant. If I do miss something, please feel free to comment about it in the comments section below. Please read the article before reading my review and remember, this is my notebook, which means these are my notes on the article and they will more-than-likely hold no relevance to you or your research.

Paper

Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nature Reviews Microbiology 2: 95–108. doi:10.1038/nrmicro821.

Review

I decided to ask the question; what is a biofilm? Usually, I would start with a review on the subject to try and answer this question and this is exactly what I decided to do. Again, as usual, I “picked” the first review article I found from a Google Scholar Search. Too bad the article isn’t OA.

  • The authors state that biofilm formations appear in fossil records dating back to 3.25 billion years ago.
  • Figure 1 is pretty spectacular and is well commented.
  • They make a compelling argument stating that; making biofilms is an ancient and integral part of prokaryotes.
    • In the early evolution of Earth, there were extreme and fluctuating conditions such as UV, pH, and temperature changes. Having a biofilm to live in created a homeostasis were the bacteria could live and learn how to communicate. This is an interesting argument and they reference a paper for it.
    • They also mention that creating biofilms could help sequester nutrients, they reference a paper for this statement as well.
  • They define the following terminology: planktonic cells are those that are freely swimming in their environment while sessile ones are in a biofilm.
  • They make a note of different ways in which bacteria will form biofilms and note that the structural similarities are possibly due to “convergent survival strategies”. Some of the convergent survival strategies include: streamers, periphyton, and stromatolite (defined in the paper).
    • I have to disagree here as I cannot believe that a group of bacteria are actively creating structures in different environments. I can, however, attribute fluid flow aiding in structural similarities between the shapes of biofilms that form in say fast flowing environments as opposed to calm quiescent environments.
  • They claim that “The proclivity of bacteria to adhere to surfaces and form biofilms in so many environments is undoubtedly related to the selective advantage that surface association offers.”
    • I think they mean that bacteria have learned how to create biofilms because they are evolutionarily advantageous.
  • They note that people have done studies where they attempt to knock out genes that show biofilm creation. In those studies, they found that knocking out the genes just retarded biofilm growth and thus it must be a fundamental and redundant gene in the bacteria….Very cool!
  • Yes! They reference an article that did biofilm modeling.
    • van Loosdrecht, M. C., Heijnen, J. J., Eberl, H., Kreft, J. & Picioreanu, C. Mathematical modelling of biofilm structures. Antonie Van Leeuwenhoek. 81, 245–256 (2002).
  • Biofilms will release their colony in a few different means:
    • Swarming dispersal.
    • Clumping dispersal.
    • Surface dispersal.
  • They state that biofilms can be thought of as hydrogels.
  • They state that there are (were in 2004) 3 proposed mechanisms to explain why biofilms are resistant to antibiotics.
    • Barrier properties of the slime matrix.
    • The physiological state of the biofilm. There are layers in the biofilm that have dormant cells and thus antibiotics end up being trapped there with not affect on the cells.
    • Subpopulations of resistant cells.
  • The authors state that Parsek and Singh (cited) proposed four criteria for defining a biofilm infection in a human.
    • The pathogenic bacteria are surface associated or adherent to a substratum.
    • Bacterial clusters, encased in a matrix of bacterial or host constituents.
    • The infection is localized.
    • The infection is resistant to antibiotic therapy.
  • Bacteria will modify their phenotypes for biofilms.

So, the second half of the paper talked about biofilms on implants and cystic fibrosis. There was a ton of stuff in this section that I didn’t quite grasp so I’ll have to revisit it in the future. Overall, this was a good review of what makes biofilms, where they form, and some characteristics of them once they are created.

 

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