PLoS ONE: Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere

by Mostafa El-Shahed and colleagues

Abstract: Background

The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.

Methodology/Principal Findings

We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU_0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.

Conclusions/Significance

The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.

Read the open-access, full-text article here:
http://dx.plos.org/10.1371/journal.pone.0012414

Now the Indian probiotic trial: would it help prevent diarrhea in the poor?

Are probiotics a feasible intervention for prevention of diarrhoea in the developing world?

 

N Hajela, GB Nair and NK Ganguly

 

Gut Pathogens 2010, 2:10doi:10.1186/1757-4749-2-10

 

With about 1.4 million of the just under 9 million child deaths attributed to diarrhoea in 2008 and 49% of them occurring in five countries namely, India, Nigeria, Democratic Republic of the Congo, Pakistan and China, there is an urgent need for interventions to prevent and control diarrhoeal diseases. Of the various interventions to prevent diarrhoea, probiotics offer potential. The past decade has witnessed the validation of their utility for the prevention, treatment and management of a variety of infective and non infective disorders. The most investigated field continues to remain infectious diarrhoea and compelling evidence comes from randomized placebo controlled trails. While results from these studies are encouraging, most of them reflect the outcomes of the developed world. Developing countries like India continue to struggle with nutritional and health challenges and bear the greatest burden of diarrhoea. A paucity of data from the developing countries limits the definite recommendation of probiotics. In these countries curd, often confused for a probiotic, is practiced as an integral part of the culture. While the nutritional benefits of these products cannot be understated, it is still uncertain whether these products can be classified as a probiotic. The emergence of probiotic foods which are scientifically validated for their efficacy and impart defined health benefits offer an excellent opportunity to improve public health. A recent randomized controlled trial conducted by the National Institute of Cholera and Enteric Diseases in Kolkata, India demonstrated a protective efficacy of 14% in preventing diarrhoea among children who received a probiotic. For the developing world, however, the vision for probiotics would mean a fundamental change in perception and developing a well-planned strategy to allow interventions like probiotics to permeate to impoverished settings, where the assault of micro organisms is on a daily basis. This would mean that probiotics be ingrained into the public health system without being seen as a medicine.

 

Read complete article here: http://www.gutpathogens.com/content/2/1/10/

Faculty of 1000’s most viewed top 10 evaluations: Evaluation of Aziz and Nizet, Sci Transl Med 2010 Jan 27 2(16):16ps4

Pathogen Micro-evolution in High Resolution (see the evaluation at F1000)

This perspective by Aziz and Nizet stresses that key hypotheses regarding microbial strain evolution or virulence cannot be addressed through conventional genotyping methods that often do not offer enough resolution of minor changes between closely related strains, such as insertion, deletion and substitution polymorphisms. Just like siblings and identical twins having their own personalities and phenotypes due to genetic, epigenetic or environmental confounders, paired/clonal isolates of bacteria, even if genetically identical, have their own colonization traits and pathogenic potentials due to their 'variome'.

Previously, people used to 'characterize' and individualize strains and isolates of bacterial pathogens by means of genetic fingerprinting or DNA profiling. However, recent revelations based on whole genome sequencing have showed that any two strains, even if (seemingly clonal) could be dramatically different in their functional capabilities, owing mainly to the single nucleotide polymorphisms (SNPs). This article, thus, potentially brings about the importance of a 'variome' in understanding evolution of pathogens, rather than putting emphasis on the core genome. In our own experience, Helicobacter pylori serially isolated from a single patient over a decade were different in containing or losing as much as ~51 open reading frames (ORFs) when whole genomes were sequenced (N Ahmed, T Taylor, F Megraud, unpublished data). These isolates were previously shown to belong to only one parental strain and were clonal according to the randomly amplified polymorphic DNA (RAPD), and MLST based genotyping {1}. As suggested in this paper, genome-wide analyses of SNPs between paired strains isolated from the same patient, or between input vs. output strains generated in a suitable animal model, could reveal important genetic 'switch' mechanisms critical for survival, adaptation and invasion potentials of the bacterial pathogens.

References: {1} Prouzet-Mauléon et al. J Clin Microbiol 2005, 43:4237-41 [PMID:16081988].

Evaluated 10 Aug 2010