Exopolysaccharide-producing strains of thermophilic lactic acid bacteria cluster into groups according to their EPS structure

AIMS: To compare galactose-negative strains of Streptococcus thermophilus and Lactobacillus delbrueckii subspecies bulgaricus isolated from fermented milk products and known to produce exopolysaccharides (EPSs). METHODS AND RESULTS: The structures of the EPSs were determined using nuclear magnetic resonance (NMR) and their genetic relationships determined using restriction endonuclease analysis (REA) and random amplification of polymorphic DNA (RAPD). Similar groupings were apparent by REA and RAPD, and each group produced an EPS with a particular subunit structure. CONCLUSION: Although none of the strains assimilated galactose, all inserted a high proportion of galactose into their EPS when grown in skimmed milk, and fell into three distinct groups. Significance and Impact of the Study: This information should help in an understanding of genetic exchanges in lactic acid bacteria.     

The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease

Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease. The kinetic studies performed in this work showed that the preexistent polymorphisms in subtype C protease, by themselves, do not provide for a greater level of resistance. Inhibition analysis with eight clinically used protease inhibitors revealed that the natural polymorphisms found in subtype C protease, in combination with drug resistance mutations, can influence enzymatic catalytic efficiency and inhibitor resistance. Structural analyses of the subtype C protease bound to nelfinavir and indinavir showed that these inhibitors form similar interactions with the residues in the active site of subtype B and C proteases. It also revealed that the naturally occurring polymorphisms could alter the position of the outer loops of the subtype C protease, especially the 60's loop.     

A Jungle in There: Bacteria in Belly Buttons are Highly Diverse,but Predictable

The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (∼1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons.     

Use of single-point genome signature tags as a universal tagging method for microbial genome surveys

We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC, uvrB, and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully used to generate Csp6I-based tags upstream of the 16S rRNA gene and allowed us to discriminate between closely related strains of Bacillus cereus and Bacillus anthracis. This concept was further used successfully to identify the individual members of a defined microbial community.     

When to bee social: interactions among environmental constraints, incentives, guarding, and relatedness in a facultatively social carpenter bee

In the facultatively social carpenter bee, Xylocopa pubescens,foundresses usually establish nests solitarily. However, nestsmay become social if a second foundress (referred to as alpha)successfully usurps the nest, with the original foundress (referredto as beta) remaining as a guard. Reproductive skew theory predictsthat beta foundresses should remain as helpers only if alphausurpers allow them a share of reproduction. Because alpha femalesdestroy much of beta's brood and beta females do not lay eggsafter takeovers, studies have concluded that usurpers offerno staying incentives or concessions in return for helping behavior.This conclusion is paradoxical, and we suggest that by refrainingfrom destroying all of beta's brood, alpha females do indeedoffer concessions to beta females. We constructed a model toexamine the conditions under which social nesting is favoredby both alpha and beta females. Female preference for socialversus solitary nesting is proportional to expected fitnessin either setting and is affected by current environmental conditions,the value of guarding behavior in protecting brood from pollenrobbery, the size of the concession offered by alpha, and thedegree of genetic relatedness between the foundresses. Our modelshows that at a minimum, establishing sociality after unrelatedusurpations always requires a concession, whereas in relatedusurpations, a concession is not always required. Generally,agreement between alpha and beta is difficult because alpharequires a much higher premium in pollen robbery protectionthan beta in order for sociality to be advantageous. Alpha femalesprefer social nesting only under the most severe environmentalconditions because usually they gain less by the presence ofa guard than by replacing beta brood with their own. In contrast,beta females always strongly prefer social nesting because thechances of successful renesting elsewhere are low and rarelyoutweigh the advantages of guarding their own brood that surviveusurpation. Effects of relatedness between foundresses on preferencefor social nesting are nonintuitive: first, alpha's preferenceincreases with relatedness, whereas beta's preference declines,and second, unrelated beta females prefer sociality more stronglythan related ones. This is because replacement of beta's offspringwith related alpha offspring partially compensates her for theloss of her own brood, even should she leave the nest.