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To the Editor: The human IgA response is composed of two antibody subclasses, [IgA.sub.1] and Ig[A.sub.2]. With a shorter hinge region, Ig[A.sub.2] is more resistant to bacterial proteases. Anecdotal evidence [...]

Author(s): Matthew P. Spindler, Jeremiah J. Faith, Junshi Wang, Paul J. Kenny Author Affiliations: Gut clues to weight gain after quitting smoking THE PAPER IN BRIEF * People who stop [...], Research has uncovered factors that underlie the weight gain associated with cessation of smoking. Here, scientists consider the implications of this finding from the perspectives of gut biology and of smoking. Gut microbes implicated in weight gain after the cessation of smoking.

We deeply sampled the organismal, genetic, and transcriptional diversity in fecal samples collected from a monozygotic (MZ) twin pair and compared the results to 1,095 communities from the gut and other body habitats of related and unrelated individuals. Using a new scheme for noise reduction in pyrosequencing data, we estimated the total diversity of species-level bacterial phylotypes in the 1.2-1.5 million bacterial 16S rRNA reads obtained from each deeply sampled cotwin to be ~800 (35.9%, 49.1% cletected in both). A combined 1.1 million read 16S rRNA dataset representing 281 shallowly sequenced fecal samples from 54 twin pairs and their mothers contained an estimated 4,018 species-level phylotypes, with each sample having a unique species assemblage (53.4 [+ or -] 0.6% and 50.3 [+ or -] 0.5% overlap with the deeply sampled cotwins). Of the 134 phylotypes with a relative abundance of >0.1% in the combined dataset, only 37 appeared in >50% of the samples, with one phylotype in the Lachnospiraceae family present in 99%. Nongut communities had significantly reduced overlap with the deeply sequenced twins' fecal microbiota (18.3 [+ or -] 0.3%, 15.3 [+ or -] 0.3%). The MZ cotwins' fecal DNA was deeply sequenced (3.8-6.3 Gbp/sample) and assembled reads were assigned to 25 genus-level phylogenetic bins. Only 17 % of the genes in these bins were shared between the cotwins. Bins exhibited differences in their degree of sequence variation, gene content including the repertoire of carbohydrate active enzymes present within and between twins (e.g., predicted cellulases, dockerins), and transcriptional activities. These results provide an expanded perspective about features that make each of us unique life forms and directions for future characterization of our gut ecosystems. microbial phylogenetic analyses | microbiota | transcriptomics | carbohydrate active enzymes doi/ 10.1073/pnas.1002355107

Protein-coding genes in mitochondrial genomes have varying degrees of asymmetric skew in base frequencies at the third codon position. The variation in skew among genes appears to be caused by varying durations of time that the heavy strand spends in the mutagenic single-strand state during replication ([D.sub.ssH). The primary data used to study skew have been the gene-by-gene base frequencies in individual taxa, which provide little information on exactly what kinds of mutations are responsible for the base frequency skew. To assess the contribution of individual mutation components to the ancestral vertebrate substitution pattern, here we analyze a large data set of complete vertebrate mitochondrial genomes in a phylogeny-based likelihood context. This also allows us to evaluate the change in skew continuously along the mitochondrial genome and to directly estimate relative substitution rates. Our results indicate that different types of mutation respond differently to the [D.sub.ssH] gradient. A primary role for hydrolytic deamination of cytosines in creating variance in skew among genes was not supported, but rather linearly increasing rates of mutation from adenine to hypoxanthine with [D.sub.ssH] appear to drive regional differences in skew. Substitutions due to hydrolytic deamination of cytosines, although common, appear to quickly saturate, possibly due to stabilization by the mitochondrial DNA single-strand-binding protein. These results should form the basis of more realistic models of DNA and protein evolution in mitochondria.

Author(s): Dachuan Zhang [1, 2]; Grace Chen [1, 2]; Deepa Manwani [3]; Arthur Mortha [4, 5]; Chunliang Xu [1, 2]; Jeremiah J. Faith [5, 6]; Robert D. Burk [3]; Yuya [...]

Seven years after the launch of the Human Microbiome Project, we still lack sufficient tools to visualize the microbiome in a living host. A new study provides experimental tools to [...]