Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.

/pdf/qiime-allows-analysis-of-high-throughput-community-2ob4mkjrat.pdf

QIIME allows analysis of high-throughput community sequencing data.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

/pdf/introducing-mothur-open-source-platform-independent-3tr77w6374.pdf

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.

Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.

Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch

Contact: [email protected]

Supplementary information:Supplementary data are available at Bioinformatics online.

/pdf/search-and-clustering-orders-of-magnitude-faster-than-blast-1c8ksdt7ke.pdf

Search and clustering orders of magnitude faster than BLAST

We showed that HCD elevated colonic oxidative stress, inflammation as well as colonocyte proliferation zone (PZ), a biomarker for colon cancer, in pig model Calprotectin (CP) and lipocalin-2 (LCN2) are non-invasive markers of intestinal inflammation, however the HCD influence on these markers and their correlation with PZ, colonic bacteria and their metabolites in a human-relevant pig model is not known We hypothesized that HCD elevated CP and LCN2 will correlate with PZ, gut bacteria and their metabolites To test this hypothesis, pigs (n = 8) were provided either standard diet (SD; 5% fat) or HCD (25% fat) for 13 wk HCD elevated (P = 0002 and P = 00006) colon digesta CP and LCN2 (ELISA) and these markers correlated (r = 0521, r = 0626; P = 005) with PZ HCD consuming animals had reduced fecal Bifidobacterium spp (16s rRNA sequencing, P = 0019) that negatively correlated with CP, LCN2 and PZ (r = -0700, r = -0609 and r = -0682, respectively; P = 005) HCD consumption also suppressed (P = 0

High-calorie diet (HCD) induced elevation in calprotectin and lipocalin-2 correlates with changes in gut bacteria and their metabolites in a porcine model

850a The treatment-naive microbiome in early-onset Crohn's Disease

Su1911 Effects of Metronidazole on the Fecal Metabolome in Healthy Dogs: An Untargeted Metabolomics Approach

Geography and location are the primary drivers

Balancing the number of stem cells and their progeny is crucial for tissue development and repair. Here we examine how muscle stem/precursor cell (MPC) numbers are tightly regulated during zebrafish somitic muscle development. MPCs expressing Pax7 are initially located in the dermomyotome (DM) external cell layer, adopt a highly stereotypical distribution and thereafter a proportion of MPCs migrate into the myotome. Regional variations in the proliferation and terminal differentiation of MPCs contribute to growth of the myotome. To probe the robustness of spatiotemporal regulation of MPCs, we compared the behaviour of wild type (wt) MPCs with those in mutant zebrafish that lack the muscle regulatory factor Myod. Myod fh261 mutants form one third fewer multinucleate fast muscle fibres than wt and show a significant expansion of the Pax7+ MPC population in the DM. Subsequently, myod fh261 mutant fibres generate more cytoplasm per nucleus, leading to recovery of muscle bulk. In addition, relative to wt siblings, there is an increased number of MPCs in myod fh261 mutants and these migrate prematurely into the myotome, differentiate and contribute to the hypertrophy of existing fibres. Thus, homeostatic reduction of the excess MPCs returns their number to normal levels, but fibre numbers remain low. The GSK3 antagonist BIO prevents MPC migration into the deep myotome, suggesting that canonical Wnt pathway activation maintains the DM in zebrafish, as in amniotes. BIO does not, however, block recovery of the myod fh261 mutant myotome, indicating that homeostasis acts on fibre intrinsic growth to maintain muscle bulk. The findings suggest the existence of a critical window for early fast fibre formation followed by a period in which homeostatic mechanisms regulate myotome growth by controlling fibre size.

http://www.biorxiv.org/content/biorxiv/early/2017/02/10/095554.full.pdf

Rob Knight

Papers

High-calorie diet (HCD) induced elevation in calprotectin and lipocalin-2 correlates with changes in gut bacteria and their metabolites in a porcine model

850a The treatment-naive microbiome in early-onset Crohn's Disease

Su1911 Effects of Metronidazole on the Fecal Metabolome in Healthy Dogs: An Untargeted Metabolomics Approach

Geography and location are the primary drivers

Myotome adaptability confers developmental robustness to somitic myogenesis in response to fibre number alteration.