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

We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

/pdf/dada2-high-resolution-sample-inference-from-illumina-ygkdeyoxho.pdf

DADA2: High-resolution sample inference from Illumina amplicon data

Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

/pdf/phyloseq-an-r-package-for-reproducible-interactive-analysis-1ez1xx3dlr.pdf

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Colonisation of the chicken caecum by afimbriate and aflagellate derivatives of Salmonella enterica serotype Enteritidis

The widespread use of silver nanoparticles (AgNPs) has prompted studies on different species and at various trophic levels, however, little is known about possible toxicological impacts on their corresponding microbiota. Here the effects of AgNPs on a defined bacterial community established from the collected stool of a healthy donor have been investigated. The anaerobic consortium was exposed to several concentrations (0 – 200 mg/L) of AgNPs (capped; 10 nm) for 48 h. Nanosilver had a negative impact on the bacterial community as evidenced by a significant reduction (~22%) in culture-generated gas production at the two highest AgNP concentrations compared to controls, as well as significant (p<0.05) changes in fatty acid methyl ester profiles even at the lowest concentration. DNA analysis confirmed these observations showing a shift in the community structure as demonstrated by cluster analysis of PCR-denaturing gradient gel electrophoresis (DGGE) profiles, as well by phylogenetic distributions obtained from 454 pyrotag 16S rRNA gene sequencing. The bacterial assemblage was significantly (p<0.01) different in the AgNP- treatment groups compared to controls. As expected, ionic silver (AgCl; 25-200 mg/L) was also antibacterial, as shown by all four assessment methods, but its effects were distinct from the AgNP-mediated changes. Thus, nano size-dependent impacts were evident. Taken together, these experiments suggest that AgNP ingestion, either deliberate or inadvertent, could have negative consequences on our intestinal microbiota.

https://www.longdom.org/open-access/nanosilvermediated-change-in-human-intestinal-microbiota-2157-7439.1000235.pdf

Nanosilver-Mediated Change in Human Intestinal Microbiota

A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium.

Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective.

Salmonella enteritidis isolated from poultry infections generated a convoluted colonial morphology after 48 h growth on colonisation factor antigen (CFA) agar at 25°C. A mutant S. enteritidis defective for the elaboration of the SEF17 fimbrial antigen, in which the agf gene cluster was inactivated by insertion of an ampicillin resistance gene cassette, and other wild-type S. enteritidis transduced to this genotype failed to produce convoluted colonies. However, growth of SEF17− mutants at 25°C on CFA agar supplemented with 0.001% Congo red resulted in partial recovery of the phenotype. Immunoelectron microscopy demonstrated that copious amounts of the SEF17 fimbrial antigen were present in the extracellular matrix of convoluted colonies of wild-type virulent S. enteritidis isolates. Bacteria were often hyperflagellated also. Immunoelectron microscopy of SEF17− mutants grown on CFA agar+0.001% Congo red demonstrated the elaboration of an as yet undefined fimbrial structure. Isolates of S. enteritidis which were described previously as avirulent and sensitive to environmental stress failed to express SEF17 or produce convoluted colonies. These data indicate an essential role for SEF17, and possibly for another fimbria and flagella, in the generation of the convoluted colonial phenotype. The relationship between virulence and colonial phenotype is discussed.

Emma Allen-Vercoe

Papers

Colonisation of the chicken caecum by afimbriate and aflagellate derivatives of Salmonella enterica serotype Enteritidis

Nanosilver-Mediated Change in Human Intestinal Microbiota

A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium.

Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective.

SEF17 fimbriae are essential for the convoluted colonial morphology of Salmonella enteritidis