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.

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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.

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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)


 Introduction: There is a critical need for complex microbiome quality control standards representing population-based samples for microbial community profiling and analysis in large scale epidemiologic studies.
 Methods: We developed standard quality control samples from five volunteers with different phenotypes, comprising one obese female, one healthy male, one male on a low-carb diet, one infant, and one male with Crohn’s Disease, and evaluated their microbial metagenomic profiles within three laboratories at two different timepoints. To quantify the percentage of microbiome variability explained by donors, laboratory and sequencing run, a distance-based coefficient of determination R2 was estimated using a permutational multivariate analysis of variance. In addition, we calculated the intraclass correlation coefficients (ICC) for the relative abundance of the most abundant species, two alpha diversity metrics (i.e., observed number of species and Shannon index) and the first principal coordinates of three beta diversity matrices (i.e., Bray-Curtis, Jaccard and Aitchison) to estimate the accuracy of fecal microbial profiles between the three different laboratories as well as within the laboratories.
 Results: The variability introduced by the phenotype of the donors explained 82.7% to 95.3% of the overall variability, which was higher than the variability introduced by the laboratories (1.8% to 3.1%) and the sequencing runs (0.6% to 1.7%) - the residual percent variance explained varied between 2.2% and 12.4%. Observations based on principal coordinates analysis showed that samples clustered by donor and not by laboratory or sequencing runs. The five donor clusters were well separated and very distinct. Based on the comparison of species relative abundances, each donor displayed very different microbial profiles; and the microbial profiles of each donor were comparable between the three different laboratories and the two sequencing runs in each laboratory. The reproducibility within and between the laboratories was good to excellent for most diversity metrics (ICCs higher than 0.97) and species relative abundances (range, ICCs=0.70-0.99); however, the reproducibility of the observed number of species was moderate (ICC=0.64 for the first laboratory, ICC=0.78 for the second laboratory, ICC=0.81 for the third laboratory, and ICC=0.42 between the laboratories).
 Conclusions: These standard quality control samples can be used as a reference in future population-based epidemiologic studies to pool or meta-analyze microbiome data.
 Citation Format: Semi Zouiouich, Smriti Karwa, Yunhu Wan, Andrew Chan, Joseph Petrosino, Emma Allen-Vercoe, Rob Knight, Jianxin Shi, Mitchell Gail, Christian Abnet, Emily Vogtmann, Rashmi Sinha. Quality control samples for future population-based microbiome studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3050.

Abstract 3050: Quality control samples for future population-based microbiome studies

A number of pediatric illnesses, both enteric and systemic, have been linked to an abnormal gut microbiota, although causality has yet to be confirmed. Several approaches have been advanced for the manipulation of the gut microbiota in order to treat or prevent microbiota-related disease conditions. These include established methods, including the use of pre-, pro-, and synbiotics, as well as more experimental techniques, including fecal microbiota transplantation and microbial ecosystem-derived therapeutics. This chapter reviews research surrounding the safety, efficacy, and sustained effects of these methods in a number of indications, with a focus on the pediatric population.

Manipulating the gut microbiota

Characterizing prophages in the genus Fusobacterium.

Intestinal colonisation with pathogens and antimicrobial resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonise intestinal AROs. However, FMT has significant practical barriers to implementation. A microbial consortium, microbial ecosystem therapeutic (MET)-2, is an alternative to FMT for the treatment of rCDI. It is unknown whether MET-2 is associated with decreases in pathogens and antimicrobial resistance genes (ARGs). We conducted a post-hoc metagenomic analysis of stool collected from two interventional studies of MET-2 (published) and FMT (unpublished) for rCDI treatment to understand if MET-2 had similar effects to FMT for decreasing pathogens and ARGs as well as increasing anaerobes. Patients were included in the current study if baseline stool had Proteobacteria relative abundance ≥10% by metagenomic sequencing. We assessed pre- and post-treatment Proteobacteria, obligate anaerobe and butyrate-producer relative abundances and total ARGs. MET-2 and FMT were associated with decreases in Proteobacteria relative abundance as well as increases in obligate anaerobe and butyrate-producer relative abundances. The microbiota response remained stable over 4 or 6 months for MET-2 and FMT, respectively. MET-2, but not FMT, was associated with a decrease in the total number of ARGs. MET-2 is a potential therapeutic strategy for ARO/ARG decolonisation and anaerobe repletion.

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Alterations in intestinal Proteobacteria and antimicrobial resistance gene burden in individuals administered microbial ecosystem therapeutic (MET-2) for recurrent Clostridioides difficile infection

La presente invention concerne de nouvelles preparations fecales synthetiques comprenant des bacteries isolees a partir d'un echantillon fecal d'un donneur sain. Les preparations fecales synthetiques sont utilisees pour le traitement des troubles du tractus gastro-intestinal, notamment la dysbiose, l'infection par Clostridium difficile et l'infection recidivante par Clostridium difficile, la prevention de la recidive de l'infection par Clostridium difficile, le traitement de la maladie de Crohn, de la rectocolite hemorragique, de la colopathie fonctionnelle, de l'affection abdominale inflammatoire, et de la diverticulose, et le traitement des intoxications alimentaires telles que la salmonelle. L'invention concerne egalement des procedes de preparation et des procedes d'utilisation des preparations fecales synthetiques.

Emma Allen-Vercoe

Papers

Abstract 3050: Quality control samples for future population-based microbiome studies

Manipulating the gut microbiota

Characterizing prophages in the genus Fusobacterium.

Alterations in intestinal Proteobacteria and antimicrobial resistance gene burden in individuals administered microbial ecosystem therapeutic (MET-2) for recurrent Clostridioides difficile infection

Procédé de traitement de troubles de l'appareil gastro-intestinal