China
Africa
Explore chapters and articles related to this topic
“Omics” Technologies in Vaccine Research
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
Although genome analysis of one strain provides valuable information about the putative antigenic proteins, it does not reveal the intra-species variations among different strains of pathogens. Mutations on the genes encoding these putative antigens may change the antigenic property or may not show the same efficacy against different strains. Therefore, a wider point of view is needed for the antigen discovery. A pan-genome is the global repertoire of genes belonging to a species obtained from its different strains, which includes three parts: (i) the core-genome with invariable and conserved genes in all strains, (ii) the dispensable genome including genes found in some strains, and (iii) the strain-specific genes found only in one strain (Kaushik and Sehgal 2008; Serruto et al. 2009).
A Genetic Framework for Addiction
Published in Hanna Pickard, Serge H. Ahmed, The Routledge Handbook of Philosophy and Science of Addiction, 2019
Philip Gorwood, Yann Le Strat, Nicolas Ramoz
Technological developments now allow an automatic genotyping at high throughput with 300,000 to 1.2 million SNPs simultaneously in a subject, thanks to DNA chips or microarrays. This method of pan-genome scan (GWAS) can be applied to large patient populations, of at least 1,000 affected subjects and controls, or family cohorts (patients and relatives) of the same size. The number of individuals included is critical to the statistical power of the associations that can be identified in the GWASs. Indeed, given the large number of SNPs genotyped, the significance level of the association must be corrected for the number of tests and preferably fixed at about 10-7 (without real consensus to date). Numerous GWASs have been made focusing on addiction, especially alcohol dependence and tobacco dependence, and among thousands of patients and controls that have been recruited through international consortia.
Campylobacter
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Hongsheng Huang, Catherine D. Carrillo, Emma Sproston
Since the advent of low-cost, rapid, whole genome sequencing (WGS) technologies, the availability of WGS information for Campylobacter species in public repositories has increased at a rapid rate. The first genome of C. jejuni, strain NCTC 11168, was published in 2000 (39), and now (at the time of writing) there are 1914 Campylobacter genomes available on the National Center for Biotechnology Information's (NCBI) microbial genome database (https://www.ncbi.nlm.nih.gov/genome/); however, 90% of these are made up of C. jejuni and C. coli species. Campylobactergenomes typically consist of a single circular chromosome with a G+C content (%) close to 30% for most species, but up to 46.6% in C. gracilis. Campylobacter species have relatively small genomes, ranging in size from 1.5 to 2.5 megabases (Mb), with approximately 1,600–2,200 genes in each genome. The presence of genomic islands and prophage is partially responsible for the size differences observed among strains (41,42). There are approximately 1,000 conserved core genes within each of the well-characterized species, C. jejuni and C. coli, and potentially 3,500 genes available from the pan genome (including both conserved and accessory genes) (43). Fewer than 700 genes are conserved across the two species (43,44), where their variation can have a large impact on the virulence and other characteristics of an individual strain (45). One of the most striking features of the Campylobacter genome is the presence of hypervariable homopolymeric tracts. Variation in the length of these sequences can impact the expression of these genes that encode flagellar glycosylation, capsular and LOS biosynthesis enzymes (46,47), and may be an important survival strategy of C. jejuni (35,39). The availability of genome sequence information has enhanced our understanding of both the biology and pathogenesis of campylobacters, and as more isolates become sequenced, and sequence-based molecular microbiology platforms become more advanced, this will continue to expand.
The evolution and competitive strategies of Akkermansia muciniphila in gut
Published in Gut Microbes, 2022
Ji-Sun Kim, Se Won Kang, Ju Huck Lee, Seung-Hwan Park, Jung-Sook Lee
The number of non-redundant strain-specific genes across different genomes varied from 2 to 108. A. muciniphila CBA5201 strain harboring the largest genome size had the largest number of unique gene families, 108, while A. muciniphila type strain KCTC 15667 T possessed the smallest number of unique gene families. The large proportion of specific genes suggested that the A. muciniphila strains harbored a high level of genomic diversity, indicating their ability to survive in various gut environments. Cumulative curves were generated using the PanGP program,40 a tool for quickly analyzing bacterial pan-genome profiles. The openness of the pan-genome was calculated based on Heap’s law model.41,42 When γ > 0, it means that pan-genomes are open state. The size of the pan-genome increased unboundedly with the increase of new genomes, including 3,811 non-redundant genes, which indicated that the A. muciniphila pan-genome was still “open” (Figure 1). This open pan-genome showed great potential for discovering novel genes with every A. muciniphila strain sequenced. In contrast to the pan-genome, the size of the core genome appeared to reach a steady-state approximation with 1,749 non-redundant genes. In addition, 45.9% of the pan-genome was found to be conserved, while the remaining 54.1% varied across the strains, indicating that the pan-genome exhibited a high level of genome variability.
Blautia—a new functional genus with potential probiotic properties?
Published in Gut Microbes, 2021
Xuemei Liu, Bingyong Mao, Jiayu Gu, Jiaying Wu, Shumao Cui, Gang Wang, Jianxin Zhao, Hao Zhang, Wei Chen
The Pan-genome is defined as the collection of all genes in a bacterial species, including core genome in all strains and dispensable genome in some strains. The open or closed characteristics of pan-genome could reflect the species diversity in genetic composition.37 As shown in Figure 3a, the number of pan-genome increased with the addition of Blautia genome, and the total number of pan-genome reached 26,728 when the 74th genome was added to the calculations. The pan-genome curve showed an upward trend, indicating that Blautia has an open pan-genome.38 In contrast, the core genes curve showed a downward trend, and gradually stabilized at 488 when the 74th genome was added.39 The core genes and unique genes of Blautia were displayed with a Venn diagram (Figure 3b). The number of core genes was 606, while the number of unique genes ranged from 3 to 995. Notedly, Blautia schinkii DSM10518 has the largest number of unique genes, which may be related to the isolation source. Because B. schinkii DSM10518 was the only strain isolated from rumen, and the other strains were isolated from human or mouse feces.
Further understanding of Pseudomonas aeruginosa’s ability to horizontally acquire virulence: possible intervention strategies
Published in Expert Review of Anti-infective Therapy, 2020
James Redfern, Mark C. Enright
Since the first genome sequence of a P. aeruginosa isolate (PAO1) was published in 2000 [30] the species has been the subject of many genome sequencing studies – at the time of writing 4660 genomes are currently in the public domain making it one of the most studied pathogen species. PAO1 is the most commonly used P. aeruginosa laboratory strain and the subject of ongoing international efforts to ascribe functions to its 5570 open reading frames, in a genome of 6,264,403bp, through the Pseudomonas Genome DB project (accessible at http://www.pseudomonas.com) [31]. P. aeruginosa genomes are approximately twice the size of that of the average bacterial species with around 6.3 million base pairs [30,32]. What is clearly apparent from genomic sequencing efforts to date is that the species has a very large pan-genome, the full complement of genes found in the species, with a very small number of core – genes found in every isolate and an extremely large accessory genome. A 2019 study [33] using genomics and analysis of gene knockouts from isolates grown under different conditions calculated that the number of core essential genes to be 321, which comprises only 6.6% of the P. aeruginosa genome. A study the previous year by Freschi and colleagues [28] estimated that the core genome was only 1.2% of the pan-genome based upon genomes that they sequenced or were publicly available in 2016. Both of these studies and other large genome sequencing projects describe a species with a minimal essential genome (compared with other bacterial species such as S. pneumoniae and C. jejuni, which has approximately 851 and 866 core genes out of an estimated 1990 and 1623 genes respectively [34]). According to the Freschi study, 50.1% of unique genes are found in single isolates.