The Neolithic revolution of bacterial genomes

Mira, Álex; Pushker, Ravindra; Rodrı́guez-Valera, Francisco

doi:10.1016/j.tim.2006.03.001

Cited by 123 publications

(90 citation statements)

References 35 publications

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“…Despite the simplicity of this model, it captures, at least qualitatively, the heterogeneity of transposition rates among transposon families (65) and environmental conditions (66,67). Unlike large expansions, which are rare events typically associated with ecological transitions affecting the entire genome (68)(69)(70)(71), small bursts occur frequently and affect a sizable fraction of transposon families. Some well-known instances of large transposon expansions become apparent in our analysis that identified taxa with unusually high burst rates, such as Xanthomonas, Burkholderia, and Francisella, in accord with previous observations (70,71).…”

Section: Discussionmentioning

confidence: 99%

“…Unlike large expansions, which are rare events typically associated with ecological transitions affecting the entire genome (68)(69)(70)(71), small bursts occur frequently and affect a sizable fraction of transposon families. Some well-known instances of large transposon expansions become apparent in our analysis that identified taxa with unusually high burst rates, such as Xanthomonas, Burkholderia, and Francisella, in accord with previous observations (70,71). In most other taxa, transposon decay is the dominant process, which is the expected trend, given that transposition is tightly regulated and a large fraction of transposon copies are inactive (72,73).…”

Section: Discussionmentioning

confidence: 99%

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Disentangling the effects of selection and loss bias on gene dynamics

Iranzo

Cuesta

Manrubia

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Disentangling the effects of selection and loss bias on gene dynamics

Iranzo

Cuesta

Manrubia

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…It is known that intracellular bacteria or bacteria that are unable to survive outside their host, such as H. parasuis, undergo genome reduction (Fraser-Liggett, 2005). This phenomenon is progressive during the course of adaptation of the bacteria, and is accompanied first by an expansion of mobile genetic elements and then by development of pseudogenes (Mira & Pushker, 2005;Mira et al, 2006 ). The present study indicated that bmaA genes of H. parasuis are undergoing genomic reduction, with each strain being in a different evolutionary state.…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, bmaA3 is affected by different frameshifts in strains Nagasaki and SH0165, but is present at full length in strain 29755. Some strain variability is also observed in sequences flanking bmaA3, with presence or absence of hypothetical proteins and pseudogenes, which can produce a particular instability in this DNA region characteristic of the development of pseudogenes (Mira et al, 2006). Alternatively, the large insertion in the bmaA2 gene of strain 29755 might be due to lateral gene transfer, as one of the inserted elements, a trimeric autotransporter gene Table S2).…”

Section: Discussionmentioning

confidence: 99%

Genomic and antigenic characterization of monomeric autotransporters of Haemophilus parasuis: an ongoing process of reductive evolution

et al. 2012

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The genome of the highly pathogenic Haemophilus parasuis Nagasaki strain (serovar 5) was sequenced to 99 % completion. A genomic comparison with two other pathogenic serovar 5 H. parasuis strains identified six genes per genome (bmaA1-bmaA6) encoding b-barrel monomeric autotransporters, bmaA2 and bmaA3 being pseudogenes in at least one strain. The remaining encoded proteins were predicted to belong to the subtilisin (BmaA1 and BmaA4) and cysteine (BmaA5 and BmaA6) protease families. Allelic polymorphism was detected in other H. parasuis strains by comparative genomic hybridization using microarrays. Recombination events were observed, some of them leading to gene disruption in one of the three strains, although synteny around bmaA genes was conserved. These results suggest that bmaA genes are undergoing a process of reductive evolution. To evaluate their use as potential vaccine antigens, the products of the passenger domains of bmaA1, bmaA4, bmaA5 and bmaA6 were produced in Escherichia coli as recombinant proteins. They were detected by immunoblotting using sera of colostrum-deprived piglets recovering from a sublethal infection with H. parasuis (Nagasaki). The existence of specific antibodies after infection with H. parasuis also demonstrated in vivo expression. Using proteomics, only BmaA6 was detected in the in vitro-grown Nagasaki strain. Interestingly, the translocator domain was found in the outer membrane, while the passenger domain was located in supernatants. These results indicate that BmaA proteins could be considered as immunogen candidates to improve H. parasuis vaccines. However, their capacity to confer protective immunity needs to be studied further.

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“…After that time, food resources became more abundant and constant, the concentration of large populations in limited areas created selective pressure that favored pathogens specialized in colonizing human hosts and probably produced the first wave of emerging human diseases (5). It has been hypothesized that bacteria specialized in human-associated niches, including our gut commensal flora, underwent intense transformation during the social and demographic changes that took place with the first Neolithic settlements (6).…”

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confidence: 99%

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Filippo

Cavalieri

Paola

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

4,788

301

3,729

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Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide. metagenomics | nutrigenomics | biodiversity | 454-pyrosequencing | shortchain fatty acids

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The Neolithic revolution of bacterial genomes

Cited by 123 publications

References 35 publications

Disentangling the effects of selection and loss bias on gene dynamics

Disentangling the effects of selection and loss bias on gene dynamics

Genomic and antigenic characterization of monomeric autotransporters of Haemophilus parasuis: an ongoing process of reductive evolution

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

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