Growth rates of Escherichia coli BJ4 colonizing the large intestine of streptomycin-treated mice were estimated by quantitative hybridization with rRNA target probes and by epifluorescence microscopy. The ribosomal contents in bacteria isolated from the cecal mucus, cecal contents, and feces were measured and correlated with the ribosomal contents of bacteria growing in vitro at defined rates. The data suggest that E. coli BJ4 grows at an overall high rate in the intestine. However, when taking into account the total intestinal volume and numbers of bacteria present in cecal mucus, cecal contents, and feces, we suggest that E. coli BJ4 in the intestine consists of two populations, one in the mucus which has an apparent generation time of 40 to 80 min and one in the luminal contents which is static.The animal intestinal tract harbors a vast number of bacteria representing a complex ecosystem in which the microorganisms are present without overgrowing the host but also without being flushed out by the host's intestinal activities, e.g., peristaltic movements and fluid flow. At least 400 to 500 different bacterial species are thought to be present at any time in the healthy human intestinal tract, and up to 10 12 bacteria are found per g of feces (3, 9). One question of interest is whether the intestinal flora grows as a homogeneous population at a low rate or as a heterogeneous population containing fast, slow, and nongrowing organisms.Accurate calculations of the rates of bacterial proliferation in the intestine have so far been represented only by average estimates at the level of populations. For example, the growth rate of Escherichia coli has been estimated in vivo, i.e., in the mouse intestine, by radioisotope techniques (8), by dilution by growth of a nonreplicating genetic marker (17,25), and simply by counting the number of viable cells (12,14). With these techniques, generation times from 30 min to 40 h have been estimated for E. coli (12,14,16,36). Also, continuous-flow cultures have been developed to mimic bacterial interactions in the gut and estimate overall growth rates (13, 27). These systems, however, do not reflect the physiological conditions in the gut, where entrapping of the bacteria in the mucus gel plays an important role. Furthermore, bacterial cell morphology, protein profiles, and growth physiology have been found to be distinct during growth in the intestine when compared with growth in laboratory media (22,33).We have previously found that in test tubes E. coli BJ4 is rod shaped, appears as large cells, and has a great potential for fast growth; however, soon after colonization of mice, E. coli BJ4 differentiates into a coccoid morphology, the so-called small variant, which grow more slowly than the rod-shaped E. coli cells in aerated test tubes (22). Here, we continue our investigation of the growth physiology of E. coli BJ4 present in its natural environment, the large intestine. Bacterial growth rates can be estimated from the cellular RNA and/or DNA contents, since the cellular RNA...
When a parent virus replicates inside its host, it must first use its own genome as the template for replication. However, once progeny genomes are produced, the progeny can in turn act as templates. Depending on whether the progeny genomes become templates, the distribution of mutants produced by an infection varies greatly. While information on the distribution is important for many population genetic models, it is also useful for inferring the replication mode of a virus. We have analyzed the distribution of mutants emerging from single bursts in the RNA bacteriophage 6 and find that the distribution closely matches a Poisson distribution. The match suggests that replication in this bacteriophage is effectively by a stamping machine model in which the parental genome is the main template used for replication. However, because the distribution deviates slightly from a Poisson distribution, the stamping machine is not perfect and some progeny genomes must replicate. By fitting our data to a replication model in which the progeny genomes become replicative at a given rate or probability per round of replication, we estimated the rate to be very low and on the on the order of 10 ؊4 . We discuss whether different replication modes may confer an adaptive advantage to viruses.In recent years, viruses have been increasingly used in the laboratory to study the fitness effects of mutations (1,4,8,10,14,15,16,25). The increase is likely due to two reasons. First, these fitness effects, which are generally quantified as the distribution of the magnitude, the sign (deleterious versus beneficial), and the interaction (additive versus nonadditive) of the mutations, are key to many evolutionary models, and viruses have become a major focus of evolutionary studies. Much of our predictive theories in evolution have come from population genetic models that make assumptions about the fitness effects of mutations. For example, depending on whether the interaction between deleterious mutations is log-additive, the models predict distinctly different advantages for the evolution of recombination (5, 15). Second, many issues addressed by such models have now also been raised in the context of viruses, especially RNA viruses, which have a much higher mutation rate than DNA viruses (11,12). Evolutionary topics as wide ranging as the quasi-species concept, game theory, the origin of life, the constancy of the molecular clock, the divergence and convergence of isolated populations, and the evolution of recombination have all been recently considered in relation to viruses (1-3, 5-7, 15, 17, 18, 22, 24, 29, 31, 32).As the more qualitative aspects of the distribution of mutational effects and interactions have become known, it has become desirable to extract more quantitative information. However, more quantitative analyses require also more exact information on another type of distribution, that of mutations and mutants in a population. The distinction between mutations and mutants is important and is made herein. A mutation is the event...
Single-celled organisms dividing by binary fission were thought not to age [1-4]. A 2005 study by Stewart et al. [5] reversed the dogma by demonstrating that Escherichia coli were susceptible to aging. A follow-up study by Wang et al. [6] countered those results by demonstrating that E. coli cells trapped in microfluidic devices are able to sustain robust growth without aging. The present study reanalyzed these conflicting data by applying a population genetic model for aging in bacteria [7]. Our reanalysis showed that in E. coli, as predicted by the model, (1) aging and rejuvenation occurred simultaneously in a population; (2) lineages receiving sequentially the maternal old pole converged to a stable attractor state; (3) lineages receiving sequentially the maternal new pole converged to an equivalent but separate attractor state; (4) cells at the old pole attractor had a longer doubling time than ones at the new pole attractor; and (5) the robust growth state identified by Wang et al. corresponds to our predicted attractor for lineages harboring the maternal old pole. Thus, the previous data, rather than opposing each other, together provide strong evidence for bacterial aging.
The physiological asymmetry between daughters of a mother bacterium is produced by the inheritance of either old poles, carrying non-genetic damage, or newly synthesized poles. However, as bacteria display long-term growth stability leading to physiological immortality, there is controversy on whether asymmetry corresponds to aging. Here we show that deterministic age structure landscapes emerge from physiologically immortal bacterial lineages. Through single-cell microscopy and microfluidic techniques, we demonstrate that aging and rejuvenating bacterial lineages reach two distinct states of growth equilibria. These equilibria display stabilizing properties, which we quantified according to the compensatory trajectories of continuous lineages throughout generations. Finally, we show that the physiological asymmetry between aging and rejuvenating lineages produces complex age structure landscapes, resulting in a deterministic phenotypic heterogeneity that is neither an artifact of starvation nor a product of extrinsic damage. These findings indicate that physiological immortality and cellular aging can both be manifested in single celled organisms.
Bacteriophages are the most numerous entities in the biosphere. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments. Previous laboratory manipulation has shown that, when multiple Cystoviruses infect a single host cell, they undergo (i) rare intrasegment recombination events and (ii) frequent genetic reassortment between segments. Analyzing linkage disequilibrium (LD) within segments, we find no significant evidence of intrasegment recombination in wild populations, consistent with (i). An extensive analysis of LD between segments supports frequent reassortment, on a time scale similar to the genomic mutation rate. The absence of LD within this group of phages is consistent with expectations for a completely sexual population, despite the fact that some segments have >50% nucleotide divergence at 4-fold degenerate sites. This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa. We discuss our results in light of the biological species concept applied to viruses.sex ͉ virus ͉ linkage disequilibrium ͉ Cystoviridae ͉ biogeography
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