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Although microbes have been classically viewed as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut bacteria shape the tissues, cells, and molecular profile of our gastrointestinal immune system. This partnership, forged over many millennia of coevolution, is based on a molecular exchange involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes for both microbes and humans. We explore how specific aspects of the adaptive immune system are influenced by intestinal commensal bacteria. Understanding the molecular mechanisms that mediate symbiosis between commensal bacteria and humans may redefine how we view the evolution of adaptive immunity and consequently how we approach the treatment of numerous immunologic disorders. 10.1126/science.1195568

Microbes rely on diverse defense mechanisms that allow them to withstand viral predation and exposure to invading nucleic acid. In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner. These hypervariable loci take up genetic material from invasive elements and build up inheritable DNA-encoded immunity over time. Conversely, viruses have devised mutational escape strategies that allow them to circumvent the CRISPR/Cas system, albeit at a cost. CRISPR features may be exploited for typing purposes, epidemiological studies, host-virus ecological surveys, building specific immunity against undesirable genetic elements, and enhancing viral resistance in domesticated microbes. 10.1126/science.1179555

Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands. Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface. All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport., In bacteria, transformation and conjugation usually mediate the transport of single-stranded DNA (ssDNA) across one or more membranes. Transformation involves the uptake of environmental DNA, whereas conjugation permits the direct [...]

The SAR11 clade consists of very small, heterotrophic marine α-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell., Pelagibacter ubique, strain HTCC1062, belongs to one of the most successful clades of organisms on the planet (1), but it has the smallest genome (1,308,759 base pairs) of any cell [...]

It is generally reasoned that lethal infections caused by opportunistic pathogens develop permissively by invading a host that is both physiologically stressed and immunologically compromised. However, an alternative hypothesis might be that opportunistic pathogens actively sense alterations in host immune function and respond by enhancing their virulence phenotype. We demonstrate that interferon-y binds to an outer membrane protein in Pseudomonas aeruginosa, OprF, resulting in the expression of a quorum-sensing dependent virulence determinant, the PA-I lectin. These observations provide details of the mechanisms by which prokaryotic organisms are directly signaled by immune activation in their eukaryotic host., Although opportunistic infection has been traditionally viewed as a passive phenomenon in which exploitative pathogens invade a weakened host, recent advances in the understanding of bacterial virulence gene regulation would [...]

The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ., The adult human intestine is home to an almost inconceivable number of microorganisms. The size of the population--up to 100 trillion--far exceeds that of all other microbial communities associated with [...]

The mammalian intestine harbors a beneficial microbiota numbering approximately [10.sup.12] organisms per gram of colonic content. The host tolerates this tremendous bacterial load while maintaining the ability to efficiently respond to pathogenic organisms. In this study, we show that the Bacteroides use a mammalian-like pathway to decorate numerous surface capsular polysaccharides and glycoproteins with L-fucose, an abundant surface molecule of intestinal epithelial cells, resulting in the coordinated expression of this surface molecule by host and symbiont. A Bacteroides mutant deficient in the ability to cover its surface with L-fucose is defective in colonizing the mammalian intestine under competitive conditions., The ability of humans to tolerate a complex gut microbiota despite their exquisite ability to distinguish self from nonself has been called an 'immunological paradox' (1). One mechanism that may [...]

Bacteria are often highly polarized, exhibiting specialized structures at or near the ends of the cell. Among such structures are actin-organizing centers, which mediate the movement of certain pathogenic bacteria within the cytoplasm of an animal host cell; organized arrays of membrane receptors, which govern chemosensory behavior in swimming bacteria; and asymmetrically positioned septa, which generate specialized progeny in differentiating bacteria. This polarization is orchestrated by complex and dynamic changes in the subcellular localization of signal transduction and cytoskeleton proteins as welt as of specific regions of the chromosome. Recent work has provided information on how dynamic subcellular localization occurs and how it is exploited by the bacterial cell, The main task of a bacterial cell is to survive and duplicate itself. The bacterium must replicate its genetic material and divide at the correct site in the cell and [...]

A metalocofactor containing iron, sulfur, copper, and nickel has been discovered in the enzyme carbon monoxide dehydrogenase/acetyl-CoA (coenzyme A) synthase from Moorella thermoacetica (f. Clostridium thermoaceticum). Our structure at 2.2 angstrom resolution reveals that the cofactor responsible for the assembly of acetyl-CoA contains a [[Fe.sub.4][S.sub.4]] cubane bridged to a copper-nickel binuclear site. The presence of these three metals together in one cluster was unanticipated and suggests a newly discovered role for copper in biology. The different active sites of this bifunctional enzyme comp[ex are connected via a channel, 138 angstroms long, that provides a conduit for carbon monoxide generated at the C-cluster on one subunit to be incorporated into acetyl-CoA at the A-duster on the other subunit., Acetogenic bacteria such as Moorella thermoacetica (f. Clostridium thermoaceticum) can grow autotrophically on the greenhouse gas C[O.sub.2]. These organisms use the Wood-Ljungdahl carbon fixation pathway to convert C[O.sub.2] to acetyl-CoA [...]

Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts., The availability of genome sequences for related bacteria is providing exciting insights into evolution, but one limitation has been the lack of identifiable bacterial fossils to provide a time flame [...]

Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have clone this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments., Life and Earth have coevolved since their beginning. So intimate has this relation been that if one seeks to discover a part of Earth that has not been fundamentally affected [...]

Most microorganisms are motile during at least part of their life cycle, because they need to find optimal conditions in a patchy world. The sheer volume of microorganisms in the biosphere means that their motile sensory behavior also contributes to the global transformation and cycling of matter. How microorganisms move and how they orient themselves using environmental cues are integral to understanding the complex structure and function of microbial communities, but although motility in response to external stimuli was first described more than 120 years ago, understanding of the cellular and molecular mechanisms involved has only been achieved more recently., All motile species of microorganism respond to different kinds of chemical stimuli. Many also respond to light intensity and to mechanical stimuli, and a few even orient themselves in magnetic [...]

The pack ice of Earth's polar oceans appears to be frozen white desert, devoid of life. However, beneath the snow lies a unique habitat for a group of bacteria and microscopic plants and animals that are encased in an ice matrix at low temperatures and light levels, with the only liquid being pockets of concentrated brines. Survival in these conditions requires a complex suite of physiological and metabolic adaptations, but sea-ice organisms thrive in the ice, and their prolific growth ensures they play a fundamental role in polar ecosystems. Apart from their ecological importance, the bacterial and algae species found in sea ice have become the focus for novel biotechnology, as well as being considered proxies for possible life forms on ice-covered extraterrestrial bodies., Sea ice is an ephemeral feature of polar regions, but also of the Baltic, Caspian, and Okhotsk Seas. At its maximum, it covers 13% of the Earth's surface area (1), [...]

A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus., Microorganisms have been isolated from various types of ancient materials, including salt crystals, deep earth cores, and fossilized animals and plants (1, 2). All such claims of ancient origin have [...]

The ability of a regulatory protein to sense the integrity of the bacterial flagellar structure was investigated. in response to a defective hook-basal body complex, the anti-σ[28] FlgM protein inhibits [...]

The bacterium Caulobacter crescentus yields two different progeny at each cell division; a chemotactically competent swarmer cell and a sessile stalked cell. The chemotaxis Proteins are synthesized in the predivisional cell and then partition only to the swarmer cell upon division. The chemoreceptors that were newly synthesized were located at the nascent swarmer pole of the predivisional cell, an indication that asymmetry was established prior to cell division. When the swarmer cell differentiated into a stalked cell, the chemoreceptor was specifically degraded by virtue of an amino acid sequence located at its carboxyl terminus. Thus, a temporally and spatially restricted proteolytic event was a component af this differentiation process., Cell divisions that yield two different progeny cells are fundamental to developmental programs in all organisms[1]. In Caulobacter crescentus, the generation of two distinct cell types at each cell division [...]

The gastric pathogen Helicobacter pylori is known to be able to use molecular hydrogen as a respiratory substrate when grown in the laboratory. We found that hydrogen is available in the gastric mucosa of mice and that its use greatly increased the stomach colonization by H. pylori. Hydrogenase activity in H. pylori is constitutive but increased fivefold upon incubation with hydrogen. Hydrogen concentrations measured in the stomachs of live mice were found to be 10 to 50 times as high as the H. pylori affinity for hydrogen. A hydrogenase mutant strain is much less efficient in its colonization of mice. Therefore, hydrogen present in animals as a consequence of normal colonic flora is an energy-yielding substrate that can facilitate the maintenance of a pathogenic bacterium., The bacterial oxidation of molecular [H.sub.2] commonly occurs in nature, as hydrogen gas released by other bacteria represents a useable high-energy reductant (1). Once [H.sub.2] is bound and 'split' by [...]

Most models of speciation require gradual change and geographic or ecological isolation for new species to arise. Homoploid hybrid speciation occurred readily between Saccharomyces cerevisiae and Saccharomyces paradoxus. Hybrids had high self-fertility (about 82%), low fertility when backcrossed to either parental species (about 7.5%), and vigorous growth under different thermal environments that favored one or the other of the parental species. Extensive karyotypic changes (tetrasomy) were observed in the hybrids, although genic incompatibilities accounted for 50% of the variation in self-fertility., Speciation is thought to arise by gradual evolution of genic incompatibilities (1), ecological specialization (2, 3), or chromosomal differences (4) that prevent mating or cause inviable or infertile hybrid offspring [...]

Microbial life may seem infinitely adaptable and durable, but microbiologists and geologists probing the most voluminous part of the biosphere--the deep subsurface--are finding it slow going., Life is a hardy sort. In recent years, microbes have been reported in the most unlikely nooks and crannies of the planet living under incredible conditions: in mine drainage with [...]

We observed physiological and metabolic activity of Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at pressures of 68 to 1680 megapascals (MPa) in diamond anvil cells. We measured biological formate oxidation at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system., Microbial communities adapt to a wide range of pressures, temperatures, salinities, pH, and oxidation states. Although the chemical and physical conditions in these extreme environments are reasonably well constrained, the [...]

SpoIIIE mediates postseptational chromosome partitioning in Bacillus subtilis, but the mechanism controlling the direction of DNA transfer remains obscure. Here, we demonstrated that SpoIIIE acts as a DNA exporter: When SpoIIIE was synthesized in the larger of the two cells necessary for sporulation, the mother cell, DNA was translocated into the smaller forespore; however, when it was synthesized in the forespore, DNA was translocated into the mother cell. Furthermore, the DNA-tracking domain of SpoIIIE inhibited SpoIIIE complex assembly in the forespore. Thus, during sporulation, chromosome partitioning is controlled by the preferential assembly of SpoIIIE in one daughter cell., The spore formation pathway of Bacillus subtills provides a valuable system for studying how bacterial cells establish the cellular polarity necessary for development (1, 2). Early in sporulation, a polar [...]

Supergene chalcocite enrichment during weathering is an economically vital natural process that may lead to severalfold increases in the copper content of sulfide deposits. A scanning electron microscope study of chalcocite ([Cu.sub.2]S) from major enriched copper deposits in northern Chile revealed myriad bacterioform bodies in original growth positions near replacement interfaces with remnant hypogene sulfide grains. These minute (0.03 to 0.2 micrometers) chalcocite bodies are interpreted as fossilized and metallized nannobacteria that promoted the fixation of mobilized copper ions. Bacterial activity may thus be a fundamental factor in supergene enrichment of copper deposits., Many of the world's major Cu deposits were formed by supergene enrichment during weathering. Enrichment took place at and beneath the ground-water table under reducing conditions and involved the progressive [...]

Soon after new oceanic crust forms at mid-ocean ridges, it begins to be corroded by seawater. This alteration of the crust is important because it affects the chemistry of the [...]

Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus., Rickettsia species live in different ecological niches inside different arthropod hosts (insects or ticks), in which most of them are transmitted vertically from the mother to the progeny (1). R. [...]

Most of the oceanic reservoir of dissolved organic matter (DOM) is of marine origin and is resistant to microbial oxidation, but little is known about the mechanisms of its formation. In a laboratory study, natural assemblages of marine bacteria rapidly (in [is less than] 48 hours) utilized labile compounds (glucose, glutamate) and produced refractory DOM that persisted for more than a year. Only 10 to 15% of the bacterially derived DOM was identified as hydrolyzab[e amino acids and sugars, a feature consistent with marine DOM. These results suggest that microbial processes alter the molecular structure of DOM, making it resistant to further degradation and thereby preserving fixed carbon in the ocean., DOM is the largest reservoir of fixed carbon in the ocean and is approximately equivalent to the reservoir of atmospheric [CO.sub.2]. The major bioelements (C, N, and P) in DOM [...]

The rapid rotation of a long helical filament called the flagellum propels bacteria such as Escherichia coli and Salmonella. The flagellum is composed of a reversible rotary motor comprising several [...]

Geologists have observed 0.1 micrometer coccoid particles (thought to reflect the presence of very small microorganisms, or'nanobacteria') in minerals and meteorites, and biologists have implicated nanobacteria as nucleators in the [...]

Pseudomonas aeruginosa causes severe infections, particularly of the lung, that are life threatening. Here, we show that P. aeruginosa infection induces apoptosis of lung epithelial cells by activation of the endogenous CD95/CD95 ligand system. Deficiency of CD95 or CD95 ligand on epithelial cells prevented apoptosis of lung epithelial cells in vivo as well as in vitro. The importance of CD95/CD95 ligand-mediated lung epithelial cell apoptosis was demonstrated by the rapid development of sepsis in CD95- or CD95 ligand--deficient mice, but not in normal mice, after P. aeruginosa infection., Several pathogens, including some bacteria, viruses, and parasites, are able to trigger apoptosis of mammalian host cells (1, 2). A paradigm for bacteria-induced apoptosis is Shigella fiexneri, which, upon invasion, [...]

BLOOMINGTON, INDIANA--Talks at Evolution 2000, held here in late June, covered the gamut of evolutionary biology, from life history changes in bacteria to the origins of modern bird diversity. Stalked [...]

The Precambrian fossil record extends back to about 3.5 billion years ago, and chemical evidence for the possible appearance of life extends several hundred million years earlier. Determining the evolution [...]

The decoding of genetic information into protein sequence relies upon the interaction of messenger RNA (mRNA), which contains information in the form of a string of three-nucleotide codons, and transfer [...]

Understanding biology at the single-cell level requires simultaneous measurements of biochemical parameters and behavioral characteristics in individual cells. Here, the output of individual flagellar motors in Escherichia coli was measured as a function of the intracellular concentration of the chemotactic signaling protein. The concentration of this molecule, fused to green fluorescent protein, was monitored with fluorescence correlation spectroscopy. Motors from different bacteria exhibited an identical steep input-output relation, suggesting that they actively contribute to signal amplification in chemotaxis. This experimental approach can be extended to quantitative in vivo studies of other biochemical networks., Biochemical networks have been the object of intensive experimental and theoretical studies. The understanding of their functioning relies mainly on data collected from populations rather than from single cells (1). [...]

CHANTILLY, VIRGINIA--A team of human sequencers using high-powered computers has just finished assembling the entire genetic sequence of the common bacterium Caulobacter crescentus. The feat, announced at a meeting(*) on [...]

The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284,156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell, Deinococcus radiodurans is a Gram-positive, red-pigmented, nonmotile bacterium that was originally identified as a contaminant of irradiated canned meat (1). It has been isolated worldwide from locations rich in organic [...]

By running experiments on microbes for thousands of generations, researchers are exploring the roles of chance and history in evolution For most living things, 24,000 generations is a daunting span [...]

Filamentous phage f1 exits its Escherichia coil host without killing the bacterial cell. It has been proposed that f1 is secreted through the outer membrane via a phage-encoded channel protein, pIV. A functional pIV mutant was isolated that allowed E. coil to grow on large maltodextrins and rendered E. coil sensitive to large hydrophilic antibiotics that normally do not penetrate the outer membrane. In planar lipid bilayers, both mutant and wild-type pIV formed highly conductive channels with similar permeability characteristics but different gating properties: the probability of the wild-type channel being open was much less than that of the mutant channel. The high conductivity of pIV channels suggests a large-diameter pore, thus implicating ply as the outer membrane phage-conducting channel., The pIV protein is one of three filamentous phage proteins that are not part of the fl virion but are required for phage export from the host bacterium. Interest in [...]

Although bacteria are often thought of as harmful, it is now recognized that the many bacteria species harbored by our intestines are essential for our well-being. Aside from their roles [...]