Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal

The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L . salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health

Draft genome sequence of Lactobacillus crispatus EM-LC1, an isolate with antimicrobial activity cultured from an elderly subject

Here we report the 1.86-Mb draft genome sequence of Lactobacillus crispatus EM-LC1, a fecal isolate with antimicrobial activity. This genome sequence is expected to provide insights into the antimicrobial activity of L. crispatus and improve our knowledge of its potential probiotic traits

Magnetic White Dwarfs from the SDSS II. The Second and Third Data Releases

Fifty-two magnetic white dwarfs have been identified in spectroscopic observations from the Sloan Digital Sky Survey (SDSS) obtained between mid-2002 and the end of 2004, including Data Releases 2 and 3. Though not as numerous nor as diverse as the discoveries from the first Data Release, the collection exhibits polar field strengths ranging from 1.5MG to ~1000MG, and includes two new unusual atomic DQA examples, a molecular DQ, and five stars that show hydrogen in fields above 500MG. The highest-field example, SDSSJ2346+3853, may be the most strongly magnetic white dwarf yet discovered. Analysis of the photometric data indicates that the magnetic sample spans the same temperature range as for nonmagnetic white dwarfs from the SDSS, and support is found for previous claims that magnetic white dwarfs tend to have larger masses than their nonmagnetic counterparts. A glaring exception to this trend is the apparently low-gravity object SDSSJ0933+1022, which may have a history involving a close binary companion.Comment: 20 pages, 4 figures Accepted for publication in the Astronomical Journa

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

BACKGROUND: A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, “Candidatus Methanomethylophilus alvus", “Candidatus Methanomassiliicoccus intestinalis” and Methanomassiliicoccus luminyensis. RESULTS: Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, “Ca. M. alvus” and “Ca. M. intestinalis” do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS: This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmat

Cataclysmic Variables from SDSS II. The Second Year

The first full year of operation following the commissioning year of the Sloan Digital Sky Survey has revealed a wide variety of newly discovered cataclysmic variables. We show the SDSS spectra of forty-two cataclysmic variables observed in 2002, of which thirty-five are new classifications, four are known dwarf novae (CT Hya, RZ Leo, T Leo and BZ UMa), one is a known CV identified from a previous quasar survey (Aqr1) and two are known ROSAT or FIRST discovered CVs (RX J09445+0357, FIRST J102347.6+003841). The SDSS positions, colors and spectra of all forty-two systems are presented. In addition, the results of follow-up studies of several of these objects identify the orbital periods, velocity curves and polarization that provide the system geometry and accretion properties. While most of the SDSS discovered systems are faint (>18th mag) with low accretion rates (as implied from their spectral characteristics), there are also a few bright objects which may have escaped previous surveys due to changes in the mass transfer rate.Comment: Accepted for publication in The Astronomical Journal, Vol. 126, Sep. 2003, 44 pages, 25 figures (now with adjacent captions), AASTeX v5.

Trigonometric Parallaxes for Two Late-Type Subdwarfs: LSR1425+71 (sdM8.0) and the Binary LSR1610-00 (sd?M6pec)

Trigonometric parallax astrometry and BVI photometry are presented for two late-type subdwarf candidates, LSR1425+71 (sdM8.0) and LSR1610-00 (sd?M6pec). For the former we measure an absolute parallax of 13.37+/-0.51 mas yielding Mv=15.25+/-0.09. The astrometry for LSR1610-00 shows that this object is an astrometric binary with a period of 1.66+/-0.01 yr. The photocentric orbit is derived from the data; it has a moderate eccentricity (e ~ 0.44+/-0.02) and a semi-major axis of 0.28+/-0.01 AU based on our measured absolute parallax of 31.02+/-0.26 mas. Our radial velocity measure of -108.1+/-1.6 km/s for LSR1610-00 at epoch 2006.179, when coupled with the observation of -95+/-1 km/s at epoch 2005.167 by Reiners & Basri, indicates a systemic radial velocity of -101+/-1 km/s for the LSR1610-00AB pair. The galactic velocity components for LSR1425+71 and LSR1610-00AB -- (U,V,W)=(84+/-6, -202+/-13, 66+/-14) km/s and (U,V,W)=(36+/-2, -232+/-2, -61+/-2) km/s, respectively. For both stars, the velocities are characteristic of halo population kinematics. However, modeling shows that both stars have orbits around the galaxy with high eccentricity that pass remarkably close to the galactic center. LSR1425+71 has a luminosity and colors consistent with its metal-poor subdwarf spectral classification, while LSR1610-00 has a luminosity and most colors indicative of being only mildly metal-poor, plus a uniquely red B-V color. The companion to LSR1610-00 must be a low-mass, substellar brown dwarf. We speculate on the paradoxical nature of LSR1610-00 and possible sources of its peculiarities.Comment: Accepted for ApJ. 37 pages, including 8 figure

Two Rare Magnetic Cataclysmic Variables with Extreme Cyclotron Features Identified in the Sloan Digital Sky Survey

Two newly identified magnetic cataclysmic variables discovered in the Sloan Digital Sky Survey (SDSS), SDSSJ155331.12+551614.5 and SDSSJ132411.57+032050.5, have spectra showing highly prominent, narrow, strongly polarized cyclotron humps with amplitudes that vary on orbital periods of 4.39 and 2.6 hrs, respectively. In the former, the spacing of the humps indicates the 3rd and 4th harmonics in a magnetic field of ~60 MG. The narrowness of the cyclotron features and the lack of strong emission lines imply very low temperature plasmas and very low accretion rates, so that the accreting area is heated by particle collisions rather than accretion shocks. The detection of rare systems like these exemplifies the ability of the SDSS to find the lowest accretion rate close binaries.Comment: Accepted for publication in the Astrophysical Journal, vol. 583, February 1, 2003; slight revisions and additions in response to referee's comments; 17 pages, 6 figures, AASTeX v4.

Faint High Latitude Carbon Stars Discovered by the Sloan Digital Sky Survey: Methods and Initial Results

We report the discovery of 39 Faint High Latitude Carbon Stars (FHLCs) from Sloan Digital Sky Survey commissioning data. The objects, each selected photometrically and verified spectroscopically, range over 16.6 < r* < 20.0, and show a diversity of temperatures as judged by both colors and NaD line strengths. At the completion of the Sloan Survey, there will be many hundred homogeneously selected and observed FHLCs in this sample. We present proper motion measures for each object, indicating that the sample is a mixture of extremely distant (>100 kpc) halo giant stars, useful for constraining halo dynamics, plus members of the recently-recognized exotic class of very nearby dwarf carbon (dC) stars. Motions, and thus dC classification, are inferred for 40-50 percent of the sample, depending on the level of statistical significance invoked. The new list of dC stars presented here, although selected from only a small fraction of the final SDSS, doubles the number of such objects found by all previous methods. (Abstract abridged).Comment: Accepted for publication in The Astronomical Journal, Vol. 124, Sep. 2002, 40 pages, 7 figures, AASTeX v5.

Optically identified BL Lacertae objects from the Sloan Digital Sky Survey

We present a sample of 386 BL Lacertae (BL Lac) candidates identified from 2860 deg^2 of the Sloan Digital Sky Survey (SDSS) spectroscopic database. The candidates are primarily selected to have quasi-featureless optical spectra and low proper motions as measured from SDSS and USNO-B positions; however, our ability to separate Galactic from extragalactic quasi-featureless objects (QFOs) on the basis of proper motion alone is limited by the lack of reliable proper motion measurements for faint objects. Fortunately, high proper motion QFOs, mostly DC white dwarfs, populate a well defined region of color space, approximately corresponding to blackbodies with temperatures in the range 7000-12000 K. QFOs with measurable redshifts or X-ray or radio counterparts (i.e., evidence of an extragalactic/AGN nature) loosely follow a track in color space that corresponds to power-law continua plus host galaxy starlight, with typical power-law slopes in the range 1<alpha_{opt}<2 (f_{nu} propto nu^{-alpha}). Based largely on this remarkably clean color separation, we subdivide the sample into 240 probable candidates and 146 additional less probable (likely stellar) candidates. The probable BL Lac candidates have multi-wavelength properties consistent with the range of previously known BL Lacs, with an apparent preponderance of objects with synchrotron peaks at relatively high energies (HBL/ XBL-type). The majority of the 154 objects with measurable redshifts have z<1, with a median of 0.45; there are also a handful of high-redshift objects extending up to z=5.03. We identify a small number of potential radio-quiet BL Lac candidates, although more sensitive radio observations are needed to confirm their radio-quiet nature.Comment: 42 pages, 11 figures (4 in color), uses aastex.cls. To appear in the June 2005 edition of AJ. Full tables are temporarily available from http://www.astro.princeton.edu/~collinge/sdss_bllac/ and will be published electronically. Summary of changes: 1) improved SDSS/USNO-B proper motion treatment; 2) improved discussion of multiwavelength propertie

An Initial Survey of White Dwarfs in the Sloan Digital Sky Survey

An initial assessment is made of white dwarf and hot subdwarf stars observed in the Sloan Digital Sky Survey. In a small area of sky (190 square degrees), observed much like the full survey will be, 269 white dwarfs and 56 hot subdwarfs are identified spectroscopically where only 44 white dwarfs and 5 hot subdwarfs were known previously. Most are ordinary DA (hydrogen atmosphere) and DB (helium) types. In addition, in the full survey to date, a number of WDs have been found with uncommon spectral types. Among these are blue DQ stars displaying lines of atomic carbon; red DQ stars showing molecular bands of C_2 with a wide variety of strengths; DZ stars where Ca and occasionally Mg, Na, and/or Fe lines are detected; and magnetic WDs with a wide range of magnetic field strengths in DA, DB, DQ, and (probably) DZ spectral types. Photometry alone allows identification of stars hotter than 12000 K, and the density of these stars for 15<g<20 is found to be ~2.2 deg^{-2} at Galactic latitudes 29-62 deg. Spectra are obtained for roughly half of these hot stars. The spectra show that, for 15<g<17, 40% of hot stars are WDs and the fraction of WDs rises to ~90% at g=20. The remainder are hot sdB and sdO stars.Comment: Accepted for AJ; 43 pages, including 12 figures and 5 table