Special issue ‘bifidobacteria: Insights from ecology to genomics of a key microbial group of the mammalian gut microbiota’

In recent years, substantial efforts have been made to dissect the composition of microbial communities that are present in the human gut, and to investigate their interactions with their host [...]

XMM-Newton and INTEGRAL observations of the black hole candidate XTE J1817-330

The galactic black hole candidate XTE J1817-330 was discovered in outburst by RXTE in January 2006. We present here the results of an XMM-Newton Target of opportunity observation (TOO), performed on 13 March 2006 (44 days after the maximum), and an INTEGRAL observation performed on 15-18 February 2006 (18 days after the maximum). The EPIC-pn camera on-board XMM-Newton was used in the fast read-out Burst mode to avoid photon pile-up, while the RGSs were used in Spectroscopy high count-rate mode. We fit both the XMM-Newton and the INTEGRAL spectra with a two-component model consisting of a thermal accretion disk and a comptonizing hot corona. The soft X-ray spectrum is dominated by an accretion disk component, with a maximum temperature decreasing from 0.96+/-0.04 keV at the time of the INTEGRAL observation to 0.70+/-m0.01 keV on 13 March. The Optical Monitors on board INTEGRAL and XMM-Newton showed the source with magnitudes V: 11.3-11.4, U:15.0-15.1 and UVW1:14.7-14.8. The soft X-ray spectrum, together with the optical and UV data, show a low hydrogen column density towards the source, and several absorption lines, most likely of interstellar origin, are detected in the RGS spectrum: OI K-alpha, OI K-beta, OII, OIII and OVII, which trace both cold and hot components of the ISM. The soft X-ray spectrum indicates the presence of a black hole, with an estimate for the upper limit of the mass of 6.0(+4.0/-2.5) Msun.Comment: Accepted for publication in A&

Riboflavin Biosynthesis and Overproduction by a Derivative of the Human Gut Commensal Bifidobacterium longum subsp. infantis ATCC 15697

Riboflavin or vitamin B2 is the precursor of the essential coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Despite increased interest in microbial synthesis of this water-soluble vitamin, the metabolic pathway for riboflavin biosynthesis has been characterized in just a handful of bacteria. Here, comparative genome analysis identified the genes involved in the de novo biosynthetic pathway of riboflavin in certain bifidobacterial species, including the human gut commensal Bifidobacterium longum subsp. infantis (B. infantis) ATCC 15697. Using comparative genomics and phylogenomic analysis, we investigated the evolutionary acquisition route of the riboflavin biosynthesis or rib gene cluster in Bifidobacterium and the distribution of riboflavin biosynthesis-associated genes across the genus. Using B. infantis ATCC 15697 as model organism for this pathway, we isolated spontaneous riboflavin overproducers, which had lost transcriptional regulation of the genes required for riboflavin biosynthesis. Among them, one mutant was shown to allow riboflavin release into the medium to a concentration of 60.8 ng mL–1. This mutant increased vitamin B2 concentration in a fecal fermentation system, thus providing promising data for application of this isolate as a functional food ingredient

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

INTEGRAL observations of the blazar Mrk 421 in outburst (Results of a multi-wavelength campaign)

We report the results of a multi-wavelength campaign on the blazar Mrk 421 during outburst. We observed four strong flares at X-ray energies that were not seen at other wavelengths (partially because of missing data). From the fastest rise in the X-rays, an upper limit could be derived on the extension of the emission region. A time lag between high-energy and low-energy X-rays was observed, which allowed an estimation of the magnetic-field strength. The spectral analysis of the X-rays revealed a slight spectral hardening of the low-energy (3 - 43 keV) spectral index. The hardness-ratio analysis of the Swift-XRT (0.2 - 10 keV) data indicated a small correlation with the intensity; i. e., a hard-to-soft evolution was observed. At the energies of IBIS/ISGRI (20 - 150 keV), such correlations are less obvious. A multiwavelength spectrum was composed and the X-ray and bolometric luminosities are calculated.Comment: 15 pages, 18 figures; accepted by Astronomy & Astrophysic

Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure

In the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment

BL Lacertae objects beyond redshift 1.3 - UV-to-NIR photometry and photometric redshift for Fermi/LAT blazars

Observations of the gamma-ray sky with Fermi led to significant advances towards understanding blazars, the most extreme class of Active Galactic Nuclei. A large fraction of the population detected by Fermi is formed by BL Lacertae (BL Lac) objects, whose sample has always suffered from a severe redshift incompleteness due to the quasi-featureless optical spectra. Our goal is to provide a significant increase of the number of confirmed high-redshift BL Lac objects contained in the 2 LAC Fermi/LAT catalog. For 103 Fermi/LAT blazars, photometric redshifts using spectral energy distribution fitting have been obtained. The photometry includes 13 broad-band filters from the far ultraviolet to the near-IR observed with Swift/UVOT and the multi-channel imager GROND at the MPG/ESO 2.2m telescope. Data have been taken quasi-simultaneously and the remaining source-intrinsic variability has been corrected for. We release the UV-to-near-IR 13-band photometry for all 103 sources and provide redshift constraints for 75 sources without previously known redshift. Out of those, eight have reliable photometric redshifts at z>1.3, while for the other 67 sources we provide upper limits. Six of the former eight are BL Lac objects, which quadruples the sample of confirmed high-redshift BL Lac. This includes three sources with redshifts higher than the previous record for BL Lac, including CRATES J0402-2615 with the best-fit solution at z~1.9.Comment: Uploaded correct Fig 4. Changed counterpart name for 2FGLJ0537.7-5716 from PKS 0541-834 (different source) to SUMSS J053748-57182

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution