Effects of initial-state dynamics on collective flow within a coupled transport and viscous hydrodynamic approach

We evaluate the effects of preequilibrium dynamics on observables in ultrarelativistic heavy-ion collisions. We simulate the initial nonequilibrium phase within A MultiPhase Transport (AMPT) model, while the subsequent near-equilibrium evolution is modeled using (2+1)-dimensional relativistic viscous hydrodynamics. We match the two stages of evolution carefully by calculating the full energy-momentum tensor from AMPT and using it as input for the hydrodynamic evolution. We find that when the preequilibrium evolution is taken into account, final-state observables are insensitive to the switching time from AMPT to hydrodynamics. Unlike some earlier treatments of preequilibrium dynamics, we do not find the initial shear viscous tensor to be large. With a shear viscosity to entropy density ratio of $0.12$, our model describes quantitatively a large set of experimental data on Pb+Pb collisions at the Large Hadron Collider(LHC) over a wide range of centrality: differential anisotropic flow $v_n(p_T) ~(n=2-6)$, event-plane correlations, correlation between $v_2$ and $v_3$, and cumulant ratio $v_2\{4\}/v_2\{2\}$.Comment: 10 pages, v2: minor revisio

Data_Sheet_1_Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.docx

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.</p

Table_1_Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.XLSX

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.</p

Image_1_Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.PDF

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.</p

The genes and encoded products of <i>B. asteroides</i> PRL2011 predicted to be involved in respiration and oxygen damage.

<p>Panel a represents a circular genome atlas of <i>B. asteroides</i> PRL2011 (circle 1) with mapped orthologs (defined as reciprocal best FastA hits with more than 30% identity over at least 80% of both protein lengths) in seven publicly available <i>Bifidobacterium</i> genomes. From the outer circle, circle (2) shows <i>B. breve</i> UCC2003, circle (3) <i>B. animalis</i> subsp. <i>lactis</i> DSM 10140, circle (4) <i>B. longum</i> subsp. <i>infantis</i> ATCC 15697, circle (5) <i>B. dentium</i> Bd1, circle (6) <i>B. longum</i> NCC2705, circle (7) <i>B. bifidum</i> PRL2010, circle (8) <i>B. adolescentis</i> ATCC 15703. Circle(9) illustrates <i>B. asteroides</i> PRL2011 G+C% deviation followed by circle (10) that highlights <i>B. asteroides</i> PRL2011 GC skew (G−C/G+C). Moreover, the outer insets indicate the main genetic loci encoding enzymes involved in respiratory metabolism, which are mapped on the circular genome atlas of <i>B. asteroides</i> PRL2011. Panel b shows a schematic representation of a cell and metabolic pathways for respiration. The different ORFs of <i>B. asteroides</i> PRL2011 encoding the presumed enzymes involved in the respiratory chain are indicated.</p

Comparative genomic analysis of <i>B. asteroides</i> PRL2011 with other fully sequenced bifidobacterial genomes, as well as <i>Gardnella vaginalis</i>.

<p>Panel a displays a Venn diagram of homologs shared between sequenced bifidobacterial-<i>Gardnella</i> genomes. Panel b shows the percentage of amino acid identity of the top-scoring self-matches for protein-coding genes in the analysed bacteria using the predicted proteome of <i>B. asteroides</i> PRL2011 as a reference. For each bacterium, the deduced protein-coding regions for each gene were compared with those derived from the <i>B. asteroides</i> PRL2011 genome. Panel c depicts a phylogenetic supertree based on the sequences of <i>Bifidobacterium-Gardnella</i> core proteins. Panel d indicates the generated phylogenetic tree based on 16S rRNA gene sequences from the same set of bacteria. Three other members of the <i>Actinobacteria</i> phylum, <i>N. farcinia</i>, <i>T. whipplei</i> and <i>L. xyli</i>, were also included in the analyses depicted in panels c and d, while the trees were rooted using <i>L. salivarius</i> as outgroup.</p

Genomic diversity in the <i>B. asteroides</i> phylogenetic group with reference to the <i>B. asteroides</i> strain PRL2011 genome.

<p>Panel a shows the comparative genomic hybridization data obtained using different members of the <i>B. asteroides</i> species. Each horizontal row corresponds to a probe on the array, and genes are ordered vertically according to their position on the PRL2011 genome. The columns represent the analysed strains, and strains are indicated by their strain codes. The colour code corresponding to the presence/absence is given at the top right of the figure: the gradient goes from black to yellow to indicate the presence, divergence or absence of a gene sequence. The predicted function of particular genes is shown on the right-hand margin. Black typed descriptions relate to most significant DNA regions that are absent in the investigated strains. Red typed descriptions represent DNA regions that encode enzymes predicted to be involved in respiration in PRL2011. Panel b details the presence (black) or absence (yellow) of key genes predicted to be involved in respiration within the <i>B. asteroides</i> phylogenetic group as well as in other genome sequenced bifidobacteria based on genomic data.</p