Lysate of Probiotic Lactobacillus casei DN-114 001 Ameliorates Colitis by Strengthening the Gut Barrier Function and Changing the Gut Microenvironment

BACKGROUND: Probiotic bacteria can be used for the prevention and treatment of human inflammatory diseases including inflammatory bowel diseases (IBD). However, the nature of active components and exact mechanisms of this beneficial effects have not been fully elucidated. Our aim was to investigate if lysate of probiotic bacterium L. casei DN-114 001 (Lc) could decrease the severity of intestinal inflammation in a murine model of IBD. METHODOLOGY/PRINCIPAL FINDINGS: The preventive effect of oral administration of Lc significantly reduces the severity of acute dextran sulfate sodium (DSS) colitis in BALB/c but not in SCID mice. In order to analyze how this beneficial effect interferes with well-known phases of intestinal inflammation pathogenesis in vivo and in vitro, we evaluated intestinal permeability using the FITC-labeled dextran method and analysed tight junction proteins expression by immunofluorescence and PCR. We also measured CD4(+)FoxP3(+) regulatory T cells proportion by FACS analysis, microbiota composition by pyrosequencing, and local cytokine production by ELISA. Lc leads to a significant protection against increased intestinal permeability and barrier dysfunction shown by preserved ZO-1 expression. We found that the Lc treatment increases the numbers of CD4(+)FoxP3(+) regulatory T cells in mesenteric lymph nodes (MLN), decreases production of pro-inflammatory cytokines TNF-α and IFN-γ, and anti-inflammatory IL-10 in Peyer's patches and large intestine, and changes the gut microbiota composition. Moreover, Lc treatment prevents lipopolysaccharide-induced TNF-α expression in RAW 264.7 cell line by down-regulating the NF-κB signaling pathway. CONCLUSION/SIGNIFICANCE: Our study provided evidence that even non-living probiotic bacteria can prevent the development of severe forms of intestinal inflammation by strengthening the integrity of intestinal barrier and modulation of gut microenvironment

Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi

Formation of all metazoan bodies is controlled by a group of selector genes including homeobox genes, highly conserved across the entire animal kingdom. The homeobox genes from Pou and Six classes are key members of the regulation cascades determining development of sensory organs, nervous system, gonads and muscles. Besides using common bilaterian models, more attention has recently been targeted at the identification and characterization of these genes within the basal metazoan phyla. Cnidaria as a diploblastic sister group to bilateria with simple and yet specialized organs are suitable models for studies on the sensory organ origin and the associated role of homeobox genes. In this work, Pou and Six homeobox genes, together with a broad range of other sensory-specific transcription factors, were identified in the transcriptome of hydrozoan jellyfish Craspedacusta sowerbyi. Phylogenetic analyses of Pou and Six proteins revealed cnidarian-specific sequence motifs and contributed to the classification of individual factors. The majority of the Craspedacusta sowerbyi Pou and Six homeobox genes are predominantly expressed in statocysts, manubrium and nerve ring, the tissues with sensory and nervous activities. The described diversity and expression patterns of Pou and Six factors in hydrozoan jellyfish highlight their evolutionarily conserved functions. This study extends the knowledge of the cnidarian genome complexity and shows that the transcriptome of hydrozoan jellyfish is generally rich in homeodomain transcription factors employed in the regulation of sensory and nervous functions

Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes

Complete Genome Sequence of the Haloaromatic Acid-Degrading Bacterium Achromobacter xylosoxidans A8 ▿

Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated biphenyls. It can use 2-chlorobenzoate and 2,5-dichlorobenzoate as sole sources of carbon and energy. This property makes it a good starting microorganism for further development toward a bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb chromosome and two large plasmids (98 kb and 248 kb). Besides genes for the utilization of xenobiotic organic substrates, it contains genes associated with pathogenesis, toxin production, and resistance. Here, we report the complete genome sequence

speciation through asexuality in fish: postzygotic reproductive isolation may be completed in spite of fertility of hybrids

Speciation process often occurs in the face of hybridisation between forming species. Hybrid genomic constitution of many clonal organisms including fish, amphibians and reptiles also indicates tight linkage between hybridization, clonality and malfunction of sex in hybrids. To address the causal links between these phenomena, we investigated the evolution of asexuality and postzygotic reproductive isolation mechanisms (postRIMs) in the Cobitis loaches, which involves three sister species (C. taenia, C. pontica and C. tanaitica) and their distant relative, C. elongatoides. Interspecific crossings revealed that initiation of asexuality is causally linked to hybridization but does not require involvement of any particular genome. Rather, it depends on genetic distance between hybridizing parental taxa: crossings of distantly related elongatoides-taenia pair produced sterile males and fertile clonal females, while crossings of closely related species, C. pontica and C. taenia, produced fertile sexually reproducing hybrids of both sexes, with only rarely occurring clonal biotypes. Previous study of elongatoides-taenia hybrid zone together with current population genetic analysis of elongatoides-tanaitica hybrid zone demonstrated the completion of speciation: no BC or F2 hybrids have been revealed and inferred F1 hybrids were clonal. However, phylogenomic analysis revealed that gene flow between these species has been quite intensive in the past, leading to massive historical introgressions. Altogether, it appears that initiation of hybrid asexuality and the completion of speciation process through formation of postRIMs are interconnected phenomena. Both processes are linked to the genetic divergence of hybridizing taxa: initially, hybridization between little diverged species leads to recombinant and fertile hybrids allowing intensive gene flow. As the hybridizing taxa continue to diverge, clonally reproducing hybrid females and sterile males become dominant and the gene flow ceases. The speciation may therefore be completed through asexuality of hybrids The work was supported by grant no. 13-12580S provided by the Czech Science Foundation (www.gacr.cz). Further support was provided by the Academy of Sciences of the Czech Republic (www.cas.cz) by the grant no. RVO 6798590

Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.

Bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. In order to avoid biases of culture-based approaches, stable isotope probing was applied in combination with sequence analysis of 16 S rRNA gene pyrotags amplified from (13)C-enriched DNA fractions. Special attention was paid to pyrosequencing data analysis in order to eliminate the errors caused by either generation of amplicons (random errors caused by DNA polymerase, formation of chimeric sequences) or sequencing itself. Therefore, sample DNA was amplified, sequenced, and analyzed along with the DNA of a mock community constructed out of 8 bacterial strains. This warranted that appropriate tools and parameters were chosen for sequence data processing. (13)C-labeled metagenomes isolated after the incubation of soil samples with all three studied aromatics were largely dominated by Proteobacteria, namely sequences clustering with the genera Rhodanobacter Burkholderia, Pandoraea, Dyella as well as some Rudaea- and Skermanella-related ones. Pseudomonads were mostly labeled by (13)C from naphthalene and benzoate. The results of this study show that many biphenyl/benzoate-assimilating bacteria derive carbon also from naphthalene, pointing out broader biodegradation abilities of some soil microbiota. The results also demonstrate that, in addition to traditionally isolated genera of degradative bacteria, yet-to-be cultured bacteria are important players in bioremediation. Overall, the study contributes to our understanding of biodegradation processes in contaminated soil. At the same time our results show the importance of sequencing and analyzing a mock community in order to more correctly process and analyze sequence data

Comparison of phylogenetic trees of HD (A) and SD (B) regions of Six class transcription factors.

<p>The phylogenetic trees were calculated by the maximum likelihood method (WAG protein substitution model, bootstrap 1000) and processed by NJ Plot software. Phylogenetically representative sequences from the following metazoan animals were selected for comparison: sponges (<i>Chalinula loosanoffi, Ephydatia fluviatilis, Sycon calcaravis</i>), cnidarians (<i>Nematostella vectensis</i>, <i>Anthopleura japonica</i>, <i>Podocoryne carnea</i>, <i>Hydra magnipapillata</i>, <i>Cladonema radiatum</i>, <i>Aurelia aurita</i>), invertebrates (<i>Saccoglossus kowalevskii</i>, <i>Drosophila melanogaster</i>, <i>Branchistoma floridae</i>) and vertebrates (<i>Danio rerio</i> and <i>Homo sapiens</i>). For the list of ID numbers of reference sequences see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036420#pone.0036420.s011" target="_blank">Text S1</a>.</p

Oral treatment with Lc increases the number of CD4⁺FoxP3⁺ T_regs in MLNs.

<p>No significant changes were found in spleen or Peyer's patches. The plots shows the expression of CD4 <i>versus</i> FoxP3 on gated Th cells (CD3⁺CD8⁻), and the values within the plots represent the mean ± standard deviation of the total numbers of CD4⁺FoxP3⁺ T cells from one representative experiment out of three independent experiments (3–5 mice per group). One-way ANOVA with Dunnett's multiple comparison test was used to evaluate the significance of differences in numbers of CD3⁺CD8⁻CD4⁺FoxP3⁺ cells between DSS/Lc-treated groups and the DSS/PBS-treated (control) group (*P<0.05).</p