First Complete Genome Sequence of a Probiotic Enterococcus faecium Strain T-110 and Its Comparative Genome Analysis with Pathogenic and Non-pathogenic Enterococcus faecium Genomes

Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.

Impact of long-term chemical fertilizer and organic amendment to Fusarium root rot of soybean

Soil suppressiveness to Fusarium root rot of soybean had been observed in a black soil field after a long-term fertilization with nitrogen(N)and phosphorus(P)fertilizer combined with pig manure as organic amendment(NPM),rather than that with only nitrogen and phosphorus fertilizer(NP)or no fertilizer(NF).To determine the microbial role on this suppressiveness,fungal and bacterial community characteristics in NPM,NP and NF treatments were investigated by q PCR and DGGE.Compared with the similar bacterial community characteristics among 3 treatments,fungal community,especially Fusarium population size and community composition in NPM treatment were different with those of NP and NF groups.Based on the isolation and pathogenicity test,pathogenic F.oxysporum,F.graminearum,F.verticillioide and F.lateritium absolutely dominated Fusarium community in NF and NP groups.Nonpathogenic F.avenaceum,F.equiseti,F.culmorum,F.redolens,F.solani and F.tricinctum dominated Fusarium community in NPM group.Isolation rate of pathogenic Fusarium in NPM reduced from 100%to 38%in NF.These results suggested that the dominance of soil non-pathogenic Fusarium population induced by organic amendment might play an important role on suppressing Fusarium root rot in the tested field.

Multiple Chromosomes in Bacteria: Low Level of Evolutionary Constraint Drives the Rapid Genetic Divergence of Chromosome II

Multiple chromosomes in bacteria are designated as a larger primary chromosome (CI) and smaller accessory chromosomes (CII and CIII). Although previous studies examined multiple chromosomes in several bacterial species, the evolutionary mechanisms for the origin of CIIs still remain unclear. In this study, the four following hypotheses were tested. 1) CIIs exhibit lower sequence conservation and sequence divergence compared to their corresponding CIs across species of Proteobacteria. 2) The differential sequence divergence of CI and CII depends on pathogenic and non-pathogenic lifestyles. 3) CIIs harbor a higher level of horizontal gene transfers (HGTs) than CIs. 4) Orthologs located on CIIs experience less purifying selection than their corresponding orthologs on CIs. Results reveal a higher level of sequence conservation of CIs than the sequence conservation of CIIs. There is no significant difference in HGT estimates between CIs and CIIs. A majority of orthologous genes of CIs and CIIs experience purifying selection;however, genes on CIIs were significantly less constrained than the corresponding ones on CIs. This finding is true for both pathogenic and non-pathogenic bacteria, but the selective constraints for non-pathogenic bacteria are relatively less constrained. It was concluded that the differential selective constraint is a potent driving force for the rapid evolution of CII. Therefore, gene expression analysis at the transcriptome and proteome levels may shed light on the gene regulation mechanisms that might affect the sequence divergence between CI and CII.