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Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.bulgaricus) is one of the economically most important representatives of the heterogeneous group of lactic acid bacteria, with a worldwide application in yogurt production. Yogurt has long been recognized as a nutritious, natural, and safe component of a healthy diet and is at the basis of the concept of probiotics (1, 2). A well documented health benefit of the consumption of yogurt containing live L. bulgaricus and Streptococcus thermophilus is an attenuation of lactose intolerance (3). In addition, immune modulation and diarrhea-alleviating effects have been reported (4), and both L. bulgaricus and S. thermophilus have been implicated in these effects (3,5). During yogurt fermentations protocooperation between these two bacteria results in an accelerated acidification, but the mechanisms involved are not completely understood (6).Among the lactic acid bacteria, L. bulgaricus belongs to the acidophilus complex, a group of lactobacilli related to Lactobacillus acidophilus, Lactobacillus johnsonii, and Lactobacillus gasseri, which have been used as probiotic cultures. Although within this group L. bulgaricus is considered unique because of its atypical GC content, until recently the lack of tools for genetic manipulation has severely hampered a more detailed analysis of this organism (7, 8, † †).Here we present the genome sequence of L. bulgaricus strain ATCC11842, originally isolated from bulgarian yogurt by S. OrlaJensen in 1919 (unpublished work). The analysis of this genome and comparison to other members of the acidophilus complex and S. thermophilus (9) have contributed to a more complete understanding of its p...

We report here the complete genome sequence of the virulent strain JIP02/86 (ATCC 49511) of Flavobacterium psychrophilum, a widely distributed pathogen of wild and cultured salmonid fish. The genome consists of a 2,861,988-base pair (bp) circular chromosome with 2,432 predicted protein-coding genes. Among these predicted proteins, stress response mediators, gliding motility proteins, adhesins and many putative secreted proteases are probably involved in colonization, invasion and destruction of the host tissues. The genome sequence provides the basis for explaining the relationships of the pathogen to the host and opens new perspectives for the development of more efficient disease control strategies. It also allows for a better understanding of the physiology and evolution of a significant representative of the family Flavobacteriaceae, whose members are associated with an interesting diversity of lifestyles and habitats.

This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (biotopes and geographical places) of bacteria from PubMed abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.