Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena.

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus Flavobacterium. In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of Flavobacterium caeni and Flavobacterium terrigena, with 16S rRNA gene sequence similarity values of 94.9% and 96.2%, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15:1 G (14.4%), iso-C16:0 (13.2%), C15:0 (12.9%), iso-C15:0 (12.9%) and iso-C17:0 3-OH (11.5%). Those of strain YIT 12746T were iso-C15:0 (21.5%), iso-C16:0 (13.3%), C15:0 (12.0%) and iso-C15:1 G (11.9%). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium, for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T=JCM 19141T=DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T=JCM 19142T=DSM 27078T) are proposed. Emended descriptions of Flavobacterium caeni and Flavobacterium terrigena are also proposed.

Comparison of Bifidobacterium breve strain Yakult transcriptomes in germ-free mice with those in fecal cultures.

Bifidobacteria are beneficial to human health, but the mechanism remains unknown. We employed oligonucleotide microarrays to identify the Bifidobacterium breve strain Yakult (BbrY) genes up-regulated specifically in mouse intestine. Based on BbrY transcriptional responses in germ-free mice and in fecal cultures, k-means clustering picked up 93 genes that were up-regulated in the mouse intestine and thereafter Venn analysis to exclude genes that were up-regulated in both the mouse intestine and the fecal culture classified 45 genes as up-regulated specifically in the mouse intestine. Most of those genes are involved in sugar transport or sugar liberation, although the functions of several genes are unknown. Most of these genes are clustered on the BbrY genome and appear to be organized into operons. Expressions of several genes were further investigated by real time PCR, revealing that their expression profiles were identical in the mouse cecum and colon. The up-regulation of genes involved in sugar liberalization and uptake suggests that BbrY could possibly maintain energy homeostasis inside the mouse intestine, which contains low quantities of readily fermentable sugars.