Publications

genome-based taxonomic classification of bacteroidetes.	the bacterial phylum bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16s rrna gene sequence. here we use a large collection of type-strain genomes from bacteroidetes and closely related ...	2016	28066339
multiple conversion between the genes encoding bacterial class-i release factors.	bacteria require two class-i release factors, rf1 and rf2, that recognize stop codons and promote peptide release from the ribosome. rf1 and rf2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. this scenario expects that the two rf gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. however, we here report two independent cases of conversion b ...	2015	26257102
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.	the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...	2014	24931479
the genome of cardinium cbtq1 provides insights into genome reduction, symbiont motility, and its settlement in bemisia tabaci.	many insects harbor inherited bacterial endosymbionts. although some of them are not strictly essential and are considered facultative, they can be a key to host survival under specific environmental conditions, such as parasitoid attacks, climate changes, or insecticide pressures. the whitefly bemisia tabaci is at the top of the list of organisms inflicting agricultural damage and outbreaks, and changes in its distribution may be associated to global warming. in this work, we have sequenced and ...	2014	24723729
optimizing information in next-generation-sequencing (ngs) reads for improving de novo genome assembly.	next-generation-sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional sanger method. however, ngs reads are shorter than sanger reads, making de novo genome assembly very challenging. because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. to improve de novo genome ...	2013	23922726
draft genome sequence of cyclobacterium qasimii strain m12-11bt, isolated from arctic marine sediment.	a 6.29-mb genome sequence of cyclobacterium qasimii strain m12-11b(t), isolated from an arctic marine sediment sample, is reported.	2013	23950138
burkholderia bcpa mediates biofilm formation independently of interbacterial contact-dependent growth inhibition.	contact-dependent growth inhibition (cdi) is a phenomenon in which gram-negative bacteria use the toxic c-terminus of a large surface-exposed exoprotein to inhibit the growth of susceptible bacteria upon cell-cell contact. little is known about when and where bacteria express the genes encoding cdi system proteins and how these systems contribute to the survival of bacteria in their natural niche. here we establish that, in addition to mediating interbacterial competition, the burkholderia thail ...	2013	23879629
evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme.	isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii).	2013	24004839
a bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals.	bacterially-produced small molecules exert profound influences on animal health, morphogenesis, and evolution through poorly understood mechanisms. in one of the closest living relatives of animals, the choanoflagellate salpingoeca rosetta, we find that rosette colony development is induced by the prey bacterium algoriphagus machipongonensis and its close relatives in the bacteroidetes phylum. here we show that a rosette inducing factor (rif-1) produced by a. machipongonensis belongs to the smal ...	2012	23066504
novel sulfonolipid in the extremely halophilic bacterium salinibacter ruber.	salinibacter ruber is an extremely halophilic bacterium, phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria. electrospray mass analyses (negative ion) of the total lipid extract of a pure culture of s. ruber shows a characteristic peak at m/z 660 as the most prominent peak in the high-mass range of the spectrum. a novel sulfonolipid, giving rise to the molecular ion [m-h]- of m/z 660, has been identified. the sulfonolipid isolated and purified by thin-lay ...	2004	15528534
bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla.	a facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as flectobacillus sp. strain mwh38 (a member of the cytophaga-flavobacterium-bacteroides phylum) by comparative 16s rrna gene sequence analysis. filament formation by flectobacillus sp. strain mwh38 and filament formation by flectobacillus major, the closest known relative of strain mwh38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate ochromonas sp. strain d ...	1999	9872755
kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneity	marine bacterioplankton diversity was examined by quantifying natural length variation in the 5' domain of small-subunit (ssu) rrna genes (rdna) amplified by pcr from a dna sample from the oregon coast. this new technique, length heterogeneity analysis by pcr (lh-pcr), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. relationships between the sizes of amplicons and ...	1998	9797317
contributing carbohydrate catabolic pathways in cyclobacterium marinus.	the primary and secondary pathways of carbohydrate metabolism were determined in a nonfermentative gram-negative ring-forming marine bacterium, cyclobacterium marinus, by radiorespirometric studies. whereas glucose is oxidized mainly via the embden-meyerhof pathway, gluconate is catabolized mainly via the entner-doudoroff pathway, both in conjunction with the tricarboxylic acid cycle as a secondary pathway and with some participation of the pentose phosphate pathway. the operation of these contr ...	1983	6848485