[Show abstract][Hide abstract]ABSTRACT: strain MPOB is the best-studied species of the genus . The species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, H and CO during the overall degradation of organic matter, and its release of products that serve as substrates for other microorganisms. The strain is able to ferment fumarate in pure culture to CO and succinate, and is also able to grow as a sulfate reducer with propionate as an electron donor. This is the first complete genome sequence of a member of the genus and a member genus in the family . Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,990,251 bp long genome with its 4,098 protein-coding and 81 RNA genes is a part of the Microbial Genome Program (MGP) and the Genomes to Life (GTL) Program project.
Full-text · Article · Oct 2012 · Standards in Genomic Sciences
[Show abstract][Hide abstract]ABSTRACT: Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments.
We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from
Full-text · Article · Mar 2011 · Journal of bacteriology
[Show abstract][Hide abstract]ABSTRACT: Accessory SecA2 cluster in L. reuteri and related bacteria. SecA2 cluster in L. reuteri 100-23, Lactobacillus gasseri JV-V03, and Streptococcus agalactiae A909. Conserved regions are labeled with grey boxes.
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[Show abstract][Hide abstract]ABSTRACT: Gene maps of SPS clusters in L. reuteri 100-23 and F275. Genomic regions that encode for proteins involved in surface polysaccharide synthesis in L. reuteri 100-23 and F275. Flanking regions that are conserved in both genomes are indicated by boxes.
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[Show abstract][Hide abstract]ABSTRACT: Comparison of genomic locations that contain host-specific genes. (A) Genome region with the pdu-cbi-cob-hem cluster in F275 and the same genomic region in 100-23. (B) Genome schematic showing the urease cluster in strain 100-23, and the same loci in F275. (C) Genomic region containing the xylose operon in 100-23 and the same loci, without xylose operon, in F275.
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[Show abstract][Hide abstract]ABSTRACT: Comparison of the genomic locations that contain large surface proteins in L. reuteri 100-23. Comparison of the sites in strains 100-23 and F275 that contain rodent-specific large surface proteins. (A) Lr_70770, (B) Lr_70697, (C) Lr_70131, Lr_70134, and Lr_70135, (D) Lr_70581, and (E) Lr_71380.
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[Show abstract][Hide abstract]ABSTRACT: Genome comparisons between L. reuteri strains and Lactobacillus fermentum. Comparisons of the genomes of Lactobacillus reuteri 100-23 (top) and F275 (bottom) with that of Lactobacillus fermentum IFO3956 (center). The BLASTN comparison using the Artemis Comparison Tool revealed an inversion in 100-23 when compared to the other two genomes.
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[Show abstract][Hide abstract]ABSTRACT: Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.
[Show abstract][Hide abstract]ABSTRACT: Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Full-text · Article · Aug 2010 · Standards in Genomic Sciences
[Show abstract][Hide abstract]ABSTRACT: Tryptophan (W) at conserved positions in Dehalococcoides RdhB sequences. (Top) Alpha helix prediction and transmembrane region prediction in the consensus RdhB. The red, green, and blue lines of the ‘TM Prediction Plot’ indicate the strength with which the corresponding residue is predicted to be located at the inner membrane, transmembrane, or outermembrane, respectively. These predictions were calculated using a Transmembrane Hidden Markov Model (TMHMM version 0.7) plugin to Geneious, contributed by Mark A. Suchard . Green horizontal cylinders indicate the location and prediction strength of presumed alpha helices, supporting the hypothesis that these are three distinct membrane-spanning helices. Though shown here only for the consensus sequence, this pattern of TM helices is consistently predicted for individual RdhB of Dehalococcoides. (Bottom) Sequence logo representing the alignment of all Dehalococcoides RdhB in the four genomes. Letter height represents the statistical support (in bits) for a residue at a given position in the sequence. Arrows (very top) emphasize the position of conserved tryptophan residues.
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[Show abstract][Hide abstract]ABSTRACT: Three strain multiple alignment of the region surrounding a putative deletion event in Dhc ethenogenes 195. The deletion appears to have occurred intragenically such that the 3′ 1400 bp of rdhA DET1535 are orthologous to the corresponding positions of DhcVS1399/cbdb_A1595, while the 5′ 100 bp are orthologous to corresponding positions in DhcVS1427/cbdb_A1624. The chimeric nature of DET1535 is further supported by local synteny, and the apparent deletion accounts for the absence of these genes in strain 195. Genes are shaded according to the following: rdhAB - red, other rdh associated genes - blue, hypothetical genes - white, other genes for which a functional annotation was assigned - light blue. For concision, annotations are often indicated at only one gene in a vertically aligned (orthologous) group. Locus ID are shown as space permits, with preference given to genes discussed in the main text. Genomic location is labeled above the black horizontal bar of each respective genome, with a much thinner horizontal line indicating a gap. A bar plot of local nucleotide identity is shown above the annotated multiple alignment and shaded to reinforce contrast in values. Green indicates windows of near perfect identity. BAV1 is not shown because this region is absent in BAV1, occurring within a larger apparent deletion in its genome.
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