[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: Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.
[Show abstract][Hide abstract] ABSTRACT: Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal kingdom Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.