scholarly journals Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

PLoS Biology ◽  
2014 ◽  
Vol 12 (8) ◽  
pp. e1001920 ◽  
Author(s):  
Nikos C. Kyrpides ◽  
Philip Hugenholtz ◽  
Jonathan A. Eisen ◽  
Tanja Woyke ◽  
Markus Göker ◽  
...  
Keyword(s):  
Type Strains ◽  
Genomic Encyclopedia

scholarly journals Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

2013 ◽  
Vol 9 (3) ◽  
pp. 1278-1284 ◽  
Author(s):  
Nikos C. Kyrpides ◽  
Tanja Woyke ◽  
Jonathan A. Eisen ◽  
George Garrity ◽  
Timothy G. Lilburn ◽  
...  
Keyword(s):  
Phase I ◽  
Microbial Genomes ◽  
The One ◽  
Type Strains ◽  
Genomic Encyclopedia

scholarly journals 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

2017 ◽  
Vol 35 (7) ◽  
pp. 676-683 ◽  
Author(s):  
Supratim Mukherjee ◽  
Rekha Seshadri ◽  
Neha J Varghese ◽  
Emiley A Eloe-Fadrosh ◽  
Jan P Meier-Kolthoff ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Phylogenetic Diversity ◽  
Scientific Discovery ◽  
Valuable Resource ◽  
Sequence Coverage ◽  
Functional Interpretation ◽  
Type Strains ◽  
Reference Genomes ◽  
Genomic Encyclopedia ◽  
Novel Protein

Abstract We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

scholarly journals Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
William B Whitman ◽  
Tanja Woyke ◽  
Hans-Peter Klenk ◽  
Yuguang Zhou ◽  
Timothy G Lilburn ◽  
...  
Keyword(s):  
Phase Iii ◽  
Type Strains ◽  
Genomic Encyclopedia

scholarly journals Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains

2019 ◽  
Vol 40 (3) ◽  
pp. 125
Author(s):  
William B Whitman ◽  
Hans-Peter Klenk ◽  
David R Arahal ◽  
Rosa Aznar ◽  
George Garrity ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Transcriptome Sequencing ◽  
Department Of Energy ◽  
Joint Genome Institute ◽  
The Us ◽  
Prokaryotic Species ◽  
Type Strains ◽  
Genomic Encyclopedia ◽  
Energy Joint Genome Institute

Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new project GEBA VI extends these efforts to functional genomics, including pangenome and transcriptome sequencing and exometabolite analyses. As part of this project, investigators with interests in specific groups of prokaryotes are invited to submit samples for analysis at JGI.

scholarly journals Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

2014 ◽  
Vol 80 (20) ◽  
pp. 6290-6302 ◽  
Author(s):  
Christian Milani ◽  
Gabriele Andrea Lugli ◽  
Sabrina Duranti ◽  
Francesca Turroni ◽  
Francesca Bottacini ◽  
...  
Keyword(s):  
Genome Structure ◽  
Genomic Data ◽  
Evolutionary Development ◽  
Bacterial Group ◽  
Content Type ◽  
Evolutionary Force ◽  
Microbial Groups ◽  
Type Strains ◽  
Genomic Encyclopedia

ABSTRACTBifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across theBifidobacteriumgenus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of theBifidobacteriumgenus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.

Ruthenium red and alcian blue effects on outer structures of methanotrophic bacteria

1988 ◽  
Vol 46 ◽  
pp. 72-73
Author(s):  
T.A. Fassel ◽  
M.J. Schaller ◽  
C.C. Remsen
Keyword(s):  
Research Effort ◽  
Ruthenium Red ◽  
Outer Cell ◽  
Methanotrophic Bacteria ◽  
En Bloc ◽  
Methylosinus Trichosporium ◽  
Wall Structures ◽  
Methylomonas Albus ◽  
Type Strains ◽  
Outer Cell Wall

Methane, a contributor to the “greenhouse effect”, is oxidized in the natural environment by methanotrophic bacteria. As part of a comprehensive research effort, we have been examining the ultrastructure of methanotrophs. These microorganisms have complex outer cell wall structures similar to those frequently found in other chemol itho- trophic bacteria. (1,2)In our work, we have focused on the “type” strains of Methylomonas albus BG8 and Methylosinus trichosporium OB3b. Between Spurr and LR White embedding resins, we found a difference 1n the preservation of an outer cup layer of BG8 external to the peripheral membranes. Cells from the same sample embedded in Spurr consistently lacked this feature (FIG. 1). This effect was overcome by an en bloc ruthenium red (RR) protocol that resulted in successful retention of the cup layer in Spurr resin (FIG. 2). For OB3b cells, the en bloc RR protocol resulted in an exterior bead feature distinguishable in thin section (FIG. 4) that previously was seen only by SEM.

scholarly journals Suitability Analysis of 17 Probiotic Type Strains of Lactic Acid Bacteria as Starter for Kimchi Fermentation

Foods ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1435
Author(s):  
Hee Seo ◽  
Jae-Han Bae ◽  
Gayun Kim ◽  
Seul-Ah Kim ◽  
Byung Hee Ryu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Growth Rates ◽  
Principal Component ◽  
Fermented Foods ◽  
Suitability Analysis ◽  
Moderate Growth ◽  
Health Promoting ◽  
Highly Correlated ◽  
Type Strains

The use of probiotic starters can improve the sensory and health-promoting properties of fermented foods. This study aimed to evaluate the suitability of probiotic lactic acid bacteria (LAB) as a starter for kimchi fermentation. Seventeen probiotic type strains were tested for their growth rates, volatile aroma compounds, metabolites, and sensory characteristics of kimchi, and their characteristics were compared to those of Leuconostoc (Le.) mesenteroides DRC 1506, a commercial kimchi starter. Among the tested strains, Limosilactobacillus fermentum, Limosilactobacillus reuteri, Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and Ligilactobacillus salivarius exhibited high or moderate growth rates in simulated kimchi juice (SKJ) at 37 °C and 15 °C. When these five strains were inoculated in kimchi and metabolite profiles were analyzed during fermentation using GC/MS and 1H-NMR, data from the principal component analysis (PCA) showed that L. fermentum and L. reuteri were highly correlated with Le. mesenteroides in concentrations of sugar, mannitol, lactate, acetate, and total volatile compounds. Sensory test results also indicated that these three strains showed similar sensory preferences. In conclusion, L. fermentum and L. reuteri can be considered potential candidates as probiotic starters or cocultures to develop health-promoting kimchi products.

A Mutation in a Saccharomyces cerevisiae Gene (RAD3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 459-466 ◽  
Author(s):  
Yingying Yang ◽  
Anthony L Johnson ◽  
Leland H Johnston ◽  
Wolfram Siede ◽  
Errol C Friedberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Excision Repair ◽  
Spontaneous Mutation ◽  
Surprising Result ◽  
Spontaneous Mutation Rate ◽  
Mismatch Correction ◽  
Nucleotide Excision ◽  
Repair Genes ◽  
Type Strains

Abstract RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMSl, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency.

Sign in / Sign up

Export Citation Format

Share Document