Genome Sequence of Rapid Beer-Spoiling Isolate Lactobacillus brevis BSO 464.

The genome of brewery-isolate Lactobacillus brevis BSO 464 was sequenced and assembly produced a chromosome and eight plasmids. This bacterium tolerates dissolved CO2/pressure and can rapidly spoil packaged beer. This genome is useful for analyzing the genetics associated with beer spoilage by lactic acid bacteria.

Role of plasmids in Lactobacillus brevis BSO 464 hop tolerance and beer spoilage.

Specific isolates of lactic acid bacteria (LAB) can grow in the harsh beer environment, thus posing a threat to brew quality and the economic success of breweries worldwide. Plasmid-localized genes, such as horA, horC, and hitA, have been suggested to confer hop tolerance, a trait required for LAB survival in beer. The presence and expression of these genes among LAB, however, do not universally correlate with the ability to grow in beer.

A better sequence-read simulator program for metagenomics.

Background: There are many programs available for generating simulated whole-genome shotgun sequence reads. The data generated by many of these programs follow predefined models, which limits their use to the authors' original intentions. For example, many models assume that read lengths follow a uniform or normal distribution.

Equivalent input produces different output in the UniFrac significance test.

Background: UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities. In this paper we identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.

Results: The phylogenetic trees that are input into UniFrac may or may not contain abundance counts.

Transcriptome sequence and plasmid copy number analysis of the brewery isolate Pediococcus claussenii ATCC BAA-344 T during growth in beer.

Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g.

RT-qPCR analysis of putative beer-spoilage gene expression during growth of Lactobacillus brevis BSO 464 and Pediococcus claussenii ATCC BAA-344(T) in beer.

Lactic acid bacteria (LAB) contamination of beer presents a continual economic threat to brewers. Interestingly, only certain isolates of LAB can grow in the hostile beer environment (e.g.

Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T.

Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and plasmids of the type strain P. claussenii ATCC BAA-344.

Genome sequence of Lactobacillus rhamnosus ATCC 8530.

Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance.

Reclassification of Paralactobacillus selangorensis Leisner et al. 2000 as Lactobacillus selangorensis comb. nov.

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed.

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.

Background: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.

Results: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets".

Thioredoxin system from Deinococcus radiodurans.

This paper describes the cloning, purification, and characterization of thioredoxin (Trx) and thioredoxin reductase (TrxR) and the structure determination of TrxR from the ionizing radiation-tolerant bacterium Deinococcus radiodurans strain R1. The genes from D. radiodurans encoding Trx and TrxR were amplified by PCR, inserted into a pET expression vector, and overexpressed in Escherichia coli.