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

Beer spoilage and low pH tolerance is linked to manganese homeostasis in selected Lactobacillus brevis strains

AIMS

Beer is a harsh medium for bacteria to survive, however, lactic acid bacteria including Lactobacillus brevis have evolved the ability to grow in beer. Here, the influence of environmental factors such as low pH, ethanol or hop content was assessed.

METHODS AND RESULTS

A transcriptomic analysis of two Lact. brevis beer-spoiling strains was performed comparing growth in nutritive media with or without the imposition of a stressor related to the beer environment. This allowed the identification of a manganese transporter encoding gene that contributes to low pH tolerance.

CONCLUSIONS

We report on the importance of a manganese transporter associated with pH tolerance and beer spoilage in Lact. brevis. The importance of manganese for Lact. brevis growth in a low pH environment was highlighted.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacterial spoilage of beer may result in product withdrawal with concomitant economic losses for the brewing industry. A limited number of genes involved in beer spoilage have been identified but none of them are universal. It is clear that other molecular players are involved in beer spoilage. The study highlights the complexity of the genetic requirements to facilitate beer spoilage and the role of multiple key players in this process.

Lactobacillus backii and Pediococcus damnosus isolated from 170-year-old beer recovered from a shipwreck lack the metabolic activities required to grow in modern lager beer

In 2010, bottles of beer containing viable bacteria of the common beer-spoilage species Lactobacillus backii and Pediococcus damnosus were recovered from a shipwreck near the Åland Islands, Finland. The 170-year quiescent state maintained by the shipwreck bacteria presented a unique opportunity to study lactic acid bacteria (LAB) evolution vis-a-vis growth and survival in the beer environment. Three shipwreck bacteria (one L. backii strain and two P. damnosus strains) and modern-day beer-spoilage isolates of the same two species were genome sequenced, characterized for hop iso-α-acid tolerance, and growth in degassed lager and wheat beer. In addition, plasmid variants of the modern-day P. damnosus strain were analyzed for the effect of plasmid-encoded genes on growth in lager beer. Coding content on two plasmids was identified as essential for LAB growth in modern lager beer. Three chromosomal regions containing genes related to sugar transport and cell wall polysaccharides were shared by pediococci able to grow in beer. Our results show that the three shipwreck bacteria lack the necessary plasmid-located genetic content to grow in modern lager beer, but carry additional genes related to acid tolerance and biofilm formation compared to their modern counterparts.

Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates

Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.

Lactobacilli and pediococci as versatile cell factories - Evaluation of strain properties and genetic tools

This review discusses opportunities and bottlenecks for cell factory development of Lactic Acid Bacteria (LAB), with an emphasis on lactobacilli and pediococci, their metabolism and genetic tools. In order to enable economically feasible bio-based production of chemicals and fuels in a biorefinery, the choice of product, substrate and production organism is important. Currently, the most frequently used production hosts include Escherichia coli and Saccharomyces cerevisiae, but promising examples are available of alternative hosts such as LAB. Particularly lactobacilli and pediococci can offer benefits such as thermotolerance, an extended substrate range and increased tolerance to stresses such as low pH or high alcohol concentrations. This review will evaluate the properties and metabolism of these organisms, and provide an overview of their current biotechnological applications and metabolic engineering. We substantiate the review by including experimental results from screening various lactobacilli and pediococci for transformability, growth temperature range and ability to grow under biotechnologically relevant stress conditions. Since availability of efficient genetic engineering tools is a crucial prerequisite for industrial strain development, genetic tool development is extensively discussed. A range of genetic tools exist for Lactococcus lactis, but for other species of LAB like lactobacilli and pediococci such tools are less well developed. Whereas lactobacilli and pediococci have a long history of use in food and beverage fermentation, their use as platform organisms for production purposes is rather new. By harnessing their properties such as thermotolerance and stress resistance, and by using emerging high-throughput genetic tools, these organisms are very promising as versatile cell factories for biorefinery applications.

Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages

Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB) fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS) or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.

Transcriptome analysis of beer-spoiling Lactobacillus brevis BSO 464 during growth in degassed and gassed beer

Lactobacillus brevis BSO 464 (Lb464) is a beer-spoilage-related (BSR) isolate of interest given its unique physiological attributes; specifically, it is highly hop-tolerant and exhibits very rapid growth in pressurized/gassed beer. RNA sequencing was performed on Lb464 grown in pressurized and non-pressurized beer to determine important genetic mechanisms for growth in these environments. The data generated were compared against data in a previous transcriptional study of another lactic acid bacterium (LAB) during growth in beer, namely, Pediococcus claussenii ATCC BAA-344(T) (Pc344). Results revealed that the most important genetic elements for Lb464 growth in beer are related to biogenic amine metabolism, membrane transport and fortification, nutrient scavenging, and efficient transcriptional regulation. Comparison with the previous transcriptional study of Pc344 indicated that the total coding capacity (plasmid profile and genome size) of a LAB isolate allows for beer-spoilage virulence and adaptation to different beer environments, i.e., the ability to grow in degassed beer (during production) or gassed beer (packaged product). Further, differences in gene expression of Lb464 and Pc344 during mid-exponential growth in beer may dictate how rapidly each isolate exhausts particular carbon sources during. The presence of headspace pressure/dissolved CO2 was found to drive Lb464 transcription during mid-exponential growth in beer towards increasing cell wall and membrane modification, transport, osmoregulation, and DNA metabolism and transposition events. This transcriptional activity resembles transcriptional patterns or signatures observed in a viable, but non-culturable state established by non-related organisms, suggesting that Lb464 overall uses complex cellular regulation to maintain cell division and growth in the stressful beer environment. Additionally, increased expression of several hypothetical proteins, the hop-tolerance gene horC, and DNA repair and recombination genes from plasmids pLb464-2, -4, and -8 were observed in the gassed beer environment. Thus, plasmids can harbor genes with specific (gassed) beer growth advantages, and confirm that plasmid transfer and acquisition as important activities for adaptation to the beer environment.

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

BACKGROUND

Metatranscriptomic landscapes can provide insights in functional relationships within natural microbial communities. Analysis of complex metatranscriptome datasets of these communities poses a considerable bioinformatic challenge since they are non-restricted with a varying number of participating strains and species. For RNA-Seq data a standard approach is to align the generated reads to a set of closely related reference genomes. This only works well for microbial communities for which a near complete catalogue of reference genomes is available at a small evolutionary distance. In this study, we focus on the design of a validated de novo metatranscriptome assembly pipeline for single-end Illumina RNA-Seq data to obtain functional and taxonomic profiles of murine microbial communities.

RESULTS

The here developed de novo assembly metatranscriptome pipeline combined rRNA removal, IDBA-UD assembler, functional annotation and taxonomic classification. Different assemblers were tested and validated using RNA-Seq data from an in silico generated mock community and in vivo RNA-Seq data from a restricted microbial community taken from a mouse model colonized with Altered Schaedler Flora (ASF). Precision and recall of resulting gene expression, functional and taxonomic profiles were compared to those obtained with a standard alignment method. The validated pipeline was subsequently used to generate expression profiles from non-restricted cecal communities of four C57BL/6J mice fed on a high-fat high-protein diet spiked with an RNA-Seq data set from a well-characterized human sample. The spike in control was used to estimate precision and recall at assembly, functional and taxonomic level of non-restricted communities.

CONCLUSIONS

A generic de novo assembly pipeline for metatranscriptome data analysis was designed for microbial ecosystems, which can be applied for microbial metatranscriptome analysis in any chosen niche.

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. Genome sequencing of the virulent beer spoilage organism Lactobacillus brevis BSO 464 revealed the presence of eight plasmids, with plasmids 1, 2, and 3 containing horA, horC, and hitA, respectively. To investigate the roles that these and the other five plasmids play in L. brevis BSO 464 growth in beer, plasmid curing with novobiocin was used to derive 10 plasmid variants. Multiplex PCRs were utilized to determine the presence or absence of each plasmid, and how plasmid loss affected hop tolerance and growth in degassed (noncarbonated) beer was assessed. Loss of three of the eight plasmids was found to affect hop tolerance and growth in beer. Loss of plasmid 2 (horC and 28 other genes) had the most dramatic effect, with loss of plasmid 4 (120 genes) and plasmid 8 (47 genes) having significant, but smaller, impacts. These results support the contention that genes on mobile genetic elements are essential for bacterial growth in beer and that beer spoilage ability is not dependent solely on the three previously described hop tolerance genes or on the chromosome of a beer spoilage LAB isolate.

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.

Metabolic strategies of beer spoilage lactic acid bacteria in beer

Beer contains only limited amounts of readily fermentable carbohydrates and amino acids. Beer spoilage lactic acid bacteria (LAB) have to come up with metabolic strategies in order to deal with selective nutrient content, high energy demand of hop tolerance mechanisms and a low pH. The metabolism of 26 LAB strains of 6 species and varying spoilage potentialwas investigated in order to define and compare their metabolic capabilities using multivariate statistics and outline possible metabolic strategies. Metabolic capabilities of beer spoilage LAB regarding carbohydrate and amino acids did not correlate with spoilage potential, but with fermentation type (heterofermentative/homofermentative) and species. A shift to mixed acid fermentation by homofermentative (hof) Pediococcus claussenii and Lactobacillus backii was observed as a specific feature of their growth in beer. For heterofermentative (hef) LAB a mostly versatile carbohydrate metabolism could be demonstrated, supplementing the known relevance of organic acids for their growth in beer. For hef LAB a distinct amino acid metabolism, resulting in biogenic amine production, was observed, presumably contributing to energy supply and pH homeostasis.

Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment

BACKGROUND

Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions. It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. The molecular mechanisms underlying its metabolic capabilities and niche adaptations were unknown up to now. In the present study, whole-genome sequencing and comparative genome analysis were used to investigate this strain's mechanisms to reside in the beer niche, with special focus on not only stress and hop resistances but also folate biosynthesis and exopolysaccharide (EPS) production.

RESULTS

The draft genome sequence of P. damnosus LMG 28219 harbored 183 contigs, including an intact prophage region and several coding sequences involved in plasmid replication. The annotation of 2178 coding sequences revealed the presence of many transporters and transcriptional regulators and several genes involved in oxidative stress response, hop resistance, de novo folate biosynthesis, and EPS production. Comparative genome analysis of P. damnosus LMG 28219 with Pediococcus claussenii ATCC BAA-344(T) (beer origin) and Pediococcus pentosaceus ATCC 25745 (plant origin) revealed that various hop resistance genes and genes involved in de novo folate biosynthesis were unique to the strains isolated from beer. This contrasted with the genes related to osmotic stress responses, which were shared between the strains compared. Furthermore, transcriptional regulators were enriched in the genomes of bacteria capable of growth in beer, suggesting that those cause rapid up- or down-regulation of gene expression.

CONCLUSIONS

Genome sequence analysis of P. damnosus LMG 28219 provided insights into the underlying mechanisms of its adaptation to the beer niche. The results presented will enable analysis of the transcriptome and proteome of P. damnosus LMG 28219, which will result in additional knowledge on its metabolic activities.

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

DOI:http://dx.doi.org/10.7554/eLife.04634.001

Many microbes—including bacteria and fungi—can affect the food and drink we consume, for better and for worse. Some spoil food, making it less tasty or even harmful to health. However, microbes can also be important ingredients: for example, yeast ferments malted barley sugars to make the alcohol and flavor of beer.

Nowadays, many beers are made under carefully controlled conditions, where the only microbes in the beer should be the strain of yeast added to the barley sugars. A more traditional ‘coolship’ method can be used to make sour beers; the barley sugars cool in an open-topped vessel and are fermented by the yeast and bacteria found naturally on the raw ingredients and in the surrounding environment.

Relatively little was known about how microbes spread around and adapt to living inside buildings. Now, Bokulich et al. have used a range of molecular and statistical techniques to examine how bacteria and fungi are dispersed throughout a North American brewery that produces beer using both conventional and coolship brewing techniques. Most of the microbes found in the building originated from the raw ingredients used to make the beer, with different parts of the brewery containing different species. Over the course of a year, some species spread to new parts of the building; a statistical method predicted the sources of these microbes, and revealed some key areas and features of the brewery that affect microbial transfer.

Bokulich et al. also looked at the spread of genes that enable their bacterial hosts to spoil beer, including those that protect bacteria from the antimicrobial action of the hops that flavor many beers. Lactic acid bacteria are the main cause of beer spoilage and so are usually to be avoided in breweries, but are also a normal ingredient in sour beer. In the brewery Bokulich et al. investigated, beer-spoilage and hop-resistance genes were found throughout the brewery, even in areas not used to produce sour beer. However, little beer spoilage occurred.

The techniques used by Bokulich et al. to track the spread of microbes and their detrimental genes could be used in the future to understand how microbes adapt to other indoor environments. Indeed, Bokulich et al. suggest that breweries could be used as models to safely understand the factors that influence microbial movement in any food-production facility as well as other building environments.

DOI:http://dx.doi.org/10.7554/eLife.04634.002

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. Other programs generate models from actual sequencing data, but are limited to reads from single-genome studies. To our knowledge, there are no programs that allow a user to generate simulated data following non-parametric read-length distributions and quality profiles based on empirically-derived information from metagenomics sequencing data.

Results

We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions. BEAR can emulate reads from various sequencing platforms, including Illumina, 454, and Ion Torrent. BEAR requires minimal user input, as it automatically determines appropriate parameter settings from user-supplied data. BEAR also uses a unique method for deriving run-specific error rates, and extracts useful statistics from the metagenomic data itself, such as quality-error models. Many existing simulators are specific to a particular sequencing technology; however, BEAR is not restricted in this way. Because of its flexibility, BEAR is particularly useful for emulating the behaviour of technologies like Ion Torrent, for which no dedicated sequencing simulators are currently available. BEAR is also the first metagenomic sequencing simulator program that automates the process of generating abundances, which can be an arduous task.

Conclusions

BEAR is useful for evaluating data processing tools in genomics. It has many advantages over existing comparable software, such as generating more realistic reads and being independent of sequencing technology, and has features particularly useful for metagenomics work.