Multiple Genome Sequences of the Important Beer-Spoiling Species
            <i>Lactobacillus backii</i>

Geißler, Andreas; Behr, Jürgen; Vogel, Rudi F.

doi:10.1128/genomea.00826-16

Cited by 6 publications

(7 citation statements)

References 11 publications

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“…Finally, an analysis of the predominant assembly complexity classification for different Lactobacillus species indicated that L. helveticus strains had the second highest mean repeat number among all Lactobacillus species, outnumbered only by L. backii (Geissler et al, 2016 ) (Figure 1B ). More importantly, due to the overall higher percentage of class III genomes, L. delbrueckii (73%), L. backii (60%), L. casei (50%), L. plantarum (43%), and L. fermentum (40%) represent Lactobacillus species that may pose considerable challenges for researchers aiming to carry out complete genome assembly projects similar to that we describe here for L. helveticus .…”

Section: Resultsmentioning

confidence: 98%

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

et al. 2018

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Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.

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Section: Resultsmentioning

confidence: 98%

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

et al. 2018

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“…Due to the significance of LAB as spoilage agents of beer, there has been a recent increase in sequenced brewing-related LAB genomes that are publicly available, including the genomes of five Lactobacillus backii isolates [17], L. brevis BSO 464 [18], Lactobacillus malefermentans KCTC 3548 [19], six P. damnosus isolates [20],[21], and Pediococcus claussenii ATCC BAA-344 T [22], as well as upwards of twenty publically available genome projects of isolates associated in some manner to the brewing environment (as of November 1, 2016, via NCBI). Application of transcriptomics to the virulent beer-spoilage organism L. brevis BSO 464 (capable of growing in packaged beer with dissolved CO 2 content/pressure) [23], and to beer-spoiling P. claussenii ATCC BAA-344 T (can grow in partially degassed beer) [24] has revealed multiple insights into LAB genetic mechanisms in relation to beer-spoilage.…”

Section: Beermentioning

confidence: 99%

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

Bergsveinson¹,

Kajala²,

Ziola

2017

AIMS Microbiology

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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.

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“…In general, butyrate-producing bacteria have health-promoting activity by maintaining epithelial barrier function and integrity, and inhibiting inflammation 37 . As for Lactobacillus backii , no report was found in human, but this organism was reported to have a beer-spoiling effect 38 . Noteworthy, many species were found more abundant in HC but depleted in CD, reflecting the significant difference between the groups, and confirming dysbiosis in CD patients.…”

Section: Discussionmentioning

confidence: 99%

Deciphering salivary microbiome signature in Crohn’s disease patients with different factors contributing to dysbiosis

Elzayat,

Malik,

Al-Awadhi

et al. 2023

Sci Rep

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Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral dysbiosis in CD is poorly understood. We aimed to explore microbiome signature and dysbiosis of the salivary microbiome in CD patients, and correlate microbiota changes to the level of inflammation. Saliva samples were collected from healthy controls (HC) and CD patients (n = 40 per group). Salivary microbiome was analyzed by sequencing the entire 16S rRNA gene. Inflammatory biomarkers (C-reactive protein and calprotectin) were measured and correlated with microbiome diversity. Five dominant species were significantly enriched in CD, namely Veillonella dispar, Megasphaera stantonii, Prevotella jejuni, Dolosigranulum pigrum and Lactobacillus backii. Oral health had a significant impact on the microbiome since various significant features were cariogenic as Streptococcus mutans or periopathogenic such as Fusobacterium periodonticum. Furthermore, disease activity, duration and frequency of relapses impacted the oral microbiota. Treatment with monoclonal antibodies led to the emergence of a unique species called Simonsiella muelleri. Combining immunomodulatory agents with monoclonal antibodies significantly increased multiple pathogenic species such as Salmonella enterica, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Loss of diversity in CD was shown by multiple diversity indices. There was a significant negative correlation between gut inflammatory biomarkers (particularly calprotectin) and α-diversity, suggesting more inflammation associated with diversity loss in CD. Salivary dysbiosis was evident in CD patients, with unique microbiota signatures and perturbed species that can serve as disease biomarkers or potential targets for microbiota modulation. The interplay of various factors collectively contributed to dysbiosis, although each factor probably had a unique effect on the microbiome. The emergence of pathogenic bacteria in the oral cavity of CD patients is alarming since they can disturb gut homeostasis and induce inflammation by swallowing, or hematogenous spread of microbiota, their metabolites, or generated inflammatory mediators.

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Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii

Cited by 6 publications

References 11 publications

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

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

Deciphering salivary microbiome signature in Crohn’s disease patients with different factors contributing to dysbiosis

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