Functional implications of the microbial community structure of undefined mesophilic starter cultures

Smid, Eddy J.; Erkuş, Oylum; Spus, M.; Wolkers-Rooijackers, J.C.M.; Alexeeva, Svetlana; Kleerebezem, Michiel

doi:10.1186/1475-2859-13-s1-s2

Cited by 81 publications

(53 citation statements)

References 44 publications

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“…These findings imply that stress responses in L. lactis are important for maintenance of cellular function and viability under near-zero-growth conditions, as well as under starvation conditions, which may reflect the evolutionary advantage of stress robustness for bacteria that encounter conditions that do not permit growth and include (temporal) nutrient starvation (30,31). Analogously, in industrial fermentation applications, increased stress robustness of lactococci may affect product characteristics by extending their viability, which may improve their contribution to aroma and flavor formation during product ripening or prolong shelf life of products that include probiotic bacteria (32). Model profiles 6 and 7 were analyzed together because these profiles are both characterized by elevated expression levels during starvation (24 h), which either remained at a high level of expression (profile 7) or declined (profile 6) during the subsequent recovery period.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

Ercan

Wels

Smid

et al. 2015

Appl Environ Microbiol

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f This paper describes the transcriptional adaptations of nongrowing, retentostat cultures of Lactococcus lactis to starvation. Near-zero-growth cultures ( ‫؍‬ 0.0001 h ؊1 ) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence in L. lactis KF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conserved cis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation in L. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.L actococcus lactis has a long history of use in the manufacturing of fermented foods. In particular, dairy starter cultures containing L. lactis are important for primary acidification of cheese milk. In addition, L. lactis contributes to the texture and formation of flavor in cheese, which are key determinants of the product's sensory quality (1, 2). Next to these industrial food fermentation applications, L. lactis is frequently found in other environments, such as (decaying) plant material, especially when nutrients become available as a consequence of primary degradation of plant polymers by other microorganisms, including yeasts and fungi (3).In nature, microbial populations mostly live in nutrient-limiting conditions due to low carbon and energy source availability (4). Under these environmental conditions, microbes either develop adaptive responses to high-affinity substrate acquisition or scavenge the ecosystem for alternative nutrients, resulting in a survival advantage (5). Similarly, in industrial fermentation applications, microbes may encounter restricted access to carbon sources for longer periods of time. For example, lactic acid bacteria (LAB) encounter long periods of low or no carbon availability during the ripening of dried sausages (6) and cheese (1), but they are able to survive under these conditions during months of ripening (6,7,...

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

Ercan

Wels

Smid

et al. 2015

Appl Environ Microbiol

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“…For example, different Lc. lactis strains have different effects on flavor formation in cheese production (624,625). Phenotypic strain variation is at least partially caused by gene content differences, which implies that mining the data from genotype-phenotype matching (GPM) approaches may reveal novel gene functions.…”

Section: Gene Function Discovery By Phenotype Diversity Mining Stratementioning

confidence: 99%

Stress Physiology of Lactic Acid Bacteria

Papadimitriou

Alegría

Bron

et al. 2016

Microbiol Mol Biol Rev

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480

404

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SUMMARYLactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g.,Lactococcus lactis), probiotic (e.g., severalLactobacillusspp.), and pathogenic (e.g.,EnterococcusandStreptococcusspp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the “stressome” of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

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“…Spontaneous fermentation provide the road map to produce food products using a small sample from the previous fermented products by adding (inoculum) to fresh media/milk to initiate the fermentation process. Subsequently it was experienced that some of the fermented foods if added to the raw material the food product quality was improved which lead to the development of back slopping (Ali and Mustafa 2009;Smid et al 2014). This back slopping improved safety and quality and shelf life of the product.…”

Section: The Futurementioning

confidence: 99%

Advances in Bioprocess Technology

Ravindra¹

2015

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Functional implications of the microbial community structure of undefined mesophilic starter cultures

Cited by 81 publications

References 44 publications

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

Stress Physiology of Lactic Acid Bacteria

Advances in Bioprocess Technology

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