Genome update: lactic acid bacteria genome sequencing is booming

Liu, Mengjin; Enckevort, Frank H. J. van; Siezen, Roland J.

doi:10.1099/mic.0.28557-0

Cited by 29 publications

(20 citation statements)

References 20 publications

(6 reference statements)

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“…longum BB536 and B. longum subsp. infantis M-63) are at various stages of completion [65]. All completely and partially annotated bifidobacterial genomes range in size from 1.9 to 2.9 Mb, on which 1,604-2,588 genes have been identified and annotated (see Table 3).…”

Section: Bifidobacterial Genomesmentioning

confidence: 99%

Carbohydrate metabolism in Bifidobacteria

2011

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Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plantderived oligo-and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.

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Section: Bifidobacterial Genomesmentioning

confidence: 99%

Carbohydrate metabolism in Bifidobacteria

2011

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“…The genomic revolution has opened new avenues for research on mixed cultures, for an increasing number of relevant genome sequences for LAB are available (90,93). In several genomes for LAB, among which L. plantarum (84), S. thermophilus (15), and Lactobacillus salivarius subsp.…”

Section: Genomics Approaches For Mixed-culture Researchmentioning

confidence: 99%

“…The recent emergence of genomics has opened new avenues for the systematic analysis of microbial metabolism and the responses of microorganisms to their environment. Additionally, genomics has boosted research on important food microbes (22,90,93). Much of this research focuses on the performance of a single strain, including its interactions with the food matrix.…”

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confidence: 99%

Unraveling Microbial Interactions in Food Fermentations: from Classical to Genomics Approaches

Sieuwerts

Bok

Hugenholtz

et al. 2008

Appl Environ Microbiol

264

178

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3Fermentation, the microbial degradation of organic compounds without net oxidation, is an important process in the global carbon cycle and is also exploited worldwide for the production and preservation of food. It is one of the oldest food-processing technologies known, with some records dating back to 6,000 B.C. (50). The link between food and microbiology was laid by Pasteur, who found that yeasts were responsible for alcoholic fermentation (106). Since that discovery, scientific and industrial interests in food microbiology started to grow and continue to increase today. The number of food products that rely on fermentation in one or more steps of their production is tremendous. They form an important constituent of the daily diet and rank among the most innovative product categories in the food industry.Most of the important microorganisms applied in the production of fermented foods have been studied for decades, yielding a wealth of information on their physiology and genetics in relation to product functionalities, such as the development of flavor, taste, and texture. The recent emergence of genomics has opened new avenues for the systematic analysis of microbial metabolism and the responses of microorganisms to their environment. Additionally, genomics has boosted research on important food microbes (22,90,93). Much of this research focuses on the performance of a single strain, including its interactions with the food matrix. However, food fermentations are typically carried out by mixed cultures consisting of multiple strains or species. Population dynamics play a crucial role in the performance of mixed-culture fermentations, and for many years, studies on mixed-culture food fermentations have focused on analyzing population dynamics using classical and molecular methods. Many of these studies are mainly descriptive, and relatively little is known about the mechanisms governing population dynamics in general and the molecular interactions that occur between the consortium members in particular. The availability of genome sequences for several species that are of industrial importance as well as technological advances in functional genomics enable new approaches to study food microbiology beyond the single species level and allow an integral analysis of the interactions and metabolic activity in mixed cultures.Here we review the current knowledge on important food fermentation processes, focusing on the bacterial interactions.In addition, we illustrate how genomics approaches may contribute to the elucidation of the interaction networks between microbes, including interactions with the food environment. This information may find application in the industry through rational optimization and increased control over mixed-culture fermentations.

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“…Genomics of Lactobacillus species is booming, and the genomes of five strains that belong to species commonly found in human fecal samples have recently been sequenced (50). Several comparative and functional genomic investigations have been conducted to gain information about the functionality of lactobacilli in the GIT (69).…”

mentioning

confidence: 99%