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Probiotics genomics.

Siezen RJ, Wilson G - Microb Biotechnol (2010)

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

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We were sitting in the Irish pub on quiz night, dumbfounded by trivia questions about ingredients of Mornay sauce and best‐selling Boy Bands, when the following question came up: What are ‘Live microorganisms which when administered in adequate amounts confer a health benefit on the host?’ At long last, we had a correct answer: PROBIOTICS! What do probiotics actually do? What is the meaning of ‘confer a health benefit’? Lactobacillus plantarum JDM1 is a widely used Chinese commercial probiotic strain which appears to have lost 100 kb relative to the non‐commercial strain WCFS1, encoding sugar transport and metabolism, possibly due to prolonged growth of this probiotic strain in rich medium... Lactobacillus rhamnosus GG and Lactobacillus rhamnosus ATCC53103, probiotic strains used widely for nearly 20 years in a variety of functional foods, differ only by deletion of 5 kb in ATCC53103, and an inversion of 8.9 kb... SpaA is the major scaffolding protein upon which the minor pili proteins SpaB and SpaC are attached... Using insertional inactivation of spaC, a truncated SpaC protein was produced which resulted in cells with a greatly reduced binding to human mucus... The targeted loss of genomic regions was experimentally validated when growth of the intestinal B.  longum in the laboratory for 1000 generations resulted in two large deletions, one in a bacteriocin‐encoding region, analogous to a predicted deletion event in the commercial strain B.  longum NCC2705... This deletion strain showed a significantly reduced competitive ability against Clostridium difficile and Escherichia coli... At present, many of the commercial probiotic strains originate from the intestine of healthy infants and adults... Current research focuses on the determination of the characteristics these bacteria use to survive and compete successfully in the intestine, and with this knowledge more effective probiotic strains can be identified... And what will be the next hype? Memory‐enhancing drinks would definitely be a commercial success on quiz night in the pub!

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Evolutionary relationships between the main gastrointestinal tract commensal lactobacilli, based on a neighbour‐joining tree of 16S rRNA gene sequences. Bootstrap values above 600 are indicated. Bacterial taxa for which whole genome sequences are available are shaded in green. The outgroup is shaded in grey. Lactobacilli for which genome sequencing is ongoing/incomplete are shaded in red. Reproduced and adapted from Ventura and colleagues (2009), with permission from Macmillan Publishers Limited, 2009.
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f1: Evolutionary relationships between the main gastrointestinal tract commensal lactobacilli, based on a neighbour‐joining tree of 16S rRNA gene sequences. Bootstrap values above 600 are indicated. Bacterial taxa for which whole genome sequences are available are shaded in green. The outgroup is shaded in grey. Lactobacilli for which genome sequencing is ongoing/incomplete are shaded in red. Reproduced and adapted from Ventura and colleagues (2009), with permission from Macmillan Publishers Limited, 2009.

Mentions: Table 2 and Fig. 1 give an overview of genome sequencing of putative probiotic bacteria that are publicly available, and Table 3 gives examples of proprietary sequences of commercial probiotics. By far the most used probiotics and the ones which have their genomes sequenced are those associated with gut health. Details of genomes sequenced before 2009 have been summarized by Mayo and colleagues (2008) and Ventura and colleagues (2009). Infants are born with a sterile gastrointestinal (GI) tract but in breast‐fed babies colonization by bifidobacteria is rapidly seen. It is thought that these bacteria confer a health benefit to the infant. The first colonizer is Bifidobacterium longum ssp. infantis, which has the largest genome of any sequenced bifidobacteria at 2.83 Mb (Sela et al., 2008). The genome has complete pathways for the synthesis of some vitamins and a novel 43 kb gene cluster encoding a system for the import and degradation of human milk oligosaccharides (HMOs). After weaning, the numbers of this bifidobacterium decline but others become more dominant. Bifidobacterium animalis ssp. lactis, a resident of the GI tract and the most commonly used probiotic in Europe and North America, has a genome size of only 1.9 Mb. These bifidobacteria lack the HMO cluster as presumably post‐weaned animals no longer require this functionality. They do, however, contain the fos gene cluster necessary to produce the enzymes to break down and utilize health‐promoting fructo‐oligosaccharides, a well‐known prebiotic and bifidogenic factor.


Probiotics genomics.

Siezen RJ, Wilson G - Microb Biotechnol (2010)

Evolutionary relationships between the main gastrointestinal tract commensal lactobacilli, based on a neighbour‐joining tree of 16S rRNA gene sequences. Bootstrap values above 600 are indicated. Bacterial taxa for which whole genome sequences are available are shaded in green. The outgroup is shaded in grey. Lactobacilli for which genome sequencing is ongoing/incomplete are shaded in red. Reproduced and adapted from Ventura and colleagues (2009), with permission from Macmillan Publishers Limited, 2009.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815941&req=5

f1: Evolutionary relationships between the main gastrointestinal tract commensal lactobacilli, based on a neighbour‐joining tree of 16S rRNA gene sequences. Bootstrap values above 600 are indicated. Bacterial taxa for which whole genome sequences are available are shaded in green. The outgroup is shaded in grey. Lactobacilli for which genome sequencing is ongoing/incomplete are shaded in red. Reproduced and adapted from Ventura and colleagues (2009), with permission from Macmillan Publishers Limited, 2009.
Mentions: Table 2 and Fig. 1 give an overview of genome sequencing of putative probiotic bacteria that are publicly available, and Table 3 gives examples of proprietary sequences of commercial probiotics. By far the most used probiotics and the ones which have their genomes sequenced are those associated with gut health. Details of genomes sequenced before 2009 have been summarized by Mayo and colleagues (2008) and Ventura and colleagues (2009). Infants are born with a sterile gastrointestinal (GI) tract but in breast‐fed babies colonization by bifidobacteria is rapidly seen. It is thought that these bacteria confer a health benefit to the infant. The first colonizer is Bifidobacterium longum ssp. infantis, which has the largest genome of any sequenced bifidobacteria at 2.83 Mb (Sela et al., 2008). The genome has complete pathways for the synthesis of some vitamins and a novel 43 kb gene cluster encoding a system for the import and degradation of human milk oligosaccharides (HMOs). After weaning, the numbers of this bifidobacterium decline but others become more dominant. Bifidobacterium animalis ssp. lactis, a resident of the GI tract and the most commonly used probiotic in Europe and North America, has a genome size of only 1.9 Mb. These bifidobacteria lack the HMO cluster as presumably post‐weaned animals no longer require this functionality. They do, however, contain the fos gene cluster necessary to produce the enzymes to break down and utilize health‐promoting fructo‐oligosaccharides, a well‐known prebiotic and bifidogenic factor.

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

We were sitting in the Irish pub on quiz night, dumbfounded by trivia questions about ingredients of Mornay sauce and best‐selling Boy Bands, when the following question came up: What are ‘Live microorganisms which when administered in adequate amounts confer a health benefit on the host?’ At long last, we had a correct answer: PROBIOTICS! What do probiotics actually do? What is the meaning of ‘confer a health benefit’? Lactobacillus plantarum JDM1 is a widely used Chinese commercial probiotic strain which appears to have lost 100 kb relative to the non‐commercial strain WCFS1, encoding sugar transport and metabolism, possibly due to prolonged growth of this probiotic strain in rich medium... Lactobacillus rhamnosus GG and Lactobacillus rhamnosus ATCC53103, probiotic strains used widely for nearly 20 years in a variety of functional foods, differ only by deletion of 5 kb in ATCC53103, and an inversion of 8.9 kb... SpaA is the major scaffolding protein upon which the minor pili proteins SpaB and SpaC are attached... Using insertional inactivation of spaC, a truncated SpaC protein was produced which resulted in cells with a greatly reduced binding to human mucus... The targeted loss of genomic regions was experimentally validated when growth of the intestinal B.  longum in the laboratory for 1000 generations resulted in two large deletions, one in a bacteriocin‐encoding region, analogous to a predicted deletion event in the commercial strain B.  longum NCC2705... This deletion strain showed a significantly reduced competitive ability against Clostridium difficile and Escherichia coli... At present, many of the commercial probiotic strains originate from the intestine of healthy infants and adults... Current research focuses on the determination of the characteristics these bacteria use to survive and compete successfully in the intestine, and with this knowledge more effective probiotic strains can be identified... And what will be the next hype? Memory‐enhancing drinks would definitely be a commercial success on quiz night in the pub!

Show MeSH