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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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Identification of pili in L. rhamnosus GG by immunogold high‐resolution electron micrography. Multiple pili are shown with gold‐labelled SpaC proteins. Reproduced with permission from Kankainen and colleagues (2009).
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f2: Identification of pili in L. rhamnosus GG by immunogold high‐resolution electron micrography. Multiple pili are shown with gold‐labelled SpaC proteins. Reproduced with permission from Kankainen and colleagues (2009).

Mentions: Several new genome sequences of probiotics have been released in 2009. Bifidobacterium animalis ssp. lactis AD011, isolated from a healthy breast‐fed infant, has a high level of immunomodulatory activity (Kim et al., 2008b). Its genome encodes multiple glycosylases than can degrade plant‐ or milk‐derived oligosaccharides, and the fos gene cluster for processing of fructo‐oligosaccharides (Kim et al., 2009). Bifidobacterium animalis ssp. lactis strains B1‐04 and DSM10140, both from commercial probiotic products, differ only by 47 single nucleotide polymorphisms and four small indels, of which one indel in a CRISPR (Barrangou et al., 2009). Lactobacillus johnsonii FI9785 is a competitive exclusion agent against pathogens in poultry (Wegmann et al., 2009). 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 (Zhang et al., 2009). 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 (Kankainen et al., 2009; Morita et al., 2009). Compared with other sequenced intestinal lactobacilli, both Lb. rhamnosus genomes have a relatively high number of proteins involved in carbohydrate and amino acid metabolism and transport, and defence mechanisms. In particular, 28 complete PTS‐type transporters and 25 putative GHs are encoded, including the alpha‐L‐fucosidase (GH29; see Cazy database http://www.cazy.org) and alpha‐mannosidase (GH38) families, which are not found in other sequenced lactobacilli. In addition, these Lb. rhamnosus genomes have three gene clusters encoding proteins with WxL domains which can attach to the peptidoglycan on cell surfaces (Siezen et al., 2006; Brinster et al., 2007); again, these gene clusters have not been found in other intestinal lactobacilli, but rather in plant‐associated Gram‐positive bacteria (Siezen et al., 2006). Most novel is the finding that Lb. rhamnosus GG has a gene cluster spaCBA, encoding three secreted pilin proteins with LPxTG‐type peptidoglycan anchors, which is not present in the highly syntenous genome of Lb. rhamnosus LC705 (Kankainen et al., 2009). 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 (Kankainen et al., 2009). The authors suggest that the presence of SpaC‐containing pili (Fig. 2) may possibly explain the longer persistence of this strain in the GI tract than strain LC705. Together with the high potential for sugar uptake and metabolism, this may explain probiotic effects of these Lb. rhamnosus strains.


Probiotics genomics.

Siezen RJ, Wilson G - Microb Biotechnol (2010)

Identification of pili in L. rhamnosus GG by immunogold high‐resolution electron micrography. Multiple pili are shown with gold‐labelled SpaC proteins. Reproduced with permission from Kankainen and colleagues (2009).
© Copyright Policy
Related In: Results  -  Collection

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

f2: Identification of pili in L. rhamnosus GG by immunogold high‐resolution electron micrography. Multiple pili are shown with gold‐labelled SpaC proteins. Reproduced with permission from Kankainen and colleagues (2009).
Mentions: Several new genome sequences of probiotics have been released in 2009. Bifidobacterium animalis ssp. lactis AD011, isolated from a healthy breast‐fed infant, has a high level of immunomodulatory activity (Kim et al., 2008b). Its genome encodes multiple glycosylases than can degrade plant‐ or milk‐derived oligosaccharides, and the fos gene cluster for processing of fructo‐oligosaccharides (Kim et al., 2009). Bifidobacterium animalis ssp. lactis strains B1‐04 and DSM10140, both from commercial probiotic products, differ only by 47 single nucleotide polymorphisms and four small indels, of which one indel in a CRISPR (Barrangou et al., 2009). Lactobacillus johnsonii FI9785 is a competitive exclusion agent against pathogens in poultry (Wegmann et al., 2009). 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 (Zhang et al., 2009). 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 (Kankainen et al., 2009; Morita et al., 2009). Compared with other sequenced intestinal lactobacilli, both Lb. rhamnosus genomes have a relatively high number of proteins involved in carbohydrate and amino acid metabolism and transport, and defence mechanisms. In particular, 28 complete PTS‐type transporters and 25 putative GHs are encoded, including the alpha‐L‐fucosidase (GH29; see Cazy database http://www.cazy.org) and alpha‐mannosidase (GH38) families, which are not found in other sequenced lactobacilli. In addition, these Lb. rhamnosus genomes have three gene clusters encoding proteins with WxL domains which can attach to the peptidoglycan on cell surfaces (Siezen et al., 2006; Brinster et al., 2007); again, these gene clusters have not been found in other intestinal lactobacilli, but rather in plant‐associated Gram‐positive bacteria (Siezen et al., 2006). Most novel is the finding that Lb. rhamnosus GG has a gene cluster spaCBA, encoding three secreted pilin proteins with LPxTG‐type peptidoglycan anchors, which is not present in the highly syntenous genome of Lb. rhamnosus LC705 (Kankainen et al., 2009). 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 (Kankainen et al., 2009). The authors suggest that the presence of SpaC‐containing pili (Fig. 2) may possibly explain the longer persistence of this strain in the GI tract than strain LC705. Together with the high potential for sugar uptake and metabolism, this may explain probiotic effects of these Lb. rhamnosus strains.

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