Genome-scale analyses of health-promoting bacteria: probiogenomics

Ventura, Marco; O’Flaherty, Sarah; Claesson, Marcus J.; Turroni, Francesca; Klaenhammer, Todd R.; Sinderen, Douwe van; O’Toole, Paul W.

doi:10.1038/nrmicro2047

Cited by 399 publications

(303 citation statements)

References 88 publications

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“…The range of phylum Firmicutes in our study, across all 161 time-0 samples, varied from 8% to 80%, whereas phylum Bacteroidetes varied from 14% to 92%. The phylum Actinobacteria includes Bifidobacterium spp., which are among the best characterized of the commensal organisms considered beneficial or probiotic in nature (47). This phylum ranged from 0% to 8% in the total dataset from 161 fecal samples, comparing with values of 0.4% (41) to 11.4% (46) in other studies of younger adults.…”

Section: Discussionmentioning

confidence: 85%

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Claesson

Cusack

O'Sullivan

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

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Section: Discussionmentioning

confidence: 85%

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Claesson

Cusack

O'Sullivan

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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1,438

1,149

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“…Both genomes are among the largest sized of the lactobacilli genomes, which typically average Ϸ2 Mbp (7,8). The genome of strain GG contains a single circular chromosome 3.01 Mbp in size, whereas strain LC705 contains a slightly smaller chromosome (2.97 Mbp) and a 64.5-kb circular plasmid, pLC1 [ Table 1 and supporting information (SI) Fig.…”

Section: Resultsmentioning

confidence: 99%

“…One postulated feature considered indispensable for some probiotic lactobacilli is adherence to human intestinal tissues, which may promote a variety of specific interactions with the host (4)(5)(6). Despite many studies demonstrating the adherent properties of lactobacilli, the molecular mechanisms governing these host-microbe interactions are only beginning to emerge as comparative and functional analyses of their genome sequences progress (7,8). Cell surface components that promote the adherence of lactobacilli include exopolysaccharides (EPSs); teichoic acids (TAs); and surface-exposed proteins, such as the S-layer and LPXTG-like proteins (4).…”

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confidence: 99%

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein

Kankainen

Paulín

Tynkkynen

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated the colinearity. A significant number of strain-specific genes were predicted in these islands (80 in GG and 72 in LC705). The GG-specific islands included genes coding for bacteriophage components, sugar metabolism and transport, and exopolysaccharide biosynthesis. One island only found in L. rhamnosus GG contained genes for 3 secreted LPXTG-like pilins (spaCBA) and a pilin-dedicated sortase. Using anti-SpaC antibodies, the physical presence of cell wall-bound pili was confirmed by immunoblotting. Immunogold electron microscopy showed that the SpaC pilin is located at the pilus tip but also sporadically throughout the structure. Moreover, the adherence of strain GG to human intestinal mucus was blocked by SpaC antiserum and abolished in a mutant carrying an inactivated spaC gene. Similarly, binding to mucus was demonstrated for the purified SpaC protein. We conclude that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial. The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues.genome ͉ probiotics ͉ adhesion ͉ pilus ͉ lactic acid bacteria

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“…The human gut is colonized with an enormous variety and amount of microorganisms, dramatically affecting human physiology and pathology [4]. The entire cohort harbors more than 1,000 prevalent bacterial species.…”

Section: Introductionmentioning

confidence: 99%

The Primary Research on the Gut Microbes in KKAy Mice

Han

et al. 2013

Indian J Microbiol

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In the first part of this paper, gut microbial difference of two genotypes mice was researched. The gut microbial community of type 2 diabetes animal model KKAy mice and normal C57BL/6J mice had clear distinctions in DGGE (denaturing gradient gel electrophoresis) profiles. The pairwise similarity coefficient (C s ) was only 26-44 % between KKAy and C57BL/6J, but C s was 82-100 % among same genotypes mice. Thirteen dominant bands were cloned from DGGE profiles to exhibit difference on gut microbial structure further. In the second part of this paper, the influence of hypoglycemic drug Pioglitazone on the gut microbes in KKAy mice was researched by gut microbial diversity analysis and principal component analysis (PCA). The results showed that Pioglitazone reduced the gut microbial diversity slightly and changed gut microbial structure of KKAy mice to that of normal C57BL/6J mice.

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Genome-scale analyses of health-promoting bacteria: probiogenomics

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Cited by 399 publications

References 88 publications

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein

The Primary Research on the Gut Microbes in KKAy Mice

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