Microbiology - Journal Articles

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ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris
(Oxford University Press, 1982) Fitzgerald, Gerald F.; Daly, C.; Brown, L. R.; Gingeras, T. R.
Processing effects on the nutritional advancement of probiotics and prebiotics
(Co-Action Publishing, 2004-07) Ananta, E.; Birkeland, S. E.; Corcoran, B.; Fitzgerald, Gerald F.; Hinz, S.; Klijn, A.; Matto, J.; Mercernier, A.; Nilsson, U.; Nyman, M.; O'Sullivan, Eilís; Parche, S.; Rautonen, N.; Ross, R. Paul; Saarela, M.; Stanton, Catherine; Stahl, U.; Suomalainen, T.; Vincken, J. P.; Virkajarvi, I.; Voragen, F.; Wesenfeld, J.; Wouters, R.; Knorr, D.; Science Foundation Ireland; European Commission
Investigates the processing effects on the nutritional advancement of probiotics and prebiotics. Efforts of health researchers to overcome difficulties that impact on the performance of functional foods; Importance of characterizing the interactions between probiotics and prebiotics in starter cultures or in functional foods prior to human consumption; Role of prebiotics on the viability and stability of probiotic cultures within food matrices during processing and storage.
Lactococcus lactis is capable of improving the riboflavin status in deficient rats
(Cambridge University Press, 2005) LeBlanc, Jean Guy; Burgess, Catherine M.; Sesma, Fernando; de Giori, Graciela Savoy; van Sinderen, Douwe; Science Foundation Ireland; European Commission; Consejo Nacional de Investigaciones Cientificas y Tecnicas, Argentina; Consejo de Investigaciones de la Universidad Nacional de Tucumán, Argentina
Lactococcus lactis is a commonly used starter strain that can be converted from a vitamin B2 consumer into a vitamin B2 'factory' by over-expressing its riboflavin biosynthesis genes. The present study was conducted to assess in a rat bioassay the response of riboflavin produced by GM or native lactic acid bacteria (LAB). The riboflavin-producing strains were able to eliminate most physiological manifestations of ariboflavinosis such as stunted growth, elevated erythrocyte glutathione reductase activation coefficient values and hepatomegalia that were observed using a riboflavin depletion–repletion model. Riboflavin status and growth rates were greatly improved when the depleted rats were fed with cultures of L. lactis that overproduced this vitamin whereas the native strain did not show the same effect. The present study is the first animal trial with food containing living bacteria that were engineered to overproduce riboflavin. These results pave the way for analysing the effect of similar riboflavin-overproducing LAB in human trials.
A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system
(BioMed Central, 2006-04-28) O'Driscoll, Jonathan; Heiter, Daniel F.; Wilson, Geoffrey G.; Fitzgerald, Gerald F.; Roberts, Richard; van Sinderen, Douwe; Science Foundation Ireland
Background: Restriction/modification systems provide the dual function of protecting host DNA against restriction by methylation of appropriate bases within their recognition sequences, and restriction of foreign invading un-methylated DNA, such as promiscuous plasmids or infecting bacteriphage. The plasmid-encoded LlaJI restriction/modification system from Lactococcus lactis recognizes an asymmetric,complementary DNA sequence, consisting of 5'GACGC'3 in one strand and 5'GCGTC'3 in the other and provides a prodigious barrier to bacteriophage infection. LlaJI is comprised of four similarly oriented genes, encoding two 5mC-MTases (M1.LlaJI and M2.LlaJI) and two subunits responsible for restriction activity R1.LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction determinants in an attempt to characterize mechanistic features of this unusual hetero-oligomeric endonuclease. Results: Detailed bioinformatics analysis confirmed the presence of a conserved GTP binding and hydrolysis domain within the C-terminal half of the R1.LlaJI amino acid sequence whilst the N-terminal half appeared to be entirely unique. This domain architecture was homologous with that of the "B" subunit of the GTP-dependent, methyl-specific McrBC endonuclease from E.coli K-12. R1.LlaJI did not appear to contain a catalytic centre, whereas this conserved motif; PD....D/EXK, was clearly identified within the amino acid sequence for R2.LlaJI. Both R1.LlaJI and R2.LlaJI were found to be absolutely required for detectable LlaJI activity in vivo. The LlaJI restriction subunits were purified and examined in vitro, which allowed the assignment of R1.LlaJI as the sole specificity determining subunit, whilst R2.LlaJI is believed to mediate DNA cleavage. Conclusion: The hetero-subunit structure of LlaJI, wherein one subunit mediates DNA binding whilst the other subunit is predicted to catalyze strand hydrolysis distinguishes LlaJI from previously characterized restriction-modification systems. Furthermore, this distinction is accentuated by the fact that whilst LlaJI behaves as a conventional Type IIA system in vivo, in that it restricts un-methylated DNA, it resembles the Type IV McrBC endonuclease, an enzyme specific for methylated DNA. A number of similar restriction determinants were identified in the database and it is likely LlaJI together with these homologous systems, comprise a new subtype of the Type II class incorporating features of Type II and Type IV systems.
A general method for selection of riboflavin-overproducing food grade micro-organisms
(BioMed Central, 2006-07) Burgess, Catherine M.; Smid, Eddy J.; Rutten, Ger; van Sinderen, Douwe; Science Foundation Ireland
Background: This study describes a strategy to select and isolate spontaneous riboflavin overproducing strains of Lactobacillus (Lb.) plantarum, Leuconostoc (Lc.) mesenteroides and Propionibacterium (P.) freudenreichii. Results: The toxic riboflavin analogue roseoflavin was used to isolate natural riboflavinoverproducing variants of the food grade micro-organisms Lb. plantarum, Lc. mesenteroides and P. freudenreichii strains. The method was successfully employed for strains of all three species. The mutation(s) responsible for the observed overproduction of riboflavin were identified for isolates of two species. Conclusion: Selection for spontaneous roseoflavin-resistant mutants was found to be a reliable method to obtain natural riboflavin-overproducing strains of a number of species commonly used in the food industry. This study presents a convenient method for deriving riboflavin-overproducing strains of bacterial starter cultures, which are currently used in the food industry, by a nonrecombinant methodology. Use of such starter strains can be exploited to increase the vitamin content in certain food products.
Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: theory and practical application to genomic and metagenomic projects
(BioMed Central, 2007-03-02) Moriarty, John; Marchesi, Julian R.; Metcalfe, Anthony; Science Foundation Ireland; Irish Government
Background: The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distributions for the number of gaps have been given in the literature, one motivation being ease of computation. Error bounds for these approximate distributions have not been given. Results: We give bounds on the probability distribution of the number of gaps when a circle is covered by fragments of fixed size. The absolute error in the approximation is typically on the order of 0.1% at 10× coverage depth. The method can be applied to coverage problems on the interval, including edge effects, and applications are given to metagenomic libraries and shotgun sequencing.
Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity
(BioMed Central, 2007-04-02) O'Connor, Eileen B.; Cotter, Paul D.; O'Connor, Paula M.; O'Sullivan, Orla; Tagg, John R.; Ross, R. Paul; Hill, Colin; Science Foundation Ireland; Irish Government; Teagasc
Background: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. Results: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. Conclusion: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system.
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis
(BioMed Central, 2008) Scanlan, Pauline D.; Shanahan, Fergus; Marchesi, Julian R.; Health Research Board
Background: The incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. A PCR and clone library methodology targeting the mcrA gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract. Results: DNA faecal extracts (207 in total) from a group of healthy controls and five gastrointestinal disease groups were investigated. Colorectal cancer, polypectomised, irritable bowel syndrome and the control group had largely equivalent numbers of individuals positive for methanogens (range 45-50%). Methanogen incidence in the inflammatory bowel disease groups was reduced, 24% for ulcerative colitis and 30% for Crohn's disease. Four unique mcrA gene restriction fragment length polymorphism profiles were identified and bioinformatic analyses revealed that the majority of all sequences (94%) retrieved from libraries were 100% identical to Methanobrevibacter smithii mcrA gene. In addition, mcrA gene sequences most closely related to Methanobrevibacter oralis and members of the order Methanosarcinales were also recovered. Conclusion: The mcrA gene serves as a useful biomarker for methanogen detection in the human gut and the varying trends of methanogen incidence in the human gut could serve as important indicators of intestinal function. Although Methanobrevibacter smithii is the dominant methanogen in both the distal colon of individuals in health and disease, the diversity of methanogens is greater than previously reported. In conclusion, the low incidence of methanogens in Inflammatory Bowel Disease, the functionality of the methanogens and impact of methane production in addition to competitive interactions between methanogens and other microbial groups in the human gastrointestinal tract warrants further investigation.
Intramammary infusion of a live culture of Lactococcus lactis for treatment of bovine mastitis: comparison with antibiotic treatment in field trials
(Cambridge University Press, 2008-04) Klostermann, Katja; Crispie, Fiona; Flynn, James; Ross, R. Paul; Hill, Colin; Meaney, William; Science Foundation Ireland; European Commission
A treatment containing a live food-grade organism, Lactococcus lactis DPC3147, was compared with conventional antibiotic therapy for its potential to treat bovine chronic subclinical or clinical mastitis in two separate field trials. Effects on disease symptoms and bacteriology were monitored in response to infusion with the culture in each trial. In the first trial, the live culture treatment was compared with an intramammary antibiotic (n=11 quarters for each treatment). Results from this small trial demonstrated that the live culture had potential to be as effective at eliminating chronic subclinical infections as an antibiotic treatment. By day 12, 7 of the 11 quarters treated with the live culture were pathogen-free compared with 5 of the 11 antibiotic-treated infected quarters. Somatic cell counts (SCC) remained relatively unchanged regardless of treatment: average log SCC pre- and post-treatment in the lactococci-treated group were 6·33±0·41 (day 0) and 6·27±0·43 cells/ml (day 12) and average log SCC pre- and post-treatment in the antibiotic-treated group were 6·34±0·37 and 6·22±0·46 cells/ml on day 0 and on day 12, respectively. In the second trial, the live culture was compared with an intramammary antibiotic for the treatment of naturally occurring clinical mastitis cases (n=25 quarters for each treatment). Following a 14-d experimental period, similar bacteriological responses were observed in 7 out of 25 live culture treated quarters and 9 out of 25 antibiotic-treated quarters. Additionally, 15 of 25 cases treated with the culture and 18 of 25 cases treated with the antibiotic did not exhibit clinical signs of the disease following treatment. The results of these trials suggest that live culture treatment with Lc. lactis DPC3147 may be as efficacious as common antibiotic treatments in some instances.
Development of multiple strain competitive index assays for Listeria monocytogenes using pIMC; a new site-specific integrative vector
(BioMed Central, 2008-06) Monk, Ian R.; Casey, Pat G.; Cronin, Michael S.; Gahan, Cormac G.; Hill, Colin; Irish Research Council for Science, Engineering and Technology
The foodborne, gram-positive pathogen, Listeria monocytogenes, is capable of causing lethal infections in compromised individuals. In the post genomic era of L. monocytogenes research, techniques are required to identify and validate genes involved in the pathogenicity and environmental biology of the organism. The aim here was to develop a widely applicable method to tag L. monocytogenes strains, with a particular emphasis on the development of multiple strain competitive index assays.
Nisin inducible production of listeriolysin O in Lactococcus lactis NZ9000
(BioMed Central, 2008-07) Bahey-El-Din, Mohammed; Griffin, Brendan T.; Gahan, Cormac G.; Science Foundation Ireland
Background: Listeria monocytogenes is a well-characterized food-borne pathogen that infects pregnant women and immunocompromised individuals. Listeriolysin O (LLO) is the major virulence factor of the pathogen and is often used as a diagnostic marker for detection of L. monocytogenes. In addition, LLO represents a potent antigen driving T cell-mediated immunity during infection. In the present work, Lactococcus lactis NZ9000 was used as an expression host to hyper-produce LLO under inducible conditions using the NICE (NIsin Controlled Expression) system. We created a modified pNZ8048 vector encoding a six-His-tagged LLO downstream of the strong inducible PnisA promoter. Results: The constructed vector (pNZPnisA:CYTO-LLO) was expressed in L. lactis NZ9000 and was best induced at mid-log phase with 0.2% v/v nisin for 4 h statically at 30°C. Purification of the His-tagged LLO was accomplished by Ni-NTA affinity chromatography and functionality was confirmed through haemolytic assays. Total LLO yield (measured as total protein content) was 4.43–5.9 mg per litre culture and the haemolytic activity was still detectable after 8 months of storage at 4°C. Conclusion: The LLO production method described in this work provides an approach to efficient LLO production in the Gram-positive Lactococcus bacterium to yield a significant source of the protein for research and diagnostic applications. Expression of LLO in L. lactis has a number of benefits over E. coli which may facilitate both in vivo and in vitro applications of this system.
Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes
(PLOS, 2008-09-12) Cotter, Paul D.; Draper, Lorraine A.; Lawton, Elaine M.; Daly, Karen M.; Groeger, David S.; Casey, Pat G.; Ross, R. Paul; Hill, Colin; Cossart, Pascale; Science Foundation Ireland
Streptolysin S (SLS) is a bacteriocin-like haemolytic and cytotoxic virulence factor that plays a key role in the virulence of Group A Streptococcus (GAS), the causative agent of pharyngitis, impetigo, necrotizing fasciitis and streptococcal toxic shock syndrome. Although it has long been thought that SLS and related peptides are produced by GAS and related streptococci only, there is evidence to suggest that a number of the most notorious Gram-positive pathogenic bacteria, including Listeria monocytogenes, Clostridium botulinum and Staphylococcus aureus, produce related peptides. The distribution of the L. monocytogenes cluster is particularly noteworthy in that it is found exclusively among a subset of lineage I strains; i.e., those responsible for the majority of outbreaks of listeriosis. Expression of these genes results in the production of a haemolytic and cytotoxic factor, designated Listeriolysin S, which contributes to virulence of the pathogen as assessed by murine- and human polymorphonuclear neutrophil–based studies. Thus, in the process of establishing the existence of an extended family of SLS-like modified virulence peptides (MVPs), the genetic basis for the enhanced virulence of a proportion of lineage I L. monocytogenes may have been revealed.
Isolation of Lactobacilli with probiotic properties from the human stomach
(Society for Applied Bacteriology; Blackwell Publishing, 2008-10) Ryan, Kieran A.; Jayaraman, Thevaraajan; Daly, Paul; Canchaya, Carlos; Curran, Susan; Fang, Fang; Quigley, Eamonn M.; O'Toole, Paul W.; Science Foundation Ireland; Irish Research Council for Science Engineering and Technology
Aims: Recent evidence suggests that the human gastric microbiota is much more diverse than previously thought. The aim of this study was to assess the potential for isolating lactobacilli from the human stomach.Methods and Results: Lactobacilli were selectively cultured from gastric biopsies from 12 patients undergoing routine endoscopy. Lactobacilli were present in four of 12 biopsies. We isolated, in total 10 different strains representing five species (Lactobacillus gasseri, L. fermentum, L. vaginalis, L. reuteri and L. salivarius). The 10 isolates varied greatly in their ability to inhibit the growth of two Gram-positive bacteria and two Gram-negative bacteria. Furthermore, the acid and bile resistance profiles of the 10 isolates spanned a wide range. Conclusions: Five different Lactobacillus species were cultured from human gastric biopsies for the first time. Significance and Impact of the Study: Diverse Lactobacillus species are more prevalent in the human stomach than previously recognized, representing an untapped source of bacteria with beneficial probiotic and/or biotechnological properties.
Enhancing bile tolerance improves survival and persistence of Bifidobacterium and Lactococcus in the murine gastrointestinal tract
(BioMed Central, 2008-10) Watson, Debbie; Sleator, Roy D.; Hill, Colin; Gahan, Cormac G.; Science Foundation Ireland; Health Research Board
The majority of commensal gastrointestinal bacteria used as probiotics are highly adapted to the specialised environment of the large bowel. However, unlike pathogenic bacteria; they are often inadequately equipped to endure the physicochemical stresses of gastrointestinal (GI) delivery in the host. Herein we outline a patho-biotechnology strategy to improve gastric delivery and host adaptation of a probiotic strain Bifidobacterium breve UCC2003 and the generally regarded as safe (GRAS) organism Lactococcus lactis NZ9000.
Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa
(Oxford University Press, 2009) Tian, Zhe-Xian; Fargier, Emilie; Mac Aogáin, Micheál; Adams, Claire; Wang, Yi-Ping; O'Gara, Fergal; European Commission; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Irish Research Council for Science, Engineering and Technology; Health Research Board; Environmental Protection Agency; National Natural Science Foundation of China
The LysR-family regulator MexT modulates the expression of the MexEF-OprN efflux system in the human pathogen Pseudomonas aeruginosa. Recently, we demonstrated that MexT regulates certain virulence phenotypes, including the type-three secretion system and early attachment independent of its role in regulating MexEF-OprN. In this study, transcriptome profiling was utilized to investigate the global nature of MexT regulation in P. aeruginosa PAO1 and an isogenic mexEF mutant. Twelve genes of unknown function were highly induced by overexpressing MexT independent of MexEF-OprN. A well-conserved DNA motif was identified in the upstream regulatory region of nine of these genes and upstream of mexE. Reporter fusion analysis demonstrated that the expression of the genes was significantly induced by MexT in P. aeruginosa and a heterogenous Escherichia coli strain and that the conserved sequence was required for this induction. The conserved DNA motif was further characterized as the MexT binding site by site-directed mutagenesis and electrophoretic mobility shift assays. Genes containing this conserved regulatory sequence were identified across other Pseudomonas species, and their expression was activated by MexT. Thus, a novel regulon directly modulated by MexT, that includes but is independent of mexEF-oprN, has been identified.
Genome-scale analyses of health-promoting bacteria: probiogenomics
(Nature Publishing Group, 2009-01) Ventura, Marco; O'Flaherty, Sarah; Claesson, Marcus J.; Turroni, Francesca; Klaenhammer, Todd R.; van Sinderen, Douwe; O'Toole, Paul W.; Science Foundation Ireland; Health Research Board; Parmalat SpA, Italy; Department of Agriculture and Food, Ireland; Ministero dell’Istruzione, dell’Università e della Ricerca, Italy; European Commission
The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.
Genetic tools for investigating the biology of commensal lactobacilli
(Frontiers in Bioscience, 2009-01-01) Fang, Fang; O'Toole, Paul W.; Science Foundation Ireland
Lactobacilli belong to the genus Lactobacillus, the largest genus among the lactic acid bacteria (LAB). They are abundant in plant material and food resources, or they may inhabit niches in or on the bodies of humans and animals, as commensals. Lactobacilli of food origin are commercially important in the production of dairy products, fermented meats, vegetables, and sourdough, and many of their properties have been well studied. Commensal lactobacilli are good candidates for development as probiotics. In recent years, the general biology and host interaction mechanisms of commensal lactobacilli have attracted great interest. Although the metabolic pathways, predicted gene functions, and some phenotypic traits, of commensal lactobacilli can be inferred or deduced to an extent by the growing number of Lactobacillus genome sequencing project, various genetic tools are still required to confirm their phenotypic properties and biological traits. The current state of the art with respect to the available complement of genetic tools including genomic resources, and more traditional approaches to investigate the biology of commensal lactobacilli, will now be reviewed.
Microbial diversity in the human intestine and novel insights from metagenomics
(Frontiers In Bioscience, 2009-01-01) Ventura, Marco; Turroni, Francesca; Canchaya, Carlos; Vaughan, Elaine E.; O'Toole, Paul W.; van Sinderen, Douwe; Science Foundation Ireland; Department of Agriculture and Food, Ireland; Ministero dell’Istruzione, dell’Università e della Ricerca, Italy; Parmalat SpA, Italy; European Commission
Bacterial communities reside in very different ecological niches on and within the human host, such as those associated with the alimentary tract. The human gastrointestinal tract is populated with as many as 100 trillion bacterial cells, whose collective genome likely reflects the co-evolution between the microbial community and its host. Recent progress has highlighted the intriguing diversity of these bacterial populations and their important contributions to human physiology. Thus, a thorough understanding of the autochthonous component of the intestinal microbiota is expected to provide crucial information not only on how to develop therapies for various gastrointestinal diseases but also on how to choose the next generation of probiotic bacteria as part of novel functional foods. Recently, novel culture-independent approaches such as metagenomics-based techniques were shown to be crucially important for the exploration of the biodiversity of the human intestinal microbiota.
Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1beta and IL-8 gene expression
(Cambridge University Press, 2009-02) Beecher, Christine; Daly, Mairead; Berry, Donagh P.; Klostermann, Katja; Flynn, James; Meaney, William; Hill, Colin; McCarthy, Tommie V.; Ross, R. Paul; Giblin, Linda; Science Foundation Ireland; Teagasc; Dairy Research Trust, Ireland
Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture, Lactococcus lactis DPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed in Interleukin (IL)-1β and IL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of a Lc. lactis leads to a rapid and considerable innate immune response.
Comparative genomics of lactic acid bacteria reveals a niche-specific gene set
(BioMed Central, 2009-03-05) O'Sullivan, Orla; O'Callaghan, John; Sangrador-Vegas, Amaia; McAuliffe, Olivia; Slattery, Lydia; Kaleta, Pawel; Callanan, Michael; Fitzgerald, Gerald F.; Ross, R. Paul; Beresford, Thomas P.; Department of Agriculture, Food and the Marine
Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM. This led us to hypothesise that a group of genes could be determined which could define an organism's niche. Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152,lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes. Conclusion: Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin. We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche.

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