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Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 327] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol 2016; 7:925. [PMID: 27379055 PMCID: PMC4908950 DOI: 10.3389/fmicb.2016.00925] [Citation(s) in RCA: 506] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.
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Affiliation(s)
- Amy O'Callaghan
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
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53
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Udatha DBRKG, Topakas E, Salazar M, Olsson L, Andersen MR, Panagiotou G. Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. BMC SYSTEMS BIOLOGY 2015; 9:77. [PMID: 26573537 PMCID: PMC4647334 DOI: 10.1186/s12918-015-0224-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/28/2015] [Indexed: 12/30/2022]
Abstract
Background The gene expression and secretion of fungal lignocellulolytic enzymes are tightly controlled at the transcription level using independent mechanisms to respond to distinct inducers from plant biomass. An advanced systems-level understanding of transcriptional regulatory networks is required to rationally engineer filamentous fungi for more efficient bioconversion of different types of biomass. Results In this study we focused on ten chemically defined inducers to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae and shed light on the complex network of transcriptional activators required. The chemical diversity analysis of the inducers, based on 186 chemical descriptors calculated from the structure, resulted into three clusters, however, the global, metabolic and extracellular protein transcription of the A. oryzae genome were only partially explained by the chemical similarity of the enzyme inducers. Genes encoding enzymes that have attracted considerable interest such as cellobiose dehydrogenases and copper-dependent polysaccharide mono-oxygenases presented a substrate-specific induction. Several homology-model structures were derived using ab-initio multiple threading alignment in our effort to elucidate the interplay of transcription factors involved in regulating plant-deconstructing enzymes and metabolites. Systematic investigation of metabolite-protein interactions, using the 814 unique reactants involved in 2360 reactions in the genome scale metabolic network of A. oryzae, was performed through a two-step molecular docking against the binding pockets of the transcription factors AoXlnR and AoAmyR. A total of six metabolites viz., sulfite (H2SO3), sulfate (SLF), uroporphyrinogen III (UPGIII), ethanolamine phosphate (PETHM), D-glyceraldehyde 3-phosphate (T3P1) and taurine (TAUR) were found as strong binders, whereas the genes involved in the metabolic reactions that these metabolites appear were found to be significantly differentially expressed when comparing the inducers with glucose. Conclusions Based on our observations, we believe that specific binding of sulfite to the regulator of the cellulase gene expression, AoXlnR, may be the molecular basis for the connection of sulfur metabolism and cellulase gene expression in filamentous fungi. Further characterization and manipulation of the regulatory network components identified in this study, will enable rational engineering of industrial strains for improved production of the sophisticated set of enzymes necessary to break-down chemically divergent plant biomass. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0224-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D B R K Gupta Udatha
- The Norwegian Structural Biology Centre, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15780, Greece.
| | - Margarita Salazar
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| | - Lisbeth Olsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Søltofts plads 223, DK-2800, Lyngby, Denmark.
| | - Gianni Panagiotou
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Hong Kong, China.
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Goh YJ, Klaenhammer TR. Genetic Mechanisms of Prebiotic Oligosaccharide Metabolism in Probiotic Microbes. Annu Rev Food Sci Technol 2015; 6:137-56. [DOI: 10.1146/annurev-food-022814-015706] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; ,
| | - Todd R. Klaenhammer
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; ,
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Egan M, Motherway MO, Kilcoyne M, Kane M, Joshi L, Ventura M, van Sinderen D. Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium. BMC Microbiol 2014; 14:282. [PMID: 25420416 PMCID: PMC4252021 DOI: 10.1186/s12866-014-0282-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bifidobacteria constitute a specific group of commensal bacteria that commonly inhabit the mammalian gastrointestinal tract. Bifidobacterium breve UCC2003 was previously shown to utilize a variety of plant/diet/host-derived carbohydrates, including cellodextrin, starch and galactan, as well as the mucin and HMO-derived monosaccharide, sialic acid. In the current study, we investigated the ability of this strain to utilize parts of a host-derived source of carbohydrate, namely the mucin glycoprotein, when grown in co-culture with the mucin-degrading Bifidobacterium bifidum PRL2010. RESULTS B. breve UCC2003 was shown to exhibit growth properties in a mucin-based medium, but only when grown in the presence of B. bifidum PRL2010, which is known to metabolize mucin. A combination of HPAEC-PAD and transcriptome analyses identified some of the possible monosaccharides and oligosaccharides which support this enhanced co-cultivation growth/viability phenotype. CONCLUSION This study describes the potential existence of a gut commensal relationship between two bifidobacterial species. We demonstrate the in vitro ability of B. breve UCC2003 to cross-feed on sugars released by the mucin-degrading activity of B. bifidum PRL2010, thus advancing our knowledge on the metabolic adaptability which allows the former strain to colonize the (infant) gut by its extensive metabolic abilities to (co-)utilize available carbohydrate sources.
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Affiliation(s)
- Muireann Egan
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| | - Mary O'Connell Motherway
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| | - Michelle Kilcoyne
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | - Marian Kane
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
| | - Douwe van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
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Mao B, Li D, Zhao J, Liu X, Gu Z, Chen YQ, Zhang H, Chen W. In vitro fermentation of lactulose by human gut bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10970-10977. [PMID: 25340538 DOI: 10.1021/jf503484d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Lactulose has been known as a prebiotic that can selectively stimulate the growth of beneficial bifidobacteria and lactobacilli. Recent studies have indicated that Streptococcus mutans, Clostridium perfringens, and Faecalibacterium prausnitzii are also able to utilize lactulose. However, the previous studies mainly focused on the utilization of lactulose by individual strains, and few studies were designed to identify the species that could utilize lactulose among gut microbiota. This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in silico and traditional culture methods. The prediction results suggested that genes for the transporters and glycosidases of lactulose are well distributed in the genomes of 222 of 453 strains of gastrointestinal-tract bacteria. The screening assays identified 35 species with the ability to utilize lactulose, of which Cronobacter sakazakii, Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas putida were reported for the first time to be capable of utilizing lactulose. In addition, significant correlations between lactulose and galactooligosaccharide metabolism were found. Thus, more attention should be paid to bacteria besides bifidobacteria and lactobacilli to further investigate the relationship between functional oligosaccharides and gut bacteria.
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Affiliation(s)
- Bingyong Mao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University , Wuxi 214122, People's Republic of China
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Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M. Diversity, ecology and intestinal function of bifidobacteria. Microb Cell Fact 2014; 13 Suppl 1:S4. [PMID: 25186128 PMCID: PMC4155821 DOI: 10.1186/1475-2859-13-s1-s4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human gastrointestinal tract represents an environment which is a densely populated home for a microbiota that has evolved to positively contribute to host health. At birth the essentially sterile gastrointestinal tract (GIT) is rapidly colonized by microorganisms that originate from the mother and the surrounding environment. Within a short timeframe a microbiota establishes within the (breastfed) infant's GIT where bifidobacteria are among the dominant members, although their numerical dominance disappears following weaning. The numerous health benefits associated with bifidobacteria, and the consequent commercial relevance resulting from their incorporation into functional foods, has led to intensified research aimed at the molecular understanding of claimed probiotic attributes of this genus. In this review we provide the current status on the diversity and ecology of bifidobacteria. In addition, we will discuss the molecular mechanisms that allow this intriguing group of bacteria to colonize and persist in the GIT, so as to facilitate interaction with its host.
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58
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Metabolism of sialic acid by Bifidobacterium breve UCC2003. Appl Environ Microbiol 2014; 80:4414-26. [PMID: 24814790 DOI: 10.1128/aem.01114-14] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3'-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain, Bifidobacterium bifidum PRL2010.
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59
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O′Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JET, Smokvina T, van Sinderen D. Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis. PLoS One 2014; 9:e94875. [PMID: 24743599 PMCID: PMC3990576 DOI: 10.1371/journal.pone.0094875] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/20/2014] [Indexed: 01/25/2023] Open
Abstract
Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized fermented dairy product for which beneficial effects on health has been studied by clinical and preclinical trials. To date little is known about the molecular mechanisms that could explain the beneficial effects that bifidobacteria impart to the host. Restriction-modification (R-M) systems have been identified as key obstacles in the genetic accessibility of bifidobacteria, and circumventing these is a prerequisite to attaining a fundamental understanding of bifidobacterial attributes, including the genes that are responsible for health-promoting properties of this clinically and industrially important group of bacteria. The complete genome sequence of B. animalis subsp. lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type II R-M systems, designated BanLI and BanLII. In order to investigate the functionality and specificity of these two putative R-M systems in B. animalis subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated methylome analysis. In addition, the contribution of the identified R-M systems to the genetic accessibility of this strain was assessed.
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Affiliation(s)
- Mary O′Connell Motherway
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Debbie Watson
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | | | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
- * E-mail:
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60
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Finelli C, Tarantino G. Non-alcoholic fatty liver disease, diet and gut microbiota. EXCLI JOURNAL 2014; 13:461-90. [PMID: 26417275 PMCID: PMC4464355 DOI: pmid/26417275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 03/31/2014] [Indexed: 02/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a severe liver disease that is increasing in prevalence with the worldwide epidemic of obesity and its related insulin-resistance state. Evidence for the role of the gut microbiota in energy storage and the subsequent development of obesity and some of its related diseases is now well established. More recently, a new role of gut microbiota has emerged in NAFLD. The gut microbiota is involved in gut permeability, low-grade inflammation and immune balance, it modulates dietary choline metabolism, regulates bile acid metabolism and produces endogenous ethanol. All of these factors are molecular mechanisms by which the microbiota can induce NAFLD or its progression toward overt non-alcoholic steatohepatitis. Modification of the gut microbiota composition and/or its biochemical capacity by specific dietary or pharmacological interventions may advantageously affect host metabolism. Large-scale intervention trials, investigating the potential benefit of prebiotics and probiotics in improving cardiometabolic health in high-risk populations, are fervently awaited.
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Affiliation(s)
- Carmine Finelli
- Center of Obesity and Eating Disorders, Stella Maris Mediterraneum Foundation, Potenza, Italy
| | - Giovanni Tarantino
- Department of Clinical Medicine and Surgery, Federico II University Medical School of Naples, Italy
- National Cancer Institute "Foundation G. Pascale" -IRCS- 83013 Mercogliano (Av), Italy
- *To whom correspondence should be addressed: Giovanni Tarantino, Department of Clinical Medicine and Surgery, Federico II University Medical School of Naples, Via Sergio Pansini, 5, 80131 Naples, Italy, E-mail:
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Peacock KS, Ruhaak LR, Tsui MK, Mills DA, Lebrilla CB. Isomer-specific consumption of galactooligosaccharides by bifidobacterial species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:12612-12619. [PMID: 24313277 PMCID: PMC3912189 DOI: 10.1021/jf403789r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Prebiotics are nondigestible substrates that stimulate the growth of beneficial microbes in the human intestine. Galactooligosaccharides (GOS) are food ingredients that possess prebiotic properties, in particular, promoting the growth of bifidobacteria in situ. However, precise mechanistic details of GOS consumption by bifidobacteria remain poorly understood. Because GOS are mixtures of polymers of different lengths and linkages, there is interest in determining which specific structures provide prebiotic effects to potentially create better supplements. This paper presents a method comprising porous graphitic carbon separation, isotopic labeling, and mass spectrometry analysis for the structure-specific analysis of GOS isomers and their bacterial consumption rate. Using this strategy, the differential bacterial consumption of GOS by the bifidobacteria species Bifidobacterium longum subsp. infantis, Bifidobacterium animalis subsp. lactis, and Bifidobacterium adolescentis was determined, indicating that the use of specific GOS isomers in infant formula may provide enrichment of distinct species.
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Affiliation(s)
- Kyle S. Peacock
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - L. Renee Ruhaak
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - Man Ki Tsui
- Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - David A. Mills
- Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
- Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
- To whom correspondence should be addressed: University of California, Davis Department of Chemistry One Shields Avenue Davis, CA, 95616 USA Phone: 1-530-752-0504 FAX: 1-530-754-8995
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Fouhy F, O’Connell Motherway M, Fitzgerald GF, Ross RP, Stanton C, van Sinderen D, Cotter PD. In silico assigned resistance genes confer Bifidobacterium with partial resistance to aminoglycosides but not to β-lactams. PLoS One 2013; 8:e82653. [PMID: 24324818 PMCID: PMC3855789 DOI: 10.1371/journal.pone.0082653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/05/2013] [Indexed: 12/25/2022] Open
Abstract
Bifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.
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Affiliation(s)
- Fiona Fouhy
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Microbiology Department, University College Cork, Cork, Ireland
| | - Mary O’Connell Motherway
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Gerald F. Fitzgerald
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Douwe van Sinderen
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
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Viborg AH, Katayama T, Abou Hachem M, Andersen MC, Nishimoto M, Clausen MH, Urashima T, Svensson B, Kitaoka M. Distinct substrate specificities of three glycoside hydrolase family 42 -galactosidases from Bifidobacterium longum subsp. infantis ATCC 15697. Glycobiology 2013; 24:208-16. [DOI: 10.1093/glycob/cwt104] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Ruiz L, Motherway MO, Lanigan N, van Sinderen D. Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003. PLoS One 2013; 8:e64699. [PMID: 23737995 PMCID: PMC3667832 DOI: 10.1371/journal.pone.0064699] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/17/2013] [Indexed: 01/20/2023] Open
Abstract
Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Mary O’Connell Motherway
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Noreen Lanigan
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
- * E-mail:
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Andersen JM, Barrangou R, Abou Hachem M, Lahtinen SJ, Goh YJ, Svensson B, Klaenhammer TR. Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04. BMC Genomics 2013; 14:312. [PMID: 23663691 PMCID: PMC3684542 DOI: 10.1186/1471-2164-14-312] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 04/18/2013] [Indexed: 02/02/2023] Open
Abstract
Background Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of uptake remain unknown for most candidate prebiotics. The differential transcriptomes of Bifidobacterium animalis subsp. lactis Bl-04, induced by 11 potential prebiotic oligosaccharides were analyzed to identify the genetic loci involved in the uptake and catabolism of α- and β-linked hexoses, and β-xylosides. Results The overall transcriptome was modulated dependent on the type of glycoside (galactosides, glucosides or xylosides) utilized. Carbohydrate transporters of the major facilitator superfamily (induced by gentiobiose and β-galacto-oligosaccharides (GOS)) and ATP-binding cassette (ABC) transporters (upregulated by cellobiose, GOS, isomaltose, maltotriose, melibiose, panose, raffinose, stachyose, xylobiose and β-xylo-oligosaccharides) were differentially upregulated, together with glycoside hydrolases from families 1, 2, 13, 36, 42, 43 and 77. Sequence analysis of the identified solute-binding proteins that determine the specificity of ABC transporters revealed similarities in the breadth and selectivity of prebiotic utilization by bifidobacteria. Conclusion This study identified the differential gene expression for utilization of potential prebiotics highlighting the extensive capabilities of Bifidobacterium lactis Bl-04 to utilize oligosaccharides. Results provide insights into the ability of this probiotic microbe to utilize indigestible carbohydrates in the human gastrointestinal tract.
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Affiliation(s)
- Joakim M Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads Building 224, Kgs. Lyngby DK-2800, Denmark
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