scholarly journals Synbiotic Matchmaking in Lactobacillus plantarum: Substrate Screening and Gene-Trait Matching To Characterize Strain-Specific Carbohydrate Utilization

2020 ◽  
Vol 86 (18) ◽  
Author(s):  
Jori Fuhren ◽  
Christiane Rösch ◽  
Maud ten Napel ◽  
Henk A. Schols ◽  
Michiel Kleerebezem
Keyword(s):  
Lactobacillus Plantarum ◽  
Specific Growth ◽  
Phenotypic Diversity ◽  
Health Effect ◽  
Gene Clusters ◽  
Substrate Utilization ◽  
Transport Systems ◽  
Carbohydrate Utilization ◽  
Single Strain ◽  
Content Type

ABSTRACT Synbiotics are food supplements that combine probiotics and prebiotics to synergistically elicit a health effect in humans. Lactobacillus plantarum exhibits remarkable genetic and phenotypic diversity, in particular in strain-specific carbohydrate utilization capacities, and several strains are marketed as probiotics. We have screened 77 L. plantarum strains for their abilities to utilize specific prebiotic fibers, revealing variable and strain-specific growth efficiencies on isomalto- and galactooligosaccharides. We identified a single strain within the screening panel that was able to effectively utilize inulin and fructooligosaccharides (FOS), which did not support efficient growth of the rest of the strains. In the panel we tested, we did not find strains that could utilize arabinoxylooligosaccharides or sulfated fucoidan. The strain-specific growth phenotype on isomaltooligosaccharides was further analyzed using high-performance anion-exchange chromatography, which revealed distinct substrate utilization phenotypes within the strain panel. The strain-specific phenotypes could be linked to the strains’ genotypes by identifying gene clusters coding for carbohydrate membrane transport systems that are predicted to be involved in the utilization of isomaltose and other (unidentified) oligosaccharides in the isomaltooligosaccharide substrate. IMPORTANCE Synbiotics combine prebiotics and probiotics to synergistically enhance the health benefits associated with these ingredients. Lactobacillus plantarum is encountered as a natural inhabitant of the gastrointestinal tract, and specific strains are marketed as probiotics based on their strain-specific health-promoting activities. Strain-specific stimulation of growth through prebiotic substrates could enhance the persistence and/or activity of L. plantarum in situ. Our study establishes a high-throughput screening model for prebiotic substrate utilization by individual strains of bacteria, which can be readily employed for synbiotic matchmaking approaches that aim to enhance the intestinal delivery of probiotics through strain-specific, selective growth stimulation.

scholarly journals Analysis of Predicted Carbohydrate Transport Systems Encoded by Bifidobacterium bifidum PRL2010

2012 ◽  
Vol 78 (14) ◽  
pp. 5002-5012 ◽  
Author(s):  
Francesca Turroni ◽  
Francesco Strati ◽  
Elena Foroni ◽  
Fausta Serafini ◽  
Sabrina Duranti ◽  
...  
Keyword(s):  
Bifidobacterium Bifidum ◽  
Transport Systems ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Carbohydrate Transport ◽  
Small Set ◽  
Transcriptome Analyses ◽  
Growth Experiments

ABSTRACTTheBifidobacterium bifidumPRL2010 genome encodes a relatively small set of predicted carbohydrate transporters. Growth experiments and transcriptome analyses ofB. bifidumPRL2010 revealed that carbohydrate utilization in this microorganism appears to be restricted to a relatively low number of carbohydrates.

scholarly journals Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Yuki Saito ◽  
Akira Shigehisa ◽  
Yohei Watanabe ◽  
Naoki Tsukuda ◽  
Kaoru Moriyama-Ohara ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

scholarly journals Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

2015 ◽  
Vol 81 (16) ◽  
pp. 5458-5470 ◽  
Author(s):  
Corina Ceapa ◽  
Jolanda Lambert ◽  
Kees van Limpt ◽  
Michiel Wels ◽  
Tamara Smokvina ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Bacterial Species ◽  
Draft Genome ◽  
Carbon Sources ◽  
Lactobacillus Rhamnosus ◽  
Genotypic Diversity ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Healthy Humans ◽  
Niche Adaptation

ABSTRACTLactobacillus rhamnosusis a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains ofL. rhamnosusin relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65L. rhamnosusstrains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification ofL. rhamnosusstrains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes ofL. rhamnosusGG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters:l-rhamnose, cellobiose,l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate withl-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the speciesL. rhamnosusand explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.

scholarly journals Complete Genome Sequence of Lactobacillus plantarum subsp. plantarum Strain LB1-2, Isolated from the Hindgut of European Honeybees, Apis mellifera L., from the Philippines

2018 ◽  
Vol 6 (14) ◽  
Author(s):  
M. Fatima C. Ilagan-Cruzada ◽  
Albert Remus R. Rosana ◽  
Andrew D. Montecillo ◽  
Noel G. Sabino ◽  
Ida F. Dalmacio
Keyword(s):  
Apis Mellifera ◽  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
The Philippines ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type

ABSTRACT Lactobacillus plantarum subsp. plantarum strain LB1-2, isolated from the hindgut of European honeybees in the Philippines, is active against Paenibacillus larvae and has broad activity against several Gram-positive and Gram-negative bacteria. The complete genome sequence reported herein contains gene clusters for multiple bacteriocins and extensive gene inventories for carbohydrate metabolism.

scholarly journals Phenotypic and genetic characterization of differential galacto-oligosaccharide utilization in Lactobacillus plantarum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jori Fuhren ◽  
Markus Schwalbe ◽  
Lucía Peralta-Marzal ◽  
Christiane Rösch ◽  
Henk A. Schols ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Phenotypic Diversity ◽  
Degree Of Polymerization ◽  
Carbohydrate Utilization ◽  
Potential Health ◽  
Probiotic Strains ◽  
Health Promoting ◽  
Phenotypic And Genetic Characterization

AbstractSeveral Lactobacillus plantarum strains are marketed as probiotics for their potential health benefits. Prebiotics, e.g., galacto-oligosaccharides (GOS), have the potential to selectively stimulate the growth of L. plantarum probiotic strains based on their phenotypic diversity in carbohydrate utilization, and thereby enhance their health promoting effects in the host in a strain-specific manner. Previously, we have shown that GOS variably promotes the strain-specific growth of L. plantarum. In this study we investigated this variation by molecular analysis of GOS utilization by L. plantarum. HPAEC-PAD analysis revealed two distinct GOS utilization phenotypes in L. plantarum. Linking these phenotypes to the strain-specific genotypes led to the identification of a lac operon encoding a β-galactosidase (lacA), a permease (lacS), and a divergently oriented regulator (lacR), that are predicted to be involved in the utilization of higher degree of polymerization (DP) constituents present in GOS (specifically DP of 3–4). Mutation of lacA and lacS in L. plantarum NC8 resulted in reduced growth on GOS, and HPAEC analysis confirmed the role of these genes in the import and utilization of higher-DP GOS constituents. Overall, the results enable the design of highly-selective synbiotic combinations of L. plantarum strain-specific probiotics and specific GOS-prebiotic fractions.

scholarly journals Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

2020 ◽  
Vol 6 (8) ◽  
Author(s):  
Carla Rodrigues ◽  
Camille d’Humières ◽  
Grégory Papin ◽  
Virginie Passet ◽  
Etienne Ruppé ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Acute Otitis Media ◽  
Gene Clusters ◽  
Laboratory Model ◽  
Invasive Infection ◽  
Single Strain ◽  
Content Type ◽  
Link Type ◽  
First Case ◽  
Community Acquired Infection

Klebsiella pneumoniae (Kp) reference strain Kp52.145 is widely used in experimental Klebsiella pathophysiology. Since 1935, only one other strain of the same sublineage (sequence type ST66, capsular serotype K2) was isolated (AJ210, Australia). Here, we describe a community-acquired invasive infection caused by a ST66-K2 Kp strain in France. Four hypermucoviscous Kp isolates responsible for acute otitis media, meningitis, bacteraemia and bacteriuria, respectively, were obtained from a patient with a history of chronic alcoholism and diabetes mellitus, and infected with HIV. The isolates were characterized by phenotypic and genomic methods. The four genetically identical ST66-K2 isolates presented a full antimicrobial susceptibility profile, including to ampicillin, corresponding to a single strain (SB5881), which was more closely related to AJ210 (135 SNPs) than to Kp52.145 (388 SNPs). Colibactin and yersiniabactin gene clusters were present on the integrative and conjugative element ICEKp10 in the chromosome. The two plasmids from Kp52.145 were detected in SB5881. In addition to carrying genes for virulence factors RmpA, aerobactin and salmochelin, plasmid II has acquired in SB5881, the conjugation machinery gene cluster from plasmid I. We report the first case of community-acquired infection caused by a hypervirulent ST66-K2 Kp strain in Europe. This demonstrates the long-term persistence of the high-virulence and laboratory model ST66-K2 sublineage. The combination of a conjugative apparatus and major virulence genes on a single plasmid may contribute to the co-occurrence of hypervirulence and multidrug resistance in single Kp strains.

scholarly journals Strain-Specific Features of Extracellular Polysaccharides and Their Impact on Lactobacillus plantarum-Host Interactions

2016 ◽  
Vol 82 (13) ◽  
pp. 3959-3970 ◽  
Author(s):  
I-Chiao Lee ◽  
Graziano Caggianiello ◽  
Iris I. van Swam ◽  
Nico Taverne ◽  
Marjolein Meijerink ◽  
...  
Keyword(s):  
Cell Surface ◽  
Lactobacillus Plantarum ◽  
Surface Properties ◽  
Gene Clusters ◽  
Host Cells ◽  
Extracellular Polysaccharides ◽  
Bacterial Strains ◽  
Strain Specificity ◽  
Content Type ◽  
Health Promoting

ABSTRACTLactobacilli are found in diverse environments and are widely applied as probiotic, health-promoting food supplements. Polysaccharides are ubiquitously present on the cell surface of lactobacilli and are considered to contribute to the species- and strain-specific probiotic effects that are typically observed. TwoLactobacillus plantarumstrains, SF2A35B and Lp90, have an obvious ropy phenotype, implying high extracellular polysaccharide (EPS) production levels. In this work, we set out to identify the genes involved in EPS production in theseL. plantarumstrains and to demonstrate their role in EPS production by gene deletion analysis. A modelL. plantarumstrain, WCFS1, and its previously constructed derivative that produced reduced levels of EPS were included as reference strains. The constructed EPS-reduced derivatives were analyzed for the abundance and sugar compositions of their EPS, revealingcps2-like gene clusters in SF2A35B and Lp90 responsible for major EPS production. Moreover, these mutant strains were tested for phenotypic characteristics that are of relevance for their capacity to interact with the host epithelium in the intestinal tract, including bacterial surface properties as well as survival under the stress conditions encountered in the gastrointestinal tract (acid and bile stress). In addition, the Toll-like receptor 2 (TLR2) signaling and immunomodulatory capacities of the EPS-negative derivatives and their respective wild-type strains were compared, revealing strain-specific impacts of EPS on the immunomodulatory properties. Taken together, these experiments illustrate the importance of EPS inL. plantarumstrains as a strain-specific determinant in host interaction.IMPORTANCEThis study evaluates the role of extracellular polysaccharides that are produced by different strains ofLactobacillus plantarumin the determination of the cell surface properties of these bacteria and their capacity to interact with their environment, including their signaling to human host cells. The results clearly show that the consequences of removal of these polysaccharides are very strain specific, illustrating the diverse and unpredictable roles of these polysaccharides in the environmental interactions of these bacterial strains. In the context of the use of lactobacilli as health-promoting probiotic organisms, this study exemplifies the importance of strain specificity.

scholarly journals Transcriptional Studies on aStreptomyces clavuligerus oppA2Deletion Mutant:N-Acetylglycyl-Clavaminic Acid Is an Intermediate of Clavulanic Acid Biosynthesis

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
R. Álvarez-Álvarez ◽  
A. Rodríguez-García ◽  
Y. Martínez-Burgo ◽  
J. F. Martín ◽  
P. Liras
Keyword(s):  
Clavulanic Acid ◽  
Parental Strain ◽  
Binding Protein ◽  
Gene Clusters ◽  
Streptomyces Clavuligerus ◽  
Culture Broth ◽  
Transport Systems ◽  
Orphan Gene ◽  
Content Type ◽  
Abc Transport

ABSTRACTTheoppA2gene encodes an oligopeptide-binding protein similar to the periplasmic substrate-binding proteins of the ABC transport systems. However,oppA2is an orphan gene, not included in an ABC operon. This gene is located in the clavulanic acid (CA) gene cluster ofStreptomyces clavuligerusand is essential for CA production. A transcriptomic study of theoppA2-null mutantS. clavuligerusΔoppA2::aacshowed changes in the expression levels of 233 genes from those in the parental strain. These include genes for ABC transport systems, secreted proteins, peptidases, and proteases. Expression of the clavulanic acid, clavam, and cephamycin C biosynthesis gene clusters was not significantly affected in theoppA2deletion mutant. The genes for holomycin biosynthesis were upregulated 2-fold on average, and the level of upregulation increased to 43-fold in a double mutant lackingoppA2and the pSCL4 plasmid. Strains in whichoppA2was mutated secreted into the culture the compoundN-acetylglycyl-clavaminic acid (AGCA), a putative intermediate of CA biosynthesis. A culture broth containing AGCA, or AGCA purified by liquid chromatography-mass spectrometry (LC-MS), was added to the cultures of various non-CA-producing mutants. Mutants blocked in the early steps of the pathway restored CA production, whereas mutants altered in late steps did not, establishing that AGCA is a late intermediate of the biosynthetic pathway, which is released from the cells when the oligopeptide-binding protein OppA2 is not available.IMPORTANCETheoppa2gene encodes an oligopeptide permease essential for the production of clavulanic acid. A transcriptomic analysis ofS. clavuligerusΔoppA2::aacin comparison to the parental strainS. clavuligerusATCC 27064 is reported. The lack of OppA2 results in different expression of 233 genes, including genes for proteases and genes for transport systems. The expression of the clavulanic acid genes in theoppA2mutant is not significantly affected, but the genes for holomycin biosynthesis are strongly upregulated, in agreement with the higher holomycin production by this strain. TheoppA2-mutant is known to releaseN-acetylglycyl-clavaminic acid to the broth. Cosynthesis assays using non-clavulanic acid-producing mutants showed that the addition of pureN-acetylglycyl-clavaminic acid to mutants in which clavulanic acid formation was blocked resulted in the recovery of clavulanic acid production, but only in mutants blocked in the early steps of the pathway. This suggests thatN-acetylglycyl-clavaminic acid is a previously unknown late intermediate of the clavulanic acid pathway.

scholarly journals Dual Zinc Transporter Systems in Vibrio cholerae Promote Competitive Advantages over Gut Microbiome

2015 ◽  
Vol 83 (10) ◽  
pp. 3902-3908 ◽  
Author(s):  
Ying Sheng ◽  
Fenxia Fan ◽  
Owen Jensen ◽  
Zengtao Zhong ◽  
Biao Kan ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Zinc Transporter ◽  
Zinc Homeostasis ◽  
Transport Systems ◽  
Growth Defect ◽  
Dependent Manner ◽  
Content Type ◽  
Transporter Systems

Zinc is an essential trace metal required for numerous cellular processes in all forms of life. In order to maintain zinc homeostasis, bacteria have developed several transport systems to regulate its uptake. In this study, we investigated zinc transport systems in the enteric pathogenVibrio cholerae, the causative agent of cholera. Bioinformatic analysis predicts that two gene clusters, VC2081 to VC2083 (annotated as zinc utilization genesznuABC) and VC2551 to VC2555 (annotated aszinc-regulatedgeneszrgABCDE), are regulated by the putative zinc uptake regulator Zur. Using promoter reporter and biochemical assays, we confirmed that Zur repressesznuABCandzrgABCDEpromoters in a Zn2+-dependent manner. Under Zn2+-limiting conditions, we found that mutations in either theznuABCorzrgABCDEgene cluster affect bacterial growth, withznuABCmutants displaying a more severe growth defect, suggesting that both ZnuABC and ZrgABCDE are involved in Zn2+uptake and that ZnuABC plays the predominant role. Furthermore, we reveal that ZnuABC and ZrgABCDE are important forV. choleraecolonization in both infant and adult mouse models, particularly in the presence of other intestinal microbiota. Collectively, our studies indicate that these two zinc transporter systems play vital roles in maintaining zinc homeostasis duringV. choleraegrowth and pathogenesis.

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