scholarly journals Defining the Bacteroides Ribosomal Binding Site

2013 ◽  
Vol 79 (6) ◽  
pp. 1980-1989 ◽  
Author(s):  
Udo Wegmann ◽  
Nikki Horn ◽  
Simon R. Carding
Keyword(s):  
Gastrointestinal Tract ◽  
Binding Site ◽  
Transcription Initiation ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Expression Vectors ◽  
Human Gastrointestinal Tract ◽  
Vast Number ◽  
Content Type ◽  
Ribosomal Binding Site

ABSTRACTThe human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genusBacteroidesare among the most abundant bacterial species in the human colon.Bacteroidetesdiverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals inBacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use ofpepIfromLactobacillus delbrueckiisubsp.lactisas a novel reporter gene forBacteroides. Furthermore, we report the identification of the 3′ end of the 16S rRNA ofBacteroides ovatusand analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5′ untranslated region of otherBacteroidalesribosomal protein genes, we conclude that our findings are relevant to all members of this order.

scholarly journals Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron

2015 ◽  
Vol 81 (12) ◽  
pp. 3973-3983 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Aakanksha Saraf ◽  
Eric C. Martens ◽  
Lubbert Dijkhuizen
Keyword(s):  
Gastrointestinal Tract ◽  
Carbohydrate Metabolism ◽  
Lactobacillus Reuteri ◽  
Bacterial Species ◽  
Transport Systems ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Positive Health ◽  
Content Type ◽  
Commensal Species

ABSTRACTProbiotic microorganisms are ingested as food or supplements and impart positive health benefits to consumers. Previous studies have indicated that probiotics transiently reside in the gastrointestinal tract and, in addition to modulating commensal species diversity, increase the expression of genes for carbohydrate metabolism in resident commensal bacterial species. In this study, it is demonstrated that the human gut commensal speciesBacteroides thetaiotaomicronefficiently metabolizes fructan exopolysaccharide (EPS) synthesized by probioticLactobacillus reuteristrain 121 while only partially degrading reuteran and isomalto/malto-polysaccharide (IMMP) α-glucan EPS polymers.B. thetaiotaomicronmetabolized these EPS molecules via the activation of enzymes and transport systems encoded by dedicated polysaccharide utilization loci specific for β-fructans and α-glucans. Reduced metabolism of reuteran and IMMP α-glucan EPS molecules may be due to reduced substrate binding by components of the starch utilization system (sus). This study reveals that microbial EPS substrates activate genes for carbohydrate metabolism inB. thetaiotaomicronand suggests that microbially derived carbohydrates provide a carbohydrate-rich reservoir forB. thetaiotaomicronnutrient acquisition in the gastrointestinal tract.

Survival of Lactobacillus delbrueckii UFV H2b20 in fermented milk under simulated gastric and intestinal conditions

2013 ◽  
Vol 4 (3) ◽  
pp. 285-289 ◽  
Author(s):  
L.L. da Conceição ◽  
E.S. Leandro ◽  
F.S. Freitas ◽  
M.N.V. de Oliveira ◽  
A.B. Ferreira-Machado ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Storage Period ◽  
Fermented Milk ◽  
Storage Conditions ◽  
Lactobacillus Delbrueckii ◽  
Refrigerated Storage ◽  
Human Gastrointestinal Tract ◽  
Log Reduction ◽  
Population Reduction ◽  
Potential Use

The survival of Lactobacillus delbrueckii UFV H2b20 was assessed in fermented milk, both during the storage period and after exposure to simulated gastric and intestinal juices, as well the detection of the gene fbpA involved in adherence to human gastrointestinal tract. L. delbrueckii UFV H2b20 remained stable and viable for 28 days under refrigerated storage conditions. After one day of storage, that strain exhibited a one-log population reduction following exposure in tandem to simulated gastric and intestinal juices. After 14 days of storage, a two-log reduction was observed following 90 min of exposure to the simulated gastric conditions. However, the strain did not survive following exposure to the simulated intestinal juice. The observed tolerance to storage conditions and resistance to the simulated gastric and intestinal conditions confirm the potential use of L. delbrueckii UFV H2b20 as a probiotic, which is further reinforced by the detection of fbpA in this strain.

scholarly journals Evidence that Oxidative Stress InducesspxA2Transcription in Bacillus anthracis Sterne through a Mechanism Requiring SpxA1 and Positive Autoregulation

2016 ◽  
Vol 198 (21) ◽  
pp. 2902-2913 ◽  
Author(s):  
Skye Barendt ◽  
Cierra Birch ◽  
Lea Mbengi ◽  
Peter Zuber
Keyword(s):  
Oxidative Stress ◽  
Bacillus Anthracis ◽  
Transcription Initiation ◽  
Bacterial Species ◽  
Negative Control ◽  
Mobility Shift ◽  
Content Type ◽  
Oxidative Protein Damage

ABSTRACTBacillus anthracispossesses two paralogs of the transcriptional regulator, Spx. SpxA1 and SpxA2 interact with RNA polymerase (RNAP) to activate the transcription of genes implicated in the prevention and alleviation of oxidative protein damage. ThespxA2gene is highly upregulated in infected macrophages, but how this is achieved is unknown. Previous studies have shown that thespxA2gene was under negative control by the Rrf2 family repressor protein, SaiR, whose activity is sensitive to oxidative stress. These studies also suggested thatspxA2was under positive autoregulation. In the present study, we show byin vivoandin vitroanalyses thatspxA2is under direct autoregulation but is also dependent on the SpxA1 paralogous protein. The deletion of eitherspxA1orspxA2reduced the diamide-inducible expression of anspxA2-lacZconstruct.In vitrotranscription reactions using purifiedB. anthracisRNAP showed that SpxA1 and SpxA2 protein stimulates transcription from a DNA fragment containing thespxA2promoter. Ectopically positionedspxA2-lacZfusion requires both SpxA1 and SpxA2 for expression, but the requirement for SpxA1 is partially overcome whensaiRis deleted. Electrophoretic mobility shift assays showed that SpxA1 and SpxA2 enhance the affinity of RNAP forspxA2promoter DNA and that this activity is sensitive to reductant. We hypothesize that the previously observed upregulation ofspxA2in the oxidative environment of the macrophage is at least partly due to SpxA1-mediated SaiR repressor inactivation and the positive autoregulation ofspxA2transcription.IMPORTANCERegulators of transcription initiation are known to govern the expression of genes required for virulence in pathogenic bacterial species. Members of the Spx family of transcription factors function in control of genes required for virulence and viability in low-GC Gram-positive bacteria. InBacillus anthracis, thespxA2gene is highly induced in infected macrophages, which suggests an important role in the control of virulence gene expression during the anthrax disease state. We provide evidence that elevated concentrations of oxidized, active SpxA2 result from an autoregulatory positive-feedback loop drivingspxA2transcription.

scholarly journals Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the Gut of a Healthy Indian Adult

2017 ◽  
Vol 5 (41) ◽  
Author(s):  
Satyabrata Bag ◽  
Tarini Shankar Ghosh ◽  
Bhabatosh Das
Keyword(s):  
Gastrointestinal Tract ◽  
Genome Sequence ◽  
Anaerobic Bacterium ◽  
Acid Metabolism ◽  
Intestinal Inflammation ◽  
Bifidobacterium Longum ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Human Gastrointestinal Tract ◽  
Content Type

ABSTRACT Bifidobacterium longum, a Gram-positive rod-shaped anaerobic bacterium, inhabits the human gastrointestinal tract and contributes significantly to oligosaccharide production, amino acid metabolism, and protection against intestinal inflammation. Here, we report the whole-genome sequence of B. longum, which was isolated from the gastrointestinal tract of a healthy Indian adult.

scholarly journals Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1

2014 ◽  
Vol 81 (4) ◽  
pp. 1319-1326 ◽  
Author(s):  
Eoghan Casey ◽  
Jennifer Mahony ◽  
Horst Neve ◽  
Jean-Paul Noben ◽  
Fabio Dal Bello ◽  
...  
Keyword(s):  
Burst Size ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Comparative Genomic ◽  
Phage Group ◽  
Content Type ◽  
Large Head ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis

ABSTRACTLdl1 is a virulent phage infecting the dairy starterLactobacillus delbrueckiisubsp.lactisLdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infectingLactobacillus delbrueckii.In vitropropagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that ofLactobacillus plantarumphage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognizedL. delbrueckiiphage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

scholarly journals Prevalence, Risk Factors, and Molecular Epidemiology of Intestinal Carbapenem-Resistant Pseudomonas aeruginosa

2021 ◽  
Author(s):  
Yanyan Hu ◽  
Yan Qing ◽  
Jiawei Chen ◽  
Congcong Liu ◽  
Jiayue Lu ◽  
...  
Keyword(s):  
Risk Factors ◽  
Pseudomonas Aeruginosa ◽  
Gastrointestinal Tract ◽  
Resistance Genes ◽  
Acquired Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Human Gastrointestinal Tract ◽  
Content Type ◽  
Carbapenem Resistant

Pseudomonas aeruginosa may become multidrug-resistant (MDR) due to multiple inherited and acquired resistance mechanisms. The human gastrointestinal tract is known as a reservoir of P. aeruginosa and its resistance genes.

scholarly journals Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult

2017 ◽  
Vol 5 (37) ◽  
Author(s):  
Satyabrata Bag ◽  
Tarini Shankar Ghosh ◽  
Bhabatosh Das
Keyword(s):  
Gastrointestinal Tract ◽  
Genome Sequence ◽  
Metabolic Pathways ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Human Gastrointestinal Tract ◽  
Gram Negative ◽  
Content Type ◽  
Host Physiology

ABSTRACT Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of P. copri isolated from the gut of a healthy Indian adult.

scholarly journals Responses of the Human GutEscherichia coliPopulation to Pathogen and Antibiotic Disturbances

mSystems ◽  
2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Taylor K. S. Richter ◽  
Jane M. Michalski ◽  
Luke Zanetti ◽  
Sharon M. Tennant ◽  
Wilbur H. Chen ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Antibiotic Treatment ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Gastrointestinal Tract ◽  
Content Type ◽  
E Coli ◽  
Pathogen Invasion

ABSTRACTStudies ofEscherichia coliin the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenicE. coli(ETEC), while overlooking the resident, nonpathogenicE. colicommunity. Relatively few genomes of nonpathogenicE. colistrains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinalE. colicommunities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained fromE. coliisolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the residentE. colicommunities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominantE. coliclone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. TheE. colicommunities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the residentE. colipopulation following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131E. colistrains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure.IMPORTANCEResearch on human-associatedE. colitends to focus on pathogens, such as enterotoxigenicE. coli(ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenicE. colicommunity that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing ofE. colibefore, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the residentE. colipopulation in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

scholarly journals Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Fuyong Li ◽  
Christopher C. Cheng ◽  
Jinshui Zheng ◽  
Junhong Liu ◽  
Rodrigo Margain Quevedo ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Genome Phylogeny

Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri . However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacillus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of L. reuteri : L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).

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