scholarly journals The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Melinda A. Engevik ◽  
Heather A. Danhof ◽  
Anne Hall ◽  
Kristen A. Engevik ◽  
Thomas D. Horvath ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Metabolic Pathways ◽  
Glycosyl Hydrolase ◽  
Acid Resistance ◽  
Human Gut ◽  
Nutrient Sources ◽  
Metabolic Plasticity ◽  
Defined Media ◽  
High Viability ◽  
Ph Range

Abstract Background Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium. Results B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment. Conclusions Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.

Direct cloning of genes encoding novel xylanases from the human gut

2005 ◽  
Vol 51 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Hidenori Hayashi ◽  
Takashi Abe ◽  
Mitsuo Sakamoto ◽  
Hiroki Ohara ◽  
Toshimichi Ikemura ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Fecal Microbiota ◽  
Coli Strain ◽  
Amino Acid Sequences ◽  
Self Organizing Map ◽  
Human Gut ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Ph Range ◽  
Self Organizing

The aim of this study was to identify a novel 1,4-β-xylanase gene from the mixed genome DNA of human fecal bacteria without bacterial cultivation. Total DNA was isolated from a population of bacteria extracted from fecal microbiota. Using PCR, the gene fragments encoding 5 different family 10 xylanases (xyn10A, xyn10B, xyn10C, xyn10D, and xyn10E) were found. Amino acid sequences deduced from these genes were highly homologous with those of xylanases from anaerobic intestinal bacteria such as Bacteroides spp. and Prevotella spp. Self-organizing map (SOM) analysis revealed that xynA10 was classified into Bacteroidetes. To confirm that one of these genes encodes an active enzyme, a full-length xyn10A gene was obtained using nested primers specific to the internal fragments and random primers. The xyn10A gene encoding the xylanase Xyn10A consists of 1146 bp and encodes a protein of 382 amino acids and a molecular weight of 43 552. Xyn10A was a single module novel xylanase. Xyn10A was purified from a recombinant Escherichia coli strain and characterized. This enzyme was optimally active at 40 °C and stable up to 50 °C at pH 6.5 and over the pH range 4.0–11.0 at 25 °C. In addition, 2 ORFs (ORF1 and ORF2) were identified upstream of xyn10A. These results suggested that many unidentified xylanolytic bacteria exist in the human gut and may contribute to the breakdown of xylan which contains dietary fiber.Key words: xylanase, human gut, fecal microbiota, phylogenetic analysis, self-organizing map.

Preparation of Single Cell Suspensions of the Intra-Epithelial Layer and Lamina Propria from Human Intestinal Tissue v1

2021 ◽  
Author(s):  
Steven B. Wells ◽  
Pranay Dogra ◽  
Josh Gray ◽  
Peter A. Szabo ◽  
Daniel Caron ◽  
...  
Keyword(s):  
Single Cell ◽  
Lamina Propria ◽  
Intestinal Tract ◽  
Distal Colon ◽  
Cell Suspensions ◽  
Epithelial Layer ◽  
Dilution Factor ◽  
Human Gut ◽  
Intestinal Tissue ◽  
Defined Media

This protocol describes a method for the isolation of the immune cells, structural and epithelial cells, and progenitors from the epithelial layer and the lamina propria of human gut sections of about one gram of tissue. By providing defined media formulations, volumes at each step, and a defined dilution factor for density centrifugation, it yields consistent single-cell suspensions across samples. This protocol can be used for any section of the intestinal tract from duodenum to distal colon.

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.

scholarly journals Deacidification by FhlA-dependent hydrogenase is involved in urease activity and urinary stone formation in uropathogenic Proteus mirabilis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wen-Yuan Lin ◽  
Shwu-Jen Liaw
Keyword(s):  
Proteus Mirabilis ◽  
Urease Activity ◽  
Stone Formation ◽  
Large Subunit ◽  
Acid Resistance ◽  
Urinary Stone ◽  
Potential Strategy ◽  
Ph Range ◽  
Tract Infections

Abstract Proteus mirabilis is an important uropathogen, featured with urinary stone formation. Formate hydrogenlyase (FHL), consisting of formate dehydrogenase H and hydrogenase for converting proton to hydrogen, has been implicated in virulence. In this study, we investigated the role of P. mirabilis FHL hydrogenase and the FHL activator, FhlA. fhlA and hyfG (encoding hydrogenase large subunit) displayed a defect in acid resistance. fhlA and hyfG mutants displayed a delay in medium deacidification compared to wild-type and ureC mutant failed to deacidify the medium. In addition, loss of fhlA or hyfG decreased urease activity in the pH range of 5–8. The reduction of urease activities in fhlA and hyfG mutants subsided gradually over the pH range and disappeared at pH 9. Furthermore, mutation of fhlA or hyfG resulted in a decrease in urinary stone formation in synthetic urine. These indicate fhlA- and hyf-mediated deacidification affected urease activity and stone formation. Finally, fhlA and hyfG mutants exhibited attenuated colonization in mice. Altogether, we found expression of fhlA and hyf confers medium deacidification via facilitating urease activity, thereby urinary stone formation and mouse colonization. The link of acid resistance to urease activity provides a potential strategy for counteracting urinary tract infections by P. mirabilis.

scholarly journals Identifying determinants of bacterial fitness in a model of human gut microbial succession

2020 ◽  
Vol 117 (5) ◽  
pp. 2622-2633 ◽  
Author(s):  
Lihui Feng ◽  
Arjun S. Raman ◽  
Matthew C. Hibberd ◽  
Jiye Cheng ◽  
Nicholas W. Griffin ◽  
...  
Keyword(s):  
Community Assembly ◽  
Metabolic Pathways ◽  
Feature Reduction ◽  
Human Infant ◽  
Human Gut ◽  
Metabolic Potential ◽  
Transcriptional Responses ◽  
Carbohydrate Utilization ◽  
Fecal Samples ◽  
Phase Strains

Human gut microbiota development has been associated with healthy growth but understanding the determinants of community assembly and composition is a formidable challenge. We cultured bacteria from serially collected fecal samples from a healthy infant; 34 sequenced strains containing 103,102 genes were divided into two consortia representing earlier and later stages in community assembly during the first six postnatal months. The two consortia were introduced alone (singly), or sequentially in different order, or simultaneously into young germ-free mice fed human infant formula. The pattern of fitness of bacterial strains observed across the different colonization conditions indicated that later-phase strains substantially outcompete earlier-phase strains, although four early-phase members persist. Persistence was not determined by order of introduction, suggesting that priority effects are not prominent in this model. To characterize succession in the context of the metabolic potential of consortium members, we performed in silico reconstructions of metabolic pathways involved in carbohydrate utilization and amino acid and B-vitamin biosynthesis, then quantified the fitness (abundance) of strains in serially collected fecal samples and their transcriptional responses to different histories of colonization. Applying feature-reduction methods disclosed a set of metabolic pathways whose presence and/or expression correlates with strain fitness and that enable early-stage colonizers to survive during introduction of later colonizers. The approach described can be used to test the magnitude of the contribution of identified metabolic pathways to fitness in different community contexts, study various ecological processes thought to govern community assembly, and facilitate development of microbiota-directed therapeutics.

Characterization of the ecological role of genes mediating acid resistance inLactobacillus reuteriduring colonization of the gastrointestinal tract

2015 ◽  
Vol 18 (7) ◽  
pp. 2172-2184 ◽  
Author(s):  
Janina A. Krumbeck ◽  
Nathan L. Marsteller ◽  
Steven A. Frese ◽  
Daniel A. Peterson ◽  
Amanda E. Ramer-Tait ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Acid Resistance ◽  
Ecological Role

Survival of Bacillus cereus Vegetative Cells and Spores during In Vitro Simulation of Gastric Passage

2012 ◽  
Vol 75 (4) ◽  
pp. 690-694 ◽  
Author(s):  
SIELE CEUPPENS ◽  
MIEKE UYTTENDAELE ◽  
KATRIEN DRIESKENS ◽  
ANDREJA RAJKOVIC ◽  
NICO BOON ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Acid Resistance ◽  
In Vitro Experiments ◽  
Vegetative Cells ◽  
Ph Values ◽  
Constant Ph ◽  
In Vitro Simulation ◽  
Ph Range

The enteric pathogen Bacillus cereus must survive gastric passage in order to cause diarrhea by enterotoxin production in the small intestine. The acid resistance and the survival after gastric passage were assessed by in vitro experiments with acidified growth medium and gastric simulation medium with B. cereus NVH 1230-88 vegetative cells and spores. First, batch incubations at constant pH values for 4 h, which represented different physiological states of the stomach, showed that spores were resistant to any gastric condition in the pH range of 2.0 to 5.0, while vegetative cells were rapidly inactivated at pH values of ≤4.0. Second, a dynamic in vitro gastric experiment was conducted that simulated the continuously changing in vivo conditions due to digestion dynamics by gradually decreasing the pH from 5.0 to 2.0 and fractional emptying of the stomach 30 to 180 min from the start of the experiment. All of the B. cereus spores and 14% (±9%) of the vegetative cells survived the dynamic simulation of gastric passage.

Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica

2009 ◽  
Vol 81 (6) ◽  
pp. 1075-1084 ◽  
Author(s):  
Markus Nett ◽  
Bradley S. Moore
Keyword(s):  
Natural Products ◽  
Metabolic Pathways ◽  
Anticancer Agent ◽  
Complex Molecules ◽  
Dna Cleaving ◽  
Metabolic Plasticity ◽  
Salinosporamide A ◽  
Salinispora Tropica ◽  
Marine Actinomycete ◽  
Key Genes

In recent years, members of the marine actinomycete genus Salinispora have proven to be a precious source of structurally diverse secondary metabolites, including the potent anticancer agent salinosporamide A and the enediyne-derived sporolides. The tremendous potential of these marine-dwelling microbes for natural products biosynthesis, however, was not fully realized until sequencing of the Salinispora tropica genome revealed the presence of numerous orphan biosynthetic loci besides a plethora of rare metabolic pathways. This contribution summarizes the biochemical exploration of this prolific organism, highlighting studies in which genome-based information was exploited for the discovery of new enzymatic processes and the engineering of unnatural natural products. Inactivation of key genes within the salinosporamide pathway has expanded its inherent metabolic plasticity and enabled access to various salinosporamide derivatives by mutasynthesis. New insights into the biosynthesis of the sporolides allowed us to increase production titers of these structurally complex molecules, thereby providing the means to search for the DNA cleaving presporolide enediyne.

Independent Effects of Acetic Acid and pH on Survival ofEscherichia coli in Simulated Acidified Pickle Products†‡

2004 ◽  
Vol 67 (1) ◽  
pp. 12-18 ◽  
Author(s):  
F. BREIDT ◽  
J. S. HAYES ◽  
R. F. McFEETERS
Keyword(s):  
Acetic Acid ◽  
Organic Acids ◽  
Acid Resistance ◽  
Ofescherichia Coli ◽  
Acid Solutions ◽  
Specific Effects ◽  
Effects Of Ph ◽  
Ph Range ◽  
Independent Effects ◽  
D Values

Our objective was to determine the effects of organic acids and pH on the rate at which selected strains ofEscherichia coli O157:H7 die in acid solutions representative of acidified pickle products (pH < 4.6). We used gluconic acid/sodium gluconate (pKa = 3.7) as a noninhibitory buffer to maintain pH at selected values in the absence of other organic acids. This was possible because we found that the inhibitory effects of this acid onE. coli strains at pH 3.1 were independent of acid concentration over a range of 2 to 200 mM. By this method, the lethal effects of acetic acid solutions (100 to 400 mM) at selected pH values between 3.1 and 4.1 were compared with the effects of pH alone (as determined using gluconate buffer). We found D-values were two- to fourfold lower with acetic acid compared with the effect of pH alone for simulated pickle brines in this pH range. Glutamic acid, an amino acid that is known to enhance acid resistance inE. coli and is a component of pickle brines, protected theE. coli strains from the specific effects of acetic acid.

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