scholarly journals Nutritional Immunity and Antibiotic Drug Treatments Influence Microbial Composition but Fail to Eliminate Urethral Catheter Biofilms in Recurrently Catheterized Patients

2019 ◽  
Author(s):  
Yanbao Yu ◽  
Harinder Singh ◽  
Tamara Tsitrin ◽  
Keehwan Kwon ◽  
Shiferaw Bekele ◽  
...  
Keyword(s):  
Immune Responses ◽  
Metal Ion ◽  
Bacterial Species ◽  
Anaerobic Bacteria ◽  
Effector Proteins ◽  
Emerging Pathogens ◽  
Microbial Composition ◽  
Antibiotic Drug ◽  
Drug Treatments ◽  
Cellular Import

AbstractPolymicrobial biofilms that form on indwelling urethral catheters used by neurogenic bladder patients are known to recur following catheter replacements. Uropathogens dominate in catheter biofilms (CBs), grow and disperse as multi-cellular aggregates. Their microbial complexity, the characteristics of host immune responses and the molecular crosstalk in this ecosystem are incompletely understood. By surveying eight patients over up to six months with meta-omics analysis methods, we shed new light on the longitudinal microbial dynamics in CBs and the microbial-host crosstalk. There was evidence of chronic innate immune responses in all patients. Pathogens dominated the microbial contents.Proteus mirabilisoften out-competed other species in cases of salt encrustation of catheters. The examination of proteomes in CBs and associated urinary pellets revealed many abundant bacterial systems for transition metal ion (TMI) acquisition. TMIs are sequestered by effector proteins released by activated neutrophils and urothelial cells, such as lactotransferrin and calgranulins, which were abundant in the host proteomes. We identified positive quantitative correlations among systems responsible for siderophore biosynthesis, TMI/siderophore uptake and TMI cellular import in bacterial species, suggesting competition for TMIs to support their metabolism and growth in CBs.Enterococcus faecaliswas prevalent as a cohabitant of CBs and expressed three lipoproteins with apparent TMI acquisition functions. Fastidious anaerobic bacteria such asVeillonella,Actinobaculum, andBifidobacteriumgrew in CB communities that appeared to be oxygen starved. Finally, antibiotic drug treatments were shown to influence microbial composition of CBs but failed to prevent re-colonization of urethral catheters with persisting and/or drug-resistant newly emerging pathogens.

scholarly journals Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment

2021 ◽  
Vol 8 ◽  
Author(s):  
Yanbao Yu ◽  
Harinder Singh ◽  
Tamara Tsitrin ◽  
Shiferaw Bekele ◽  
Yi-Han Lin ◽  
...  
Keyword(s):  
Neurogenic Bladder ◽  
Metal Ion ◽  
Anaerobic Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Effector Proteins ◽  
Rrna Gene ◽  
Chronic Infections ◽  
Nadh:Quinone Oxidoreductase ◽  
Antibiotic Drug ◽  
Iron And Zinc

Biofilms composed of multiple microorganisms colonize the surfaces of indwelling urethral catheters that are used serially by neurogenic bladder patients and cause chronic infections. Well-adapted pathogens in this niche are Escherichia coli, Proteus, and Enterococcus spp., species that cycle through adhesion and multilayered cell growth, trigger host immune responses, are starved off nutrients, and then disperse. Viable microbial foci retained in the urinary tract recolonize catheter surfaces. The molecular adaptations of bacteria in catheter biofilms (CBs) are not well-understood, promising new insights into this pathology based on host and microbial meta-omics analyses from clinical specimens. We examined catheters from nine neurogenic bladder patients longitudinally over up to 6 months. Taxonomic analyses from 16S rRNA gene sequencing and liquid chromatography–tandem mass spectrometry (LC-MS/MS)–based proteomics revealed that 95% of all catheter and corresponding urinary pellet (UP) samples contained bacteria. CB biomasses were dominated by Enterobacteriaceae spp. and often accompanied by lactic acid and anaerobic bacteria. Systemic antibiotic drug treatments of patients resulted in either transient or lasting microbial community perturbations. Neutrophil effector proteins were abundant not only in UP but also CB samples, indicating their penetration of biofilm surfaces. In the context of one patient who advanced to a kidney infection, Proteus mirabilis proteomic data suggested a combination of factors associated with this disease complication: CB biomasses were high; the bacteria produced urease alkalinizing the pH and triggering urinary salt deposition on luminal catheter surfaces; P. mirabilis utilized energy-producing respiratory systems more than in CBs from other patients. The NADH:quinone oxidoreductase II (Nqr), a Na+ translocating enzyme not operating as a proton pump, and the nitrate reductase A (Nar) equipped the pathogen with electron transport chains promoting growth under hypoxic conditions. Both P. mirabilis and E. coli featured repertoires of transition metal ion acquisition systems in response to human host-mediated iron and zinc sequestration. We discovered a new drug target, the Nqr respiratory system, whose deactivation may compromise P. mirabilis growth in a basic pH milieu. Animal models would not allow such molecular-level insights into polymicrobial biofilm metabolism and interactions because the complexity cannot be replicated.

scholarly journals Widely Conserved Attenuation of Plant MAMP-Induced Calcium Influx by Bacteria Depends on Multiple Virulence Factors and May Involve Desensitization of Host Pattern Recognition Receptors

2019 ◽  
Vol 32 (5) ◽  
pp. 608-621 ◽  
Author(s):  
Meltem Lammertz ◽  
Hannah Kuhn ◽  
Sebastian Pfeilmeier ◽  
Jacob Malone ◽  
Cyril Zipfel ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Immune Responses ◽  
Pseudomonas Syringae ◽  
Prolonged Exposure ◽  
Calcium Influx ◽  
Bacterial Species ◽  
Cytosolic Calcium ◽  
Pattern Recognition Receptors ◽  
Effector Proteins ◽  
Virulence Determinants

Successful pathogens must efficiently defeat or delay host immune responses, including those triggered by release or exposure of microbe-associated molecular patterns (MAMPs). Knowledge of the molecular details leading to this phenomenon in genuine plant–pathogen interactions is still scarce. We took advantage of the well-established Arabidopsis thaliana–Pseudomonas syringae pv. tomato DC3000 pathosystem to explore the molecular prerequisites for the suppression of MAMP-triggered host defense by the bacterial invader. Using a transgenic Arabidopsis line expressing the calcium sensor apoaequorin, we discovered that strain DC3000 colonization results in a complete inhibition of MAMP-induced cytosolic calcium influx, a key event of immediate-early host immune signaling. A range of further plant-associated bacterial species is also able to prevent, either partially or fully, the MAMP-triggered cytosolic calcium pattern. Genetic analysis revealed that this suppressive effect partially relies on the bacterial type III secretion system (T3SS) but cannot be attributed to individual members of the currently known arsenal of strain DC3000 effector proteins. Although the phytotoxin coronatine and bacterial flagellin individually are dispensable for the effective inhibition of MAMP-induced calcium signatures, they contribute to the attenuation of calcium influx in the absence of the T3SS. Our findings suggest that the capacity to interfere with early plant immune responses is a widespread ability among plant-associated bacteria that, at least in strain DC3000, requires the combinatorial effect of multiple virulence determinants. This may also include the desensitization of host pattern recognition receptors by the prolonged exposure to MAMPs during bacterial pathogenesis.

scholarly journals A31 COMPLEX ROLE OF DIETARY FIBERS IN IBD: MICROBES MEDIATE FIBER-INDUCED INFLAMMATION

2021 ◽  
Vol 4 (Supplement_1) ◽  
pp. 148-150
Author(s):  
H Armstrong ◽  
R Valcheva ◽  
D Santer ◽  
Z Zhang ◽  
A Rieger ◽  
...  
Keyword(s):  
Immune Responses ◽  
Anaerobic Fermentation ◽  
Ex Vivo ◽  
Severe Disease ◽  
Cytokine Secretion ◽  
Dietary Fibers ◽  
Gut Health ◽  
T84 Cells ◽  
Microbial Composition ◽  
Barrier Integrity

Abstract Background Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, typically promoting gut health. However, many IBD patients describe experiencing sensitivity to fibers. β-glucan, found on the surface of fungal cells during fungal infection, has been shown to bind to fiber receptors, such as Dectin-1, on host immune cells, resulting in a pro-inflammatory response. These fungal fibres share properties with dietary fibers. Aims As an altered gut microbial composition has been associated with IBD, we hypothesized that the loss of fiber-fermenting microbes populating the gut in IBD could lead to dietary fibers not being efficiently broken down into their beneficial biproducts (e.g. short chain fatty acids; SCFA), resulting in binding of intact fibers to pro-inflammatory host cell receptors. Methods Immune and epithelial cell lines and colonic biopsies cultured ex vivo were incubated with oligofructose or inulin (5g/L), or pre-fermented fibers (24hr anaerobic fermentation). Immune responses were measured by cytokine secretion (ELISA), and expression (qPCR). Barrier integrity was measured by transepithelial resistance (TEER). Food frequency questionnaire (FFQ) data of patient fiber consumption were correlated with gut microbes (shotgun sequencing) and immune responses to fiber in patient biopsies. Results Unfermented oligofructose induced IL-1β secretion in leukocytes (macrophage, T cell, neutrophil) and in colon biopsies from pediatric Crohn disease (CD; n=38) and ulcerative colitis (UC; n=20) patients cultured ex vivo, but not in non-IBD patients (n=21). IL-1β secretion was greater in patients with more severe disease. Pre-fermentation of oligofructose by whole-microbe intestinal washes from non-IBD patients or remission patients reduced secretion of IL-1β, while whole microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce cytokine secretion. Fiber effects on IL-1β secretion in biopsies positively correlated with effects on barrier integrity in T84 cells. Fiber-associated immune responses in patient biopsies cultured ex vivo (ELISA) correlated with fiber avoidance (FFQ) and gut microbiome (sequencing) in matching patient samples. Conclusions Our findings demonstrate that intolerance and avoidance of prebiotic fibers in select IBD patients is associated with the inability to ferment these fibers, leading to pro-inflammatory immune responses and intestinal barrier disruption. This highlights select disease state scenarios, in which administration of fermentable fibers should be avoided and tailored dietary interventions should be considered in IBD patients. Funding Agencies CIHRWeston Foundation

scholarly journals Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Detman ◽  
Michał Bucha ◽  
Laura Treu ◽  
Aleksandra Chojnacka ◽  
Łukasz Pleśniak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Bacterial Species ◽  
Stable Carbon Isotope ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Core Microbiome ◽  
Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

scholarly journals BAK1 Is Not a Target of the Pseudomonas syringae Effector AvrPto

2011 ◽  
Vol 24 (1) ◽  
pp. 100-107 ◽  
Author(s):  
Tingting Xiang ◽  
Na Zong ◽  
Jie Zhang ◽  
Jinfeng Chen ◽  
Mingsheng Chen ◽  
...  
Keyword(s):  
Cell Surface ◽  
Immune Responses ◽  
Pseudomonas Syringae ◽  
Plant Cell ◽  
Crucial Role ◽  
Pathogenic Bacteria ◽  
Effector Proteins ◽  
Receptor Like Kinase ◽  
Receptor Kinases ◽  
New Evidence

Plant cell surface-localized receptor kinases such as FLS2, EFR, and CERK1 play a crucial role in detecting invading pathogenic bacteria. Upon stimulation by bacterium-derived ligands, FLS2 and EFR interact with BAK1, a receptor-like kinase, to activate immune responses. A number of Pseudomonas syringae effector proteins are known to block immune responses mediated by these receptors. Previous reports suggested that both FLS2 and BAK1 could be targeted by the P. syringae effector AvrPto to inhibit plant defenses. Here, we provide new evidence further supporting that FLS2 but not BAK1 is targeted by AvrPto in plants. The AvrPto-FLS2 interaction prevented the phosphorylation of BIK1, a downstream component of the FLS2 pathway.

scholarly journals Bacterial Flagellar Filament: A Supramolecular Multifunctional Nanostructure

2021 ◽  
Vol 22 (14) ◽  
pp. 7521
Author(s):  
Marko Nedeljković ◽  
Diego Emiliano Sastre ◽  
Eric John Sundberg
Keyword(s):  
Immune Responses ◽  
Basal Body ◽  
Vaccine Development ◽  
Bacterial Species ◽  
High Variability ◽  
Bacterial Survival ◽  
Bacterial Flagellum ◽  
Capping Proteins ◽  
Flagellar Filament ◽  
Flagellar Assembly

The bacterial flagellum is a complex and dynamic nanomachine that propels bacteria through liquids. It consists of a basal body, a hook, and a long filament. The flagellar filament is composed of thousands of copies of the protein flagellin (FliC) arranged helically and ending with a filament cap composed of an oligomer of the protein FliD. The overall structure of the filament core is preserved across bacterial species, while the outer domains exhibit high variability, and in some cases are even completely absent. Flagellar assembly is a complex and energetically costly process triggered by environmental stimuli and, accordingly, highly regulated on transcriptional, translational and post-translational levels. Apart from its role in locomotion, the filament is critically important in several other aspects of bacterial survival, reproduction and pathogenicity, such as adhesion to surfaces, secretion of virulence factors and formation of biofilms. Additionally, due to its ability to provoke potent immune responses, flagellins have a role as adjuvants in vaccine development. In this review, we summarize the latest knowledge on the structure of flagellins, capping proteins and filaments, as well as their regulation and role during the colonization and infection of the host.

scholarly journals Antibiotics in early life and childhood pre-B-ALL. Reasons to analyze a possible new piece in the puzzle

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
T. M. Cardesa-Salzmann ◽  
A. Simon ◽  
N. Graf
Keyword(s):  
Immune Responses ◽  
Early Life ◽  
Lymphoblastic Leukemia ◽  
Antibiotic Use ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Hematopoietic Stem ◽  
Childhood All ◽  
Host Immune Responses

AbstractAcute lymphoblastic leukemia (ALL) is the most common pediatric cancer with precursor B-cell ALL (pB-ALL) accounting for ~ 85% of the cases. Childhood pB-ALL development is influenced by genetic susceptibility and host immune responses. The role of the intestinal microbiome in leukemogenesis is gaining increasing attention since Vicente-Dueñas’ seminal work demonstrated that the gut microbiome is distinct in mice genetically predisposed to ALL and that the alteration of this microbiome by antibiotics is able to trigger pB-ALL in Pax5 heterozygous mice in the absence of infectious stimuli. In this review we provide an overview on novel insights on the role of the microbiome in normal and preleukemic hematopoiesis, inflammation, the effect of dysbiosis on hematopoietic stem cells and the emerging importance of the innate immune responses in the conversion from preleukemic to leukemic state in childhood ALL. Since antibiotics, which represent one of the most widely used medical interventions, alter the gut microbial composition and can cause a state of dysbiosis, this raises exciting epidemiological questions regarding the implications for antibiotic use in early life, especially in infants with a a preleukemic “first hit”. Sheading light through a rigorous study on this piece of the puzzle may have broad implications for clinical practice.

scholarly journals Host F-box protein 22 enhances the uptake of Brucella by macrophages and drives a sustained release of pro-inflammatory cytokines through degradation of the anti-inflammatory effector proteins of Brucella.

2021 ◽  
Author(s):  
Girish Radhakrishnan ◽  
Varadendra Mazumdar ◽  
Kiranmai Joshi ◽  
Binita Roy Nandi ◽  
Swapna Namani ◽  
...  
Keyword(s):  
Immune Responses ◽  
Inflammatory Cytokines ◽  
Effector Proteins ◽  
Host Protein ◽  
Limited Information ◽  
Phagocytic Cells ◽  
Scf Complex ◽  
Enhanced Production ◽  
Anti Inflammatory ◽  
Pro Inflammatory Cytokines

Brucella species are intracellular bacterial pathogens, causing the world-wide zoonotic disease, brucellosis.  Brucella invade professional and non-professional phagocytic cells, followed by resisting intracellular killing and establishing a replication permissive niche. Brucella also modulate the innate and adaptive immune responses of the host for their chronic persistence. The complex intracellular cycle of Brucella majorly depends on multiple host factors but limited information is available on host and bacterial proteins that play essential role in the invasion, intracellular replication and modulation of host immune responses. By employing an siRNA screening, we identified a role for the host protein, FBXO22 in Brucella -macrophage interaction. FBXO22 is the key element in the SCF E3 ubiquitination complex where it determines the substrate specificity for ubiquitination and degradation of various host proteins.  Downregulation of FBXO22 by siRNA or CRISPR-Cas9 system, resulted diminished uptake of Brucella into macrophages, which was dependent on NF-κB-mediated regulation of phagocytic receptors. FBXO22 expression was upregulated in Brucella -infected macrophages that resulted induction of phagocytic receptors and enhanced production of pro-inflammatory cytokines through NF-κB. Furthermore, we found that FBXO22 recruits the effector proteins of Brucella , including the anti-inflammatory proteins, TcpB and OMP25 for degradation through the SCF complex. We did not observe any role for another F-box containing protein of SCF complex, β-TrCP in Brucella -macrophage interaction. Our findings unravel novel functions of FBXO22 in host-pathogen interaction and its contribution to pathogenesis of infectious diseases.

scholarly journals Identification and Quantification by Targeted Metabolomics of Antibiotic-Responsive Urinary Small Phenolic Molecules Derived from the Intestinal Microbiota in Mice

2019 ◽  
Vol 4 (1) ◽  
pp. 85
Author(s):  
Mark E. Obrenovich ◽  
George Eugene Jaskiw ◽  
Renliang Zhang ◽  
Belinda Willard ◽  
Curtis J. Donskey
Keyword(s):  
High Performance ◽  
Bacterial Species ◽  
Anaerobic Bacteria ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Mouse Urine ◽  
Urinary Levels ◽  
Low Levels ◽  
Pathogen Colonization ◽  
The Relationship

Background: Urinary levels of small molecules generated by the gut microbiota (GMB) constitute potential biomarkers for the state of the GMB. Such metabolites include numerous small phenolic molecules linked to anaerobic bacteria, particularly Clostridium species. Due to multiple technical challenges, however, the relationship between these chemicals and the GMB remains poorly characterized. Improved, high-performance liquid chromatography-mass spectrometry (LC-MS)-based metabolomic analysis can now reliably separate and quantify low levels of multiple small phenolic molecules and their structural isomers.Methods: CF-1 (female mice) were treated over 2 consecutive days with either i) vehicle, ii) one of 2 different antibiotic regimens (clindamycin or piperacillin/tazobactam) known to inhibit intestinal anaerobes and promote colonization by Clostridium difficile and other pathogens or iii) an antibiotic (aztreonam) that suppresses facultative Gram-negative bacteria but not enterococci or anaerobes and does not promote pathogen colonization Urine collected 24 hours after the last treatment was analyzed by LC-MS.Results: We identified over 25 compounds, many of which had not been previously reported in mouse urine. Eleven small phenolic molecules showed significant antibiotic-related changes. Urinary levels of the hydroxyphenylpropionic acids were suppressed by clindamycin and piperacillin/tazobactam treatment, but were elevated in aztreonam-treated mice. In addition, aztreonam treatment was associated with elevated levels of the dihydroxyhydrocinnamic acids.Conclusions: Profiles of differential changes in urinary small phenolic molecules may provide an index of anaerobic bacterial species in the GMB and could prove useful in monitoring susceptibility to overgrowth of pathogens such as C. difficile.

scholarly journals What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

2016 ◽  
Vol 55 (1) ◽  
pp. 24-42 ◽  
Author(s):  
Erik Munson ◽  
Karen C. Carroll
Keyword(s):  
Susceptibility Testing ◽  
Novel Species ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Taxonomic Status ◽  
Emerging Pathogens ◽  
Taxonomic Changes ◽  
Clinically Significant ◽  
Organism Identification ◽  
Evolutionary Microbiology

ABSTRACTTechnological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by theInternational Journal of Systematic and Evolutionary Microbiology. Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by theJournal of Clinical Microbiologyon a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

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