scholarly journals Metaproteomic Profiling of Fungal Gut Colonization in Gnotobiotic Mice

2021 ◽  
Author(s):  
Veronika Kuchařová Pettersen ◽  
Antoine Dufour ◽  
Marie-Claire Arrieta
Keyword(s):  
Bacterial Species ◽  
Fungal Species ◽  
Mammalian Host ◽  
Marginal Effect ◽  
Host Immune System ◽  
Proteomic Profiling ◽  
Functional Changes ◽  
Fungal Colonisation ◽  
Gut Colonization ◽  
Gnotobiotic Mice

Abstract Background: Eukaryotic microbes can modulate mammalian host health and disease states, yet the molecular contribution of gut fungi remains nascent. We previously showed that mice exclusively colonised with fungi displayed increased sensitivity to allergic airway inflammation and had fecal metabolite profiles similar to germ-free mice. This marginal effect on the host metabolome suggested that fungi do not primarily use metabolites to modulate the host immune system.Methods: To describe functional changes attributed to fungal colonisation, we performed mass spectrometry-based analyses of feces (Label-Free Quantitative; LFQ) and the small intestine (labeling with Tandem Mass Tag; TMT) of gnotobiotic mice colonised with defined consortia of twelve bacterial species, five fungal species, or both. We also evaluated the effect of microbiome perturbances on the metaproteome by analysing feces from mouse pups treated with an antibiotic or antifungal.Results: We detected 6,675 proteins in the mice feces, of which 3,845 had determined LFQ levels. Analysis of variance showed changes in the different gnotobiotic mouse groups; specifically, 46% of 2,860 bacterial, 15% of 580 fungal, and 76% of 405 mouse quantified proteins displayed differential levels. The antimicrobial treatments resulted in lasting changes in the bacterial and fungal proteomes, suggesting that the antimicrobials impacted the entire community. Fungal colonisation resulted in changes in host proteins functional in innate immunity as well as metabolism, predicting specific roles of gut fungi on host systems during early developmental stages. Several of the detected fungal proteins (3% of 1,492) have been previously reported as part of extracellular vesicles and having immunomodulating properties. Using an isobaric labelling TMT approach for profiling low abundant proteins of the jejunal tissue, we confirmed that the five fungal species differentially impacted the host intestinal proteome compared to the bacterial consortium. The detected changes in mouse jejunal proteins (4% of 1,514) were mainly driven by metabolic proteins. Conclusions: We used quantitative proteomic profiling of gnotobiotic conditions to show how colonisation with selected fungal species impacts the host gut proteome. Our results suggest that an increased abundance of certain gut fungal species in early life may affect the developing intracellular attributes of epithelial and immune cells.

scholarly journals Metaproteomic Profiling of Fungal Gut Colonization in Gnotobiotic Mice

2020 ◽  
Author(s):  
Veronika Kuchařová Pettersen ◽  
Antoine Dufour ◽  
Marie-Claire Arrieta
Keyword(s):  
Allergic Airway Inflammation ◽  
Fungal Species ◽  
Fungal Colonization ◽  
Mammalian Host ◽  
Functional Changes ◽  
Disease States ◽  
Gut Colonization ◽  
Increased Sensitivity ◽  
Gnotobiotic Mice ◽  
Eukaryotic Microbes

ABSTRACTEukaryotic microbes can modulate mammalian host health and disease states, yet the molecular contribution of gut fungi remains nascent. We previously showed that mice exclusively colonized with fungi displayed increased sensitivity to allergic airway inflammation and fecal metabolite profiles similar to germ-free mice. To gain insights into the functional changes attributed to fungal colonization, we performed quantitative proteomic analyses of feces and small intestine of four-week-old gnotobiotic mice colonized with bacteria, fungi, or both. A comparison of fecal metaproteomic profiles between the mouse groups yielded broad changes in the relative levels of bacterial (46% of 2,860) and mouse (76% from 405) proteins. Many of the detected fungal proteins (3% of 1,492) have been previously reported as part of extracellular vesicles and having immunomodulating properties. Changes in the levels of mouse proteins derived from the jejunum (4% of 1,514) were mainly driven by proteins functional in lipid metabolism and apoptosis. Using metaproteomic profiling of gnotobiotic conditions, we show that fungal colonization profoundly impacts the host gut proteome. Our results suggest that an increased abundance of certain gut fungal species in early life may impact the developing intracellular balance of epithelial and immune cells.

scholarly journals Long-Term Bacterial and Fungal Dynamics following Oral Lyophilized Fecal Microbiota Transplantation in Clostridioides difficile Infection

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Craig Haifer ◽  
Sudarshan Paramsothy ◽  
Thomas J. Borody ◽  
Annabel Clancy ◽  
Rupert W. Leong ◽  
...  
Keyword(s):  
Fecal Microbiota Transplantation ◽  
Bacterial Species ◽  
Fecal Microbiota ◽  
Fungal Species ◽  
Health Concern ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Gut Colonization ◽  
The Impact

ABSTRACT Oral lyophilized fecal microbiota transplantation (FMT) is effective in recurrent Clostridioides difficile infection (CDI); however, limited data exist on its efficacy in primary CDI and long-term microbial engraftment. Patients with primary or recurrent CDI were prospectively enrolled to receive oral FMT. Changes in the bacterial and fungal communities were characterized prior to and up to 6 months following treatment. A total of 37 patients with CDI (15 primary, 22 recurrent) were treated with 6 capsules each containing 0.35-g lyophilized stool extract. A total of 33 patients (89%) had sustained CDI cure, of whom 3 required a second course. There were no safety signals identified. FMT significantly increased bacterial diversity and shifted composition toward donor profiles in responders but not in nonresponders, with robust donor contribution observed to 6 months following FMT (P < 0.001). Responders showed consistent decreases in Enterobacteriaceae and increases in Faecalibacterium sp. to levels seen in donors. Mycobiome profiling revealed an association with FMT failure and increases in one Penicillium taxon, as well as coexclusion relationships between Candida sp. and bacterial taxa enriched in both donors and responders. Primary CDI was associated with more robust changes in the bacterial community than those with recurrent disease. Oral FMT leads to durable microbial engraftment in patients with primary and recurrent CDI, with several microbial taxa being associated with therapy outcome. Novel coexclusion relationships between bacterial and fungal species support the clinical relevance of transkingdom dynamics. IMPORTANCE Clostridioides difficile infection (CDI) is a substantial health concern worldwide, complicated by patterns of increasing antibiotic resistance that may impact primary treatment. Orally administered fecal microbiota transplantation (FMT) is efficacious in the management of recurrent CDI, with specific bacterial species known to influence clinical outcomes. To date, little is known about the efficacy of FMT in primary CDI and the impact of the mycobiome on therapeutic outcomes. We performed matched bacterial and fungal sequencing on longitudinal samples from a cohort of patients treated with oral FMT for primary and recurrent CDI. We validated many bacterial signatures following oral therapy, confirmed engraftment of donor microbiome out to 6 months following therapy, and demonstrated coexclusion relationships between Candida albicans and two bacterial species in the gut microbiota, which has potential significance beyond CDI, including in the control of gut colonization by this fungal species.

Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

2020 ◽  
Vol 20 (29) ◽  
pp. 2681-2691
Author(s):  
Athina Geronikaki ◽  
Victor Kartsev ◽  
Phaedra Eleftheriou ◽  
Anthi Petrou ◽  
Jasmina Glamočlija ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Drug Targets ◽  
Bacterial Species ◽  
Pharmaceutical Research ◽  
Docking Studies ◽  
Fungal Species ◽  
Docking Analysis ◽  
E Coli ◽  
Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

scholarly journals The novel Dbl homology/BAR domain protein, MsgA, of Talaromyces marneffei regulates yeast morphogenesis during growth inside host cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Harshini Weerasinghe ◽  
Hayley E. Bugeja ◽  
Alex Andrianopoulos
Keyword(s):  
Pathogenic Fungi ◽  
Host Cells ◽  
Microbial Pathogens ◽  
Mammalian Host ◽  
Host Immune System ◽  
Nucleotide Exchange ◽  
Phagocytic Cells ◽  
Macrophage Infection ◽  
Bar Domain ◽  
Talaromyces Marneffei

AbstractMicrobial pathogens have evolved many strategies to evade recognition by the host immune system, including the use of phagocytic cells as a niche within which to proliferate. Dimorphic pathogenic fungi employ an induced morphogenetic transition, switching from multicellular hyphae to unicellular yeast that are more compatible with intracellular growth. A switch to mammalian host body temperature (37 °C) is a key trigger for the dimorphic switch. This study describes a novel gene, msgA, from the dimorphic fungal pathogen Talaromyces marneffei that controls cell morphology in response to host cues rather than temperature. The msgA gene is upregulated during murine macrophage infection, and deletion results in aberrant yeast morphology solely during growth inside macrophages. MsgA contains a Dbl homology domain, and a Bin, Amphiphysin, Rvs (BAR) domain instead of a Plekstrin homology domain typically associated with guanine nucleotide exchange factors (GEFs). The BAR domain is crucial in maintaining yeast morphology and cellular localisation during infection. The data suggests that MsgA does not act as a canonical GEF during macrophage infection and identifies a temperature independent pathway in T. marneffei that controls intracellular yeast morphogenesis.

scholarly journals Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Processes ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 784
Author(s):  
Chao Wang ◽  
Lin Sun ◽  
Haiwen Xu ◽  
Na Na ◽  
Guomei Yin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Fungal Diversity ◽  
North China ◽  
Bacterial Species ◽  
Fungal Species ◽  
Family Farms ◽  
Aerobic Stability ◽  
Whole Plant ◽  
Lactobacillus Kefiri

Whole-plant corn silages on family farms were sampled in Erdos (S1), Baotou (S2), Ulanqab (S3), and Hohhot (S4) in North China, after 300 d of ensiling. The microbial communities, metabolites, and aerobic stability were assessed. Lactobacillusbuchneri, Acinetobacter johnsonii, and unclassified Novosphingobium were present at greater abundances than others in S2 with greater bacterial diversity and metabolites. Lactobacillus buchneri, Lactobacillus parafarraginis, Lactobacillus kefiri, and unclassified Lactobacillus accounted for 84.5%, and 88.2%, and 98.3% of bacteria in S1, S3, and S4, respectively. The aerobic stability and fungal diversity were greater in S1 and S4 with greater abundances of unclassified Kazachstania, Kazachstania bulderi, Candida xylopsoci, unclassified Cladosporium, Rhizopus microspores, and Candida glabrata than other fungi. The abundances of unclassified Kazachstania in S2 and K. bulderi in S3 were 96.2% and 93.6%, respectively. The main bacterial species in S2 were L. buchneri, A. johnsonii, and unclassified Novosphingobium; Lactobacillus sp. dominated bacterial communities in S1, S3, and S4. The main fungal species in S1 and S4 were unclassified Kazachstania, K. bulderi, C. xylopsoci, unclassified Cladosporium, R. microspores, and C. glabrata; Kazachstania sp. dominated fungal communities in S2 and S3. The high bacterial diversity aided the accumulation of metabolites, and the broad fungal diversity improved the aerobic stability.

scholarly journals Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus

2019 ◽  
Author(s):  
Feng Zhu ◽  
Yanmei Ju ◽  
Wei Wang ◽  
Qi Wang ◽  
Ruijin Guo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Validation Cohort ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Operating Characteristics ◽  
Discovery Cohort ◽  
Peripheral Tissues ◽  
Functional Changes ◽  
Microbial Biomarkers

AbstractEmerging evidence has linked the gut microbiota to schizophrenia. However, the functional changes in the gut microbiota and the biological role of individual bacterial species in schizophrenia have not been explored systematically. Here, we characterized the gut microbiota in schizophrenia using shotgun metagenomic sequencing of feces from a discovery cohort of 90 drug-free patients and 81 controls, as well as a validation cohort of 45 patients taking antipsychotics and 45 controls. We screened 83 schizophrenia-associated bacterial species and constructed a classifier comprising 26 microbial biomarkers that distinguished patients from controls with a 0.896 area under the receiver operating characteristics curve (AUC) in the discovery cohort and 0.765 AUC in the validation cohort. Our analysis of fecal metagenomes revealed that schizophrenia-associated gut–brain modules included short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters including glutamate, γ-aminobutyric acid, and nitric oxide. The schizophrenia-enriched gut bacterial species include several oral cavity-resident microbes, such as Streptococcus vestibularis. We transplanted Streptococcus vestibularis into the gut of the mice with antibiotic-induced microbiota depletion to explore its functional role. We observed that this microbe transiently inhabited the mouse gut and this was followed by hyperactivity and deficit in social behaviors, accompanied with altered neurotransmitter levels in peripheral tissues. In conclusion, our study identified 26 schizophrenia-associated bacterial species representing potential microbial targets for future treatment, as well as gut–brain modules, some of which may give rise to new microbial metabolites involved in the development of schizophrenia.

scholarly journals GC-MS Analysis and Antimicrobial Assessment of Syzygium cumini (L.) Skeels Seed Ethanol Extract

2021 ◽  
pp. 271-283
Author(s):  
S. Mabel Parimala ◽  
A. Antilin Salomi
Keyword(s):  
Bacterial Species ◽  
Ethanol Extract ◽  
Microtiter Plate ◽  
Salmonella Typhi ◽  
Fungal Species ◽  
Gas Chromatography Mass Spectrometry ◽  
Diffusion Method ◽  
Syzygium Cumini ◽  
Microtiter Plate Assay ◽  
Agar Well Diffusion Method

People use plants to treat infections, and this has led to search of antimicrobials from medicinal plants. In this work, we evaluated the ethanol extract of Syzygium cumini seeds for their antibacterial and antifungal activities. Extraction was performed by maceration method using ethanol. The antimicrobial efficacy of the extract was assessed by agar well diffusion method against ten bacterial species, Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Staphylococcus aureus and Streptococcus mutans, and five fungal species, Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Candida albicans and Mucor sp. Minimum inhibitory concentrations (MICs) of the extract were determined by resazurin microtiter plate assay.  Phytochemicals in the extract was identified by gas chromatography mass spectrometry (GC-MS) information.  In agar well diffusion method, Gram-negative bacteria such as P. aeruginosa and S. marcescens, Gram-positive bacteria such as B. subtilis and E. faecalis and fungi A. fumigatus were more susceptible showing larger zones of inhibition.  In resazurin method, low MICs were recorded for bacteria, B. cereus (<7.8 µg) and P. aeruginosa (15.6 µg) and fungi, A. fumigatus (31.2 µg).  Fifteen compounds were identified by GC-MS profiling of the extract.  The antimicrobial activity of the extract can be rightly related to the secondary metabolites in the ethanol extract of Syzygium cumini seeds.

Characterizing the Microbiome of the Contracted Breast Capsule Using Next Generation Sequencing

2020 ◽  
Author(s):  
Jonathan Cook ◽  
Casey J Holmes ◽  
Roger Wixtrom ◽  
Martin I Newman ◽  
Jason N Pozner
Keyword(s):  
Next Generation Sequencing ◽  
Capsular Contracture ◽  
Bacterial Species ◽  
Fungal Species ◽  
Augmentation Mammoplasty ◽  
Next Generation ◽  
Level Of Evidence ◽  
Cutibacterium Acnes ◽  
Microbial Dna ◽  
Generation Sequencing

Abstract Background Recent work suggests that bacterial biofilms play a role in capsular contracture (CC). However, traditional culture techniques provide only a limited understanding of the bacterial communities present within the contracted breast. Next generation sequencing (NGS) represents an evolution of polymerase chain reaction technology that can sequence all DNA present in a given sample. Objectives The aim of this study was to utilize NGS to characterize the bacterial microbiome of the capsule in patients with CC following cosmetic breast augmentation. Methods We evaluated 32 consecutive patients with Baker grade III or IV CC following augmentation mammoplasty. Specimens were obtained from all contracted breasts (n = 53) during capsulectomy. Tissue specimens from contracted capsules as well as intraoperative swabs of the breast capsule and implant surfaces were obtained. Samples were sent to MicroGenDX Laboratories (Lubbock, TX) for NGS. Results Specimens collected from 18 of 32 patients (56%) revealed the presence of microbial DNA. The total number of positive samples was 22 of 53 (42%). Sequencing identified a total of 120 unique bacterial species and 6 unique fungal species. Specimens with microbial DNA yielded a mean [standard deviation] of 8.27 [4.8] microbial species per patient. The most frequently isolated species were Escherichia coli (25% of all isolates), Diaphorobacter nitroreducens (12%), Cutibacterium acnes (12%), Staphylococcus epidermidis (11%), fungal species (7%), and Staphylococcus aureus (6%). Conclusions NGS enables characterization of the bacterial ecosystem surrounding breast implants in unprecedented detail. This is a critical step towards understanding the role this microbiome plays in the development of CC. Level of Evidence: 4

scholarly journals Common adaptive strategies underlie within-host evolution of bacterial pathogens

2020 ◽  
Author(s):  
Yair E Gatt ◽  
Hanah Margalit
Keyword(s):  
Bacterial Infections ◽  
Large Scale ◽  
Bacterial Species ◽  
Adaptive Strategies ◽  
Single Species ◽  
Adaptive Strategy ◽  
Host Immune System ◽  
Glycerol Phosphate ◽  
Genomic Changes ◽  
Virulence Attenuation

Abstract Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge towards similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. While the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure or function were changed in other species utilizing the same adaptive strategy (e.g. mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species-specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa), and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.

scholarly journals Prevalence and Clinicomycological studies of Otomycosis: A review

2019 ◽  
Vol 28 ◽  
pp. 121-135
Author(s):  
KK Nipa ◽  
AHM Kamal ◽  
A Imtiaj
Keyword(s):  
Bacterial Species ◽  
Folk Medicine ◽  
Fungal Species ◽  
Research Needs ◽  
Predisposing Factor ◽  
Global Context ◽  
Education Improvement ◽  
The World ◽  
Causative Agents ◽  
Socioeconomic Status And Health

Otomycosis is a chronic ear disease of external auditory canal and it is more prevalent in warm, humid and dusty environment, although it is now found throughout the world. The most commonly found causative agents as of fungal species are Aspergillus and Candida along with preponderance of various fungal and bacterial species has also been reported. The aim of this review is to focus on the prevalence of causal agents of otomycosis in the global context and its clinical management. A total of 63 research articles have been reviewed, which deals prevalence of otomycosis. Its clinicomycological studies both separately and altogether with folk medicine in relation to treatment of otomycosis were also reviewed. Findings of various reports revealed that the Aspergillus and Candida species are the main causal agents of otomycosis. But many reports indicate that a few of other fungal species along with bacteria particularly Staplylococcus aureus and Pseudomonas aeruginosa are also responsible for accelerating this disease in human all over the world. In many reports, improper self-cleaning of ear has been found as major predisposing factor of otomycosis. This review suggests that health education, improvement of socioeconomic status and health caring facilities should be increased for reducing prevalence of otomycosis. However, more research needs to be carried out because of its severe parallel effects to the human health. J. bio-sci. 28: 121-135, 2020

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