Profiling of Oral Microbiota and Cytokines in COVID-19 Patients

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that the oral cavity mucosa harbors high levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease, serine 2 (TMPRSS2), highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. Here, we studied the oral microbiota structure and inflammatory profile of 26 naive severe coronavirus disease 2019 (COVID-19) patients and 15 controls by 16S rRNA V2 automated targeted sequencing and magnetic bead-based multiplex immunoassays, respectively. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Rothia mucilaginosa were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Groups (SIGs). COVID-19-related pro-inflammatory cytokines were found in both oral and serum samples, along with a specific bacterial consortium able to counteract them. We introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an Area Under Curve (AUC) equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would be usable in clinics against COVID-19, using bacterial consortia as biomarkers or to reduce local inflammation.

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Profiling of oral microbiota and cytokines in COVID-19 patients

10.1101/2020.12.13.422589 ◽

2020 ◽

Author(s):

Valerio Iebba ◽

Nunzia Zanotta ◽

Giuseppina Campisciano ◽

Verena Zerbato ◽

Stefano Di Bella ◽

...

Keyword(s):

Distinct Species ◽

Bacterial Consortium ◽

Magnetic Bead ◽

Oral Microbiota ◽

Serum Samples ◽

Inflammatory Profile ◽

First Time ◽

Neisseria Perflava ◽

Microbiota Structure ◽

Pro Inflammatory Cytokines

ABSTRACTSARS-CoV-2 presence has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that oral cavity mucosa harbors high levels of ACE2 and TMPRSS2, highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. In the present study, for the first time, we demonstrate the oral microbiota structure and inflammatory profile of COVID-19 patients. Hospitalized COVID-19 patients and matched healthy controls underwent naso/oral-pharyngeal and oral swabs. Microbiota structure was analyzed by 16S rRNA V2 automated targeted sequencing, while oral and sera concentrations of 27 cytokines were assessed using magnetic bead-based multiplex immunoassays. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Granulicatella elegans were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Group (SIGs). Pro-inflammatory cytokines were distinctive for COVID-19 in both oral and serum samples, and we found a specific bacterial consortium able to counteract them, following a novel index called C4 firstly proposed here. We even introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an AUC equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would pave the way for a theranostic approach in fighting COVID-19, trying to enlighten the intimate relationship among microbiota and SARS-CoV-2 infection.

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Asthma and COVID-19: who wins the contested territory of the lower airways?

Research Society and Development ◽

10.33448/rsd-v10i12.20110 ◽

2021 ◽

Vol 10 (12) ◽

pp. e17101220110

Author(s):

Taís de Lima e Fraga ◽

Waldemar de Paula Junior ◽

Marileia Chaves Andrade

Keyword(s):

Target Cells ◽

Chronic Asthma ◽

Th2 Response ◽

Angiotensin Converting Enzyme 2 ◽

Asthmatic Patients ◽

Coronavirus Infection ◽

Inflammatory Profile ◽

Limited Possibility ◽

Pro Inflammatory Cytokines

Among the numerous published studies on COVID-19 in a pandemic year, few listed asthma as a comorbidity, making it therefore difficult to draw any solid conclusions. The respiratory allergy and controlled exposures to allergens are associated with significant reductions in the expression of angiotensin-converting enzyme 2 (ACE2), receptor for SARS-CoV-2 entry into human cells. There is a hypothesis that patients with chronic asthma, due to the type 2 inflammatory profile, may be potentially resistant to developing a severe clinical course of COVID-19. The low IFN-g-mediated response in the respiratory tract of asthmatic patients could limit ACE2 expression in the target cells of SARS-CoV-2 infection. The inflammatory profile of the airways in patients with chronic asthma is mainly related to a Th2 response in type-2 asthma, with production of IL-4, IL-13 and IL-5, presenting antagonistic relationship with pro-inflammatory cytokines such as IFN-g, produced at high levels in severe COVID-19. Published studies, for the most part, are retrospective and may have loss of information or present material with limited possibility for more robust and conclusive analysis. It is important to discuss how patients with atopic or nonatopic asthma seem to protect themselves from new coronavirus infection and how asthma affects COVID-19 and the course of the disease, since there is no increased mortality in asthmatic patients with COVID-19 compared to non-asthmatic patients.

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A comparison between different anti-retroviral therapy regimes on soluble inflammation markers: a pilot study

AIDS Research and Therapy ◽

10.1186/s12981-020-00316-w ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Martina Maritati ◽

Trentini Alessandro ◽

Nunzia Zanotta ◽

Manola Comar ◽

Tiziana Bellini ◽

...

Keyword(s):

Drug Regimen ◽

Antiretroviral Drugs ◽

Serum Samples ◽

The Third ◽

Cytokines And Chemokines ◽

Antiretroviral Drug ◽

Group 3 ◽

Group 2 ◽

Inflammatory Profile ◽

Group 1

Abstract Background Although HIV-related deaths have decreased dramatically following the introduction of antiretroviral therapy (ART), HIV infection itself causes increased morbidity and mortality for both non-AIDS-related events or chronic inflammation and immune activation. The use of certain antiretroviral drugs can contribute to this process. Methods We investigated 26 potential biomarkers in serum samples from HIV-1 infected patients virologically suppressed under ART. The main objective of our study was to evaluate if virological suppression achieved with a triple drug regimen containing tenofovir disoproxil fumarate co-formulated with emtricitabine (TDF/FTC) as backbone, could correlate with a better immunological and inflammatory profile in relation to the third class of antiretroviral drug administered. The eligible patients were then divided into 3 groups in relation to the third drug associated with TDF/FTC: nucleoside reverse transcriptase inhibitors (NNRTI) (Group 1, n = 16), protease inhibitors (PI) (Group 2, n = 17) and integrase inhibitors (INI) (Group 3, n = 16). Results Inflammatory cytokines and chemokines were more represented in Group 2 than in Group 3 (IL-1Ra, p = 0.013; IL-12p70 p = 0.039; TNF-α p = 0.041; IL-8, p = 0.027; MIP1 β, p = 0.033). Eotaxin showed lower levels in Group 1 compared to Group 2 (p = 0.010), while IP-10 was significantly lower in Group 1 compared to both Group 2 and Group 3 (p = 0.003 and p = 0.007, respectively). Conclusions Our results seem to discourage the administration of PI as a third drug in a virologically effective antiretroviral regimen, as its use is linked to the detection of higher levels of pro-inflammatory mediators in comparison with INI and NNRTI.

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Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR)

Animals ◽

10.3390/ani10122378 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2378

Author(s):

Cristian Piras ◽

Viviana Greco ◽

Enrico Gugliandolo ◽

Alessio Soggiu ◽

Bruno Tilocca ◽

...

Keyword(s):

Ecological Niche ◽

Bacterial Species ◽

Raw Milk ◽

Bacterial Consortium ◽

Cow Milk ◽

Milk Analysis ◽

Animal Products ◽

Bacterial Consortia ◽

Expression Of Genes ◽

Ecological Pressure

The environment, including animals and animal products, is colonized by bacterial species that are typical and specific of every different ecological niche. Natural and human-related ecological pressure promotes the selection and expression of genes related to antimicrobial resistance (AMR). These genes might be present in a bacterial consortium but might not necessarily be expressed. Their expression could be induced by the presence of antimicrobial compounds that could originate from a given ecological niche or from human activity. In this work, we applied (meta)proteomics analysis of bacterial compartment of raw milk in order to obtain a method that provides a measurement of circulating AMR involved proteins and gathers information about the whole bacterial composition. Results from milk analysis revealed the presence of 29 proteins/proteoforms linked to AMR. The detection of mainly β-lactamases suggests the possibility of using the milk microbiome as a bioindicator for the investigation of AMR. Moreover, it was possible to achieve a culture-free qualitative and functional analysis of raw milk bacterial consortia.

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The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins

PLoS ONE ◽

10.1371/journal.pone.0158288 ◽

2016 ◽

Vol 11 (8) ◽

pp. e0158288 ◽

Cited By ~ 2

Author(s):

Tejal Madhwani ◽

Andrew J. McBain

Keyword(s):

Magnetic Bead ◽

Oral Microbiota

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BACTERIAL CONSORTIA FOR RETTING OF COCONUT HUSKS IN TANKS

CORD ◽

10.37833/cord.v15i01.322 ◽

1999 ◽

Vol 15 (01) ◽

pp. 34

Author(s):

Anita Das Ravindranath ◽

Saroi Bhosle

Keyword(s):

Bacterial Consortium ◽

Bacterial Consortia ◽

Coconut Husk ◽

Coir Fibre

A bacterial consortium developed on coconut husk leachates could ret coconut husk steeped for retting in rap water in a period of three months. The quality of the coir fibre obtained was comparable to traditionally retted fibre. The consortia could also bestow a greater degree of softness to the mechanically extracted coir fibre. Coir extraction can therefore be practiced by supplying the consortia for retting of husk for production of fibre and enhance the commercial utilization of the husk in coconut growing regions of Asia.

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Establishing and Optimizing a Bacterial Consortia for Effective Biodegradation of Petroleum Contaminants: Advancing Classical Microbiology via Experimental and Mathematical Approach

Water ◽

10.3390/w13223311 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3311

Author(s):

Baichun Wu ◽

Jingmin Deng ◽

Hao Niu ◽

Jiahao Liang ◽

Muhammad Arslan ◽

...

Keyword(s):

Partial Correlation ◽

High Efficiency ◽

Bacterial Species ◽

Rhodococcus Erythropolis ◽

Bacterial Consortium ◽

Bacterial Strains ◽

Bacterial Consortia ◽

Orthogonal Experiments ◽

Petroleum Contaminants ◽

Different Strains

In classical microbiology, developing a high-efficiency bacterial consortium is a great challenge for faster biodegradation of petroleum contaminants. In this study, a systematic experimental and mathematical procedure was adopted to establish a bacterial consortium for the effective biodegradation of heavy oil constituents. A total of 27 bacterial consortia were established as per orthogonal experiments, using 8 petroleum-degrading bacterial strains. These bacteria were closer phylogenetic relatives of Brevundimonas sp. Tibet-IX23 (Y1), Bacillus firmus YHSA15, B. cereus MTCC 9817, B. aquimaris AT8 (Y2, Y6 and Y7), Pseudomonas alcaligenes NBRC (Y3), Microbacterium oxydans CV8.4 (Y4), Rhodococcus erythropolis SBUG 2052 (Y5), and Planococcus sp. Tibet-IX21 (Y8), and were used in different combinations. Partial correlation analysis and a general linear model hereafter were applied to investigate interspecific relationships among different strains and consortia. The Y1 bacterial species showed a remarkable synergy, whereas Y3, Y4, and Y6 displayed a strong antagonism in all consortia. Inoculation ratios of different strains significantly influenced biodegradation. An optimal consortium was constructed with Y1, Y2, Y5, Y7, and Y8, which revealed maximum degradation of 11.238 mg/mL OD600 for oil contaminants. This study provides a line of evidence that a functional consortium can be established by mathematical models for improved bioremediation of petroleum-contaminated environment.

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Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore

mSystems ◽

10.1128/msystems.00161-20 ◽

2020 ◽

Vol 5 (2) ◽

Cited By ~ 4

Author(s):

Carla C. Uranga ◽

Pablo Arroyo ◽

Brendan M. Duggan ◽

William H. Gerwick ◽

Anna Edlund

Keyword(s):

Liquid Chromatography ◽

Oral Health ◽

Genome Mining ◽

Oral Bacteria ◽

Community Member ◽

Oral Microbiota ◽

Content Type ◽

Positive Effects ◽

A Genome ◽

Rothia Mucilaginosa

ABSTRACT Next-generation sequencing studies of saliva and dental plaque from subjects in both healthy and diseased states have identified bacteria belonging to the Rothia genus as ubiquitous members of the oral microbiota. To gain a deeper understanding of molecular mechanisms underlying the chemical ecology of this unexplored group, we applied a genome mining approach that targets functionally important biosynthetic gene clusters (BGCs). All 45 genomes that were mined, representing Rothia mucilaginosa, Rothia dentocariosa, and Rothia aeria, harbored a catechol-siderophore-like BGC. To explore siderophore production further, we grew the previously characterized R. mucilaginosa ATCC 25296 in liquid cultures, amended with glycerol, which led to the identification of the archetype siderophore enterobactin by using tandem liquid chromatography-mass spectrometry (LC-MS/MS), high-performance liquid chromatography (HPLC), and nuclear magnetic resonance (NMR) spectroscopy. Normally attributed to pathogenic gut bacteria, R. mucilaginosa is the first commensal oral bacterium found to produce enterobactin. Cocultivation studies including R. mucilaginosa or purified enterobactin revealed that enterobactin reduced growth of certain strains of cariogenic Streptococcus mutans and pathogenic strains of Staphylococcus aureus. Commensal oral bacteria were either unaffected, reduced in growth, or induced to grow adjacent to enterobactin-producing R. mucilaginosa or the pure compound. Taken together with Rothia’s known capacity to ferment a variety of carbohydrates and amino acids, our findings of enterobactin production add an additional level of explanation to R. mucilaginosa’s prevalence in the oral cavity. Enterobactin is the strongest Fe(III) binding siderophore known, and its role in oral health requires further investigation. IMPORTANCE The communication language of the human oral microbiota is vastly underexplored. However, a few studies have shown that specialized small molecules encoded by BGCs have critical roles such as in colonization resistance against pathogens and quorum sensing. Here, by using a genome mining approach in combination with compound screening of growth cultures, we identified that the commensal oral community member R. mucilaginosa harbors a catecholate-siderophore BGC, which is responsible for the biosynthesis of enterobactin. The iron-scavenging role of enterobactin is known to have positive effects on the host’s iron pool and negative effects on host immune function; however, its role in oral health remains unexplored. R. mucilaginosa was previously identified as an abundant community member in cystic fibrosis, where bacterial iron cycling plays a major role in virulence development. With respect to iron’s broad biological importance, iron-chelating enterobactin may explain R. mucilaginosa’s colonization success in both health and disease.

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Simultaneous Bioremediation of Phenol and Cr (VI) from Tannery Wastewater Using Bacterial Consortium

International Journal of Applied Sciences and Biotechnology ◽

10.3126/ijasbt.v3i1.11889 ◽

2015 ◽

Vol 3 (1) ◽

pp. 50-55 ◽

Cited By ~ 6

Author(s):

Amrik Bhattacharya ◽

Anshu Gupta ◽

Amarjeet Kaur ◽

Darshan Malik

Keyword(s):

Bacterial Consortium ◽

Agitation Speed ◽

Tannery Wastewater ◽

Tannery Effluent ◽

Simultaneous Removal ◽

Bacterial Strains ◽

Static Mode ◽

Simultaneous Reduction ◽

Bacterial Consortia ◽

Removal Of Contaminants

In the present study a consortium of four naturally isolated bacterial strains was evaluated as remediation tool for simultaneous removal ofphenol and Cr (VI) from tannery effluent. Application of bacterial consortia to effluent (pH 4.6) resulted in 100 and 78% removal of initial 47mg L-1 phenol and 16 mg L-1 Cr (VI), respectively at 96 h of treatment. The consortium was also active in removal of contaminants with lowerremoval rate in presence of extraneous higher concentrations of both phenol and Cr (VI). Treatment in static mode also resulted in removal ofpollutants, however with increase in agitation speed simultaneous reduction of contaminants becomes faster. Overall it can be inferred fromthe study that the above formulated bacterial consortium could effectively be used for treatment of phenol and Cr (VI) laden tannery and otherindustrial effluents.DOI: http://dx.doi.org/10.3126/ijasbt.v3i1.11889 Int J Appl Sci Biotechnol, Vol. 3(1): 50-55

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Digital immunoassay for biomarker concentration quantification using solid-state nanopores

Nature Communications ◽

10.1038/s41467-021-25566-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Liqun He ◽

Daniel R. Tessier ◽

Kyle Briggs ◽

Matthaios Tsangaris ◽

Martin Charron ◽

...

Keyword(s):

Solid State ◽

Single Molecule ◽

Dynamic Range ◽

Point Of Care ◽

Magnetic Bead ◽

Thyroid Stimulating Hormone ◽

Target Protein ◽

Diagnostic Tools ◽

Dna Nanostructures ◽

Serum Samples

ABSTRACTSingle-molecule counting is the most accurate and precise method for determining the concentration of a biomarker in solution and is leading to the emergence of digital diagnostic platforms enabling precision medicine. In principle, solid-state nanopores—fully electronic sensors with single-molecule sensitivity—are well suited to the task. Here we present a digital immunoassay scheme capable of reliably quantifying the concentration of a target protein in complex biofluids that overcomes specificity, sensitivity, and consistency challenges associated with the use of solid-state nanopores for protein sensing. This is achieved by employing easily-identifiable DNA nanostructures as proxies for the presence (“1”) or absence (“0”) of the target protein captured via a magnetic bead-based sandwich immunoassay. As a proof-of-concept, we demonstrate quantification of the concentration of thyroid-stimulating hormone from human serum samples down to the high femtomolar range. Further optimization to the method will push sensitivity and dynamic range, allowing for development of precision diagnostic tools compatible with point-of-care format.

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