SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

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Sa244 INFLUENCE OF HELICOBACTER PYLORI ON THE MICROBIAL COMPOSITION OF HUMAN GASTRIC MUCOSA: ANALYSIS BASED ON DNA AND RNA 16S AMPLICON SEQUENCING

Gastroenterology ◽

10.1016/s0016-5085(21)01813-8 ◽

2021 ◽

Vol 160 (6) ◽

pp. S-463

Author(s):

Elena Kupriyanova ◽

Maria Markelova ◽

Sayar Abdulkhakov ◽

Tatyana Grigoryeva ◽

Airat Safin ◽

...

Keyword(s):

Helicobacter Pylori ◽

Gastric Mucosa ◽

Amplicon Sequencing ◽

Human Gastric Mucosa ◽

Microbial Composition ◽

Dna And Rna ◽

16S Amplicon Sequencing

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Microbial composition of enigmatic bird parasites:WolbachiaandSpiroplasmaare the most important bacterial associates of quill mites (Acari: Syringophilidae)

10.1101/377218 ◽

2018 ◽

Author(s):

Eliza Glowska ◽

Zuzanna K. Filutowska ◽

Miroslawa Dabert ◽

Michael Gerth

Keyword(s):

Subcutaneous Tissue ◽

Detection Threshold ◽

Bird Species ◽

Amplicon Sequencing ◽

Biological Properties ◽

Mite Species ◽

Symbiotic Association ◽

Microbial Composition ◽

Quill Mites ◽

16S Amplicon Sequencing

AbstractThe microbiome is an integral component of many animal species, potentially affecting behaviour, physiology, and other biological properties. Despite this importance, bacterial communities remain vastly understudied in many groups of invertebrates, including mites. Quill mites (Acariformes: Syringophilidae) are a poorly known group of permanent bird ectoparasites that occupy quills of feathers and feed on bird subcutaneous tissue and fluids. Most species have strongly female biased sex ratios and it was hypothesized that this is caused by endosymbiotic bacteria. Their peculiar lifestyle further makes them potential vectors for bird diseases. Previously,Anaplasma phagocytophilumand a high diversity ofWolbachiastrains were detected in quill mites via targeted PCR screens. Here, we use an unbiased 16S amplicon sequencing approach to determine other Bacteria that potentially impact quill mite biology.We performed 16S V4 amplicon sequencing of 126 quill mite individuals from eleven species parasitizing twelve bird species (four families) of passeriform birds. In addition toWolbachia, we foundSpiroplasmaas potential symbiont of quill mites. Interestingly, consistently highSpiroplasmatitres were only found in individuals of two mite species associated with finches of the genusCardfuelis, suggesting a history of horizontal transfers ofSpiroplasmavia the bird host. Furthermore, there was evidence forSpiroplasmanegatively affectingWolbachiatitres. We found no evidence for the previously reportedAnaplasmain quill mites, but detected the potential pathogensBrucellaandBartonellaat low abundances. Other amplicon sequence variants (ASVs) could be assigned to a diverse number of bacterial taxa, including several that were previously isolated from bird skin. We observed a relatively uniform distribution of these ASVs across mite taxa and bird hosts, i.e, there was a lack of host-specificity for most detected ASVs. Further, many frequently found ASVs were assigned to taxa that show a very broad distribution with no strong prior evidence for symbiotic association with animals. We interpret these findings as evidence for a scarcity or lack of resident microbial associates (other than inherited symbionts) in quill mites, or for abundances of these taxa below our detection threshold.

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Oral Microbiome and Gingival Transcriptome Profiles of Ligature-Induced Periodontitis

Journal of Dental Research ◽

10.1177/0022034520906138 ◽

2020 ◽

Vol 99 (6) ◽

pp. 746-757 ◽

Cited By ~ 5

Author(s):

J. Ebersole ◽

S. Kirakodu ◽

J. Chen ◽

R. Nagarajan ◽

O.A. Gonzalez

Keyword(s):

Amplicon Sequencing ◽

Young Group ◽

Oral Microbiome ◽

Specific Gene ◽

Immune Genes ◽

Gene Profiles ◽

16S Amplicon Sequencing ◽

Health And Disease ◽

Relationship Of ◽

The Relationship

This investigation evaluated the relationship of the oral microbiome and gingival transcriptome in health and periodontitis in nonhuman primates ( Macaca mulatta). Subgingival plaque samples and gingival biopsies were collected from healthy sites and at sites undergoing ligature-induced periodontitis. Microbial samples were analyzed with 16S amplicon sequencing to identify bacterial profiles in young (3 to 7 y) and adult (12 to 23 y) animals. The gingival transcriptome was determined with a microarray analysis and focused on the expression level of 452 genes that are associated with the development of inflammation and innate and adaptive immune responses. Of the 396 total operational taxonomic units (OTUs) identified across the samples, 81.8% were detected in the young group and 99.5% in the adult group. Nevertheless, 58 of the OTUs composed 88% of the signal in adults, and 49 OTUs covered 91% of the OTU readouts in the young group. Correlation analyses between the microbiome members and specific gingival genes showed a high number of significant bacteria-gene correlations in the young healthy tissues, which decreased by 75% in diseased tissues. In contrast, these correlations increased by 2.5-fold in diseased versus healthy tissues of adult animals. Complexes of bacteria were delineated that related to specific sets of immune genes, differing in health and disease and in the young versus adult animals. The correlated gene profiles demonstrated selected pathway overrepresentation related to particular bacterial complexes. These results provide novel insights into microbiome changes with disease and the relationship of these changes to specific gene profiles and likely biologic activities occurring in healthy and diseased gingival tissues in this human-like periodontitis model.

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Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1908600116 ◽

2019 ◽

Vol 117 (2) ◽

pp. 1148-1159 ◽

Cited By ~ 19

Author(s):

Norma M. Morella ◽

Francis Cheng-Hsuan Weng ◽

Pierre M. Joubert ◽

C. Jessica E. Metcalf ◽

Steven Lindow ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Amplicon Sequencing ◽

Host Genotype ◽

Microbial Composition ◽

Internal Transcribed Spacer Region ◽

Tomato Plants ◽

16S Amplicon Sequencing ◽

Host Evolution ◽

Plant Microbiome

There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.

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16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients

PeerJ ◽

10.7717/peerj.10995 ◽

2021 ◽

Vol 9 ◽

pp. e10995

Author(s):

Muhammad Yasir ◽

Arooj K. Qureshi ◽

Esam I. Azhar

Keyword(s):

Microbial Diversity ◽

Hot Springs ◽

Hot Spring ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Microbial Composition ◽

Sediment Samples ◽

Bacterial Phyla ◽

16S Amplicon Sequencing ◽

Culture Dependent

Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.

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Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

10.1101/627794 ◽

2019 ◽

Cited By ~ 3

Author(s):

Norma M. Morella ◽

Francis Cheng-Hsuan Weng ◽

Pierre M. Joubert ◽

C. Jessica E. Metcalf ◽

Steven Lindow ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Amplicon Sequencing ◽

Host Genotype ◽

Microbial Composition ◽

Plant Host ◽

Independent Manner ◽

16S Amplicon Sequencing ◽

The Impact ◽

Plant Microbiome

AbstractThere is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across five plant genotypes for four eight-week long passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (ITS amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond.Significance StatementThere is great interest in selecting for host-associated microbiomes that confer particular functions to their host, and yet it remains unknown whether selection for a robust and stable microbiome is possible. Here, we use a microbiome passaging approach to measure the impact of host-mediated selection on the tomato phyllosphere (above ground) microbiome. We find robust community selection across replicate lines that is shaped by plant host genotype in early passages, but changes in a genotype-independent manner in later passages. Work such as ours is crucial to understanding the general principles governing microbiome assembly and adaptation, and is widely applicable to both sustainable agriculture and microbiome-related medicine.

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Differences in Diet and Gut Microbiota Between Lactating and Non-lactating Asian Particolored Bats (Vespertilio sinensis): Implication for a Connection Between Diet and Gut Microbiota

Frontiers in Microbiology ◽

10.3389/fmicb.2021.735122 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jingjing Li ◽

Yujia Chu ◽

Wenwen Yao ◽

Hui Wu ◽

Jiang Feng

Keyword(s):

Comparative Analysis ◽

Gut Microbiota ◽

Relative Abundance ◽

Amplicon Sequencing ◽

Microbial Composition ◽

High Protein Content ◽

Gut Microbes ◽

Energy Demands ◽

16S Amplicon Sequencing ◽

Lactating Females

In mammals, lactation is considered the most energetically costly phase for females. To meet nutritional and energy demands, lactating females usually change feeding patterns by eating food that is higher in protein and calories. Their gut microbes respond accordingly to help adapt to the changes in diet. In this study, we examined differences in diet and gut microbial composition between lactating and non-lactating Asian particolored bats (Vespertilio sinensis) using COI and 16S amplicon sequencing. When compared with non-lactating bats, we found that the diversity and composition of lactating bats’ diets differed; the proportion of Diptera increased and Coleoptera and Orthoptera decreased significantly. This could be attributed to the easy availability and high protein content of Diptera. Comparative analysis of the gut microbiota of lactating and non-lactating females showed that although the diversity of gut microbiota did not change, the relative abundance of specific gut microbiota associated with a particular diet did change. For example, when the consumption of Coleoptera decreased in lactating bats, the relative abundance of Lactobacillaceae was also reduced. Lactobacillaceae are thought to be involved in the digestion of Coleopteran exoskeletons. This study suggests that during lactation, Asian particolored bats eat a diet that yields higher levels of protein, and at the same time, the abundance of specific gut microbes change to help their hosts adapt to these changes in diet.

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Plasma therapy a possible hope to fight against COVID-19

10.35543/osf.io/yhq7v ◽

2020 ◽

Author(s):

Ravikant Piyush ◽

Aroni Chatterjee ◽

Shashikant Ray

Keyword(s):

Middle East ◽

Severe Acute Respiratory Syndrome ◽

Viral Disease ◽

Plasma Therapy ◽

Therapeutic Drugs ◽

Wild Fire ◽

The World ◽

Short Span ◽

Game Changer

The world is currently going through a disastrous event and a catastrophic upheaval caused by the coronavirus disease 2019 (COVID-19). The pandemic has resulted in loss of more than 150000 deaths across the globe. Originating from China and spreading across all continents within a short span of time, it has become a matter of international emergency. Different agencies are adopting diverse approaches to stop and spread of this viral disease but still now nothing confirmatory has come up. Due to lack of vaccines and proper therapeutic drugs, the disease is still spreading like wild fire without control. An Old but very promising method- the convalescent plasma therapy could be the key therapy to stop this pandemic. This method has already proven its mettle on several occasions previously and has been found to be effective in curing the pandemics induced by Ebola, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the same group of β-Coronavirus that has resulted in the above diseases. Therefore, the role of plasma therapy is being explored for treatment of this disease. In this review, we have mainly focused on the role of convalescent plasma therapy and why its use should be promoted in fight against COVID-19, as it could turn out to be a game changer.

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Pre-Procedural COVID-19 Nasopharyngeal Swab Has Good Concordance with Bronchoalveolar Lavage in Patients at Low Risk for Viral Infection

Respiration ◽

10.1159/000514928 ◽

2021 ◽

pp. 1-5

Author(s):

Catherine L. Oberg ◽

Reza Ronaghi ◽

Erik E. Folch ◽

Colleen L. Channick ◽

Tao He ◽

...

Keyword(s):

Bronchoalveolar Lavage ◽

Low Risk ◽

Lower Airway ◽

Nasopharyngeal Swab ◽

Symptom Screening ◽

The World ◽

Good Concordance ◽

Sensitivity Specificity ◽

Overall Reliability ◽

Rule Out

Background: The coronavirus disease 2019 (COVID-19) pandemic has drastically affected hospital and operating room (OR) workflow around the world as well as trainee education. Many institutions have instituted mandatory preoperative SARS-CoV-2 PCR nasopharyngeal swab (NS) testing in patients who are low risk for COVID-19 prior to elective cases. This method, however, is challenging as the sensitivity, specificity, and overall reliability of testing remains unclear. Objectives: The objective of this study was to assess the concordance of a negative NS in low risk preoperative patients with lower airway bronchoalveolar lavage (BAL) specimens obtained from the same patients. Methods: We prospectively sent intraoperative lower airway BAL samples collected within 48 h of a negative mandatory preoperative NS for SARS-CoV-2 PCR testing. All adult patients undergoing a scheduled bronchoscopic procedure for any reason were enrolled, including elective and nonelective cases. Results: One-hundred eighty-nine patients were included. All BAL specimens were negative for SARS-CoV-2 indicative of 100% concordance between testing modalities. Conclusions: These results are promising and suggest that preoperative nasopharyngeal SARS-CoV-2 testing provides adequate screening to rule out active COVID-19 infection prior to OR cases in a population characterized as low risk by negative symptom screening. This information can be used for both pre-procedural screening and when reintroducing trainees into the workforce.

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Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽

10.3390/metabo11080472 ◽

2021 ◽

Vol 11 (8) ◽

pp. 472

Author(s):

Yeong-Ji Oh ◽

Ye-Rin Park ◽

Jungil Hong ◽

Do-Yup Lee

Keyword(s):

Amplicon Sequencing ◽

Taxonomic Composition ◽

Metabolic Phenotype ◽

Rrna Gene ◽

Functional Evaluation ◽

Initial Condition ◽

Microbial Composition ◽

Light Emitting ◽

Blue Led ◽

Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

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