scholarly journals Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Phillip A. Engen ◽  
Ankur Naqib ◽  
Cheryl Jennings ◽  
Stefan J. Green ◽  
Alan Landay ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Disease Progression ◽  
High Throughput ◽  
Ribosomal Rna ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Proof Of Concept ◽  
Viral Transport ◽  
16S Ribosomal Rna Gene

AbstractWe investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed significant microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection samples already collected for SARS-CoV-2 testing (viral transport media) and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.

scholarly journals Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients

2021 ◽  
Author(s):  
Phillip A. Engen ◽  
Ankur Naqib ◽  
Cheryl Jennings ◽  
Stefan J. Green ◽  
Alan Landay ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Disease Progression ◽  
High Throughput ◽  
Ribosomal Rna ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Proof Of Concept ◽  
Ribosomal Rna Gene ◽  
16S Ribosomal Rna Gene

Abstract We investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection procedures for SARS-CoV-2 testing and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.

Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

2021 ◽  
Author(s):  
Yanbo Liu ◽  
Mengxiao Sun ◽  
Pei Hou ◽  
Wenya Wang ◽  
Xiangkun Shen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Qualitative Analysis ◽  
Volatile Compounds ◽  
High Throughput ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Solid Phase ◽  
Gas Chromatography Mass Spectrometry ◽  
Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

scholarly journals High-throughput sequencing revealed differences of microbial community structure and diversity between healthy and diseased Caulerpa lentillifera

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhourui Liang ◽  
Fuli Liu ◽  
Wenjun Wang ◽  
Pengyan Zhang ◽  
Xiutao Sun ◽  
...  
Keyword(s):  
Information Processing ◽  
Community Structure ◽  
Microbial Community ◽  
16S Rdna ◽  
High Throughput ◽  
Microbial Community Structure ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
Rdna Sequencing ◽  
Caulerpa Lentillifera

Abstract Background Caulerpa lentillifera is one of the most important economic green macroalgae in the world. Increasing demand for consumption has led to the commercial cultivation of C. lentillifera in Japan and Vietnam in recent decades. Concomitant with the increase of C. lentillifera cultivation is a rise in disease. We hypothesise that epiphytes or other microorganisms outbreak at the C. lentillifera farm may be an important factor contributing to disease in C. lentillifera. The main aims are obtaining differences in the microbial community structure and diversity between healthy and diseased C. lentillifera and key epiphytes and other microorganisms affecting the differences through the results of high-throughput sequencing and bioinformatics analysis in the present study. Results A total of 14,050, 2479, and 941 operational taxonomic units (OTUs) were obtained from all samples using 16S rDNA, 18S rDNA, and internal transcribed spacer (ITS) high-throughput sequencing, respectively. 16S rDNA sequencing and 18S rDNA sequencing showed that microbial community diversity was higher in diseased C. lentillifera than in healthy C. lentillifera. Both PCoA results and UPGMA results indicated that the healthy and diseased algae samples have characteristically different microbial communities. The predominant prokaryotic phyla were Proteobacteria, Planctomycetes, Bacteroidetes, Cyanobacteria, Acidobacteria, Acidobacteria and Parcubacteria in all sequences. Chlorophyta was the most abundant eukaryotic phylum followed by Bacillariophyta based on 18S rDNA sequencing. Ascomycota was the dominant fungal phylum detected in healthy C. lentillifera based on ITS sequencing, whereas fungi was rare in diseased C. lentillifera, suggesting that Ascomycota was probably fungal endosymbiont in healthy C. lentillifera. There was a significantly higher abundance of Bacteroidetes, Cyanobacteria, Bacillariophyta, Ulvales and Tetraselmis in diseased C. lentillifera than in healthy C. lentillifera. Disease outbreaks significantly change carbohydrate metabolism, environmental information processing and genetic information processing of prokaryotic communities in C. lentillifera through predicted functional analyses using the Tax4Fun tool. Conclusions Bacteroidetes, Cyanobacteria, Bacillariophyta, Ulvales and Tetraselmis outbreak at the C. lentillifera farm sites was an important factor contributing to disease in C. lentillifera.

scholarly journals Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Metabolites ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 414
Author(s):  
Naren Gaowa ◽  
Wenli Li ◽  
Sonia Gelsinger ◽  
Brianna Murphy ◽  
Shengli Li
Keyword(s):  
Cell Cycle ◽  
Community Structure ◽  
Microbial Community ◽  
Ribosomal Rna ◽  
Microbial Community Structure ◽  
Control Diet ◽  
Structure Variation ◽  
Ruminal Acidosis ◽  
Bull Calves ◽  
Whole Transcriptome

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.

scholarly journals Effect of C/N ratios on nitrogen removal and microbial communities in the anaerobic baffled reactor (ABR) with an anammox-coupling-denitrification process

2018 ◽  
Vol 78 (11) ◽  
pp. 2338-2348 ◽  
Author(s):  
Chongjun Chen ◽  
Min Zhang ◽  
Xuliang Yu ◽  
Juan Mei ◽  
Ying Jiang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput ◽  
Nitrogen Removal ◽  
Microbial Community Structure ◽  
Anammox Bacterium ◽  
Miseq Sequencing ◽  
Anaerobic Baffled Reactor ◽  
Denitrification Process

Abstract Effects of different C/N (NO2–N) ratios on nitrogen removal and microbial community structure were investigated using an anaerobic baffled reactor (ABR). Results indicated that the C/N ratio exerted an important effect on nitrogen removal in the anammox-coupling-denitrification process associated with the ABR. When the C/N ratio was 1.29, the ABR could achieve the highest total nitrogen (TN) removal efficiency of 99.9%. Most of TN was removed in the 1st and 2nd compartment, accounting for about 81.0–97.6% of total TN removal. The nitrogen removal resulted from the interaction among anammox, heterotrophic denitrificans, and other microbes within the ABR. The contribution of anammox to nitrogen removal varied from 6.8% to 32.4%. High-throughput MiSeq sequencing analyses revealed that the C/N ratio was one of the most important factors regulating the microbial community structure, and the predominant phylum changed from Proteobacteria to Chloroflexi with the elevated C/N ratio. In addition, the Candidatus Brocadia was the major anammox bacterium, and its percentage varied from 1.0–2.9% at day 9 to 2.8–9.1% at day 46.

scholarly journals Mercury Methylating Microbial Community Structure in Boreal Wetlands Explained by Local Physicochemical Conditions

2021 ◽  
Vol 8 ◽  
Author(s):  
Jingying Xu ◽  
Van Liem-Nguyen ◽  
Moritz Buck ◽  
Stefan Bertilsson ◽  
Erik Björn ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Current Knowledge ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Nutrient Concentrations ◽  
Molecular Barcoding ◽  
Physicochemical Conditions ◽  
Wide Range

The potent neurotoxin methylmercury (MeHg) is a major concern due to its negative effects on wildlife and human health. Boreal wetlands play a crucial role in Hg cycling on a global scale, and therefore, it is crucial to understand the biogeochemical processes involved in MeHg formation in this landscape element. By combining high-throughput hgcA amplicon sequencing with molecular barcoding, we reveal diverse clades of potential HgII methylators in a wide range of wetland soils. Among Bacteria, Desulfuromonadota (14% of total reads), Desulfurobacterota_A, and Desulfurobacterota (up to 6% of total reads), previously classified as Deltaproteobacteria, were important members of the hgcA+ microbial community in the studied wetlands. We also identified Actinobacteriota (9.4% of total reads), Bacteroidota (2% of total reads), and Firmicutes (1.2% of total reads) as members of the hgcA+ microbial community. Within Archaea, Methanosarcinales represented up to 2.5% of the total reads. However, up to half of the hgcA+ community could not be resolved beyond domain Bacteria. Our survey also shows that local physicochemical conditions, such as pH, nutrient concentrations, water content, and prevailing redox states, are important for shaping the hgcA+ microbial community structure across the four studied wetlands. Furthermore, we observed a significant correlation between HgII methylation rate constants and the structure of the hgcA+ microbial community. Our findings expand the current knowledge on the hgcA+ microbial community composition in wetlands and the physicochemical factors underpinning spatial heterogeneity in such communities.

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