scholarly journals Compositional Features of Distinct Microbiota Base on Serum Extracellular Vesicle Metagenomics Analysis in Moderate to Severe Psoriasis Patients

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2349
Author(s):  
Chih-Jung Chang ◽  
Jing Zhang ◽  
Yu-Ling Tsai ◽  
Chun-Bing Chen ◽  
Chun-Wei Lu ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Bacterial Communities ◽  
Extracellular Vesicle ◽  
Taxonomic Composition ◽  
Severe Psoriasis ◽  
Sequence Variant ◽  
Transmission Electron ◽  
Bacterial Microbiota ◽  
Functional Capacities ◽  
Ralstonia Insidiosa

The bacterial microbiota in the skin and intestine of patients with psoriasis were different compared with that of healthy individuals. However, the presence of a distinct blood microbiome in patients with psoriasis is yet to be investigated. In this study, we investigated the differences in bacterial communities in plasma-derived extracellular vesicles (EVs) between patients with moderate to severe psoriasis (PSOs) and healthy controls (HCs). The plasma EVs from the PSO (PASI > 10) (n = 20) and HC (n = 8) groups were obtained via a series of centrifugations, and patterns were examined and confirmed using transmission electron microscopy (TEM) and EV-specific markers. The taxonomic composition of the microbiota was determined by using full-length 16S ribosomal RNA gene sequencing. The PSO group had lower bacterial diversity and richness compared with HC group. Principal coordinate analysis (PCoA)-based clustering was used to assess diversity and validated dysbiosis for both groups. Differences at the level of amplicon sequence variant (ASV) were observed, suggesting alterations in specific ASVs according to health conditions. The HC group had higher levels of the phylum Firmicutes and Fusobacteria than in the PSO group. The order Lactobacillales, family Brucellaceae, genera Streptococcus, and species Kingella oralis and Aquabacterium parvum were highly abundant in the HC group compared with the PSO group. Conversely, the order Bacillales and the genera Staphylococcus and Sphihgomonas, as well as Ralstonia insidiosa, were more abundant in the PSO group. We further predicted the microbiota functional capacities, which revealed significant differences between the PSO and HC groups. In addition to previous studies on microbiome changes in the skin and gut, we demonstrated compositional differences in the microbe-derived EVs in the plasma of PSO patients. Plasma EVs could be an indicator for assessing the composition of the microbiome of PSO patients.

scholarly journals High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

2019 ◽  
Author(s):  
William J. Watterson ◽  
Melikhan Tanyeri ◽  
Andrea R. Watson ◽  
Candace M. Cham ◽  
Yue Shan ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Fold Increase ◽  
Taxonomic Composition ◽  
Biased Sampling ◽  
Human Gut ◽  
Rare Taxa ◽  
Conventional Culture ◽  
16S Ribosomal Rna Gene ◽  
Slow Growing ◽  
New Strategies

AbstractTraditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

scholarly journals Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Juan F. Alzate ◽  
Miguel Toro-Londoño ◽  
Felipe Cabarcas ◽  
Gisela Garcia-Montoya ◽  
Ana Galvan-Diaz
Keyword(s):  
Bacterial Communities ◽  
Intestinal Parasites ◽  
Intestinal Lumen ◽  
Bacterial Populations ◽  
Microbial Competition ◽  
E Coli ◽  
Daycare Centers ◽  
Microbial Profile ◽  
Bacterial Microbiota ◽  
Bacterial Richness

Abstract Recent studies have shown how intestinal parasites can modulate gut microbiota. This observation is not surprising since the human intestinal lumen, like any other niche, is a battlefield of microbial competition, and Eukaryotes can affect bacterial populations. Intestinal pathogenic protist has been associated with reshaping the microbial community structure; however, the interactions between the colonic bacterial communities and parasites like Blastocystis spp., Entamoeba coli, and Endolimax nana have been poorly studied. In this work, we studied the distal intestinal bacterial microbiota of 49 children attending 7 public daycare centers in Medellin, Colombia, and compared the bacterial microbiota structure in the presence or absence of the protists Blastocystis spp., E. coli, and E. nana. Parasite colonization was associated with an increase in bacterial richness. Moreover, Blastocystis spp. presented a positive relationship with Prevotella, since this bacterium was selectively enriched in children carrying it. Remarkably, the E. coli colonized children showed a microbial profile that was closer to uninfected controls, although some bacterial taxa displayed to be enriched. This is the case for Akkermansia, which showed to be favored in E. coli colonized individuals, while notably reduced in the Blastocystis spp. parasitized group.

scholarly journals Enrichment of plasma extracellular vesicles for reliable quantification of their size and concentration for biomarker discovery

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marija Holcar ◽  
Jana Ferdin ◽  
Simona Sitar ◽  
Magda Tušek-Žnidarič ◽  
Vita Dolžan ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Plasma Source ◽  
Extracellular Vesicle ◽  
Size Exclusion ◽  
Enzyme Linked Immunosorbent Assay ◽  
Enrichment Method ◽  
Transmission Electron ◽  
Relative Standard ◽  
Exclusion Chromatography ◽  
Reliable Quantification

AbstractHuman plasma is a complex fluid, increasingly used for extracellular vesicle (EV) biomarker studies. Our aim was to find a simple EV-enrichment method for reliable quantification of EVs in plasma to be used as biomarker of disease. Plasma of ten healthy subjects was processed using sedimentation rate- (sucrose cushion ultracentrifugation—sUC) and size- (size exclusion chromatography—SEC) based methods. According to nanoparticle tracking analysis (NTA), asymmetrical flow field-flow fractionation coupled to detectors (AF4-UV-MALS), miRNA quantification, transmission electron microscopy and enzyme-linked immunosorbent assay, enrichment of EVs from plasma with sUC method lead to high purity of EVs in the samples. High nanoparticle concentrations after SEC resulted from substantial contamination with lipoproteins and other aggregates of EV-like sizes that importantly affect downstream EV quantification. Additionally, sUC EV-enrichment method linked to quantification with NTA or AF4-UV-MALS is repeatable, as the relative standard deviation of EV size measured in independently processed samples from the same plasma source was 5.4% and 2.1% when analyzed by NTA or AF4-UV-MALS, respectively. In conclusion, the sUC EV-enrichment method is compatible with reliable measurement of concentration and size of EVs from plasma and should in the future be tested on larger cohorts in relation to different diseases. This is one of the first studies using AF4-UV-MALS to quantify EVs in blood plasma, which opens new possible clinical utility for the technique.

scholarly journals Characterization of bacterial communities of rhizosphere and rhizoplane of Early Zhukovsky potato

2020 ◽  
Vol 222 ◽  
pp. 02050
Author(s):  
Marat Lutfulin ◽  
Darya Zaripova ◽  
Oksana Moiseeva ◽  
Semen Vologin ◽  
Ayslu Mardanova
Keyword(s):  
Bacterial Communities ◽  
Functional Role ◽  
Agricultural Crop ◽  
Potato Root ◽  
Bacterial Microbiota ◽  
16S R Rna ◽  
Significant Difference ◽  
Dominant Bacteria

Identification of patterns of formation of bacterial communities of the rhizosphere and rhizoplane of potato (Solanum tuberosum L.), the most important agricultural crop, is necessary for the introduction and maintenance of sustainable organic farming. The purpose of this work was the study of the biodiversity of the bacterial microbiota of the rhizosphere and rhizoplane of Early Zhukovsky potato, cultivated on gray forest soils. Comparative analysis based on sequencing of the 16S R RNA gene showed a significant difference in the representation of different groups of bacteria in these potato root compartments. Thus, the proportions of the dominant bacteria in the rhizosphere and rhizoplane of the Proteobacteria phylum reach 47.66% ± 7.22 % and 86.35 % ± 0.53%, respectively (P < 0.05). In contrast, the representation of phylum Bacteroidetes and Firmicutes in the rhizosphere is significantly higher and reaches 41.45 % ± 10.42% and 6.49 % ± 3.23%, respectively, compared to the rhizoplane (7.84 % ± 1.24 % and 0.43 % ± 0.48 %, (P < 0.05). At the same time, Actinobacteria phylum bacteria are present in both compartments in approximately equal amounts (4.40 % ± 1.81% in the rhizosphere and 5.37 % ± 1.42% in the rhizoplane). Thus, it was found that potato forms different bacterial communities in the rhizosphere and rhizoplane in quantitative proportions, which is probably determined by the functional role of these microorganisms in the plant physiology.

scholarly journals Extracellular Vesicle-derived circular RNAs confers chemoresistance in Colorectal cancer

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kha Wai Hon ◽  
Nurul Syakima Ab-Mutalib ◽  
Nik Muhd Aslan Abdullah ◽  
Rahman Jamal ◽  
Nadiah Abu
Keyword(s):  
Colorectal Cancer ◽  
Extracellular Vesicle ◽  
Circular Rnas ◽  
Serum Samples ◽  
Transmission Electron ◽  
Potential Biomarker ◽  
Drug Sensitivity Assay ◽  
Drug Induction ◽  
Early Biomarker ◽  
Sirna Knockdown

Abstract Chemo-resistance is associated with poor prognosis in colorectal cancer (CRC), with the absence of early biomarker. Exosomes are microvesicles released by body cells for intercellular communication. Circular RNAs (circRNAs) are non-coding RNAs with covalently closed loops and enriched in exosomes. Crosstalk between circRNAs in exosomes and chemo-resistance in CRC remains unknown. This research aims to identify exosomal circRNAs associated with FOLFOX-resistance in CRC. FOLFOX-resistant HCT116 CRC cells (HCT116-R) were generated from parental HCT116 cells (HCT116-P) using periodic drug induction. Exosomes were characterized using transmission electron microscopy (TEM), Zetasizer and Western blot. Our exosomes were translucent cup-shaped structures under TEM with differential expression of TSG101, CD9, and CD63. We performed circRNAs microarray using exosomal RNAs from HCT116-R and HCT116-P cells. We validated our microarray data using serum samples. We performed drug sensitivity assay and cell cycle analysis to characterize selected circRNA after siRNA-knockdown. Using fold change >2 and p < 0.05, we identified 105 significantly upregulated and 34 downregulated circRNAs in HCT116-R exosomes. Knockdown of circ_0000338 improved the chemo-resistance of CRC cells. We have proposed that circ_0000338 may have dual regulatory roles in chemo-resistant CRC. Exosomal circ_0000338 could be a potential biomarker for further validation in CRC.

scholarly journals ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1418 ◽  
Author(s):  
Adam R. Rivers ◽  
Kyle C. Weber ◽  
Terrence G. Gardner ◽  
Shuang Liu ◽  
Shalamar D. Armstrong
Keyword(s):  
Ribosomal Rna ◽  
Large Subunit ◽  
Marker Gene ◽  
Its Region ◽  
Small Subunit ◽  
Sequence Variant ◽  
Ribosomal Rna Gene ◽  
Conserved Regions ◽  
Conserved Genes ◽  
Internally Transcribed Spacer

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.

scholarly journals Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana Castaño ◽  
Alexander Prosenkov ◽  
Diego Baragaño ◽  
Nerea Otaegui ◽  
Herminio Sastre ◽  
...  
Keyword(s):  
Organic Contaminants ◽  
Bacterial Communities ◽  
Intergenic Spacer ◽  
Cost Effective ◽  
Taxonomic Composition ◽  
Sulfate Reducing ◽  
Oxidation Reduction ◽  
Before And After ◽  
Complete Study

Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.

scholarly journals Microbiota Dysbiosis in Fungal Rhinosinusitis

2019 ◽  
Vol 8 (11) ◽  
pp. 1973 ◽  
Author(s):  
Yen-Ting Lu ◽  
Shao-Hung Wang ◽  
Ming-Li Liou ◽  
Ting-An Shen ◽  
Ying-Chou Lu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Chronic Rhinosinusitis ◽  
Bacterial Communities ◽  
Middle Meatus ◽  
Fungal Rhinosinusitis ◽  
Bacterial Microbiota ◽  
Histological Characteristics ◽  
Distinct Distribution

Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.

Association of the 16SrII-D Phytoplasma with African Marigold (Tagetes erecta) Phyllody in Oman

Plant Disease ◽  
2021 ◽  
Vol 105 (1) ◽  
pp. 27-30
Author(s):  
Ali M. Al-Subhi ◽  
Rashid A. Al-Yahyai ◽  
Abdullah M. Al-Sadi
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Sieve Tube ◽  
Tagetes Erecta ◽  
Herbaceous Plant ◽  
Sultan Qaboos University ◽  
Sequence Identity ◽  
Transmission Electron ◽  
African Marigold ◽  
Tagetes Erecta L

The African marigold (Tagetes erecta L.) is an ornamental, herbaceous plant commonly found in Oman. In 2019, African marigold plants showing phyllody and virescence symptoms, which are typical symptoms of phytoplasmas disease, were found in at Sultan Qaboos University in Oman. Transmission electron microscopy of marigold leaf midrib from phyllody disease plants showed the presence of numerous phytoplasma bodies in the sieve tube of all of the symptomatic samples. DNA was extracted from asymptomatic and symptomatic marigold plant samples, followed by PCR of the 16S ribosomal RNA (rRNA) and imp genes. The PCR assays showed that the symptomatic plants are positive for phytoplasma. The DNA sequence analysis and phylogenetic trees showed that the 16S rDNA and imp gene sequences from all marigold phyllody strains shared 100% sequence identity to 16SrII-D subgroup sequences in the GenBank. This is the first report of a phytoplasma of the 16SrII-D subgroup associated with the African marigold (T. erecta) worldwide.

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