scholarly journals Microbial composition, diversity, and activity varies across different types of basal ice

2021 ◽  
Author(s):  
Shawn M. Doyle ◽  
Brent C. Christner
Keyword(s):  
Organic Matter ◽  
16S Rrna ◽  
Meta Analysis ◽  
Microbial Composition ◽  
Glacial Ice ◽  
Microbiome Composition ◽  
Basal Ice ◽  
Different Types ◽  
Insight Into ◽  
Read Abundance

ABSTRACTBasal ice often contains entrained subglacial debris and sediment which can serve as a source of nutrients and organic matter and provide habitat for microorganisms adapted to frozen conditions. However, basal ice comes in many different forms and comparatively little is known about how microbial composition, diversity, and activity vary across different types of basal ice. Here, we investigated these parameters in four different types of basal ice from two different glaciers and then used a meta-analysis to compare our findings with microbiome studies of other permanently frozen environments. We found microbiome composition varies substantially between basal ice types, even within the same glacier. Further, the microbiomes of sediment-rich basal ices were distinct from those found in glacial ice and instead were most like those found in permafrost. Consistent with this, microbial diversity was also comparable to that found in permafrost and was much higher relative to glacial ice. Patterns of 16S rRNA read abundance from RNA relative to DNA implicated certain taxa as potentially active in basal ice with ice temperature appearing to be an important predictor for the diversity of taxa inferred to be active. Our results improve our understanding of the microbial ecology of different basal ice types and provide insight into which types are likely habitats for metabolizing microbial communities.

scholarly journals Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microsporidian Infection ◽  
Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

scholarly journals The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 309
Author(s):  
Alisa Kazarina ◽  
Elina Petersone-Gordina ◽  
Janis Kimsis ◽  
Jevgenija Kuzmicka ◽  
Pawel Zayakin ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Modern Human ◽  
Oral Microbiome ◽  
Dental Calculus ◽  
Microbial Composition ◽  
Metagenome Analysis ◽  
Microbiome Composition ◽  
Microbial Adaptation ◽  
Microbial Dna ◽  
Insight Into

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

The influence of natural organic matter on the adsorption of microcystin-LR by powdered activated carbon

2019 ◽  
Vol 5 (2) ◽  
pp. 256-267 ◽  
Author(s):  
Asnika Bajracharya ◽  
Yen-Ling Liu ◽  
John J. Lenhart
Keyword(s):  
Organic Matter ◽  
Activated Carbon ◽  
Natural Organic Matter ◽  
Powdered Activated Carbon ◽  
Different Types ◽  
Insight Into

In this study, microcystin-LR (MC-LR) adsorption to four different types of powdered activated carbon (PAC) was evaluated to provide insight into the use of PAC to treat water containing MC-LR.

scholarly journals NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

F1000Research ◽  
2018 ◽  
Vol 5 ◽  
pp. 1791 ◽  
Author(s):  
Javier Ramiro-Garcia ◽  
Gerben D. A. Hermes ◽  
Christos Giatsis ◽  
Detmer Sipkema ◽  
Erwin G. Zoetendal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Read Length ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Microbial Composition ◽  
Sample Composition ◽  
Mock Communities

Background: Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises meta-analyses, although this fact is often disregarded. Results: To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as a frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed for the evaluation of important causes of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 97.78%. On average 99.95% and 88.43% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.21% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not achieved with QIIME. Conclusions: Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.

scholarly journals NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1791 ◽  
Author(s):  
Javier Ramiro-Garcia ◽  
Gerben D. A. Hermes ◽  
Christos Giatsis ◽  
Detmer Sipkema ◽  
Erwin G. Zoetendal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Read Length ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Microbial Composition ◽  
Sample Composition ◽  
Mock Communities

Background Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises true meta-analyses, although this fact is often disregarded. Results To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as the currently most frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina’s HiSeq2000 platform. This allowed evaluating important factors of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR–error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 96%. On average 99.94% and 92.02% of the reads could be assigned to at least family or genus level, respectively, while assignment to ‘spurious genera’ represented on average only 0.02% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not the case when samples were analysed using QIIME. Conclusions Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.

Insight into Interactions of Microplastics with Different Types and Compositions of Dissolved Organic Matter

2021 ◽  
Author(s):  
Ling Ding ◽  
Yuanyuan Luo ◽  
Xiaoqin Yu ◽  
Zhuozhi Ouyang ◽  
Peng Liu ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Different Types ◽  
Insight Into

scholarly journals Application of the Subspace-Based Methods in Health Monitoring of Civil Structures: A Systematic Review and Meta-Analysis

2020 ◽  
Vol 10 (10) ◽  
pp. 3607
Author(s):  
Hoofar Shokravi ◽  
Hooman Shokravi ◽  
Norhisham Bakhary ◽  
Mahshid Heidarrezaei ◽  
Seyed Saeid Rahimian Koloor ◽  
...  
Keyword(s):  
System Identification ◽  
Systematic Reviews ◽  
Health Monitoring ◽  
Meta Analysis ◽  
Civil Structures ◽  
Literature Reviews ◽  
Research Gap ◽  
Meta Analyses ◽  
Subspace System Identification ◽  
Insight Into

A large number of research studies in structural health monitoring (SHM) have presented, extended, and used subspace system identification. However, there is a lack of research on systematic literature reviews and surveys of studies in this field. Therefore, the current study is undertaken to systematically review the literature published on the development and application of subspace system identification methods. In this regard, major databases in SHM, including Scopus, Google Scholar, and Web of Science, have been selected and preferred reporting items for systematic reviews and meta-analyses (PRISMA) has been applied to ensure complete and transparent reporting of systematic reviews. Along this line, the presented review addresses the available studies that employed subspace-based techniques in the vibration-based damage detection (VDD) of civil structures. The selected papers in this review were categorized into authors, publication year, name of journal, applied techniques, research objectives, research gap, proposed solutions and models, and findings. This study can assist practitioners and academicians for better condition assessment of structures and to gain insight into the literature.

The participation of Palestinian-Israeli politicians in public and commercial television and radio in Israel as capability

2021 ◽  
pp. 174804852199056
Author(s):  
Baruch Shomron ◽  
Amit Schejter
Keyword(s):  
Capabilities Approach ◽  
Media Representations ◽  
Community Members ◽  
Commercial Television ◽  
Radio Stations ◽  
Modes Of Representation ◽  
Current Affairs ◽  
Different Types ◽  
The Media ◽  
Insight Into

This study examines how media representations of Palestinian-Israeli politicians, can help community members realize their capabilities. The study’s database is comprised of 1,207 interviews conducted with Palestinian-Israeli politicians on news and current affairs programs on the three national television channels and the two national radio stations in Israel, for 24 months (2016-2017). We identified and analyzed the differences in the modes of representation between national and local Palestinian-Israeli politicians and between Palestinian-Israeli parliament members in the Joint List and Palestinian-Israeli parliament members in Zionist parties, all through the capabilities prism. In this study, we demonstrated how different types of Palestinian-Israeli politicians may potentially affect the realization of different political functions and capabilities. Analyzing political representations in the media through the theoretical framework of the ‘capabilities approach’ contributes to a more comprehensive insight into the roles the media can play promoting people’s wellbeing and human rights, relative to traditional media theories.

Double, triple or quadruple hits? Exploring the impact of cybercrime on victims in the Netherlands

2021 ◽  
pp. 026975802110106
Author(s):  
Raoul Notté ◽  
E.R. Leukfeldt ◽  
Marijke Malsch
Keyword(s):  
Public Opinion ◽  
Literature Review ◽  
The Netherlands ◽  
Public Discourse ◽  
Moral Judgments ◽  
Victim Blaming ◽  
High Prevalence ◽  
Different Types ◽  
The Impact ◽  
Insight Into

This article explores the impact of online crime victimisation. A literature review and 41 interviews – 19 with victims and 22 with experts – were carried out to gain insight into this. The interviews show that most impacts of online offences correspond to the impacts of traditional offline offences. There are also differences with offline crime victimisation. Several forms of impact seem to be specific to victims of online crime: the substantial scale and visibility of victimhood, victimisation that does not stop in time, the interwovenness of online and offline, and victim blaming. Victims suffer from double, triple or even quadruple hits; it is the accumulation of different types of impact, enforced by the limitlessness in time and space, which makes online crime victimisation so extremely invasive. Furthermore, the characteristics of online crime victimisation greatly complicate the fight against and prevention of online crime. Finally, the high prevalence of cybercrime victimisation combined with the severe impact of these crimes seems contradictory with public opinion – and associated moral judgments – on victims. Further research into the dominant public discourse on victimisation and how this affects the functioning of the police and victim support would be valuable.

scholarly journals Updated Review and Meta-Analysis of Probiotics for the Treatment of Clinical Depression: Adjunctive vs. Stand-Alone Treatment

2021 ◽  
Vol 10 (4) ◽  
pp. 647
Author(s):  
Viktoriya L. Nikolova ◽  
Anthony J. Cleare ◽  
Allan H. Young ◽  
James M. Stone
Keyword(s):  
Meta Analysis ◽  
Clinical Depression ◽  
Controlled Clinical Trial ◽  
Reactive Protein ◽  
Treatment Type ◽  
Antidepressant Effects ◽  
Clinical Trial Evidence ◽  
Randomised Controlled ◽  
Trial Evidence ◽  
Insight Into

Recent years have seen a rapid increase in the use of gut microbiota-targeting interventions, such as probiotics, for the treatment of psychiatric disorders. The objective of this update review was to evaluate all randomised controlled clinical trial evidence on the efficacy of probiotics for clinical depression. Cochrane guidelines for updated reviews were followed. By searching PubMed and Web of Science databases, we identified 546 new records since our previous review. A total of seven studies met selection criteria, capturing 404 people with depression. A random effects meta-analysis using treatment type (stand-alone vs. adjunctive) as subgroup was performed. The results demonstrated that probiotics are effective in reducing depressive symptoms when administered in addition to antidepressants (SMD = 0.83, 95%CI 0.49–1.17), however, they do not seem to offer significant benefits when used as stand-alone treatment (SMD = −0.02, 95%CI −0.34–0.30). Potential mechanisms of action may be via increases in brain-derived neurotrophic factor (BDNF) and decreases in C-reactive protein (CRP), although limited evidence is available at present. This review offers stronger evidence to support the clinical use of probiotics in depressed populations and provides an insight into the mode of administration more likely to yield antidepressant effects.

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