Is Toxin-Producing Planktothrix sp. an Emerging Species in Lake Constance?

Recurring blooms of filamentous, red-pigmented and toxin-producing cyanobacteria Planktothrix rubescens have been reported in numerous deep and stratified prealpine lakes, with the exception of Lake Constance. In a 2019 and 2020 Lake Constance field campaign, we collected samples from a distinct red-pigmented biomass maximum below the chlorophyll-a maximum, which was determined using fluorescence probe measurements at depths between 18 and 20 m. Here, we report the characterization of these deep water red pigment maxima (DRM) as cyanobacterial blooms. Using 16S rRNA gene-amplicon sequencing, we found evidence that the blooms were, indeed, contributed by Planktothrix spp., although phycoerythrin-rich Synechococcus taxa constituted most of the biomass (>96% relative read abundance) of the cyanobacterial DRM community. Through UPLC–MS/MS, we also detected toxic microcystins (MCs) in the DRM in the individual sampling days at concentrations of ≤1.5 ng/L. Subsequently, we reevaluated the fluorescence probe measurements collected over the past decade and found that, in the summer, DRM have been present in Lake Constance, at least since 2009. Our study highlights the need for a continuous monitoring program also targeting the cyanobacterial DRM in Lake Constance, and for future studies on the competition of the different cyanobacterial taxa. Future studies will address the potential community composition changes in response to the climate change driven physiochemical and biological parameters of the lake.

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Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.747814 ◽

2021 ◽

Vol 11 ◽

Author(s):

Roland Wirth ◽

Bernadett Pap ◽

Gergely Maróti ◽

Péter Vályi ◽

Laura Komlósi ◽

...

Keyword(s):

Amplicon Sequencing ◽

Abundant Species ◽

Periodontal Pathogen ◽

Host Immune System ◽

Periodontal Pathogens ◽

Pocket Depth ◽

Probing Pocket Depth ◽

The Individual ◽

Biofilm Development

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.

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Isolation of Polymer-Degrading Bacteria and Characterization of the Hindgut Bacterial Community from the Detritus-Feeding Larvae of Tipula abdominalis (Diptera: Tipulidae)

Applied and Environmental Microbiology ◽

10.1128/aem.00213-07 ◽

2007 ◽

Vol 73 (17) ◽

pp. 5683-5686 ◽

Cited By ~ 15

Author(s):

Dana M. Cook ◽

Emily DeCrescenzo Henriksen ◽

Rima Upchurch ◽

Joy B. Doran Peterson

Keyword(s):

Microbial Community ◽

Initial Study ◽

Gene Clone ◽

Rrna Gene ◽

Bacterial Isolates ◽

Future Studies ◽

Degrading Bacteria ◽

Novel Bacteria ◽

Tipula Abdominalis

ABSTRACT The Tipula abdominalis larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.

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Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.678319 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wenyi Xu ◽

Tianda Chen ◽

Yuwei Pei ◽

Hao Guo ◽

Zhuanyu Li ◽

...

Keyword(s):

Large Scale ◽

Low Cost ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Shotgun Sequencing ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Cost Efficient ◽

Taxonomic Assignments

Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.

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Characterization of bacterial community shift in human Ulcerative Colitis patients revealed by Illumina based 16S rRNA gene amplicon sequencing

Gut Pathogens ◽

10.1186/1757-4749-6-22 ◽

2014 ◽

Vol 6 (1) ◽

pp. 22 ◽

Cited By ~ 46

Author(s):

Sandeep A Walujkar ◽

Dhiraj P Dhotre ◽

Nachiket P Marathe ◽

Parimal S Lawate ◽

Renu S Bharadwaj ◽

...

Keyword(s):

Ulcerative Colitis ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Community Shift

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Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

BMC Microbiology ◽

10.1186/s12866-021-02094-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yoshiyuki Matsuo ◽

Shinnosuke Komiya ◽

Yoshiaki Yasumizu ◽

Yuki Yasuoka ◽

Katsura Mizushima ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Species Level ◽

Full Length ◽

Rrna Gene ◽

Short Read ◽

Short Read Sequencing ◽

Long Read

Abstract Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. Results We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. Conclusions Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene.

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Development of a robust protocol for the characterization of the pulmonary microbiota

Communications Biology ◽

10.1038/s42003-021-01690-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Nathan Dumont-Leblond ◽

Marc Veillette ◽

Christine Racine ◽

Philippe Joubert ◽

Caroline Duchaine

Keyword(s):

Amplicon Sequencing ◽

Rrna Gene ◽

Validity Of Results ◽

Healthy Human ◽

Bacterial Dna ◽

Starting Point ◽

Sampling Procedures ◽

Negative Controls ◽

The Impact

AbstractThe lack of methodological standardization diminishes the validity of results obtained and the conclusions drawn when studying the lung microbiota. We report the validation of a complete 16S rRNA gene amplicon sequencing workflow, from patient recruitment to bioinformatics, tailored to the constrains of the pulmonary environment. We minimize the impact of contaminants and establish negative controls to track and account for them at every step. Enzymatic and mechanical homogenization combined to commercially available extraction kits allow for a fast and reliable extraction of bacterial DNA. The DNA extraction kits have a significant impact on the bacterial composition of the controls. The bacterial signatures of extracted cancerous and healthy human tissues from 5 patients are highly distinguishable from methodological controls. Our work expands our understanding of low microbial burdened environments analysis. This article is to be a starting point towards methodological standardization and the implementation of proper sampling procedures in the study of lung microbiota.

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Use of next-generation amplicon sequencing to study Blastocystis genetic diversity in a rural human population from Mexico

Parasites & Vectors ◽

10.1186/s13071-019-3814-z ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 4

Author(s):

Liliana Rojas-Velázquez ◽

Jenny G. Maloney ◽

Aleksey Molokin ◽

Patricia Morán ◽

Angélica Serrano-Vázquez ◽

...

Keyword(s):

Intestinal Parasite ◽

Intestinal Parasites ◽

Amplicon Sequencing ◽

Farm Animals ◽

Rrna Gene ◽

Next Generation ◽

Future Studies ◽

Contaminated Food ◽

Transmission Pathways ◽

Subtype 3

Abstract Background The intestinal parasite Blastocystis is found in humans and animals around the world. It is spread through the consumption of contaminated food and water and has been associated with a variety of intestinal symptoms. Blastocystis is one of the most common intestinal parasites in humans, yet its prevalence and distribution in humans in North America is not well characterized. Methods Next-generation amplicon sequencing of a region of the Blastocystis SSU rRNA gene was applied to DNA extracted from fecal specimens obtained from 182 inhabitants of a rural population in Mexico to characterize Blastocystis prevalence, subtype distribution, and intra-host subtype diversity in humans. Results Of the 182 samples tested in this study, 68.1% (124) contained one or more Blastocystis subtypes. Subtype 3 was the most common subtype observed and was found in 81.5% of the positive samples. Subtype 1, 16.9% of the positive samples, and subtype 2, 17.7% of the positive samples, were also found in this population. Mixed infections were observed in 13.7% of the positive samples. In this population, the odds of having Blastocystis increased in adulthood (> 15 years; OR: 1.72, P < 0.0001), and the odds of having subtype 1 increased in the presence of farm animals (OR: 1.51, P = 0.03). The odds of having subtype 1, subtype 2, or a mixed infection decreased in the presence of cement flooring (OR: − 1.61, P = 0.005; OR: − 1.14, P = 0.03; OR: − 1.48, P = 0.02) possibly indicating socioeconomic factors are involved in the risk of acquiring one of these subtypes. Conclusions These data contribute to our understanding of the epidemiology of Blastocystis infection in humans and can be used to shape future studies which aim to better characterize the transmission pathways and health outcomes of Blastocystis infections.

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Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde

10.1101/266957 ◽

2018 ◽

Author(s):

Ana P. Semedo-Aguiar ◽

José B. Pereira-Leal ◽

Ricardo B. Leite

Keyword(s):

Microbial Diversity ◽

Global Climate ◽

Amplicon Sequencing ◽

Toxin Production ◽

Cape Verde ◽

Cyanobacterial Blooms ◽

Rrna Gene ◽

Water Reservoirs ◽

Cyanobacterial Toxin ◽

Close Relationship

AbstractThe Cape Verde islands are part of the African Sahelian arid belt that possesses an irregular rainy season between August and October. This erratic rain pattern has prompted the need for water reservoirs, now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and eutrophication of water bodies, particularly in reservoirs. To date there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde.Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs (Poilão, Saquinho and Faveta). In Faveta Microcystis sp., a genus well known for toxin production and bloom-formation, dominated our samples, while a green algae of the genus Cryptomonas and Gammaproteobacteria dominated Saquinho and Poilão.Taking advantage of the dominance of Microcystis in the Faveta reservoir, we were able to reconstruct and assemble its genome, extracted from a metagenome of bulk DNA from Faveta water. We named it Microcystis cf. aeruginosa CV01, for which a phylogenetic analysis revealed to have a close relationship with other genomes from those taxa, as well as other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This assessment of Cape Verdean freshwater microbial diversity and potential for toxin production reinforces the need to better understand the microbial ecology as a whole of water reservoirs on the rise.

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Microbiota differences of the comb jelly Mnemiopsis leidyi in native and invasive sub-populations

10.1101/601419 ◽

2019 ◽

Cited By ~ 1

Author(s):

Cornelia Jaspers ◽

Nancy Weiland-Bräuer ◽

Martin Fischer ◽

Sven Künzel ◽

Ruth A. Schmitz ◽

...

Keyword(s):

Amplicon Sequencing ◽

Sister Group ◽

Invasion Success ◽

Mnemiopsis Leidyi ◽

Rrna Gene ◽

Indigenous Species ◽

Controlled Environments ◽

Non Indigenous Species ◽

The Impact

ABSTRACTThe translocation of non-indigenous species around the world, especially in marine systems, is a matter of concern for biodiversity conservation and ecosystem functioning. While specific traits are often recognized to influence establishment success of non-indigenous species, the impact of the associated microbial community for the fitness, performance and invasion success of basal marine metazoans remains vastly unknown. In this study we compared the microbiota community composition of the invasive ctenophore Mnemiopsis leidyi in different native and invasive sub-populations along with characterization of the genetic structure of the host. By 16S rRNA gene amplicon sequencing we showed that the sister group to all metazoans, namely ctenophores, harbored a distinct microbiota on the animal host, which significantly differed across two major tissues, namely epidermis and gastrodermis. Additionally, we identified significant differences between native and invasive sub-populations of M. leidyi, which indicate, that the microbiota community is likely influenced by the genotypic background of the ctenophore. To test the hypothesis that the microbiota is genotypically selected for by the ctenophore host, experiments under controlled environments are required.

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EVALUATION OF OCCURRENCE OF HYPERDONTIA IN NON-SYNDROMIC POPULATION FROM BIHAR REGION

International Journal of Medical and Biomedical Studies ◽

10.32553/ijmbs.v3i10.740 ◽

2019 ◽

Vol 3 (10) ◽

Author(s):

Dr. Minti Kumari ◽

Dr. Madhuri Kumari ◽

Dr Anurag Rai ◽

Dr. Navin Kumar

Keyword(s):

Panoramic Radiograph ◽

Permanent Dentition ◽

Dental Anomalies ◽

Supernumerary Teeth ◽

Panoramic Radiographs ◽

Future Studies ◽

Asian Populations ◽

Males And Females ◽

The Individual ◽

Clinical Records

It is evident that hyperdontia is more common in the permanent dentition than in the primary. There is a considerable difference between males and females in the prevalence of these teeth in permanent dentition; hyperdontia is twice as common in males as in females. However, this approximation varies in terms of location, other associating syndromes that may be present, and the ethnicity of the individual. In terms of ethnicity, it can be seen that hyperdontia is in fact less common in Caucasian than in Asian populations. There is evidence to show that an individual is more likely to have hyperdontia if other members of their family also have the condition. Hence the present study was planned for evaluation of occurrence of hyperdontia in non-syndromic population from Bihar Region. The present study was planned in Public Health Dentistry, Patna Dental College and Hospital, Patna, Bihar. Total 195 patients referred to Department of Dentistry were evaluated in the present study. Panoramic radiographs and clinical records of patients above the age of 18 years and without any syndromic features were selected for the study. All the radiographs were examined for the presence of supernumerary teeth, their location, morphology, and number. Morphologically, teeth were classified as conical, tuberculate, supplemental, and odontoma. Early diagnosis of dental anomalies can prevent some esthetic, orthodontic, and periodontal problems, and knowledge of the prevalence and distribution of the anomalies may help clinicians to the detection of these anomalies at early stages. Our study evaluated the prevalence of selected dental anomalies; future studies should investigate the prevalence of dental anomalies of all types. Keywords: Hyperdontia, non-syndromic, panoramic radiograph, supernumerary teeth, etc.

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