scholarly journals Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

2020 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A Sierra ◽  
Fangxi Xu ◽  
Yasmi Crystal ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Operational Taxonomic Units ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning

2021 ◽  
Vol 2 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A. Sierra ◽  
Fangxi Xu ◽  
Xin Li ◽  
...  
Keyword(s):  
Machine Learning ◽  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

Objectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment non-response using machine learning.Methods: An observational pilot study (N = 20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment non-response was assessed using lasso regression and artificial neural networks.Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between non-responders and those who responded to SDF therapy. No differences were found between non-responders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron.Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Christian Apolinaris Lombogia ◽  
Max Tulung ◽  
Jimmy Posangi ◽  
Trina Ekawati Tallei
Keyword(s):  
Community Structure ◽  
Illumina Miseq ◽  
Gut Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Adult Worker ◽  
Gut Microbial Community ◽  
Apis Nigrocincta

Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.

scholarly journals 16S rRNA–Based Analysis Reveals Differences in the Bacterial Community Present in Tissues of Choromytilus chorus (Mytilidae, Bivalvia) Grown in an Estuary and a Bay in Southern Chile

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 209
Author(s):  
Tamara Valenzuela ◽  
Joaquin I. Riling ◽  
Giovanni Larama ◽  
Jacquelinne J. Acuña ◽  
Marco Campos ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Venn Diagram ◽  
Linear Discriminant ◽  
Operational Taxonomic Units ◽  
Marine Bivalves ◽  
Diagram Analysis

Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this study, the composition and predicted functions of the bacterial community in tissues of C. chorus specimens grown in an estuary (Nehuentue) and a bay (Hueihue) were investigated. Using 16S rRNA genes as targets, the bacterial abundance in tissues was estimated by quantitative PCR and sequenced via Illumina MiSeq. The abundances of bacteria ranged from 103 to 105 copies of 16S rRNA genes g−1 tissue. In the Nehuentue estuary, the bacterial communities in the tissues were dominated by the Tenericutes phylum, whereas the Tenericutes and Proteobacteria phyla dominated in mussels from Hueihue Bay. Higher numbers of operational taxonomic units (OTUs) were observed in tissues from the Nehuentue Estuary than in those from Hueihue Bay. Differences in bacterial community compositions in tissues between both locations were confirmed by nonmetric multidimensional scaling (nMDS) and Venn diagram analysis. In addition, linear discriminant analysis effect size (LEfSe) revealed that the Mollicutes class and Actynomycetales order were key phylotypes in tissues from the Nehuentue Estuary and Hueihue Bay, respectively. Our analysis also predicted a high abundance of sequences assigned to heterotrophy; however, relatively high functional diversity was also found in tissues from Hueihue Bay. This work represents our first attempt to elucidate the C. chorus microbiota in contrasting Chilean aquatic environments.

scholarly journals Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Matthew R. Olm ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Proteins ◽  
Large Scale ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Discrimination ◽  
Bacterial Genomes ◽  
Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

scholarly journals A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2492 ◽  
Author(s):  
Catherine M. Burke ◽  
Aaron E. Darling
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Single Molecule ◽  
Illumina Miseq ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Taxonomy

BackgroundThe bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision.ResultsWe describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection.ConclusionsThis method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.

scholarly journals Microbial contamination of a University dental clinic in Brazil

2017 ◽  
Vol 15 (4) ◽  
pp. 248
Author(s):  
Gisely Naura Venâncio ◽  
Victor Hugo Marques Coelho ◽  
Thiago Fontanella Cestari ◽  
Maxine Ennata Alves de Almeida ◽  
Carolinie Batista Nobre da Cruz
Keyword(s):  
Culture Media ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dental Clinics ◽  
Dental Office ◽  
Dental Surface ◽  
The University ◽  
The Chairs ◽  
And Staphylococcus Aureus

Pathogens of the oral cavity of a patient can be transferred to the dental office surfaces by direct contact, aerosol instruments and blood or saliva. The objective of this study was to investigate the microbiological contamination presents in the stands, chairs and spittoons in the University Nilton Lins dental clinics, in Manaus, Amazonas. Samples were collected with sterile swabs and seeded in different microbiological culture media for the isolation of microorganisms collected from each room. Then, assays were carried out for identification of strains isolated from each environment, such as: Gram stain, DNA purification, Amplification of 16s rRNA genes and sequencing. All these experiments were performed in the LBS / ILMD / FIOCRUZ. It was found 40 CFU / mL in the stands, 43 on the chairs and 47 in the spittoons and it was also possible to identify microorganisms like Klebsiella pneumoniae, Shigella sonnei and Staphylococcus aureus. The greatest number of CFUs was found in Clinic 3 and it was observed that the spittoon was the dental surface with the highest number of CFUs. Some of the bacterial species isolated are opportunists, suggesting that more severe biosecurity measures must be taken in order to prevent cross-infection.Pathogens of the oral cavity of a patient can be transferred to the dental office surfaces by direct contact, aerosol instruments and blood or saliva. The objective of this study was to investigate the microbiological contamination presents in the stands, chairs and spittoons in the University Nilton Lins dental clinics, in Manaus, Amazonas. Samples were collected with sterile swabs and seeded in different microbiological culture media for the isolation of microorganisms collected from each room. Then, assays were carried out for identification of strains isolated from each environment, such as: Gram stain, DNA purification, Amplification of 16s rRNA genes and sequencing. All these experiments were performed in the LBS / ILMD / FIOCRUZ. It was found 40 CFU / mL in the stands, 43 on the chairs and 47 in the spittoons and it was also possible to identify microorganisms like Klebsiella pneumoniae, Shigella sonnei and Staphylococcus aureus. The greatest number of CFUs was found in Clinic 3 and it was observed that the spittoon was the dental surface with the highest number of CFUs. Some of the bacterial species isolated are opportunists, suggesting that more severe biosecurity measures must be taken in order to prevent cross-infection.

scholarly journals Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study

Atmosphere ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 45
Author(s):  
Angelina Metaxatos ◽  
Sydonia Manibusan ◽  
Gediminas Mainelis
Keyword(s):  
Field Application ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Airborne Bacteria ◽  
Urban Air ◽  
Operational Taxonomic Units ◽  
Bacterial Aerosol ◽  
Bacterial Aerosols ◽  
Taxonomic Categories

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.

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