Dental biofilm and its ecological interrelationships in ovine periodontitis

Introduction. Periodontitis, one of the most common oral disorders in sheep, is caused by a mixed and opportunistic microbiota that severely affects the health and welfare of animals. However, little is known about the ecological processes involved and the composition of the microbiota associated with the development of the disease. Hypothesis/Gap Statement. Using high-throughput sequencing of the 16S ribosomal RNA gene and network analysis it would be possible to discriminate the microbiomes of clinically healthy sheep and those with periodontitis and possibly identify the key microorganisms associated with the disease. Aim. The present study aimed to characterise the composition of dental microbiomes and bacterial co-occurrence networks in clinically healthy sheep and animals with periodontitis. Methodology. Dental biofilm samples were collected from ten sheep with periodontitis and ten clinically healthy animals. Bacteria were identified using high-throughput sequencing of the 16S ribosomal RNA gene. Results. The most prevalent genera in the dental microbiota of sheep with periodontitis were Petrimonas , Acinetobacter , Porphyromonas and Aerococcus . In clinically healthy animals, the most significant genera were unclassified Pasteurellaceae, Pseudomonas, and Neisseria. Fusobacterium was found at high prevalence in the microbiomes of both groups. The dental microbiota of sheep in the two clinical conditions presented different profiles and the diversity and richness of bacteria was greater in the diseased animals. Network analyses showed the presence of a large number of antagonistic interactions between bacteria in the dental microbiota of animals with periodontitis, indicating the occurrence of a dysbiotic community. Through the interrelationships, members of the Prevotella genus are likely to be key pathogens, both in the dental microbiota of healthy animals and those with periodontitis. Porphyromonas stood out among the top three nodes with more centrality and the largest number of hubs in the networks of animals with periodontitis. Conclusion. The dental biofilm microbiota associated with ovine periodontitis is dysbiotic and with significant antagonistic interactions, which discriminates healthy animals from diseased animals and highlights the importance of key bacteria, such as Petrimonas , Porphyromonas , Prevotella and Fusobacterium species.

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Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol

Methods in Molecular Biology - Gene Expression Analysis ◽

10.1007/978-1-4939-7834-2_7 ◽

2018 ◽

pp. 149-169 ◽

Cited By ~ 26

Author(s):

Ankur Naqib ◽

Silvana Poggi ◽

Weihua Wang ◽

Marieta Hyde ◽

Kevin Kunstman ◽

...

Keyword(s):

High Throughput ◽

Ribosomal Rna ◽

16S Ribosomal Rna ◽

Two Stage ◽

Ribosomal Rna Gene ◽

16S Ribosomal Rna Gene

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

10.21203/rs.3.rs-334241/v1 ◽

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.

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kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing

BMC Genomics ◽

10.1186/s12864-021-07696-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xue Lin ◽

Yingying Hua ◽

Shuanglin Gu ◽

Li Lv ◽

Xingyu Li ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Somatic Mutations ◽

R Package ◽

Frequency Of Occurrence ◽

Link Type ◽

Genomic Landscape ◽

One Step ◽

Flanking Regions

Abstract Background Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means. Results There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions. Conclusions The kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.

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Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene

Journal of UOEH ◽

10.7888/juoeh.38.223 ◽

2016 ◽

Vol 38 (3) ◽

pp. 223-232 ◽

Cited By ~ 14

Author(s):

Kazumasa FUKUDA ◽

Midori OGAWA ◽

Hatsumi TANIGUCHI ◽

Mitsumasa SAITO

Keyword(s):

Microbial Communities ◽

Ribosomal Rna ◽

16S Ribosomal Rna ◽

Approaches To Studying ◽

Ribosomal Rna Gene ◽

Molecular Approaches ◽

16S Ribosomal Rna Gene

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Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

Applied and Environmental Microbiology ◽

10.1128/aem.01938-17 ◽

2017 ◽

Vol 83 (22) ◽

Cited By ~ 40

Author(s):

Konstantia Gkarmiri ◽

Shahid Mahmood ◽

Alf Ekblad ◽

Sadhna Alström ◽

Nils Högberg ◽

...

Keyword(s):

Brassica Napus ◽

Stable Isotope ◽

Oilseed Rape ◽

High Throughput ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Stable Isotope Probing ◽

Biofuel Production ◽

Content Type ◽

Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

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Evaluation of 16S, map1 and pCS20 probes for detection of Cowdria and Ehrlichia species

Epidemiology and Infection ◽

10.1017/s0950268899002101 ◽

1999 ◽

Vol 122 (2) ◽

pp. 323-328 ◽

Cited By ~ 18

Author(s):

M. T. E. P. ALLSOPP ◽

C. M. HATTINGH ◽

S. W. VOGEL ◽

B. A. ALLSOPP

Keyword(s):

16S Rrna ◽

Ribosomal Rna ◽

Pcr Amplification ◽

16S Ribosomal Rna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Amblyomma Hebraeum ◽

Ribosomal Rna Gene ◽

Group Iii ◽

16S Ribosomal Rna Gene

A panel of 16S ribosomal RNA gene probes has been developed for the study of the epidemiology of heartwater; five of these detect different cowdria genotypes, one detects five distinct genotypes; one detects any Group III Ehrlichia species other than Cowdria and one detects any Group II Ehrlichia species. These probes have been used on PCR-amplified rickettsial 16S rRNA genes from over 200 Amblyomma hebraeum ticks. Control ticks were laboratory-reared and either uninfected or fed on sheep experimentally infected with different cowdria isolates, field ticks were collected from animals in heartwater-endemic areas. All tick-derived DNA samples were also examined by PCR amplification and probing for two other cowdria genes (map1 and pCS20) which have previously been used for heartwater epidemiology. This paper describes the first direct comparison of all currently available DNA probes for heartwater-associated organisms.

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