scholarly journals GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
W. M. Tong ◽  
Yuki Chan
Keyword(s):  
Graphical User Interface ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Wide Range ◽  
R Shiny ◽  
Microbiome Data ◽  
The 16S Rrna Gene ◽  
Graphical User Interface Tool ◽  
Shiny Application

Amplicon sequencing of the 16S rRNA gene is commonly performed for the assessment and comparison of microbiomes. Here, we introduce GenePiper, an open-source R Shiny application that provides an easy-to-use interface, a wide range of analytical methods, and optimized graphical outputs for offline microbiome data analyses.

scholarly journals How Diverse Is the Genus Wolbachia? Multiple-Gene Sequencing Reveals a Putatively New Wolbachia Supergroup Recovered from Spider Mites (Acari: Tetranychidae)

2008 ◽  
Vol 75 (4) ◽  
pp. 1036-1043 ◽  
Author(s):  
Vera I. D. Ros ◽  
Vicki M. Fleming ◽  
Edward J. Feil ◽  
Johannes A. J. Breeuwer
Keyword(s):  
Spider Mite ◽  
Sequence Data ◽  
Nematode Species ◽  
Mite Species ◽  
Rrna Gene ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
Multiple Gene ◽  
Wide Range ◽  
The 16S Rrna Gene

ABSTRACT At least 20% of all arthropods and some nematode species are infected with intracellular bacteria of the genus Wolbachia. This highly diverse genus has been subdivided into eight “supergroups” (A to H) on the basis of nucleotide sequence data. Here, we report the discovery of a new Wolbachia supergroup recovered from the spider mite species Bryobia species V (Acari: Tetranychidae), based on the sequences of three protein-coding genes (ftsZ, gltA, and groEL) and the 16S rRNA gene. Other tetranychid mites possess supergroup B Wolbachia strains. The discovery of another Wolbachia supergroup expands the known diversity of Wolbachia and emphasizes the high variability of the genus. Our data also clarify the existing supergroup structure and highlight the use of multiple gene sequences for robust phylogenetic analysis. In addition to previous reports of recombination between the arthropod-infecting supergroups A and B, we provide evidence for recombination between the nematode-infecting supergroups C and D. Robust delineation of supergroups is essential for understanding the origin and spread of this common reproductive parasite and for unraveling mechanisms of host adaptation and manipulation across a wide range of hosts.

scholarly journals The microbial community of the gut differs between piglets fed sow milk, milk replacer or bovine colostrum

2017 ◽  
Vol 117 (7) ◽  
pp. 964-978 ◽  
Author(s):  
Ann-Sofie R. Poulsen ◽  
Nadieh de Jonge ◽  
Sugiharto Sugiharto ◽  
Jeppe L. Nielsen ◽  
Charlotte Lauridsen ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Bovine Colostrum ◽  
Milk Replacer ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Faecal Samples ◽  
Milk Replacers ◽  
The 16S Rrna Gene ◽  
Gut Microbiota Composition

AbstractThe aim of this study was to characterise the gut microbiota composition of piglets fed bovine colostrum (BC), milk replacer (MR) or sow milk (SM) in the post-weaning period. Piglets (n36), 23-d old, were randomly allocated to the three diets. Faecal samples were collected at 23, 25, 27 and 30 d of age. Digesta from the stomach, ileum, caecum and mid-colon was collected at 30 d of age. Bacterial DNA from all samples was subjected to amplicon sequencing of the 16S rRNA gene. Bacterial enumerations by culture and SCFA analysis were conducted as well. BC-piglets had the highest abundance ofLactococcusin the stomach (P<0·0001) and ileal (P<0·0001) digesta, whereas SM-piglets had the highest abundance ofLactobacillusin the stomach digesta (P<0·0001). MR-piglets had a high abundance of Enterobacteriaceae in the ileal digesta (P<0·0001) and a higher number of haemolytic bacteria in ileal (P=0·0002) and mid-colon (P=0·001) digesta than SM-piglets. BC-piglets showed the highest colonic concentration of iso-butyric and iso-valeric acid (P=0·02). Sequencing and culture showed that MR-piglets were colonised by a higher number of Enterobacteriaceae, whereas the gut microbiota of BC-piglets was characterised by a change in lactic acid bacteria genera when compared with SM-piglets. We conclude that especially the ileal microbiota of BC-piglets had a closer resemblance to that of SM-piglets in regard to the abundance of potential enteric pathogens than did MR-piglets. The results indicate that BC may be a useful substitute for regular milk replacers, and as a feeding supplement in the immediate post-weaning period.

A new species of Puddle Frog, genus Phrynobatrachus (Amphibia: Anura: Phrynobatrachidae) from Ghana

Zootaxa ◽  
2018 ◽  
Vol 4374 (4) ◽  
pp. 565 ◽  
Author(s):  
CALEB OFORI-BOATENG ◽  
ADAM D. LEACHÉ ◽  
BRIGHT OBENG-KANKAM ◽  
N’GORAN GERMAIN KOUAMÉ ◽  
ANNIKA HILLERS ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Species ◽  
Sequence Data ◽  
Face Mask ◽  
West African ◽  
Rrna Gene ◽  
Forest Region ◽  
Mtdna Sequence ◽  
A New Species ◽  
The 16S Rrna Gene

We describe a new species of Phrynobatrachus from the eastern part of the Upper Guinea forest region, Ghana, West Africa. Morphologically, the new species can be distinguished from all of its congeners by the combination of a slender body, short and pointed snout, a relatively warty dorsum, a black-spotted throat in both sexes, a gular flap in males, a dark spotted chest, a white-greyish venter with occasional blackish spots, rudimentary pedal webbing, none to slightly dilated finger tips and strongly delated toe tips, presence of both inner and outer metatarsal tubercles and absence of a dark face mask, eyelid tubercles and longer dorsal ridges. We collected mitochondrial DNA (mtDNA) sequence data from the 16S rRNA gene to measure the genetic diversity of the new species, and to estimate phylogenetic relationships. The new species is a distinct and monophyletic evolutionary lineage most closely related to Phrynobatrachus gutturosus, P. fraterculus and P. maculiventris. The discovery of this new species highlights that the biodiversity of West African forests is still incompletely known and that the few remaining forests need urgent protection. 

scholarly journals A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Davide Porcellato ◽  
Roger Meisal ◽  
Alberto Bombelli ◽  
Judith A. Narvhus
Keyword(s):  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Lactation Period ◽  
Strong Negative Correlation ◽  
Udder Health ◽  
Milk Samples ◽  
Lactating Cows ◽  
Definition Of ◽  
The 16S Rrna Gene

AbstractThe importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.

scholarly journals A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

2020 ◽  
Vol 58 (6) ◽  
Author(s):  
Stefan Moritz Neuenschwander ◽  
Miguel Angel Terrazos Miani ◽  
Heiko Amlang ◽  
Carmen Perroulaz ◽  
Pascal Bittel ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Sequence Data ◽  
Automated Analysis ◽  
Amplicon Sequencing ◽  
Turnaround Time ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Taxonomic Identification ◽  
Consensus Analysis

ABSTRACT Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling a flexible number of samples per run and an adjustable sequencing time. Here, we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (long read consensus analysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, simulated read and amplicon mixtures were used to assess LORCAN’s behavior when dealing with samples with known cross-contamination levels. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single-base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability, and availability of amplicon sequencing in diagnostic settings.

scholarly journals Prokaryotic Community Structures in a Thermophilic Anaerobic Digestion Reactor Converting Poly(l-Lactic Acid) for a Long Period Revealed by 16S rRNA Gene Amplicon Sequencing

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Takeshi Yamada ◽  
Masako Hamada ◽  
Misaki Kurobe ◽  
Jun Harada ◽  
Surya Giri ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Anaerobic Digestion ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Thermophilic Anaerobic Digestion ◽  
Taxonomic Class ◽  
Class Level

Little information on poly(l-lactic acid) (PLLA) treatment-associated microbiota in thermophilic anaerobic digestion reactors is available. Here, we provide 16S rRNA gene sequence data on microbiota in a thermophilic anaerobic digestion reactor converting PLLA to methane for 336 days. Data comprising 99,566 total high-quality reads were tabulated at the taxonomic class level.

scholarly journals The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

2018 ◽  
Vol 7 (1) ◽  
pp. 4 ◽  
Author(s):  
Kelly Ugarelli ◽  
Peeter Laas ◽  
Ulrich Stingl
Keyword(s):  
Carbon Sink ◽  
Amplicon Sequencing ◽  
Thalassia Testudinum ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Carbon Cycles ◽  
Syringodium Filiforme ◽  
Turtle Grass ◽  
Shoreline Protection ◽  
The 16S Rrna Gene

Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassia testudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽  
2013 ◽  
Vol 141 (5) ◽  
pp. 646-651 ◽  
Author(s):  
GASTÓN MORÉ ◽  
NIKOLA PANTCHEV ◽  
DALAND C. HERRMANN ◽  
MAJDA GLOBOKAR VRHOVEC ◽  
SABINE ÖFNER ◽  
...  
Keyword(s):  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Apicomplexan Parasites ◽  
Large Numbers ◽  
Wide Range ◽  
18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

scholarly journals Desulfitibacter alkalitolerans gen. nov., sp. nov., an anaerobic, alkalitolerant, sulfite-reducing bacterium isolated from a district heating plant

2006 ◽  
Vol 56 (12) ◽  
pp. 2831-2836 ◽  
Author(s):  
Marie Bank Nielsen ◽  
Kasper Urup Kjeldsen ◽  
Kjeld Ingvorsen
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
District Heating ◽  
Rrna Gene ◽  
Corrosion Monitoring ◽  
Optimum Growth ◽  
Genes Encoding ◽  
Nitrate And Nitrite ◽  
The 16S Rrna Gene ◽  
Heating Plant

A novel alkalitolerant, anaerobic bacterium, designated strain sk.kt5T, was isolated from a metal coupon retrieved from a corrosion-monitoring reactor of a Danish district heating plant (Skanderborg, Jutland). The cells of strain sk.kt5T were motile, rod-shaped (0.4–0.6×2.5–9.6 μm), stained Gram-positive and formed endospores. Strain sk.kt5T grew at pH 7.6–10.5 (with optimum growth at pH 8.0–9.5), at temperatures in the range 23–44 °C (with optimum growth at 35–37 °C), at NaCl concentrations in the range 0–5 % (w/v) (with optimum growth at 0–0.5 %) and required yeast extract for growth. Only a limited number of substrates were utilized as electron donors, including betaine, formate, lactate, methanol, choline and pyruvate. Elemental sulfur, sulfite, thiosulfate, nitrate and nitrite, but not sulfate or Fe(III) citrate, were used as electron acceptors. The G+C content of the DNA was 41.6 mol%. Phylogenetic analyses of the sequence data for the dsrAB genes [encoding the major subunits of dissimilatory (bi)sulfite reductase] and the 16S rRNA gene placed strain sk.kt5T within a novel lineage in the class Clostridia of the phylum Firmicutes. Taken together, the physiological and genotypic data suggest that strain sk.kt5T represents a novel species within a novel genus, for which the name Desulfitibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Desulfitibacter alkalitolerans is sk.kt5T (=JCM 12761T=DSM 16504T).

scholarly journals Single Cell Viewer (SCV): An interactive visualization data portal for single cell RNA sequence data

2019 ◽  
Author(s):  
Shuoguo Wang ◽  
Constance Brett ◽  
Mohan Bolisetty ◽  
Ryan Golhar ◽  
Isaac Neuhaus ◽  
...  
Keyword(s):  
Single Cell ◽  
Sequence Data ◽  
Single Cells ◽  
Link Type ◽  
Technological Advances ◽  
R Shiny ◽  
Data Volume ◽  
Exploratory Data ◽  
Cell Data ◽  
Shiny Application

AbstractMotivationThanks to technological advances made in the last few years, we are now able to study transcriptomes from thousands of single cells. These have been applied widely to study various aspects of Biology. Nevertheless, comprehending and inferring meaningful biological insights from these large datasets is still a challenge. Although tools are being developed to deal with the data complexity and data volume, we do not have yet an effective visualizations and comparative analysis tools to realize the full value of these datasets.ResultsIn order to address this gap, we implemented a single cell data visualization portal called Single Cell Viewer (SCV). SCV is an R shiny application that offers users rich visualization and exploratory data analysis options for single cell datasets.AvailabilitySource code for the application is available online at GitHub (http://www.github.com/neuhausi/single-cell-viewer) and there is a hosted exploration application using the same example dataset as this publication at http://periscopeapps.org/[email protected]; [email protected]

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