Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.

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Fecal Microbiota, Lactic Acid and Short Chain Fatty Levels of Infants Following Rotavirus Infection Revealed by Illumina Miseq High-Throughput Sequencing and HPLC Method

Jundishapur Journal of Microbiology ◽

10.5812/jjm.68389 ◽

2019 ◽

Vol 12 (6) ◽

Author(s):

Lin Li ◽

Dongxu Huang ◽

Austin Nevin ◽

Peng Fei ◽

Ling Guo

Keyword(s):

Lactic Acid ◽

High Throughput ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Fecal Microbiota ◽

Hplc Method ◽

Short Chain ◽

Rotavirus Infection

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Analysis of the effects of nanosilver on bacterial community in the intestinal fluid of silkworms using high-throughput sequencing

Bulletin of Entomological Research ◽

10.1017/s0007485319000634 ◽

2019 ◽

Vol 110 (3) ◽

pp. 309-320

Author(s):

Chen Lin ◽

Zhou Wei ◽

Zhou Yi ◽

Tan Tingting ◽

Du Huamao ◽

...

Keyword(s):

Bacterial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Intestinal Bacteria ◽

Illumina Miseq ◽

The Body ◽

Dependent Manner ◽

Negative Effects ◽

Silkworm Larvae ◽

Intestinal Bacterial Community

AbstractNanosilver is an environment-friendly, harmless alternative of traditional disinfectants which can be potentially applied in the sericulture industry. However, the effects of nanosilver on the intestinal bacterial community of the silkworms (Bombyx mori L.) are unclear. In this study, Illumina MiSeq high-throughput sequencing technology was used to assess the intestinal bacterial community in both male and female silkworms while treated with different concentrations of nanosilver. We found that nanosilver significantly influenced the composition of silkworm intestinal bacterial community on the different taxonomic levels. Most conspicuously, the abundance of Firmicutes was increased by the treatment of 20 mg L−1 nanosilver but decreased by that of 100 mg L−1 nanosilver at the phylum level. The same trend was observed in Bacilli at the class level and in Enterococcus at the genus level. In some extreme cases, application of nanosilver eliminated the bacterium, e.g., Brevibacillus, but increased the population of several other bacteria in the host intestine, such as Blautia, Terrisporobacter, Faecalibacterium, and some bacteria could only be found in nanosilver treatment groups, e.g., Dialister. In addition, although nanosilver generally showed negative effects on the cocooning rate in a dose-dependent manner, we found that 20 mg L−1 nanosilver treatment significantly increased the body weight of silkworms and did not show negative effects on the survival rate. These results indicated that the intestinal bacteria community of silkworm larvae was significantly changed after nanosilver treatment which might consequently influence host growth and development.

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DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

Bulletin of Entomological Research ◽

10.1017/s0007485315000681 ◽

2015 ◽

Vol 105 (6) ◽

pp. 717-727 ◽

Cited By ~ 83

Author(s):

G.-J. Brandon-Mong ◽

H.-M. Gan ◽

K.-W. Sing ◽

P.-S. Lee ◽

P.-E. Lim ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Ease Of Use ◽

Malaise Trap ◽

Detection Rates ◽

Operational Taxonomic Units ◽

Arthropod Species ◽

Primer Sets ◽

Arthropod Biodiversity

AbstractMetabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80–90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.

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High-throughput sequencing in the population analysis of bacterial pathogens of humans

International Journal of Medical Microbiology ◽

10.1016/s1438-4221(00)80089-2 ◽

2000 ◽

Vol 290 (2) ◽

pp. 183-190 ◽

Cited By ~ 18

Author(s):

Martin C.J. Maiden

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Population Analysis ◽

Bacterial Pathogens

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FINE GRAINED LONGITUDINAL ANALYSIS OF COCOA BEAN FERMENTATION PROVIDES INSIGHTS INTO THE DYNAMICS OF MICROBIAL POPULATIONS

10.1101/702225 ◽

2019 ◽

Cited By ~ 1

Author(s):

M. E. Pacheco-Montealegre ◽

L. L. Dávila-Mora ◽

L. M. Botero-Rute ◽

A. Reyes ◽

A. Caro-Quintero

Keyword(s):

Molecular Markers ◽

High Throughput ◽

High Throughput Sequencing ◽

Population Analysis ◽

Starter Cultures ◽

Cocoa Bean ◽

Microbial Fermentation ◽

Single Strain ◽

Ecological Zones ◽

Cocoa Bean Fermentation

ABSTRACTCocoa bean fermentation is an important microbial driven process where metabolites that affect chocolate quality and aroma are produced. Although considerable research has been devoted to the yeast and bacteria species involved in this process, less attention has been paid to the role of populations and strains, which hinders its selection, monitoring and use. Here we present a study that evaluates the microbial diversity associated to the tools and bean mass during spontaneous cocoa fermentation and in two distinct agro-ecological zones in Colombia. Using high-throughput sequencing of molecular markers for bacteria and yeast, we established the dynamics at the species-level (OTUs) and strains-level (oligotypes). Our results show that cocoa bean fermentation is catalyzed by a composite of strains within each OTU and not by one single strain. Eventhough we found only a few bacterial OTUs, one Enterobacter, three of Lactic Acid Bacteria and two of Acetic Acid Bacteria, these could be further split into 6, 23 and 19 oligotypes, respectively. Only two fungal OTUs were found. Comparison between fermentations suggest that local protocols generated a specific footprint in the dynamics of the microbial communities and that tools are reservoirs of some of those groups. The population analysis shows that the oligotypes that become most dominant are the same in the two locations, coupling co-abundance and dominance analysis we suggest that a combination of Enterobacter and Acetobacter oligotypes seem more optimal for the starter cultures. In conclusion, the results presented here show that exploring the fine level dynamics of microbial fermentation is necessary to understand the patterns of the dominance of specific populations and can be used as a valuable approach to select and monitor specific bacteria for the design of starter cultures in the food industry.IMPORTANCEIn Colombia, the lack of tools to validate and standardize fermentation protocols are one of the principal reasons why Colombian cocoa beans are not recognized as “fine-flavor” and widely marketed. Because of the large influence of the microbial fermentation in cocoa quality, the present study explores the microbial dynamics using high-throughput sequencing of molecular markers in two of the most important producer regions in Colombia. The results show that the identification of dominant and transitive strains can be used to select, design and monitor starter cultures and/or the effect of adjustments in the fermentation protocols.

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Population genomics of bank vole populations reveals associations between immune related genes and the epidemiology of Puumala hantavirus in Sweden

10.1101/148163 ◽

2017 ◽

Author(s):

Audrey Rohfritsch ◽

Maxime Galan ◽

Mathieu Gautier ◽

Karim Gharbi ◽

Gert Olsson ◽

...

Keyword(s):

High Throughput ◽

Bank Vole ◽

High Throughput Sequencing ◽

Population Genomics ◽

Reservoir Host ◽

Model Organisms ◽

Myodes Glareolus ◽

A Genome ◽

Outlier Loci ◽

Immune Related Genes

AbstractInfectious pathogens are major selective forces acting on individuals. The recent advent of high-throughput sequencing technologies now enables to investigate the genetic bases of resistance/susceptibility to infections in non-model organisms. From an evolutionary perspective, the analysis of the genetic diversity observed at these genes in natural populations provides insight into the mechanisms maintaining polymorphism and their epidemiological consequences. We explored these questions in the context of the interactions between Puumala hantavirus (PUUV) and its reservoir host, the bank vole Myodes glareolus. Despite the continuous spatial distribution of M. glareolus in Europe, PUUV distribution is strongly heterogeneous. Different defence strategies might have evolved in bank voles as a result of co-adaptation with PUUV, which may in turn reinforce spatial heterogeneity in PUUV distribution. We performed a genome scan study of six bank vole populations sampled along a North/South transect in Sweden, including PUUV endemic and non-endemic areas. We combined candidate gene analyses (Tlr4, Tlr7, Mx2 genes) and high throughput sequencing of RAD (Restriction-site Associated DNA) markers. We found evidence for outlier loci showing high levels of genetic differentiation. Ten outliers among the 52 that matched to mouse protein-coding genes corresponded to immune related genes and were detected using ecological associations with variations in PUUV prevalence. One third of the enriched pathways concerned immune processes, including platelet activation and TLR pathway. In the future, functional experimentations should enable to confirm the role of these these immune related genes with regard to the interactions between M. glareolus and PUUV.

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