Effect of Plantaricin 163 in Combination with Thymol and Surfactin on Crucian Carp (Carassius auratus)

2019 ◽  
Vol 82 (8) ◽  
pp. 1283-1291 ◽  
Author(s):  
HECHAO DU ◽  
XIUXIU LI ◽  
ZHAOXIN LU ◽  
XIAOMEI BIE ◽  
HAIZHEN ZHAO ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Crucian Carp ◽  
Thiobarbituric Acid ◽  
Commercial Application ◽  
Operational Taxonomic Units ◽  
Spoilage Bacteria ◽  
Plate Counts ◽  
Natural Preservatives ◽  
Control Samples

ABSTRACT The use of natural preservatives has attracted considerable attention owing to their generally safe and environmentally friendly properties. In this study, we investigated the effects of the preservative A1, composed of plantaricin 163, thymol, and surfactin, on bacterial communities and storage quality of refrigerated crucian carp. A total of 522 operational taxonomic units belonging to 20 phyla and 272 genera were identified by high-throughput sequencing, showing a comprehensive coverage of bacterial composition of crucian carp. In untreated samples after spoilage, Brochothrix was the predominant genus, followed by Aeromonas and Pseudomonas. After treatment with A1, the growth of these spoilage bacteria was significantly inhibited according to high-throughput sequencing and plate counts, and Lactococcus became the most abundant organism at the end of storage. Meanwhile, compared with control samples, the shelf life of A1-treated samples extended from 3 to 12 days on the basis of the sensory evaluation and the total viable counts. Furthermore, the total volatile basic nitrogen, thiobarbituric acid, and pH values for A1-treated samples were significantly lower than that of control samples. The results indicate that preservative A1 has potential commercial application in the preservation of refrigerated crucian carp.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

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

2015 ◽  
Vol 105 (6) ◽  
pp. 717-727 ◽  
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.

scholarly journals The promise of a DNA taxonomy

2004 ◽  
Vol 359 (1444) ◽  
pp. 669-679 ◽  
Author(s):  
Mark L. Blaxter
Keyword(s):  
High Throughput ◽  
Small Proportion ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Molecular Data ◽  
Similar Extent ◽  
Molecular Barcoding ◽  
Dna Taxonomy ◽  
Biologically Relevant ◽  
Operational Taxonomic Units

Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of ‘species’ fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional ‘species’. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re–analysis and meta–analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high–throughput sequencing methodologies, however, place the idea of a universal, multi–locus molecular barcoding system in the realm of the possible.

scholarly journals Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3472 ◽  
Author(s):  
Ross Cunning ◽  
Ruth D. Gates ◽  
Peter J. Edmunds
Keyword(s):  
Coral Reef ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virgin Islands ◽  
Us Virgin Islands ◽  
Operational Taxonomic Units ◽  
The North ◽  
Application Specific ◽  
North And South ◽  
Symbiotic Microalgae

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.

An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing

2021 ◽  
Author(s):  
Eden Esteves ◽  
Paul Whyte ◽  
John Mills ◽  
Gale Brightwell ◽  
Tanushree B Gupta ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Amplicon Sequencing ◽  
Alpha And Beta Diversity ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Meat Spoilage ◽  
Beef Carcasses ◽  
Spoilage Bacteria ◽  
Beef Carcass

Abstract The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored in this study. A total of 120 carcass and 120 rump steak swabs were collected immediately after slaughtering and boning, respectively from five meat plants, anaerobically incubated and enriched d at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeqTM, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). The microbiota recovered from both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5–20% and 0.1–29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0–0.8% on carcass and 0–1.8% on rump steak swabs, respectively. Alpha and Beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. This study highlights the presence of potential spoilage bacteria, mainly anaerobic genera on and between carcass and rump steaks, as an indication of contamination on and between these samples.

scholarly journals High-throughput sequencing of fungal communities across the perennial ice block of Scărișoara Ice Cave

2018 ◽  
Vol 59 (77) ◽  
pp. 134-146 ◽  
Author(s):  
Antonio Mondini ◽  
Johanna Donhauser ◽  
Corina Itcus ◽  
Constantin Marin ◽  
Aurel Perșoiu ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Temporal Distribution ◽  
Ice Age ◽  
Climate Variations ◽  
Operational Taxonomic Units ◽  
Ph Values ◽  
Low Diversity ◽  
Fungal Distribution ◽  
Perennial Ice

ABSTRACTThis survey presents the first high-throughput characterisation of fungal distribution based on ITS2 Illumina sequencing of uncultured microbiome from a 1500 years old perennial ice deposit in Scărișoara Ice Cave, Romania. Of the total of 1 751 957 ITS2 sequences, 64% corresponded to 182 fungal operational taxonomic units, showing a low diversity, particularly in older ice strata, and a distinct temporal distribution pattern. Ascomycota was the major phylum in all ice samples, dominating the 400 and 1500 years old ice strata deposited during the cold Little Ice Age (LIA) and Dark Ages Cold Period, while Basidiomycota was mostly present in 900-years old ice formed during the Medieval Warm Period (MWP). Chytridiomycota and Mucoromycota phyla were present in recently formed and 400-years old ice, respectively. Among the 80 identified genera, Cryptococcus victoriae, commonly found in glacial habitats, was identified in all strata. A positive correlation between fungal distribution and ice conductivity, Ca, Na and Sr concentrations was observed across the ice block, with pH values trailing climate variations during LIA and MWP, respectively. Our record highlighted the presence of a complex climate and environmental-driven fungal community in perennial ice strata accumulated during the last 1500 years in Scărișoara Ice Cave.

scholarly journals Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Yan Zhao ◽  
Kun Li ◽  
Houqiang Luo ◽  
Longchuan Duan ◽  
Caixia Wei ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Water Contamination ◽  
High Throughput Sequencing ◽  
Free Access ◽  
Operational Taxonomic Units ◽  
Genus Level ◽  
Significant Difference ◽  
Access To Water ◽  
Poultry Droppings

Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).

scholarly journals Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, U.S. Virgin Islands

2017 ◽  
Author(s):  
Ross Cunning ◽  
Ruth D Gates ◽  
Peter J Edmunds
Keyword(s):  
Coral Reef ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virgin Islands ◽  
Us Virgin Islands ◽  
Operational Taxonomic Units ◽  
The North ◽  
Application Specific ◽  
North And South ◽  
Symbiotic Microalgae

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this 'within-sample clustering' to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying 'dominant' and 'background' niches, and coral hosts that are more 'flexible' or 'specific' in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.

scholarly journals Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, U.S. Virgin Islands

2017 ◽  
Author(s):  
Ross Cunning ◽  
Ruth D Gates ◽  
Peter J Edmunds
Keyword(s):  
Coral Reef ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virgin Islands ◽  
Us Virgin Islands ◽  
Operational Taxonomic Units ◽  
The North ◽  
Application Specific ◽  
North And South ◽  
Symbiotic Microalgae

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this 'within-sample clustering' to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying 'dominant' and 'background' niches, and coral hosts that are more 'flexible' or 'specific' in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.

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