A database for ITS2 sequences from nematodes

Workentine, Matthew L.; Chen, Rebecca; Zhu, Shawna; Gavriliuc, Stefan; Shaw, N.; Rijke, Jill de; Redman, Elizabeth; Avramenko, Russell W.; Wit, Janneke; Poissant, Jocelyn; Gilleard, John S.

doi:10.1186/s12863-020-00880-0

Cited by 43 publications

(27 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A conservative approach was used for taxonomic assignment of amplicon sequence variants (ASV) in which three different assignment methods were used (Additional file 1 : Table S1): (1) IDTaxa using the default conservative threshold of 60, which corresponds to the confidence at which to truncate the output taxonomic classification [ 49 ]; (2) assignTaxonomy [ 46 , 50 ] and (3) BLASTn [ 51 ]. The nematode ITS2 rDNA database 1.1.0 [ 52 ] containing 9811 complete and non-redundant sequences, with a few additional manual corrections of species assignation corresponding to morphotypes, was used for both IDTaxa and assignTaxonomy. For BLASTn, the three best hits were considered only if they reached a threshold of 90% similarity against NCBI database sequences (2021/04/13).…”

Section: Methodsmentioning

confidence: 99%

Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

et al. 2021

Self Cite

View full text Add to dashboard Cite

Background Gastrointestinal nematodes are ubiquitous for both domestic and wild ungulates and have varying consequences for health and fitness. They exist as complex communities of multiple co-infecting species, and we have a limited understanding of how these communities vary in different hosts, regions and circumstances or of how this affects their impacts. Methods We have undertaken ITS2 rDNA nemabiome metabarcoding with next-generation sequencing on populations of nematode larvae isolated from 149 fecal samples of roe deer of different sex and age classes in the two isolated populations of Chizé and Trois Fontaines in France not co-grazing with any domestic ungulate species. Results We identified 100 amplified sequence variants (ASVs) that were assigned to 14 gastrointestinal nematode taxa overall at either genus (29%) or species (71%) level. These taxa were dominated by parasites classically found in cervids—e.g. Ostertagia leptospicularis, Spiculopteragia spp. Higher parasite species diversity was present in the Trois Fontaines population than in the Chizé population including the presence of species more typically seen in domestic livestock (Haemonchus contortus, Bunostomum sp., Cooperia punctata, Teladorsagia circumcincta). No differences in parasite species diversity or community composition were seen in the samples collected from three zones of differing habitat quality within the Chizé study area. Young roe deer hosted the highest diversity of gastrointestinal nematodes, with more pronounced effects of age apparent in Trois Fontaines. The effect of host age differed between gastrointestinal nematode species, e.g. there was little effect on O. leptospicularis but a large effect on Trichostrongylus spp. No effect of host sex was detected in either site. Conclusions The presence of some livestock parasite species in the Trois Fontaines roe deer population was unexpected given the isolation of this population away from grazing domestic livestock since decades. Overall, our results illustrate the influence of host traits and the local environment on roe deer nemabiome and demonstrate the power of the nemabiome metabarcoding approach to elucidate the composition of gastrointestinal nematode communities in wildlife. Graphical Abstract

show abstract

Section: Methodsmentioning

confidence: 99%

Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…To assess the possibility of taxa not being detected due to the variable length of the nematode ITS2 region, the forward reads were also analysed in parallel as described above, omitting the merging step. Taxonomy was assigned to ASVs using the naïve Bayesian classifier [ 47 ] implemented in DADA2 and a custom version of the Nematode ITS2 v.1.0.0 database [ 34 , 48 ] ( http://www.nemabiome.ca ) including an additional 19 reference sequences from adult nematodes and eggs identified during morphological examinations of the samples in this study (GenBank accession no. MZ478650-MZ478668).…”

Section: Methodsmentioning

confidence: 99%

Section: Bioinformatics and Statistical Analysesmentioning

confidence: 99%

Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

2021

View full text Add to dashboard Cite

Background Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population. Methods Faeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments. Results DNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples. Conclusions DNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes. Graphical abstract

show abstract

“…An amplicon sequence variant (ASV) table was then created and chimeras removed. A recently developed database of nematode rDNA ITS-2 reference sequences was used [ 32 ]. Finally, IdTaxa was used as the classification algorithm to classify the ASVs from the pipeline at the highest resolution using the database.…”

Section: Methodsmentioning

confidence: 99%

Seasonal epidemiology of gastrointestinal nematodes of cattle in the northern continental climate zone of western Canada as revealed by internal transcribed spacer-2 ribosomal DNA nemabiome barcoding

et al. 2021

Self Cite

View full text Add to dashboard Cite

Background Gastrointestinal nematode (GIN) epidemiology is changing in many regions of the world due to factors such as global warming and emerging anthelmintic resistance. However, the dynamics of these changes in northern continental climate zones are poorly understood due to a lack of empirical data. Methods We studied the accumulation on pasture of free-living infective third-stage larvae (L3) of different GIN species from fecal pats deposited by naturally infected grazing cattle. The field study was conducted on three organic farms in Alberta, western Canada. Grass samples adjacent to 24 fecal pats were collected from each of three different pastures on each farm. Internal transcribed spacer-2 nemabiome metabarcoding was used to determine the GIN species composition of the harvested larvae. The rotational grazing patterns of the cattle ensured that each pasture was contaminated only once by fecal pat deposition. This design allowed us to monitor the accumulation of L3 of specific GIN species on pastures under natural climatic conditions without the confounding effects of pasture recontamination or anthelmintic treatments. Results In seven out of the nine pastures, grass L3 counts peaked approximately 9 weeks after fecal deposition and then gradually declined. However, a relatively large number of L3 remained in the fecal pats at the end of the grazing season. Nemabiome metabarcoding revealed that Cooperia oncophora and Ostertagia ostertagi were the two most abundant species on all of the pastures and that the dynamics of larval accumulation on grass were similar for both species. Daily precipitation and temperature across the whole sampling period were similar for most of the pastures, and multiple linear regression showed that accumulated rainfall 1 week prior to sample collection had a significant impact on the pasture L3 population, but accumulated rainfall 3 weeks prior to sample collection did not. Conclusions The results suggest that the pasture L3 population was altered by short-term microclimatic conditions conducive for horizontal migration onto grass. Overall, the results show the importance of the fecal pat as a refuge and reservoir for L3 of cattle GIN on western Canadian pastures, and provide an evidence base for the risk assessment of rotational grazing management in the region. Graphical Abstract

show abstract

A database for ITS2 sequences from nematodes

Cited by 43 publications

References 19 publications

Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

Seasonal epidemiology of gastrointestinal nematodes of cattle in the northern continental climate zone of western Canada as revealed by internal transcribed spacer-2 ribosomal DNA nemabiome barcoding

Contact Info

Product

Resources

About