scholarly journals Sheep Nemabiome Diversity and Its Response to Anthelmintic Treatment in Swedish Sheep Herds

2020 ◽  
Author(s):  
Peter Halvarsson ◽  
Johan Höglund
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Nematode Species ◽  
Anthelmintic Treatment ◽  
Host Age ◽  
Nematode Parasites ◽  
South Central ◽  
Nematode Diversity ◽  
Commercial Farms ◽  
Multiple Species

Abstract Background: A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first-time the nematode community structure (nemabiome) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments. Methods: A total of 158 larval cultures were collected (n=35 in 2007 and n=126 in 2014-2016) from groups of sheep on 61 commercial farms in the south-central part of country were most animals are grazed. Among the samples, 2 x 44 (56%) were paired collected from the same groups pre- and post-treatment with macrocyclic lactones, benzimidazoles or levamisole. The sequences were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.Results: Nematode ITS2 sequences were found in all samples except two, despite that the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded on average 1,011 sequences per sample. Totally 26 operational taxonomical units (OTU) among which 18 (69%) had ≥99 % identity to sequences in the NCBI database were recognized. The OTUs found represented nematode species among which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of IVM and ABZ. Interestingly, despite zero egg count after use of levamisole, these samples still contained nematode DNA and especially H. contortus. Conclusions: Our findings provide evidence for that nemabiome analysis combined with diversity index analysis provide a sensitive and objective methodology in the study of the efficacy of anthelmintic treatment.

scholarly journals Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Peter Halvarsson ◽  
Johan Höglund
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Nematode Species ◽  
Abundant Species ◽  
Anthelmintic Treatment ◽  
Host Age ◽  
Larval Culture ◽  
Nematode Parasites ◽  
South Central ◽  
Nematode Diversity

Abstract Background A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments. Methods A total of 158 fecal samples were collected (n = 35 in 2007 and n = 123 in 2013–2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 × 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R. Results Nematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1008 sequences per sample. In total, 16 operational taxonomical units (OTU), all with ≥ 98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which ten are commonly associated with sheep. Multiple species were identified in all pre-anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus. Conclusions Our findings provide evidence that nemabiome analysis combined with diversity index analysis provides an objective methodology in the study of the efficacy of anthelmintic treatment as both high and low abundant species were detected.

scholarly journals Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

2021 ◽  
Author(s):  
Peter Halvarsson ◽  
Johan Höglund
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Nematode Species ◽  
Abundant Species ◽  
Anthelmintic Treatment ◽  
Host Age ◽  
Larval Culture ◽  
Nematode Parasites ◽  
South Central ◽  
Nematode Diversity

Abstract BackgroundA novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first-time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.MethodsA total of 158 fecal samples were collected (n=35 in 2007 and n=123 in 2013-2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 x 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.ResultsNematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1,008 sequences per sample. In total 16 operational taxonomical units (OTU), all had ≥98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.ConclusionsOur findings provide evidence that nemabiome analysis combined with diversity index analysis provide an objective methodology in the study of the efficacy of anthelmintic treatment, as both high and low abundant species were detected.

scholarly journals Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

2020 ◽  
Author(s):  
Peter Halvarsson ◽  
Johan Höglund
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Nematode Species ◽  
Abundant Species ◽  
Anthelmintic Treatment ◽  
Host Age ◽  
Larval Culture ◽  
Nematode Parasites ◽  
South Central ◽  
Nematode Diversity

Abstract BackgroundA novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first-time the nematode community structure (nemabiome) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.MethodsA total of 158 fecal samples were collected (n=35 in 2007 and n=123 in 2013-2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of country where most animals are grazed. Among the samples, 2 x 44 (56%) were paired collections from the same groups pre- and post-treatment with macrocyclic lactones, benzimidazoles or levamisole. The sequences were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.ResultsNematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1,008 sequences per sample. In total 16 operational taxonomical units (OTU), all had ≥98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazol. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.ConclusionsOur findings provide evidence that nemabiome analysis combined with diversity index analysis provide a sensitive and objective methodology in the study of the efficacy of anthelmintic treatment, as both high and low abundant species were detected.

scholarly journals Molecular Diversity of Nematode Parasites in Afrotropical Reed Frogs (Hyperolius spp.)

Diversity ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 265
Author(s):  
Ulrich Sinsch ◽  
J. Maximilian Dehling ◽  
Patrick Scheid ◽  
Carsten Balczun
Keyword(s):  
Dna Sequences ◽  
Nematode Species ◽  
Sub Saharan Africa ◽  
Parasitic Nematodes ◽  
Marker Genes ◽  
Nematode Parasites ◽  
Diversity Assessment ◽  
Wide Range ◽  
Nematode Diversity ◽  
Sub Saharan

The diversity of nematodes infecting amphibians is understudied in tropical Africa and unknown in Rwanda. Diversity assessment is hampered by the fact that species descriptions refer mostly to morphological features that are unlinked to DNA sequences of marker genes available in public databases. In this paper, we explore the abundance and diversity of parasitic nematodes in reed frogs Hyperolius kivuensis (n = 115), H. parallelus (n = 45) and H. viridiflavus (n = 100) collected in Rwanda. Five nematode species were identified morphologically as Orneoascaris chrysanthemoides, O. schoutedeni, Gendria leberrei, Aplectana chamaeleonis and Rhabdias collaris. Corresponding DNA sequences of 18S and COI genes were determined and subsequently deposited in GenBank. Aplectana chamaeleonis showed the highest prevalence (8.7%), but O. chrysanthemoides the highest mean intensity of infection (6.0) and largest number (24) of individuals in H. kivuensis. To the best of our knowledge, all amphibian hosts are new records for these nematode species, which are known to infect a wide range of amphibian and reptile species. Our findings suggest that nematode diversity is probably lower than previously assumed due to low host specificity. As morphological species identification is often challenging, our data facilitate molecular identification of adult and specifically larval nematodes found in amphibians of Sub-Saharan Africa.

scholarly journals Diversity and community ecology of metazoan parasites in Pimelodus ornatus (Siluriformes: Pimelodidae) from the Amazonas River in Brazil

2021 ◽  
Vol 30 (3) ◽  
Author(s):  
Elvis Silva Lima ◽  
Marcos Sidney Brito Oliveira ◽  
Marcos Tavares-Dias
Keyword(s):  
Species Richness ◽  
Food Web ◽  
Community Ecology ◽  
Parasite Species ◽  
Diversity Index ◽  
Nematode Species ◽  
Parasite Community ◽  
First Record ◽  
Metazoan Parasites ◽  
Shannon’S Diversity Index

Abstract The present study investigated the metazoan parasite community in Pimelodus ornatus from the Amazon River, in the state of Amapá (Brazil). Of 71 fish examined, 70.4% were parasitized by Demidospermus sp. (Monogenea), Cucullanus pinnai, Procamallanus (Spirocamallanus) inopinatus and Contracaecum sp. (Nematoda) and plerocercoids from Proteocephalidae gen. sp. (Cestoda). The dominance was of nematode species such as Procamallanus (S.) inopinatus and Contracaecum sp. The parasites showed a highly aggregated dispersion and a predominance of hosts infected by one species of parasite. The parasite community was characterized by a low Shannon diversity index, low evenness and low species richness. The richness of parasite species, Shannon's diversity index, abundance of P. (S.) inopinatus and Proteocephalidae gen. sp. showed a positive correlation with the length of the hosts. Therefore, the size of the hosts had an influence on the parasite community and infracommunities, as well as their intermediate position in the food web. This is the first record of P. (S.) inopinatus and Contracaecum sp. for P. ornatus.

Linking fish and crustacean taxonomic composition with seasonal contrasts in the soft-bottom intertidal zone

2020 ◽  
Author(s):  
M. A. Gondal ◽  
S. Iqbal ◽  
U. Atique ◽  
N. U. Saher ◽  
N. A. Qureshi ◽  
...  
Keyword(s):  
Species Richness ◽  
Water Temperature ◽  
Fish Species ◽  
Diversity Index ◽  
Taxonomic Composition ◽  
Primary Objective ◽  
Negative Effect ◽  
Fish Species Composition ◽  
One Year ◽  
Sw Monsoon

Abstract The primary objective of this study was to investigate the seasonal fish and crustacean variations concerning taxonomic composition, species richness, and diversity in sandy beach habitat. For this purpose, we investigated the Sonmiani Hor lagoon area during four distinct seasons, i.e., northeast (NE) monsoon, pre-monsoon, south-west (SW) monsoon, and post-monsoon for one year. During each haul, the net was pulled about 100m along the beach in 0.5m depth. The results showed a strong linear correlation between the diversity index and equitability in fishes (r = 0.978). The diversity index was strong negatively correlated with the abundance and biomass (r = -0.978, -0.972, respectively). The physical attributes like sea surface water temperature and salinity showed a strong negative effect on species assemblages (r = -0.981 and -0.943, respectively). The mean air and water temperature illustrated approximately 3°C difference during NE and pre-monsoon seasons. However, salinity, pH, and electrical conductivity did not show any significant seasonal variabilities. Under the ecological indices, the fish species displayed higher diversity (H’ = 3.19) during SW monsoon, whereas the lowest diversity was observed during pre-monsoon (H’ = 1.58). The equitability and species richness, however, remained more noticeable during SW monsoon (J’ = 0.81). The total number of individuals of fish and crustaceans reached 4799 with 3813 fish individuals and 986 individuals of crustaceans. A total of 27 families of fish while five crustacean families comprising of 30 genera and 38 fish species while ten genera and 17 species of crustaceans were recorded. Liza subviridis displayed the highest abundance among the sampled fish species. In conclusion, fish species constituted a significant part of the coastal fauna in the study area. The seasonal variations displayed distinct variations in fish species composition and diversity.

Assemblage Patterns of Hymenoptera at Different Elevations of Gunung Datuk, Rembau

2017 ◽  
Vol 14 (2) ◽  
pp. 1 ◽  
Author(s):  
Noor Nasuha Abd Aziz ◽  
Siti Khairiyah Mohd Hatta ◽  
Idris Abd Ghani ◽  
Saiyid Jalaluddin Saiyid Shaifuddin
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
High Elevation ◽  
Significant Difference ◽  
Index Site ◽  
Evenness Index ◽  
Abundance And Diversity ◽  
Richness Index ◽  
Paired T Test ◽  
Malaise Traps

A study on abundance and diversity of Hymenoptera was conducted in Gunung Datuk, Rembau. Samplings were conducted from November 2014 to February 2015 using six Malaise traps. Three traps were placed at Site 1 at 700m height for high elevation and the remaining traps were placed at Site 2 at 200m height for low elevation. A total number of 221 Hymenopteran were collected which consist of nine families namely Ichneumonidae, Formicidae, Braconidae, Bethylidae, Evaniidae, Tiphiidae, Vespidae, Pompilidae and Apidae. In this study, 93 individuals were obtained from Site 1, comprising nine families and 43 morphospecies while 127 individuals were obtained from Site 2 with nine families and 45 morphospecies. Formicidae was the most dominant family collected from both sites with a total of 104 individuals while the least family recorded was Apidae with only one individual. Shannon’s Weiner Diversity Index (H’) showed Site 1 had the higher diversity value with H’ = 3.17 compared to Site 2 with value H’ = 3.12. For Evenness Index, Site 1 had higher value compared to Site 2 with E’ = 0.84 and E’ = 0.82 respectively. Moreover, for Margalef Richness Index, Site 1 recorded R’ = 9.24 while site two recorded R’ = 9.08 which concluded that Site 1 had higher species richness compared to Site 2. Paired t-test showed that both sites had no significant difference with p>0.05. Overall study showed that the diversity and abundance of Hymenoptera in Gunung Datuk were low since the value of H’ is less than 3.50.

Diversity metrics, species turnovers and nestedness of bird assemblages in a deep karst sinkhole

2017 ◽  
Vol 63 (2) ◽  
pp. 8-16 ◽  
Author(s):  
Corrado Battisti ◽  
Marco Giardini ◽  
Francesca Marini ◽  
Lorena Di Rocco ◽  
Giuseppe Dodaro ◽  
...  
Keyword(s):  
Species Richness ◽  
Random Distribution ◽  
Diversity Index ◽  
Species Turnover ◽  
Floristic Composition ◽  
Bird Assemblages ◽  
Β Diversity ◽  
Stick Model ◽  
Karst Sinkhole

We reported a study on breeding birds occurring inside an 80 m-deep karst sinkhole, with the characterization of the assemblages recorded along its semi-vertical slopes from the upper edge until the bottom. The internal sides of the sinkhole have been vertically subdivided in four belts about 20 m high. The highest belt (at the upper edge of the cenote) showed the highest values in mean number of bird detections, mean and normalized species richness, and Shannon diversity index. The averaged values of number of detections and species richness significantly differ among belts. Species turnover (Cody’s β-diversity) was maximum between the highest belts. Whittaker plots showed a marked difference among assemblages shaping from broken-stick model to geometric series, and explicited a spatial progressive stress with a disruption in evenness towards the deepest belts. Bird assemblages evidenced a nested subset structure with deeper belts containing successive subsets of the species occurring in the upper belts. We hypothesize that, at least during the daytime in breeding season, the observed non-random distribution of species along the vertical stratification is likely due to (i) the progressive simplification both of the floristic composition and vegetation structure, and (ii) the paucity of sunlight as resources from the upper edge to the inner side of the cenote.

scholarly journals Species richness and diversity in shrub savanna using ordinary kriging

2016 ◽  
Vol 51 (8) ◽  
pp. 958-966 ◽  
Author(s):  
Anderson Pedro Bernardina Batista ◽  
José Márcio de Mello ◽  
Marcel Régis Raimundo ◽  
Henrique Ferraço Scolforo ◽  
Aliny Aparecida dos Reis ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Species Richness ◽  
Spatial Dependence ◽  
Ordinary Kriging ◽  
Diversity Index ◽  
Spatial Models ◽  
Shannon Diversity Index ◽  
Shannon Diversity ◽  
Species Richness And Diversity ◽  
Number Of Species

Abstract: The objective of this work was to analyze the spatial distribution and the behavior of species richness and diversity in a shrub savanna fragment, in 2003 and 2014, using ordinary kriging, in the state of Minas Gerais, Brazil. In both evaluation years, the measurements were performed in a fragment with 236.85 hectares, in which individual trees were measured and identified across 40 plots (1,000 m2). Species richness was determined by the total number of species in each plot, and diversity by the Shannon diversity index. For the variogram study, spatial models were fitted and selected. Then, ordinary kriging was applied and the spatial distribution of the assessed variables was described. A strong spatial dependence was observed between species richness and diversity by the Shannon diversity index (<25% spatial dependence degree). Areas of low and high species diversity and richness were found in the shrub savanna fragment. Spatial distribution behavior shows relative stability regarding the number of species and the Shannon diversity index in the evaluated years.

scholarly journals Increased mosquito abundance and species richness in Connecticut, United States 2001–2019

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tanya A. Petruff ◽  
Joseph R. McMillan ◽  
John J. Shepard ◽  
Theodore G. Andreadis ◽  
Philip M. Armstrong
Keyword(s):  
United States ◽  
Species Richness ◽  
Community Composition ◽  
Pathogen Transmission ◽  
Public Health Importance ◽  
Data Set ◽  
Mosquito Abundance ◽  
Total Species Richness ◽  
Multiple Species ◽  
Total Species

Abstract Historical declines in multiple insect taxa have been documented across the globe in relation to landscape-level changes in land use and climate. However, declines have either not been universally observed in all regions or examined for all species. Because mosquitoes are insects of public health importance, we analyzed a longitudinal mosquito surveillance data set from Connecticut (CT), United States (U.S.) from 2001 to 2019 to identify changes in mosquito community composition over time. We first analyzed annual site-level collections and metrics of mosquito community composition with generalized linear/additive mixed effects models; we also examined annual species-level collections using the same tools. We then examined correlations between statewide collections and weather variables as well as site-level collections and land cover classifications. We found evidence that the average trap night collection of mosquitoes has increased by ~ 60% and statewide species richness has increased by ~ 10% since 2001. Total species richness was highest in the southern portion of CT, likely due to the northward range expansion of multiple species within the Aedes, Anopheles, Culex, and Psorophora genera. How the expansion of mosquito populations in the northeast U.S. will alter mosquito-borne pathogen transmission in the region will require further investigation.

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