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 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 A checklist of gilled mushrooms (Basidiomycota: Agaricomycetes) with diversity analysis in Hollongapar Gibbon Wildlife Sanctuary, Assam, India

2015 ◽  
Vol 7 (15) ◽  
pp. 8272 ◽  
Author(s):  
Girish Gogoi ◽  
Vipin Parkash
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Abundant Species ◽  
Shannon Diversity Index ◽  
Diversity Analysis ◽  
Wildlife Sanctuary ◽  
Shannon Diversity ◽  
Number Of Species ◽  
Simpson Diversity Index ◽  
Richness Index

<p>Hollongapar Gibbon Wildlife Sanctuary is comprised of five distinct compartments.  A total of 138 species of gilled mushrooms belonging to 48 genera, 23 families, five orders of the class Agaricomycetes, division Basidiomycota, have been collected and analyzed. The order Agaricales was was found with the highest number of species (113), followed by Russulales (14), Polyporales (5), Cantharellales (4) and Boletales (2). The species <em>Coprinellus disseminatus </em>and <em>Megacollybia rodmani</em> have shown the highest (8.26) and the lowest density (0.05), respectively.  A total of 24 species, e.g., <em>Termitomyces albuminosus, Marasmius curreyi, Marasmiellus candidus, Leucocoprinus medioflavus, Mycena leaiana, Hygrocybe miniata, Collybia chrysoropha, Gymnopus confluens</em> were common with frequency percentage of 11.9, whereas <em>Megacollybia rodmani</em> with less frequency percentage (2.4) was found only in few quadrates of the sanctuary.  The highly abundant species were <em>Termitomyces medius</em> (91.7) and <em>Coprinellus disseminatus </em>(86.8), and less abundant species were <em>Psilocybe wayanadensis</em> (1.0) and <em>Lepiota</em> sp. (1.0) in the study site.  The order of the species richness index (<em>R</em>) compartment wise was 2&gt;3&gt;4&gt;5&gt;1. Both the Shannon diversity index and Simpson diversity index of agarics was maximum (1.88, 0.98) in compartment 2, whereas minimum (1.72, 0.95) in compartment 1 and 5, respectively.  Moreover, the compartment 2 was found very much similar with compartment 3 and very less similar with compartment 1.</p><div> </div>

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.

Spatial patterns of meiofauna and diversity of nematode species assemblages in the Uvea lagoon (Loyalty Islands, South Pacific)

2008 ◽  
Vol 88 (5) ◽  
pp. 931-940 ◽  
Author(s):  
Y. Guo ◽  
M.-N. Helleouet ◽  
G. Boucher
Keyword(s):  
Species Richness ◽  
Spatial Patterns ◽  
Environmental Parameters ◽  
Nematode Species ◽  
Abundant Species ◽  
Diversity Indices ◽  
Species Assemblages ◽  
Leeward Side ◽  
Local Composition ◽  
Total Species Richness

Meiofauna assemblages were investigated at 15 stations on triplicated samples in the Uvea Atoll (Loyalty Islands) in relation to 9 selected environmental parameters. Spatial patterns and variability of meiofauna density were quantified according to location, macrofauna and nematode species assemblages. Meiofauna was dominated by ciliates and nematodes. Densities of total meiofauna and of most of the meiofauna taxa were significantly higher in the back reef North Pléiades stations than the leeward side of the Island. The highest correlation between biotic patterns and environmental parameters that best explains the pattern was with sediment thickness and to a lesser extent organic matter, C/N ratio and depth. One hundred and thirty-four nematode species were identified with four dominant species Chromadora macrolaimoides, an undescribed species of Bolbonema, Daptonema svalbardense and Prochromadorella septempapillata. Three significantly different nematode species assemblages were detected in two of the previously described macrofauna assemblages by cluster analysis and multidimensional scaling methods suggesting that nematodes are more sensible ecological indicators than macrofauna. Diversity indices based on dominance were not significantly different among the three nematode species assemblages but indices based on species richness and rarefaction were significantly higher leeward of Uvea Island. Estimates of total species richness showed no sign of stabilizing with sample size. However, rare species stabilized very quickly, whereas abundant species were added with increasing sampling coverage, indicating a high spatial variability of the local composition of nematodes.

Diversity of Mosquitoes (Diptera: Culicidae) in the Bom Retiro Private Natural Heritage Reserve, Rio de Janeiro State, Brazil

2022 ◽  
Author(s):  
Amanda Queiroz Bastos ◽  
Cecilia Ferreira de Mello ◽  
Júlia dos Santos Silva ◽  
Hélcio Reinaldo Gil-Santana ◽  
Shayenne Olsson Freitas Silva ◽  
...  
Keyword(s):  
Species Richness ◽  
Rio De Janeiro ◽  
Diversity Index ◽  
Abundant Species ◽  
Immature Stages ◽  
Larval Habitats ◽  
Natural Heritage ◽  
Wiener Diversity Index ◽  
Water Tanks ◽  
Janeiro State

Abstract This study registers the diversity of Culicidae in the Bom Retiro Private Natural Heritage Reserve (RPPNBR), Rio de Janeiro state, Brazil, based on the collection of the immature stages in natural and artificial larval habitats. Larvae and pupae were collected monthly at two sites of the RPPNBR from May 2014 to July 2015 using dippers and aquatic pipettes. The diversity of the mosquito community was described using the Shannon–Wiener Diversity Index (H′), as well as diversity, richness, and dominance of species found in different larval habitats (lake, bamboos, bromeliads, and artificial vessels). The Mann–Whitney test was used to calculate differences between the two natural and artificial habitats. Overall, 15,659 specimens belonging to 25 species, ten genera, and two subfamilies were collected. The most abundant species collected at sites that were reforested recently were Culex pleuristriatus Theobald, 1903, Limatus durhamii (Theobald, 1901), Aedes albopictus (Skuse, 1895), Culex neglectus (Lutz, 1904), and Culex retrosus (Lane & Whitman, 1951). In a forest preserved site, the most abundant species were Cx. neglectus, Culex iridescens (Lutz, 1905), Sabethes identicus (Dyar & Knab, 1907), Wyeomyia arthrostigma (Lutz, 1905), and Li. durhamii. With respect to larval habitats, 0.1% of the specimens were collected along the edge of a lake, 5.5% in bamboos, 35.9% in bromeliads, and 58.4% in artificial containers. Only 5.5% of the specimens were collected in the forest preserved site, with the remaining samples from the site with altered vegetation. A greater species richness and diversity were found in forest-altered sites compared to the forest preserved site. Several species were collected in the water accumulated in the nylon lids of plastic water tanks. Such vessels can promote an increase in mosquito population density in the environment surrounding the study area.

scholarly journals Biodiversity and Spatiotemporal Variation of Longhorn Beetles (Coleoptera: Cerambycidae) in Tropical Forest of Thailand

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 45
Author(s):  
Sirapat Yotkham ◽  
Piyawan Suttiprapan ◽  
Natdanai Likhitrakarn ◽  
Chayanit Sulin ◽  
Wichai Srisuka
Keyword(s):  
Species Richness ◽  
National Parks ◽  
Forest Type ◽  
Diversity Index ◽  
Negative Relationship ◽  
Abundant Species ◽  
Cold Season ◽  
Longhorn Beetles ◽  
Richness Pattern ◽  
Malaise Traps

Longhorn beetles are highly diversified and important for agriculture and health of the environment. However, the fauna and ecology of these beetles are not well known in Thailand. This study is the first to report the biodiversity, elevation, and seasonal distribution of longhorn beetles. Specimens were collected by malaise traps from 41 localities in 24 national parks throughout the country during 2006–2009. The traps were operated at each site for 12 consecutive months with a monthly service. A total of 199 morphotaxa in 36 tribes of 6 subfamilies were identified from 1376 specimens. Of these, 40.7% and 14.5% of total taxa were singletons and doubletons, respectively. The Shannon diversity index and observed species richness at Panernthung, Loei Forest Unit and Mae Fang Hotspring were high at 0.96 (30), 0.88 (50), and 0.86 (34), respectively. Local richness ranged between 3 and 50 species, while the species richness estimator showed between 6 and 1275 species. The most relatively abundant species, Nupserha lenita, Pterolophia sp.1, Oberea sp.3, Acalolepta pseudospeciosa, and Ac. rustricatrix represented 4.80%, 4.80%, 4.80%, 4.5%, and 4.43% of the species, respectively. The species with the widest distribution range of percentage of species occurrence (% SO) was Pt. sp.1 (63.4%), followed by Ac. rustricatrix (39%) and Moechotypa suffusa (39%). In a significantly negative relationship between species richness and elevation (p > 0.05, R2 = 0.04), the species richness pattern showed a hump-shaped curve that peaked at the middle elevation (501–1000 m asl). Regarding seasonal variation, most of the species occurred during the hot season (March–April) and peaked in early rainy season (May), while a low number of species were found during the mid-rainy (June–October) and cold season (November–February). Ordination analysis indicated that the distribution of most species was associated with regions and forest type, and most of the species correlated with forest located at middle and low elevation. The results of this study indicated the very high biodiversity of longhorn beetles in Thailand, which suggests that an understanding of their seasonal and elevational distribution will be of value to agriculture management and conservation. They also indicated that malaise traps are appropriate for the evaluation of biodiversity.

scholarly journals Short Communication: The species diversity and composition of roadside trees in five cities in Sumatra, Indonesia

2018 ◽  
Vol 19 (5) ◽  
pp. 1615-1621 ◽  
Author(s):  
WIRYONO . ◽  
YANSEN . ◽  
ADITYA . ◽  
DAVID JUARA LAMHOT ◽  
JURIAH HUTAHAEAN
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Introduced Species ◽  
Native Species ◽  
Short Communication ◽  
Diversity Index ◽  
Wiener Index ◽  
Abundant Species ◽  
Number Of Individuals ◽  
Aesthetic Values

Wiryono, Yansen, Aditya, Lamhot DJ, Hutahaean J. 2018. Short Communication: The species diversity and composition ofroadside trees in five cities in Sumatra, Indonesia. Biodiversitas 19: 1615-1621. Roadside trees make living in a city more enjoyable dueto their aesthetic values and ecosystem services. The ecological benefits of roadside trees may be enhanced by increasing the speciesdiversity and the proportion of native species. The objective of this study was to know the species diversity and composition of roadsidetrees in the cities of Palembang, Bengkulu, Curup, Pematang Siantar and Argamakmur, in Sumatra Island, Indonesia, varying in size andaltitude. Data of trees were collected from selected streets and analyzed to determine the species richness (S), Shannon-Wiener index ofdiversity (Hʹ) and Ellenberg index of community similarity (ISE). The results showed that the species richness in a city ranged from 7 to26, with the diversity index between 1.05 and 2.08. The large and medium cities had higher S and Hʹ. More introduced species werefound, both in number of species and number of individuals, than the native ones. The similarity among cities in species compositionranged from 47 to 82%. Overall, Swietenia macrophylla, an introduced species, was the most abundant species. The S and Hʹ values ofall cities were considered low and the composition of tree species did not support the conservation of native species. It is, therefore,essential to increase the species diversity of street trees, especially by planting native species.

scholarly journals Diversity of social wasps (Hymenoptera, Vespidae) in Cerrado biome of the southern of the state of Minas Gerais, Brazil

2012 ◽  
Vol 102 (3) ◽  
pp. 292-297 ◽  
Author(s):  
Matheus H. Simões ◽  
Mariana D. Cuozzo ◽  
Fernando A. Frieiro-Costa
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
Riparian Forest ◽  
Abundant Species ◽  
Social Wasps ◽  
Minas Gerais ◽  
The State ◽  
Wet Season ◽  
Cerrado Biome ◽  
Made In

An inventory of social wasps in Cerrado biome of the southern of the state of Minas Gerais was performed. A comparison between field and Riparian Forest areas was made in relation to species richness; correlations between diversity, sample methods and environmental factors were conducted. A total of 32 species was registered and Polybia fastidiosuscula de Saussure, 1854 was the most abundant species. The higher richness was in the Cerrado Field, as well as the highest diversity index. The temperature and rainfall had significant correlation with species richness and a significant variation in richness between dry and wet seasons was observed. Polybia fastidiosuscula was more abundant in the Riparian Forest during the dry season and in the Cerrado Field during wet season. The study area showed a great diversity of social wasps, with record both widely distributed species such as rare species, which indicates the quality and potential area for future studies.

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