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390 results for “Commensals”
Data and R Code for 'Domestication via the commensal pathway in a fish-invertebrate mutualism'
<p>This document contains all data and R code required to replicate the analyses in 'Domestication via the commensal pathway in a fish-invertebrate mechanism' as published in Nature Communications. The R Markdown provided includes descriptions of all variables and the code used for the analysis of the following eight datasets:</p> <p>1. Transects<br> 2. Census of farms<br> 3. Paired choice experiments<br> 4. Predation experiment 1<br> 5. Predation experiment 2<br> 6. Timed observations<br> 7. Farm algae composition<br> 8. Longfin damselfish body condition</p> <p>In addition, the R Markdown also includes descriptions of all variables for two additional datasets:</p> <p>9. Estimates of mysid swarm density<br> 10. Mysid waste excretion and nutrient availability</p> <p>A PDF version of the R Markdown with all output is also provided. Please see the methods section of the associated manuscript for further information on data collection and analysis procedures.</p> <p>Author contributions to data collection and analysis: RMB, JMC, ZLC, TLS & WEF collected the data; WEF, RMB, JMC, ZLC & AM implemented the analyses. </p> <p>Correspond with: rohan.m.brooker@gmail.com</p>
Adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor
<p>Sequencing data for pooled isolate samples of <em>Pseudomonas aeruginosa</em> obtained in experimental evolution project "Adaptation of <em>Pseudomonas aeruginosa</em> to repeated invasion into a commensal competitor". To generate sequencing data, the gDNA from 10 isolates for each culture condition was pooled in equimolar ratios and libraries were sequenced using the Illumina NovaSeq6000 platform using a 250 bp paired-end protocol, submitted for x510 depth sequencing. Dataset provides raw sequencing data (untrimmed) for pooled starting culture isolates, monoculture evolved lines, and coculture evolved lines.</p>
Interspecific coprophagia by wild red foxes: DNA metabarcoding reveals a potentially widespread form of commensalism among animals
<p>Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large-scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox' main prey, short-tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems as well as the implications for ecological communities. Tools such as metabarcoding offer a way forward.</p>
Strains used in the paper "Bacteriophage cultivation for commensal human gut bacteria"
<p>Sequences of 16S rRNA genes of 411 strains for taxonomic detection;</p> <p>Genomic sequence of of 42 strains for taxonomic detection;</p> <p>Genomic sequence of Bacteroides fragilis and Parabacteroides merdae strains used for genomic analysis in phage-host range analysis experiments. </p>
Fig. 5 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 5 Phylogenetic reconstruction of the 18S rRNA gene tree of the novel Sarcocystis species and other tissue cyst-forming coccidia based on 1465 homologous positions of 40 aligned nucleotide sequences under the minimum evolution (ME) criterion; selected eimeriid coccidia served as outgroup. The new sequences of Sarcocystis sp. from China are highlighted by black symbols. Branch support values are shown for 1000 bootstrap replicates of three independent alignments with a site coverage of 95%. The shaded box highlights the taxa included in the so-called S. zuoi complex
Fig. 6 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 6 ML analysis of the ITS1 region of Sarcocystis sp., S. zuoi and other species of the Sarcocystidae; members of the Toxoplasmatinae served as outgroup. Bootstrap branch support values are shown in triplicate, indicating results from three independent alignments and analyses.The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 204 homologous positions of 33 nucleotide sequences
Fig. 1 a–f in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 1 a–f Light microscopic and ultrastructural morphology of sarcocysts of Sarcocystis sp. in SD rats 5 months after inoculation with sporocysts isolated from rat snakes in Thailand. a Typical sporocyst from a fecal sample of Coelognathus radiatus; sporocysts from C. flavolineatus were identical in size and appearance; asterisk indicates single sporozoite. b Live sarcocyst, freed from muscle tissue; note the broad, palisade-like villar protrusions that could at times resemble those of Sarcocystis singaporensis with which this species can co-occur; however, the protrusions lack the basal stalks typical for the former species; the arrow highlights the septated compartments in the interior of the sarcocyst, and the inset shows a micrograph of live cystozoites freshly released from a cyst (arrowheads). c Typical structure of a cyst wall protrusion (isolate from C. flavolineatus); the arrows point to the electron-dense, knob-like structures of the primary cyst wall, whereby the knobs could apparently fuse to form an electron-dense borderline in larger protrusions (inset: arrowhead); also note the electron-light, thin layer of ground substance (GS) underneath the protrusions. d Typical cystozoites of the new species, which contained only two rhoptries (arrowheads) among relatively few micronemes (asterisks); additionally, the cystozoites exhibited vesicle-like structures in the anterior third of the cell containing electron-light, reticulate matter (arrow); the inset shows such a vesicle-like compartment at higher magnification, which was apparently not bound by a membrane (white arrow) and often located near micronemes (white asterisk); dense granules were present but rarely observed. e Interior and cyst wall of a mature sarcocyst (isolate from C. radiatus); metrocytes (asterisks) exclusively divided by endodyogeny, producing only two cystozoites (CZ). f Full-length section through a 15-µm-long protrusion of the sarcocyst wall; note that larger protrusions often occurred close to the tips of a cyst and showed a base with folds. AP, apicoplast; MI, mitochondrion; NU, nucleus; PT, villar protrusions
Fig. 4 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 4 Two separate phylogenies of the 28S rRNA gene (longer and shorter sequence fragments) of the new Sarcocystis sp. sampled in China, newly sequenced S. zuoi from China and novel Sarcocystis isolates from Borneo. Symbols indicate the new sequences of this study, whereby taxa considered conspecific are grouped by shape. GenBank accession numbers are given behind each taxon name. a Maximum likelihood (ML) analysis of an alignment of 29 sequences and 1383 homologous positions. Branch support by bootstrapping (1000 replicate trees) is shown next to the branches, whereby the results of three independent analyses based on independent alignments are shown. The scale bar indicates the number of substitutions per site. All positions with <85% site coverage were eliminated, i.e. fewer than 15% alignment gaps, missing data and ambiguous bases were allowed at any position (partial deletion option). Selected eimeriid coccidia served as outgroup. b ML analysis of a trimmed alignment including five shorter sequences of Sarcocystis sampled in Borneo compared with the samples of Sarcocystis sp. from China; a total of 16 sequences and 366 homologous positions with site coverage of 95% were compared. Sarcocystis pantherophisi served as outgroup. The corresponding natural intermediate hosts are also indicated
Fig. 2 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 2 Light microscopic and ultrastructural morphology of sarcocysts from Maxomys whiteheadi in Borneo (a–c) and wild Rattus norvegicus in China (d, e). Note, due to ethanol fixation some ultrastructural details of the samples from Borneo are poorly resolved. a Richardsen's dye-stained 1.0-µm thin section through a mature sarcocyst showing the villar protrusions (PT) of the cyst wall and numerous relatively small cystozoites (CZ). b Same sample as before under the electron microscope; note the thin layer of ground substance underneath the protrusions. c Enlarged part of the interior of the sarcocyst showing cystozoites—although with limited resolution—that possess a pair of rhoptries each, which is characteristic for this Sarcocystis species (black and white arrows; compare with Fig. 1d). d Live sarcocyst isolated from striated muscle tissue of a wild Norway rat in China; the inset shows live cystozoites that were freshly released from a cyst. e Ultrastructure of the same sarcocyst as before; note that the villar protrusions are highly similar to the samples from Borneo and Thailand regarding size and shape (Fig. 1e); again, cystozoites only exhibit one pair of rhoptries (arrows) and relatively few micronemes
Fig. 3 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.
Fig. 3 Graph showing the size of sporocysts (length plotted against diameter, in μm; error bars indicate s.e.) of the Sarcocystis isolates from the colubrid snakes Coelognathus flavolineatus and C. radiatus in Thailand and closely related Sarcocystis. Every isolate/ species is indicated by a different symbol (legend), whereby sporocyst samples with the same shape index (= length/diameter) share the same background shading: white = 1.3; dark = 1.5; Sarcocystis pantherophisi = 1.2. Here, S. pantherophisi is included as reference for the snake host Sarcocystis lineage S2, while all other species belong to lineage S1 (except for S. murinotechis, for which no genetic information is available)
Figure 2 in Distribution of commensal rodents in some shops of three districts in Malakand region, Pakistan
Figure 2.Variation in population dynamics of rodents (Rattus rattus and Mus musculus) in different seasons of the year.
Commensal microbiome dysbiosis in keloid disease
<p>Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that related to commensal microbiota and skin fibrosis remain mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterize microbial composition and divergence between the pathological and normal skin tissue. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.</p>
Fig. 1 in A White Stork (Ciconia ciconia (Linnaeus, 1758)) nest - an unique case of multiple nesting commensalism of five species from Dragoman (W Bulgaria)
Fig. 1. Eurasian Tree Sparrows nesting in a nest of White Stork, Dragoman, 19.05.2019. Photo: Z. Boev.
Fig. 4 in A White Stork (Ciconia ciconia (Linnaeus, 1758)) nest - an unique case of multiple nesting commensalism of five species from Dragoman (W Bulgaria)
Fig. 4. Eurasian Collared Dove nesting in a nest of White Stork, Dragoman, 19.05.2019. Photo: Z. Boev.
Fig. 3 in New record of commensal scale worms, Arctonoe vittata (Grube, 1855) and Hyperhalosydna striata (Kinberg, 1856) (Polychaeta: Polynoidae) from Korean waters
Fig. 3. Various host invertebrates of Arctonoe vittata (Grube, 1855) found in this study. A, Solaster dawsoni Verrill, 1880; B and C, Aphelasterias japonica (Bell, 1851); D, Haliotis discus hannai Ino, 1953; E, Scelidotoma gigas (Martens, 1881); F, Triopha catalinae (Cooper, 1863); G and H, Cadlina japonica Baba, 1937; I, Niveotectura pallida (Gould, 1859); J, Apostichopus japonicus (Selenka, 1867).
Fig. 2 in New record of commensal scale worms, Arctonoe vittata (Grube, 1855) and Hyperhalosydna striata (Kinberg, 1856) (Polychaeta: Polynoidae) from Korean waters
Fig. 2. Hyperhalosydna striata (Kinberg, 1856), NIBRIV0000326200. A, Anterior end with elytra, dorsal view; B, Proboscis, frontal view; C, Right elytron from segment 11; D, Posterior end, dorsal view; E, Anterior end without elytra, dorsal view (arrow indicate dorsal cirrophore); F, Notopodium with notochaeta (arrow) from segment 14; G, Cirrigerous parapodium from segment 14, anterior view; H, Posterior end, ventral view; I, Posterior segments with nephridial papillae, ventral view; J, Neurochaeta from segment 14. Scale bar: A-E, H = 1 mm; F, J = 0.05 mm; G = 0.3 mm; I = 0.2 mm.
Fig. 5 in New record of commensal scale worms, Arctonoe vittata (Grube, 1855) and Hyperhalosydna striata (Kinberg, 1856) (Polychaeta: Polynoidae) from Korean waters
Fig. 5. Distribution of Arctonoe vittata (Grube, 1855) and Hyperhalosydna striata (Kinberg, 1856) in eastern Asia based on the present study (P) and literatures (1-19). 1: Uschakov (1982), 2: Uchida (1992), 3: Imajima (2001), 4: Uchida (1988), 5: Moore (1903), 6: Okuda (1936), 7: Imajima (2001), 8: Imajima and Hartman (1964); Imajima (2001), 9: Imajima (2001), 10: Okuda (1936), 11 and 12: Imajima (2001), 13: Okuda (1936), 14: Imajima (1988), 15-19: Uschakov (1955).
The skin commensal yeast Malassezia triggers a Th17-response that coordinates anti-fungal immunity and exacerbates skin inflammation
<p>Data accompanying the publication: Sparber et al. The skin commensal yeast <em>Malassezia</em> triggers a Th17-response that coordinates anti-fungal immunity and exacerbates skin inflammation. 2019. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2019.02.002</p>
Fig. 1 in Commensalism in the fossil record: Eunicid polychaete bioerosion on Pliocene solitary corals
Fig. 1. Palaeogeographical map of the Western Mediterranean during the Piacenzian (Early Pliocene) showing the location of the basins that have provided the study material: 1, Liguria (NW Italy); 2, Alpes−Maritimes (SE France); 3, Roussillon (SE France); 4, Alt Empordà (Catalonia, NE Spain); 5, Baix Llobregat (Catalonia, NE Spain); 6, Baix Ebre (Catalonia, NE Spain); 7, Níjar−Almería (Andalusia, SE Spain); 8, Vélez−Málaga (Andalusia, SE Spain); 9, Estepona (Andalusia, SE Spain).
Fig. 5 in Commensalism in the fossil record: Eunicid polychaete bioerosion on Pliocene solitary corals
Fig. 5. Recent polychaete Lumbrineris flabellicola (Fage, 1936) infesting alive caryophyllids. Pictures by Alan and Eve Southward, from the Marine Biological Association, UK; reproduced with permission.
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OpenNeuro
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