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70 results for “Gut contents”
Mummichog (Fundulus heteroclitus) counts and gut content analysis from lift trap transect collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The lift traps were used to capture mummichogs accessing the high marsh platform. Mummichogs were collected to study the effect of marsh-edge geomorphology on mummichog distribution and foraging. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
Mummichog (Fundulus heteroclitus) gut content analysis from Breder trap transect collections in tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and eat invertebrate prey, coupling the high marsh and aquatic creek food webs by gathering energy produced on the high marsh and making it available to the aquatic food web. Changes in the geomorphology of saltmarsh creek edges greatly influence the survival, biomass, and resource use of mummichog populations. Here we use gut content analysis assess the diet of mummichog on the high marsh platform during a flooding spring-cycle tide in July 2018 across 3 PIE creeks known to present different geomorphologic patterns in their low marsh zones. These data allow us to quantify the amount of terrestrial invertebrate prey mummichog consume on a single flooding tide and determine the impact altered low marsh geomorphology has on the trophic relationships in PIE food webs. These mummichog were captured in Breder traps; information about the consumer communities captured in these traps was recorded separately (LTE-TIDE-BrederTrap-Demographics). These data were included in part of the study “Habitat decoupling via saltmarsh creek geomorphology alters connection between spatially-coupled food webs” (Lesser et al. 2020) and were a portion of an MBL REU project.
Dog gut gene catalog. Supplemental data for "Similarity of the dog and human gut microbiomes in gene content and response to diet"
<p>Gene catalogue for the dog gut microbiome including</p> <ol> <li>FASTA file of nucleotide sequences (including padding, see coords file for exact coordinates)</li> <li>FASTA file of amino-acid sequences</li> <li>coords file (gene coordinates)</li> <li>Taxonomic predictions</li> <li>Functional predictions</li> </ol> <p>See the paper "<em>Similarity of the dog and human gut microbiomes in gene content and response to diet</em>" by Coelho et al. in Microbiome for details. We ask that you cite that publication when using this dataset in published literature</p>
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.
Arthropod food webs in the foreland of a retreating glacier: Gut content analysis and structural equation modeling (SEM)
<p>Below- and above-ground arthropod communities were explored at a glacier foreland area in low Arctic Southwest Greenland aiming for a better understanding of the mechanisms behind the arthropod succession driven by increasing temperatures in the context of an Arctic climate change scenario. Arthropods were sampled in 2015 and 2016 along a downslope transect where the microclimate became warmer downhill a chronosequence towards a climax vegetation. The arthropod data sets were analyzed in relation to an environmental data set. Bottom-up controlled population developments were important in the early phase of the vegetation development while top-down prevailed in the later phase of the vegetation development. The shift from bottom-up to top-down cascades between arthropod predators and their potential prey populations was mainly driven by increasing temperatures away from the glacier. Structural equation modeling (SEM) shows bottom-up and top-down controlled food chains as bottom-up control was important for spider and harvestman populations while top-down control was important for ground beetle populations. These mechanisms are closely related to the hunting strategies of the predators as bottom-up mechanisms are connected to a sit-and-wait behavior while top-down mechanisms are related to active-search behavior. The SEM analyzes were supported by DNA metabarcoding as well as by the literature. A consequence of the strong top-down cascades in the later phase of the succession is high rates of intra-guild predation (IGP) among all arthropod predators. Particularly in the guts of the linyphiid spider, <em>Collinsia holmgreni </em>Thorell 1871, trophic linkages to other linyphiid and lycosid spiders were detected. The IGP ratio of <em>C. holmgreni</em> was negatively correlated with the activity density of available ground-living prey. Probably as a consequence of the high IGP among the linyphiid spiders, cold-adapted linyphiid species like <em>C. holmgreni</em> decreased in numbers downhill and became extinct in the warmer climax vegetation, where lycosid spiders dominated. SEM shows that the declining activity densities of the soil fauna, such as collembolans and mites, due to predation, are responsible for the increase in organic matter content in the topsoil.</p>
Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
<p>Understanding how mesopredators partition their diet and the identity of consumed prey can assist in understanding the ecological role predators and prey play in ecosystem trophodynamics. Here, we assessed the diet of three common coral reef mesopredators; <em>Pseudochromis flavivertex</em>, <em>Pseudochromis fridmani</em>, and <em>Pseudochromis olivaceus</em> from the family Pseudochromidae, commonly known as dottybacks, using a combination of i) visual stomach content analysis, ii) stomach content DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ<sup>15</sup>N, δ<sup>13</sup>C). In addition, <em>P. flavivertex</em> is found in two distinct color morphs in the Red Sea, providing an opportunity to analyze intra-morph differences. These techniques revealed partitioning in the dietary composition and resource use among species. Arthropods comprised the main dietary component of <em>P. flavivertex</em> (18S > 60%; COI > 10%), and <em>P. olivaceus</em> (18S = 57.2%) while <em>P. fridmani</em> ingested predominantly mollusks (18S = 51.3%, COI = 24.6%). Despite being small predators, microplastics were found in the gut content of some of these fishes. Stable isotope analysis showed differences in species' isotopic niche breadth and trophic position. <em>Pseudochromis olivaceus</em> presented the largest isotopic niche (SEA<sub>C</sub> = 1.61‰<sup>2</sup>), while <em>P. fridmani</em> showed the smallest isotopic niche (SEA<sub>C</sub> = 0.45‰<sup>2</sup>) among species. Although the two techniques used for stomach content analysis did not show differences in the diet within color morphs of <em>P. flavivertex</em>, they differed in the isotopic niche and resource use. Despite our limited sampling, our findings provide evidence of species-specific differences in the trophic ecology of dottybacks and demonstrate their important role as predators of cryptic invertebrates and small fishes. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.</p>
Coilaco, Guampoe and Trancura gut content dataset
<p>This dataset contains feeding interactions of the organisms in three rivers (Coilaco, Guampoe and Trancura Rivers) within the catchment of the Toltén River in south Chile, South America</p>
Broadstone Stream gut content data
<p>This dataset contains feeding interactions on the organisms in Broadstone Stream. It also contains body sizes of individuals, and abundances.</p>
Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment
<p>In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (<em>Chaetodon</em> <em>lunulatus</em>) resident at coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater versus gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S rRNA and ITS2 rRNA sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that can include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (coral reefs, kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.</p>
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
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Data from: To pool or not to pool: Pooled metabarcoding does not affect estimates of prey diversity in spider gut content analysis
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Estimating required sample sizes for gut content metabarcoding studies of dietary diversity in spiders
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Identification of potential western bean cutworm (<em>Striacosta albicosta</em>) predators in field corn through molecular gut-content analysis
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Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment
Open the record for dataset details and reuse information.
Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
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Arthropod food webs in the foreland of a retreating Greenland glacier: Integrating molecular gut content analysis with Structural Equation Modelling
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Data from: Reconstructing hyperdiverse food webs: gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs
1. Anthropogenic stressors have strong impacts on ecosystems. To understand their influence, detailed knowledge about trophic relationships among species is critical. However, this requires both exceptional resolution in dietary assessments and sampling breadth within communities, especially for highly-diverse, tropical ecosystems. 2. We used gut content metabarcoding across a broad range of coral reef fishes (8 families, 22 species) in Mo'orea, French Polynesia to test whether this technique has the potential to capture the structure of a hyperdiverse marine food web. Moreover, we explored whether taxonomic groups (families) and traditional, broad-scale trophic assignments explained fish diet across four different metrics of quantifying predator-prey interactions. 3. Metabarcoding yielded a large number (4,341) of unique operational taxonomic units (i.e. prey) with high-resolution taxonomic assignments (i.e. often to the level of genus or species). We demonstrate that across multiple metrics, taxonomic group at the family level is a consistently better, albeit still weak, predictor of empirical trophic relationships than frequently-used, broad-scale functional assignments. Our method also reveals a complex trophic network with fine-scale partitioning among species, further emphasizing the importance of examining fish diets beyond broad trophic categories. 4. We demonstrate the capacity of metabarcoding to reconstruct diverse and complex food webs with exceptional resolution, a significant advancement from traditional food web reconstruction. Further, this method allows us to pinpoint the trophic niche of species with niche-based modelling, even across hyperdiverse species assemblages such as coral reefs. In conjunction with complementary techniques such as stable isotope analysis, applying metabarcoding to whole communities will provide unparalleled information about energy and nutrient fluxes and inform their susceptibility to disturbances even in the world's most diverse ecosystems.
Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
Data from: Trace fossils of possible parasites inside the gut contents of a hadrosaurid dinosaur, Upper Cretaceous Judith River Formation, Montana
Tiny sinuous trace fossils have been found within probable gut contents of an exceptionally preserved specimen of a hadrosaurid dinosaur, Brachylophosaurus canadensis, from the Judith River Formation of Montana. Approximately 280 examples of the trace fossils were observed in 19 samples of gut region material. The tubular structures typically are about 0.3 mm across. Many have thin calcareous linings or layers, and some exhibit fine surficial striae. At least two dozen of these trace fossils share walls with adjacent tubular traces, and this association can extend for several millimeters. While the trace fossils share some characteristics with fine rhizoliths, these features are most consistent with tiny burrows, or possibly body impressions, of worms (vermiform organisms) of uncertain biologic affinity. Such trace fossils have not been reported previously, and herein described as Parvitubulites striatus n. gen. n. sp. Either autochthonous (parasites) or allochthonous (scavengers) worms may have created the trace fossils, but taphonomic factors suggest that autochthonous burrowers are more likely. Several lines of evidence, such as constant diameters and matching directional changes, suggest that the paired trace fossils were made by two individuals moving at the same time, which implies sustained intraspecific contact. Parvitubulites striatus provides a rare record of interactions between terrestrial, meiofaunal-sized, soft-bodied invertebrates and a dinosaur carcass. The evidence that the worms may have parasitized a living hadrosaur and subsequently left traces of intraspecific behavior between individual worms adds unique information to our understanding of Mesozoic trophic interactions.
Data from: Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents
Species of grasshopper have been divided into three diet classifications based on mandible morphology: forbivorous (specialist on forbs), graminivorous (specialist on grasses), and mixed feeding (broad-scale generalists). For example, Melanoplus bivittatus and Dissosteira carolina are presumed to be broad-scale generalists, Chortophaga viridifasciata is a specialist on grasses, and Melanoplus femurrubrum is a specialist on forbs. These classifications, however, have not been verified in the wild. Multiple specimens of these four species were collected, and diet analysis was performed using DNA metabarcoding of the gut contents. The rbcLa gene region was amplified and sequenced using Illumina MiSeq sequencing. Levins' measure and the Shannon–Wiener measure of niche breadth were calculated using family-level identifications and Morisita's measure of niche overlap was calculated using operational taxonomic units (OTUs). Gut contents confirm both D. carolina and M. bivittatus as generalists and C. viridifasciata as a specialist on grasses. For M. femurrubrum, a high niche breadth was observed and species of grasses were identified in the gut as well as forbs. Niche overlap values did not follow predicted patterns, however, the low values suggest low competition between these species.
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Allen Brain Atlas
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