DNA metabarcoding Uncover the Diet of Subterranean Rodents in China

Zhang, Xuxin; Zou, Yao; Nan, Xuemei; Han, Chongxuan

doi:10.1101/2021.09.20.461124

Cited by 3 publications

(3 citation statements)

References 53 publications

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“…The RDP classifier bayesian algorithm version 2.11 ( ) was used on the QIIME (QIIME version 1.9.1) platform for classification analysis of representative sequences of OTUs from the sliva138/16S bacterial classification database with a default confidence threshold of 0.7. Core species analysis was used to indicate that the sample size was sufficient ( 27 ). The fecal alpha diversity among the two groups was evaluated via Sobs, Shannon and Simpson indices.…”

Section: Methodsmentioning

confidence: 99%

The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years

Fan

Zang²,

Dai³

et al. 2022

Front. Immunol.

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BackgroundIt is critical to investigate the underlying pathophysiological mechanisms in the development of atopic dermatitis. The microbiota hypothesis suggested that the development of allergic diseases may be attributed to the gut microbiota of mother-offspring pairs. The purpose of this study was to investigate the relationship among maternal-offspring gut microbiota and the subsequent development of atopic dermatitis in infants and toddlers at 2 years old.MethodsA total of 36 maternal-offspring pairs were enrolled and followed up to 2 years postpartum in central China. Demographic information and stool samples were collected perinatally from pregnant mothers and again postpartum from their respective offspring at the following time intervals: time of birth, 6 months, 1 year and 2 years. Stool samples were sequenced with the 16S Illumina MiSeq platform. Logistic regression analysis was used to explore the differences in gut microbiota between the atopic dermatitis group and control group.ResultsOur results showed that mothers of infants and toddlers with atopic dermatitis had higher abundance of Candidatus_Stoquefichus and Pseudomonas in pregnancy and that infants and toddlers with atopic dermatitis had higher abundance of Eubacterium_xylanophilum_group at birth, Ruminococcus_gauvreauii_group at 1 year and UCG-002 at 2 years, and lower abundance of Gemella and Veillonella at 2 years. Additionally, the results demonstrated a lower abundance of Prevotella in mothers of infants and toddlers with atopic dermatitis compared to mothers of the control group, although no statistical difference was found in the subsequent analysis.ConclusionThe results of this study support that gut microbiota status among mother-offspring pairs appears to be associated with the pathophysiological development of pediatric atopic dermatitis.

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Section: Methodsmentioning

confidence: 99%

The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years

Fan

Zang²,

Dai³

et al. 2022

Front. Immunol.

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“…Generally, the lower parts of the forbs are enlarged and their nutrient content is more abundant. The distribution of the biomass of forbs determines the population density of plateau zokors in different regions to a certain extent (Zhang et al, 2010(Zhang et al, , 2022. Plateau zokors at different degradation levels and RG feed on the same species of plants but with different proportions.…”

Section: Changes In the Diet Of Plateau Zokors After Grassland Degrad...mentioning

confidence: 99%

Increased availability of preferred food and decreased foraging costs from degraded grasslands lead to rodent pests in the Qinghai-Tibet Plateau

et al. 2022

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The increased population density of rodent species during ongoing grassland degradation further deteriorates its conditions. Understanding the effects of grassland degradation on rodent feeding habits is of great value for optimizing grassland management strategies. In this study, lightly degraded (LD), moderately degraded (MD), severely degraded (SD), and reseeded grassland (RG) were selected and their plant resources and soil physical properties were investigated. In addition, the study used ITS2 barcode combined with the Illumina MiSeq sequencing method to analyze the food composition and proportion of plateau zokors in different grassland conditions. The results showed that, with grassland degradation, plant biomass decreased, but the relative proportion of forbs increased (LD: 32.05 ± 3.89%; MD: 28.97 ± 2.78%; SD: 49.16 ± 4.67% and RG: 10.93 ± 1.53%). Forbs were the main food of the plateau zokor, accounting for more than 90% of their diet, and the animal had a clear preference for Potentilla species; the soil compaction of feeding habits showed a decreasing trend in the 10–25 cm soil layer, suggesting a decreased foraging cost. Nutritional analysis showed that the stomach content of crude protein in zokors feeding on MD grassland was significantly higher than that of animals feeding on the other grassland types. Structural equation modeling showed that soil physical properties and the relative biomass of forbs had significant (P < 0.05) and extremely significant (P < 0.001) impacts on the population density of plateau zokors, with direct impact contribution rates of 0.20 and 0.63. As the severity of grassland degradation increased, although the aboveground and underground biomass of the plants decreased, the proportion of food preferred by the plateau zokor increased, and the corresponding changes in the feeding environment resulted in decreased foraging energy expenditure, thereby increasing the suitability of the degraded grassland for the plateau zokor. Compared with degraded grassland, the food diversity and evenness of zokors increased, the food niche width enlarged, and the proportion of weeds decreased in RG, which increased the difficulty of obtaining food. Reseeding in grassland management is therefore an effective way to control plateau zokors.

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“…During the last decade, DNA metabarcoding for dietary analysis has become a popular approach (Taberlet et al., 2018 ), mainly due to its cost efficiency and superior taxonomic resolution compared to morphological methods (da Silva et al., 2019 ; Soininen et al., 2009 ; Valentini et al., 2009 ). Thus, it has become a common method for resolving the diverse diets of small rodents (Aylward et al., 2022 ; Lopes et al., 2020 ; Sato et al., 2019 ; Zhang & Han, 2021 ). DNA metabarcoding also has the potential to provide information about the relative biomass proportions of ingested food via different approaches (Deagle et al., 2019 )—though neither is optimal in every study system (if in any).…”

Section: Introductionmentioning

confidence: 99%

Is the diet cyclic phase‐dependent in boreal vole populations?

Neby,

Ims,

Kamenova

et al. 2024

Ecology and Evolution

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Herbivorous rodents in boreal, alpine and arctic ecosystems are renowned for their multi‐annual population cycles. Researchers have hypothesised that these cycles may result from herbivore–plant interactions in various ways. For instance, if the biomass of preferred food plants is reduced after a peak phase of a cycle, rodent diets can be expected to become dominated by less preferred food plants, leading the population to a crash. It could also be expected that the taxonomic diversity of rodent diets increases from the peak to the crash phase of a cycle. The present study is the first to use DNA metabarcoding to quantify the diets of two functionally important boreal rodent species (bank vole and tundra vole) to assess whether their diet changed systematically in the expected cyclic phase‐dependent manner. We found the taxonomic diet spectrum broad in both vole species but with little interspecific overlap. There was no evidence of systematic shifts in diet diversity metrics between the phases of the population cycle in either species. While both species' diet composition changed moderately between cycle phases and seasons, these changes were small compared to other sources of diet variation—especially differences between individuals. Thus, the variation in diet that could be attributed to cyclic phases is marginal relative to the overall diet flexibility. Based on general consumer‐resource theory, we suggest that the broad diets with little interspecific overlap render it unlikely that herbivore–plant interactions generate their synchronous population cycles. We propose that determining dietary niche width should be the first step in scientific inquiries about the role of herbivore–plant interactions in cyclic vole populations.

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DNA metabarcoding Uncover the Diet of Subterranean Rodents in China

Cited by 3 publications

References 53 publications

The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years

The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years

Increased availability of preferred food and decreased foraging costs from degraded grasslands lead to rodent pests in the Qinghai-Tibet Plateau

Is the diet cyclic phase‐dependent in boreal vole populations?

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