Dispersal, niche breadth and population extinction: colonization ratios predict range size in N orth A merican dragonflies

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107541/1/jane12181.pd

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations

Dietary soy protein reverses obesity-induced liver steatosis and alters fecal microbial composition independent of isoflavone level

IntroductionMetabolic dysfunction-associated steatotic liver disease (MASLD) is a major public health concern that is exacerbated by the obesity pandemic. Dietary interventions have the potential to alleviate obesity-associated MASLD through variable mechanisms, including optimizing the gut microbiota. Previously, we reported that soy protein concentrate (SPC) with low or high levels of isoflavone (LIF or HIF) protected young obese Zucker rats from developing liver steatosis. The current study was designed to test whether SPC-LIF and SPC-HIF diets would reverse liver steatosis and alter fecal microbial composition in adult obese Zucker rats with existing steatosis.MethodsSix-week-old male obese Zucker rats (n = 26) were fed a casein control diet (CAS) for 8 weeks and 7 rats were randomly selected and sacrificed to confirm liver steatosis. The remaining rats were randomly assigned to receive CAS, SPC-LIF, or SPC-HIF diet (n = 6–7/group) for an additional 10 weeks.ResultsCompared to CAS diet, feeding SPC-LIF and SPC-HIF diets resulted in significantly lower liver weight, liver steatosis score, and liver microvesicular score (p < 0.05), but did not lead to difference in body weight, liver macrovesicular score, serum ALT, or serum AST. Isoflavone levels (e.g., LIF vs. HIF) did not affect any of these measurements except in the SPC-HIF group, which had an additional decrease in liver weight (p < 0.05) compared to the SPC-LIF group. The SPC-HIF group also had significantly higher levels of the aglycone forms of daidzein, genistein, and equol as well as the total levels of daidzein, genistein, and equol compared to SPC-LIF or CAS diet fed rats (p < 0.05). The distribution of microbial communities based on measures of beta diversity of both SPC-LIF and SPC-HIF groups were significantly different to that of the CAS group (p ≤ 0.005). Alpha-diversity did not differ between any of the groups.ConclusionTaken together, dietary soy protein can reverse liver steatosis in adult Zucker rats, and the reversal of steatosis is accompanied by alterations in gut microbial composition

Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities

Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted ‘omics’ techniques have accelerated research into microbiome–cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.ISSN:0966-842

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.ISSN:2001-037

Data from: Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities we designed a trap-plant bioassay experiment. Replicate Populus, Quercus, and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of 4 loci (i.e. 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability

Data from: Dispersal, niche breadth, and population extinction/colonization ratios predict range size in North American dragonflies

1. Species’ range sizes are shaped by fundamental differences in species’ ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species’ risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. 2. Despite hypotheses that dispersal behaviour is a strong determinant of species range areas, few data are available to directly compare the relationship between dispersal behaviour and range size. Here, we overcome this limitation by combining data from a multi-species dispersal experiment with additional species-level trait data that are commonly hypothesized to affect range size (e.g. niche-breadth, local abundance, and body size, etc.). This enables us to examine the relationship between these species-level traits and range size across North America for fifteen dragonfly species. 3. Ten models based on a priori predictions about the relationship between species traits and range size were evaluated and two models were identified as good predictors of species range size. These models indicated that only two species’ level traits, dispersal behaviour and niche breadth were strongly related to range size. The evidence from these two models indicated that dragonfly species that disperse more often and further had larger North American ranges. 4. Extinction and colonization dynamics are expected to be a key linkage between dispersal behaviour and range size in dragonflies. To evaluate how extinction and colonization dynamics among dragonflies were related to range size we used an independent data set of extinction and colonization rates for eleven dragonfly species and assessed the relationship between these populations rates and North American range areas for these species. 5. We found a negative relationship between North American range size and species’ extinction to colonization ratios. Our results indicate that metapopulation dynamics act to shape the extent of species’ continental distributions. These population dynamics are likely to interact with dispersal behaviour, particularly at species range margins, to determine range limits and ultimately species range sizes

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/ year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (<i>Bison bison</i>)

<div><p>North American bison (<i>Bison bison</i>) are becoming increasingly important to both grassland management and commercial ranching. However, a lack of quantitative data on their diet constrains conservation efforts and the ability to predict bison effects on grasslands. In particular, we know little about the seasonality of the bison diet, the degree to which bison supplement their diet with eudicots, and how changes in diet influence gut microbial communities, all of which play important roles in ungulate performance. To address these knowledge gaps, we quantified seasonal patterns in bison diet and gut microbial community composition for a bison herd in Kansas using DNA sequencing-based analyses of both chloroplast and microbial DNA contained in fecal matter. Across the 11 sampling dates that spanned 166 days, we found that diet shifted continuously over the growing season, allowing bison to take advantage of the seasonal availability of high-protein plant species. Bison consumed more woody shrubs in spring and fall than in summer, when forb and grass intake predominated. In examining gut microbiota, the bacterial phylum <i>Tenericutes</i> shifted significantly in relative abundance over the growing season. This work suggests that North American bison can continuously adjust their diet with a high reliance on non-grasses throughout the year. In addition, we find evidence for seasonal patterns in gut community composition that are likely driven by the observed dietary changes.</p></div

Relative abundance of microbial phyla as indicated by sequencing of 16S ribosomal RNA genes.

<p>The effect of time on each microbial phylum was tested using repeated measures ANOVA with Bonferroni correction. The phylum <i>Tenericutes</i> exhibited a significant shift in relative abundance over the growing season (<i>P</i> < 0.001).</p