Specific Taxa Research Articles

First morphological and molecular investigation of the mycobiota associated with Astragalus nebrodensis in its natural environment (Madonie mountains, Sicily)

Although Astragalus nebrodensis plays a fundamental ecological role, mycorrhizal fungi associated with this species have never been investigated in natural habitats. Our aim was to check the presence and occurrence of Arbuscular Mycorrhizal Fungi (AMF) in roots of A. nebrodensis in a natural habitat and to screen the fungal diversity in the surrounding soil, considering the positive influence of mycotrophic shrub species on soil microbiota. A morphological analysis was performed on A. nebrodensis roots samples from the Madonie mountains (Sicily, Italy), while high-throughput-sequencing was carried out in A. nebrodensis roots and in the associated soil. Observations of A. nebrodensis roots revealed typical structures of AMF. Sequencing revealed that Ascomycota was the most abundant phylum in both roots and soil samples, followed by Basidiomycota and Mucoromycota. A. nebrodensis roots host a fungal community with lower richness as compared to soil and specific taxa were differentially abundant between roots and soil. The endomycorrhizal symbiosis in A. nebrodensis from a natural habitat is reported here for the first time. The fungal diversity between the two matrices (soil vs roots) supports the notion of a specialised and well-established root microbiome in A. nebrodensis enabling it to survive the stressful conditions of its harsh environment.

WASP: the World Archives of Species Perception.

While human perception can play a role in influencing public support for species conservation, the mechanisms underlying human perception remain poorly understood. Some previous studies on perception have focused on a few specific taxa, which makes the understanding of the public perception of species at large a resource- and time-intensive task. Here, we introduce the World Archives of Species Perception project that consists of an animal survey and a plant survey to construct the first systematic database to study the human perception of the floral and faunal diversity at a global scale. We provide a description of our survey method, species selection, survey implementation and a discussion of the potential uses of our databases in multidisciplinary research. In the animal survey, we cover 1980 International Union for Conservation of Nature (IUCN)-evaluated species, representing 25 classes, 192 orders, 1037 families and 1705 genera. In the plant survey, we cover 2000 IUCN-evaluated species, representing 13 classes, 93 orders, 386 families and 1968 genera. Data from the survey will be collected and made available 24 months after the publication of the article. Database URL http://wasp-project.net/.

Abstract MP28: The Association Between the Saliva Microbiome and Biomarkers of Cardiometabolic Disease in ORIGINS

Introduction: The present study sought to characterize taxonomic and functional characteristics of the saliva microbiome and their cross-sectional association with cardiometabolic biomarkers. Hypothesis: Features of the saliva microbiome will be associated with cardiometabolic risk. Methods: Saliva microbiome composition from 265 ORIGINS participants was defined with 16S rRNA sequencing (Illumina, DADA2). Functional composition (KEGG orthologs; KOs) was inferred with PICRUSt2. Alpha Diversity was computed with the Shannon Index. Blood pressure was defined as normal (SBP<120, DBP<80, and no antihypertensive medication) vs elevated/high (hypertension: SBP≥120, DBP≥80 and/or antihypertensive medication). Prediabetes was defined as 5.7≤HbA1≤6.4% or 100≤fasting plasma glucose≤125 mg/dL. HOMA-IR was calculated from insulin and glucose. HOMA-IR and CRP were dichotomized as high/low using thresholds of 3 mg/L and 1.9, respectively. Multivariable multinomial regression with cross-validation was conducted for each feature (species, KOs) and outcome, ranking regression coefficients from most positively to most inversely associated features. Microbiota and KO ratios (Micro-R, KO-R) were computed as the log-ratio of the sum of abundances of taxa/KOs in the top vs bottom tertiles of cross-validated ranks, such that higher ratios are potentially adverse. Adjusted multivariable logistic regressions produced ORs summarizing the association between Shannon, Micro-R, and KO-R and each cardiometabolic outcome. Results: Participants were 71% female, 22% Black, 40% Hispanic, and 18% white, with mean age of 33±10 years. Prevalence of hypertension was 36%, prediabetes was 17%, high CRP was 23%, and high HOMA-IR was 25%. Estimated ORs for the association between microbiome metrics and cardiometabolic outcomes are summarized in Figure 1. Conclusion: Microbiome scores based on specific taxa or KOs are associated with hypertension, prediabetes, and increased inflammation and insulin resistance.

Body Size Estimation in Toads (Anura: Bufonidae): Applicability to the Fossil Record

Organisms’ body size is an important biological trait that is related to the environment and constrained by physiology. It is also one of few biological characteristics that can be inferred from fossil specimens. Variation in body size both within and across fossil communities can provide insight into their response to past climatic events, as well as morphological or ecological evolution in specific taxa. Among vertebrates, frogs and toads (Anura) are of particular interest given their sensitivity to environmental variation. Here, we propose a method for estimating body size in toads, one of the most ecologically and taxonomically diverse frog families (Bufonidae) that is cosmopolitan in distribution and contains aquatic, terrestrial, arboreal, and fossorial species. We used computed tomography scans (CT-scans) of 36 living species of toads to digitally segment five bones that are frequently found as fossil (ilium, sacrum, urostyle, humerus, and radioulna). We took nine different measurements on those bones to be used as proxies for body size and for each specimen collected a measurement of body size, snout–urostyle length (SUL). We used ordinary least square regression analysis (OLS) with 95% confidence and prediction intervals to determine if those measurements are useful to estimate body size from isolated bones and in the fossil record. Our regression analyses indicate that these measurements can serve as proxies to estimate body size in bufonids (with coefficients of determination between 0.80–0.95). The measurements with the highest coefficient of determinations are those of the ilium and humeri, both of which are abundant in the fossil record and taxonomically informative. Last, we tested our method on examples of living and fossils toads of North and South America. Our method is the first quantitative approach to estimate size in toads based on isolated bones and enables us to continue to explore the correlation between size and ecology in toads in the past.

Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection.

Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.

Evolutionary patterns of host switching, lifestyle mode, and the diversification history in symbiotic zoantharians

Symbioses play important roles in forming the structural and distributional patterns of marine diversity. Understanding how interspecies interactions through symbioses contribute to biodiversity is an essential topic. Host switching has been considered as one of the main drivers of diversification in symbiotic systems. However, its process and patterns remain poorly investigated in the marine realm. Hexacoral species of the order Zoantharia (=zoantharians) are often epizoic on other marine invertebrates and generally use specific taxa as hosts. The present study investigates the patterns of host switching and the diversification history of zoantharians based on the most comprehensive molecular phylogenetic analyses to date, using sequences from three mitochondrial and three nuclear markers from representatives of 27 of 29 genera. Our results indicate that symbiotic zoantharians, in particular those within suborder Macrocnemina, diversified through repeated host switching. In addition, colonization of new host taxa appears to have driven morphological and ecological specialization in zoantharians. These findings have important implications for understanding the role of symbioses in the morphological and ecological evolution of marine invertebrates.

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.

A closer look into the microbiome of microalgal cultures.

Although bacteria are commonly co-occurring in microalgal cultivation and production systems, little is known about their community structure and how it might be affected by specific microalgal groups or growth conditions. A better understanding about the underlying factors that determine the growth of specific bacterial populations is not only important for optimizing microalgal production processes, but also in the context of product quality when the algal biomass is to be used for future food or feed. We analyzed the bacterial community composition associated with nine microalgal strains in stock culture, maintained in two different growth media, to explore how specific taxonomic microalgal groups, microalgal origin, or the growth medium affect the bacterial community composition. Furthermore, we monitored the bacterial community composition for three Phaeodactylum strains during batch cultivation in bubble columns to examine if the bacterial composition alters during cultivation. Our results reveal that different microalgal genera, kept at the same cultivation conditions over many years, displayed separate and unique bacterial communities, and that different strains of the same genus had very similar bacterial community compositions, despite originating from different habitats. However, when maintained in a different growth medium, the bacterial composition changed for some. During batch cultivation, the bacterial community structure remained relatively stable for each Phaeodactylum strain. This indicates that microalgae seem to impact the development of the associated bacterial communities and that different microalgal genera could create distinct conditions that select for dominance of specific bacteria. However, other factors such as the composition of growth medium also affect the formation of the bacterial community structure.

Mandibular shape as a proxy for the identification of functional feeding traits of midge larvae (Diptera: Chironomidae)

The identification of functional feeding traits in aquatic macroinvertebrates often requires a morphology-based identification of species, which is important for trait-based methods of biological assessment. The extent of functional homogenization is compared along scales of impairment, where trait-based information is used as an input in models that examine degradation pathways. However, trait-based information is not always readily available for all groups of aquatic insects, especially for species diverse families, such as chironomids (Diptera: Chironomidae). Taxonomic challenges and ambiguous traits complicate the use of chironomid larvae in trait-based bioassessment. Here, we examine the use of geometric morphometric analysis (GMA), deep learning (Convolutional Neural Networks), and computer vision (deep CNN) applied to the mouthparts (mandibles) of chironomid larvae as a proxy for identifying the relationship between the functional morphology and food acquisition behaviour. We determined the variability in morphology of mandibles for 23 taxa of chironomid larvae from different genera, subfamilies, and their Functional Feeding Group (FFG). Analysis using GMA showed that the five different FFGs examined had different mandibular traits that significantly varied in shape and size. A deep CNN model was then built that was able to classify the 23 taxa into their respective FFG automatically with 92.31 % accuracy. A gradient-weighted Class Activation Mapping (Grad-CAM) algorithm found that the most important part of mandibles for classification were the gula and mandibular joint. We introduced three additional species to the deep CNN models to test whether automatic classification would directly and automatically identify traits of the specimens independently from taxonomic identification. The deep CNN process avoids issues surrounding both taxonomic identification and previous knowledge of a specific taxon’s feeding trait, and in all cases the model classified taxa correctly based on their mandibular traits. The use of deep learning approaches could substantially enhance the use of trait-based approaches and increase the reliability and use of chironomids in bioassessment.

BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata

Abstract DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize identification success. BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open‐source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location. BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high‐throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy‐based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats. BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error‐prone manual steps and enabling efficient collaborative workflows.

Hedgerows have contrasting effects on pollinators and natural enemies and limited spillover effects on apple production

Agricultural intensification has resulted in a decline in insect biodiversity and threatens the provision of valuable ecosystem services. Agri-environment schemes (AESs) have been implemented in an effort to conserve biodiversity on farmland and increase agricultural sustainability, but their effectiveness can vary widely. To better determine which factors influence AES effectiveness, the relative roles of local habitat features, habitat quality, and landscape context need to be further explored. The aim of this study was to determine the most important factors influencing field margin AES effectiveness in commercial apple orchards, in terms of arthropod biodiversity conservation and ecosystem service provision. We surveyed wild bees and aphid natural enemies in field margins and apple trees in 20 orchards, ten bordered by hedgerow field margins (an AES) and ten with herbaceous field margins (no hedgerows present, not an AES). We considered field margin floral resources and the cover of semi-natural habitat in the surrounding landscape as indicators of local habitat quality and landscape context, respectively. We furthermore quantified pollination and pest control as measures of ecosystem service delivery and the relationship between arthropod communities and apple yield (initial and final fruit set) and quality. We found that hedgerow presence strongly predicted both pollinator and natural enemy communities and that these relationships were more pronounced than those with local habitat quality and landscape context. Hedgerows were negatively related to wild bee richness and abundance within the orchard, and positively related to natural enemy richness and abundance at the field margin but not within the orchard. We found no relationships between local and landscape factors and ecosystem service delivery, and no relationship between wild bee communities and apple yield, suggesting that apple is not pollen limited in our study system. There was, however, a negative relationship between natural enemy richness and initial fruit set. We conclude that annually cut hedgerows can benefit the conservation of natural enemies, but have limited arthropod-mediated private benefits for apple production, and likely need to be supplemented with additional local habitat resources for the conservation of wild bees. Our findings indicate that local habitat factors can strongly influence biodiversity regardless of landscape context, but that AESs likely need to be designed with separate biodiversity and ecosystem service targets, and specific taxonomic groups, in mind.

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples.

Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.

Macro-invertebrate abundance on green roofs versus ground level sites in the city of Antwerp, Belgium

Here, the abundance of macro-invertebrates (Arthropoda and Gastropoda) of eight green roofs and their adjacent ground level habitats in the city of Antwerp, Belgium, is compared. All higher-level taxa found were present in both types of habitats without significant differences in their overall abundance between green roofs and ground level habitats. However, we found significant differences in abundances between the two types of habitats, when specific taxa were compared. Beetles (Coleoptera), isopods (Isopoda) and bees (Anthophila) were more abundant at ground level sites compared to green roofs, while for true bugs (Heteroptera) and cicadas (Auchenorrhyncha) the opposite was found. Our results support the idea that extensive green roofs in Belgium can provide a suitable habitat for different invertebrate taxa, but further research is needed to identify the true drivers behind differences in abundance between ground level and adjacent green roofs.

Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments.

Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.

Association between Dysbiosis in the Gut Microbiota of Primary Osteoporosis Patients and Bone Loss.

In recent decades, gut microbiome research has experienced significant growth, driven by technological advances that enable quantifying bacterial taxa with greater precision. Age, diet, and living environment have emerged as three key factors influencing gut microbes. Dysbiosis, resulting from alterations in these factors, may lead to changes in bacterial metabolites that regulate pro- and anti-inflammatory processes and consequently impact bone health. Restoration of a healthy microbiome signature could mitigate inflammation and potentially reduce bone loss associated with osteoporosis or experienced by astronauts during spaceflight. However, current research is hindered by contradictory findings, insufficient sample sizes, and inconsistency in experimental conditions and controls. Despite progress in sequencing technology, defining a healthy gut microbiome across global populations remains elusive. Challenges persist in identifying accurate gut bacterial metabolics, specific taxa, and their effects on host physiology. We suggest greater attention be directed towards this issue in Western countries as the cost of treating osteoporosis in the United States reaches billions of dollars annually, with expenses projected to continue rising.

An insight into the commercial piglet’s microbial gut colonization: from birth towards weaning

BackgroundThe establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform.ResultsThe present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2–5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets’ gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows.ConclusionsIn conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.

Uncertainty in coprophilous fungal spore concentration estimates

The abundance of coprophilous (dung-inhabiting) fungal spores (CFS) in sedimentary records is an increasingly popular proxy for past megaherbivore abundance that is used to study megaherbivore-vegetation interactions, timing of megaherbivore population declines and extinctions, and the introduction of domesticated herbivores. This method often relies on counting CFS alongside pollen and tracers of known concentration such as exotic pollen or synthetic microspherules. Prior work has encouraged reporting CFS abundances as accumulation rates (spores/unit2/year) or concentration (spores/unit3) instead of percentages relative to the total pollen abundance, because CFS percentages can be sensitive to fluctuations in pollen influx. In this work, we quantify the uncertainty associated with estimating concentration values at different total counts and find that high uncertainty is associated with concentration estimates using low to moderate total counts (n = 20 to 200) of individual fungal spore types and tracers. We also demonstrate the effect of varying tracer proportions, and find that larger tracer proportions result in narrower confidence intervals. Finally, the probability of encountering a CFS spore from a specific taxon occurring in moderate concentrations (1,000 spores/unit2) dramatically decreases after a low tracer count (∼50). The uncertainties in concentration estimates caused by calculating tracer proportion are a likely cause of the high observed variance in many CFS time series, especially when CFS or tracer concentrations are low. Thus, we recommend future CFS studies increase counts and report the uncertainty surrounding concentration values. For some records, reporting spore data as presence/absence rather than concentrations or counts is preferable, such as when performing high counts is not feasible.

Mucosal Microbiota Associated With Eosinophilic Esophagitis and Eosinophilic Gastritis.

The aim of the study was to determine the mucosal microbiota associated with eosinophilic esophagitis (EoE) and eosinophilic gastritis (EoG) in a geographically diverse cohort of patients compared to controls. We conducted a prospective study of individuals with eosinophilic gastrointestinal disease (EGID) in the Consortium of Eosinophilic Gastrointestinal Disease Researchers, including pediatric and adult tertiary care centers. Eligible individuals had clinical data, mucosal biopsies, and stool collected. Total bacterial load was determined from mucosal biopsy samples by quantitative polymerase chain reaction (PCR). Community composition was determined by small subunit rRNA gene amplicons. One hundred thirty-nine mucosal biopsies were evaluated corresponding to 93 EoE, 17 EoG, and 29 control specimens (18 esophageal) from 10 sites across the United States. Dominant community members across disease activity differed significantly. When comparing EoE and EoG with controls, the dominant taxa in individuals with EGIDs was increased ( Streptococcus in esophagus; Prevotella in stomach). Specific taxa were associated with active disease for both EoE ( Streptococcus , Gemella ) and EoG ( Leptotrichia ), although highly individualized communities likely impacted statistical testing. Alpha diversity metrics were similar across groups, but with high variability among individuals. Stool analyses did not correlate with bacterial communities found in mucosal biopsy samples and was similar in patients and controls. Dominant community members ( Streptococcus for EoE, Prevotella for EoG) were different in the mucosal biopsies but not stool of individuals with EGIDs compared to controls; taxa associated with EGIDs were highly variable across individuals. Further study is needed to determine if therapeutic interventions contribute to the observed community differences.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16–31.05 % and 30.37–15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Addressing Amazonian Fish Diversity Using Environmental DNA (eDNA): A First Glance

Environmental DNA (eDNA) is considered to be an innovative method that can be used in the detection and identification of species present in aquatic environments, adding the advantage of describing the ichthyofauna without capturing the organisms. Out of the two possible approaches of eDNA, the metabarcoding approach aims to identify the diversity of a specific taxon and its composition using a universal DNA primer. This approach has grown considerably in recent years, although most studies focus on temperate regions, which causes a lack of clarity about the potential of the method in tropical regions since these have very distinct abiotic characteristics, as well as a higher diversity of fauna and flora. Therefore, as a way to verify the potential use of eDNA metabarcoding, this study focused on the Neotropical region, specifically the Amazon basin, a place with the highest ichthyofaunistic biodiversity in the world. As such, the goal of this study was to detect the composition of the main taxonomic groups of fish in the small stream Tarumã-Mirim, an acidic blackwater river that is located nearby Manaus city and is part of an environmental protection area near the city of Manaus, Brazil. For that, water samples of 6 L were collected along the river at 5 points (totaling 30 L). The water samples were stored in ice boxes and transported to the laboratory for filtration in fiberglass filters. Following the filtration and the extraction of eDNA, the samples were amplified in PCRs machines, using the universal primers MiFish developed by Miya et al., (2015). The next steps were: the construction of eDNA libraries, the sequencing on Illumina – Miseq platform, and a bioinformatic analysis. For the taxonomic identification of the eDNA sequences we used the sequences deposited in GenBank and the reference database developed specifically for Amazonian fish. The application and efficiency of eDNA metabarcoding for the samples, identified 42 molecular operational taxonomic units (MOTUs), which were grouped into six orders and eight families. A refined approach identified seven species and one genus. In addition, since eDNA samples were obtained along the entire river, it was possible to build a distribution map of fish species. Despite the limitation in identifying the abundance of all taxonomic groups present in the Tarumã-Mirim River, the metabarcoding approach for the eDNA was able to identify the species that have their contemporary distribution in the Amazonian rivers, as well as the detection of the three main groups of fish. Thus, the method may serve as a complement to ecological studies for the detection, identification and monitoring the Amazonian ichthyofauna. These results show that the eDNA approach needs to be optimized in tropical regions since the biotic and abiotic characteristics, which are peculiar to the tropics (acidic waters, high temperatures, etc.), may affect the adequate detection of the rich biodiversity of such sites