Specific Taxa Research Articles

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

Long-term growing season aridity and grazing seasonality effects on perennial grass biomass in a Chihuahuan Desert rangeland

Growing season aridity and livestock grazing seasonality can influence primary productivity of perennial grasses in dryland systems. For this study, we used a long-term dataset (1967–2004) to investigate the independent and joint effects of growing season aridity and season of grazing (yearlong continuous, fall, winter/spring, or summer season grazing) on the mean annual primary productivity of the perennial grasses Bouteloua eriopoda (black grama), Aristida spp. (threeawn), and Sporobolus spp. (dropseed) in a southwestern United States Chihuahuan Desert rangeland system. Over the 37-year study period, total perennial grass biomass decreased as aridity increased, but the extent of this relationship depended upon season of grazing and specific grass taxon. Aridity-related decreases in total perennial grass biomass were most severe in the summer grazing treatment. Our findings indicate that over time, summer and fall grazing can potentially exacerbate the negative effects of increasing aridity on perennial grass biomass. As arid and semi-arid rangelands globally face increasing aridity associated with a changing climate, land managers can modulate the season of grazing, dependent on dominant taxa present, to minimize these effects. Our study and those from other arid land locations indicate continuous grazing at light to conservative intensities can better sustain key perennial grasses than strategies involving concentrated seasons of grazing. However, growing season aridity levels must also be taken into consideration.

The Role of the Intestinal Microbiome in Antibiotic Associated Neutropenia

Prolonged antibiotic administration has been associated with bone marrow suppression in approximately 10-15% of patients. The mechanisms that underlie the association between prolonged antibiotic therapy and bone marrow suppression, including neutropenia, remain poorly understood. Our recent studies in murine models demonstrated that prolonged broad-spectrum antibiotics suppress hematopoiesis by depletion of the intestinal microbiota. Furthermore, oral administration of the microbial metabolites nucleotide-binding oligomerization domain-containing protein 1 ligand (NOD1L) and desaminotyrosine (DAT) was sufficient to restore normal hematopoiesis in antibiotic-treated mice. Additionally, Type I IFN signaling in hematopoietic cells was noted to be critical for the intestinal microbiota to promote hematopoiesis, as administration of IFNα during antibiotic therapy rescued normal hematopoiesis. These findings support a paradigm in which products of the intestinal microbiota enter the bloodstream and travel to the bone marrow where they promote the production of growth cytokines that support normal hematopoiesis. To elucidate whether changes in the microbiome similar to those observed in mice also occur in humans treated with prolonged courses of antibiotics, we carried out a multicenter non-treatment, non-intervention study. We enrolled patients aged 0-17 years receiving long-term (>2 weeks) intravenous (IV) or oral (PO) antibiotic courses across two tertiary children's hospitals. We excluded patients with history of abnormal blood counts, bone marrow failure, gastrointestinal infection / syndromes / abnormalities, immunodeficiency, malignancy, severe malnutrition, use of prophylactic antibiotics or use of antibiotics immediately before admission. Patients noted to develop neutropenia while receiving antibiotics were enrolled in the retrospective arm. A stool sample was collected at 2 timepoints: at the start and at the completion of antibiotics for the prospective arm of the study; at the onset of neutropenia while on antibiotics and at resolution of neutropenia after completion of antibiotics for the retrospective arm. Here, we report an interim analysis performed for an initial cohort of 5 patients with antibiotic-associated neutropenia and 10 controls matched for age and race/ethnicity. For clinical data analysis, we assessed continuous variables using parametric and non-parametric tests when appropriate while using χ2 or Fisher's exact tests for categorical variables. Stool samples were sent for 16s rDNA sequencing to determine whether there are significant changes in the composition (individual microbial taxa) and diversity (both alpha and beta) of the gut microbiome between groups; as well as for untargeted metabolomic profiling to assess whether changes in the relative abundance of specific microbiome-related metabolites, including but not limited to NOD1L and DAT, are associated with the development of neutropenia with prolonged antibiotic treatment. Analyses of these data are currently ongoing. Neutropenia occurred in 9.4% of our prospective patient samples (3 out of 32 patients). Median age was 13y (range 6 mo. - 17y) for the neutropenic group and 11y (range 1-15y) for the control group. Forty percent of patients were female in both groups (Table 1). Total length of IV antibiotic and ICU admission were positively correlated with neutropenia in this cohort (Table 2). To our knowledge, this is the first clinical study linking changes in the intestinal microbiota with antibiotic associated neutropenia. The incidence of antibiotic-associated neutropenia was comparable to what has been previously reported. The analysis of stool samples from this cohort through 16sDNA sequencing and untargeted metabolomic profiling will outline specific changes in microbiome load, diversity, as well as specific taxa and metabolites potentially related to the development of neutropenia. Altogether, we hope to utilize an improved understanding of the molecular pathways, mediators and receptors by which the microbiome sustains normal hematopoiesis to prevent and treat antibiotic-associated bone marrow suppression. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Respiratory Microbiome Profile of Pediatric Pulmonary Hypertension Patients Associated With Congenital Heart Disease.

Pulmonary hypertension (PH) associated with congenital heart disease (CHD) is the most common type of PH in pediatric patients. The airway microbiome profile in CHD-PH patients remains rarely studied. A total of 158 children were recruited for collection of oropharyngeal swabs to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome, to establish a correlation between these bacterial groups and echocardiography indicators in CHD-PH patients. Bacterial α- and β-diversity of the airway microbiome indicated a significantly lower richness in the CHD-PH group and compositional differences associated with the specific taxa and their relative abundances in the upper respiratory tract. Principal coordinate analysis showed that the pharynx microbiota composition in the CHD-PH group varied from that in the CHD or control group. The linear discriminant analysis effect size also highlighted an increased presence of Streptococcus and Rothia in pediatric CHD-PH patients. Comparison of microbial composition between pediatric and adult PH patients showed significant differences and separation of microbiota. The correlation between bacterial abundance and transthoracic echocardiography indexes in CHD-associated PH indicated that different groups of microbiomes may be related to different PH grades. In summary, our study reported the systematic definition and divergent profile of the upper respiratory tract microbiota in pediatric PH patients, CHD and reference subjects, as well as between pediatric and adult PH patients.

Epigenetics for crop adaptation to climate change

Epigenetics for crop adaptation to climate change

Commensal oral microbiota impacts ulcerative oral mucositis clinical course in allogeneic stem cell transplant recipients

Oral mucositis (OM) is a complex acute cytotoxicity of antineoplastic treatment that affects 40–85% of patients undergoing hematopoietic stem-cell transplantation. OM is associated with prolonged hospitalization, increased extensive pharmacotherapy, need for parenteral nutrition, and elevated treatment costs. As OM onset relates to the mucosal microenvironment status, with a particular role for microbiota-driven inflammation, we aimed to investigate whether the oral mucosa microbiota was associated with the clinical course of OM in patients undergoing allogeneic hematopoietic stem-cell transplantation. We collected oral mucosa samples from 30 patients and analyzed the oral mucosa microbiota by 16S rRNA sequencing. A total of 13 patients (43%) developed ulcerative OM. We observed that specific taxa were associated with oral mucositis grade and time to oral mucositis healing. Porphyromonas relative abundance at preconditioning was positively correlated with ulcerative OM grade (Spearman ρ = 0.61, P = 0.028) and higher Lactobacillus relative abundance at ulcerative OM onset was associated with shortened ulcerative OM duration (P = 0.032). Additionally, we generated a machine-learning-based bacterial signature that uses pre-treatment microbial profiles to predict whether a patient will develop OM during treatment. Our findings suggest that further research should focus on host-microbiome interactions to better prevent and treat OM.

Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes

Successive plantings of Prunus species produce suboptimal growth and yield in many California soils due to a poorly understood soilborne disease complex, Prunus replant disease (PRD). We explored the hypothesis that PRD is mediated by microbial taxa in roots of Nemaguard peach, a rootstock for almond and other stone fruits. In a greenhouse bioassay, portions of 10 replant soils were treated with fumigation or pasteurization or left untreated as a control before being planted with peach seedlings. Ten weeks after planting, seedlings were considered PRD-affected if their top fresh weights in the control were significantly reduced, compared to the weights in pasteurization and fumigation treatments; plants with equivalent top weights in all treatments were considered to be non-affected. The roots were washed from the soil, frozen, extracted for total DNA, and used for metabarcoding of rRNA gene amplicons from bacteria, fungi, and oomycetes. High-throughput amplicon sequencing revealed that root microbial community shifts resulted from preplant treatments, and specific taxa were associated with PRD induction among controls. Random forest (RF) analysis discriminated effectively between PRD-affected and non-affected root communities. Among the 30 RF top-ranked amplicon sequence variant (ASV) predictors, 26 were bacteria, two were oomycetes, and two were fungi. Among them, only Streptomyces scabiei, Steroidobacter denitrificans, Streptomyces bobili, and Pythium mamillatum had root abundances ≥5% that were either associated positively (former two ASVs) or negatively (latter two) with PRD. Thus, our findings were consistent with microbial mediation of PRD in roots and suggested taxa that may be involved in the mediation.

Christensenella regulated by Huang-Qi-Ling-Hua-San is a key factor by which to improve type 2 diabetes.

There is a lot of evidence that oral hypoglycemic drugs work by affecting gut microbes, but the key strains responsible for this effect are not well known. Huang-Qi-Ling-Hua-San (HQLHS), composed of Astragalus Membranaceus, Ganoderma lucidum, Inonotus obliquus, and Momordica charantia L., is a specially designed Chinese medicine formula to treat type 2 diabetes (T2D). In this study, a mouse model of T2D induced by high-fat diet and streptozotocin was used to explore the mechanism of HQLHS in improving hyperglycemia and hyperlipidemia through multiple rounds of animal experiments, such as HQLHS feeding, fecal microbiota transplantation (FMT), and live bacteria feeding, so as to explore the potential target intestinal flora in its hypoglycemic effect. Results show that such specific taxa as Bifidobacterium, Turicibacter, Alistipes, Romboutsia, and Christensenella were identified to be preferably enriched by HQLHS and then assumed to be the target microbes. Herein, FMT was used to test if the upregulated beneficial bacteria by HQLHS play a therapeutic role. The strain Christensenella minuta DSM 22607 and the strain Christensenella timonensis DSM 102800 were selected to test the beneficial effect of Christensenella taxa on T2D. Diabetic animals supplemented with these strains showed the improvement in blood glucose and lipid metabolism, the promotion of GLP-1 secretion, the increase in antioxidant capacity, the inhibition of hepatic gluconeogenesis, the suppression of intestinal glucose absorption, the enhancement of intestinal barrier, reduced LPS-induced inflammation, and the reduction of branched amino acids (BCAAs) content in the liver. Overall, these data demonstrate that Christensenella plays a beneficial role in T2D and is a target for the action of HQLHS therapy.

Association between ultra-processed food consumption and gut microbiota in senior subjects with overweight/obesity and metabolic syndrome.

The production and consumption of ultra-processed foods (UPF) has increased considerably during the last years worldwide. Collective evidence shows the association between UPF consumption and adverse health outcomes, including inflammatory gastro-intestinal disorders and obesity. The gut microbiota has been suggested as potential mediator of the effects of UPF consumption on metabolism and health. However, few studies have been conducted in order to elucidate these aspects. Therefore, the aim of the present study was to assess the cross-sectional associations between UPF consumption and gut microbiota in a population of senior subjects (n = 645) within the frame of the PREDIMED-Plus trial. Eligible participants were men and women (aged 55–75 years), without documented history of cardiovascular disease at enrollment, with overweight/obesity (body mass index ≤ 27 and <40 kg/m2) and metabolic syndrome. Using the information of food frequency questionnaires, the consumption of UPF, expressed as a percentage of total dietary energy intake in kcal/day, was calculated considering those food items classified in group 4 of NOVA system. Population was categorized according to tertiles of UPF consumption. Taxonomic fecal microbiota information, along with blood biochemical parameters, anthropometric measurements and clinical data were obtained. Bioinformatics analysis was performed to study the association between fecal microbiota composition and UPF consumption. We observed that subjects allocated in the highest tertile of UPF consumption (21.4 ± 5.0 % kcal/day) presented lower adherence to MedDiet (p < 0.001) and higher total energy intake (p < 0.001). The taxonomic analysis of the fecal microbiota revealed a significant (Benjamini-Hochberg adjusted p < 0.2) positive association between specific taxa and tertiles (T) of UPF consumption: Alloprevotella (p = 0.041 vs. T2; p = 0.065 vs. T3), Negativibacillus (p = 0.096 vs. T3), Prevotella (p = 0.116 vs. T3), and Sutterella (p = 0.116 vs. T2). UPF consumption was positively associated with lower adherence to MedDiet and higher total energy intake in senior subjects with overweight obesity and metabolic syndrome. In addition, positive association with specific fecal microbiota taxa related to inflammatory gastro-intestinal diseases and low consumption of fruits and vegetables, was observed.

Roads to Construct and Re-build Plant Microbiota Community.

Plant microbiota has influenced plant growth and physiology significantly. Plant and plant-associated microbes have flexible interactions that respond to changes in environmental conditions. These interactions can be adjusted to suit the requirements of the microbial community or the host physiology. In addition, it can be modified to suit microbiota structure or fixed by the host condition. However, no technology is realized yet to control mechanically manipulated plant microbiota structure. Here, we review step-by-step plant-associated microbial partnership from plant growth-promoting rhizobacteria to the microbiota structural modulation. Glutamic acid enriched the population of Streptomyces, a specific taxon in anthosphere microbiota community. Additionally, the population density of the microbes in the rhizosphere was also a positive response to glutamic acid treatment. Although many types of research are conducted on the structural revealing of plant microbiota, these concepts need to be further understood as to how the plant microbiota clusters are controlled or modulated at the community level. This review suggests that the intrinsic level of glutamic acid in planta is associated with the microbiota composition that the external supply of the biostimulant can modulate.

Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis

ABSTRACTBackgroundA low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet is increasingly used to manage symptoms in irritable bowel syndrome (IBS). Although this approach may alter the colonic microbiome, the nature of these changes has not been comprehensively synthesized.ObjectivesThe aim of this study was to conduct a systematic review with meta-analysis of randomized controlled trials examining the impact of a low FODMAP diet on the composition and function of the microbiome in patients with IBS.MethodsA systematic search was conducted for randomized controlled trials evaluating the effects of a low FODMAP diet on the colonic microbiome in patients with IBS in MEDLINE, EMBASE, CENTRAL, and Web of Science from inception to April 2022. Outcomes included diversity of the microbiome, specific bacterial abundances, fecal SCFA concentration, and fecal pH. For fecal SCFA concentrations and pH, meta-analyses were performed via a random-effects model.ResultsNine trials involving 403 patients were included. There were no clear effects of the low FODMAP diet on diversity of the microbiome. A low FODMAP diet consistently led to lower abundance of Bifidobacteria, but there were no clear effects on diversity of the microbiome or abundances of other specific taxa. There were no differences in total fecal SCFA concentration between the low FODMAP diet and control diets (standardized mean difference: −0.25; 95% CI: −0.63, 0.13; P = 0.20), nor were there differences for fecal concentrations of specific SCFAs or fecal pH.ConclusionsIn patients with IBS, the effects of a low FODMAP diet on the colonic microbiome appear to be specific to Bifidobacteria with no consistent impacts on other microbiome metrics, including diversity, fecal SCFA concentrations, and fecal pH. Further, adequately powered trials are needed to confirm these findings.This review was registered at https://www.crd.york.ac.uk/prospero/ as CRD42020192243.

Metazoan parasite diversity of the endemic South African intertidal klipfish, Clinus superciliosus: Factors influencing parasite community composition.

The current trend in marine parasitology research, particularly in South Africa, is to focus on a specific parasite taxon and not on the total parasite community of a specific fish host. However, these records do not always reveal the ecological role of parasites in ecosystems. Thus, the present study aimed to determine which factors influence the parasite community composition of the endemic southern African intertidal klipfish, Clinus superciliosus (n=75). Metazoan parasites were sampled from four localities (two commercial harbours - west coast; and two relatively pristine localities - southeast coast) along the South African coast. A total of 75 klipfish were examined for parasites, where 30 distinct taxa, representing seven taxonomic groups were found: Acanthocephala (4 taxa), Cestoda (2 taxa), Crustacea (5 taxa), Digenea (11 taxa), Hirudinea (2 taxa), Monogenea (1 taxon) and Nematoda (5 taxa). Results indicated that the main driver of diversity was locality, with the highest diversity on the southeast coast, most likely due to higher water temperatures and upwelling compared to the west coast. The parasite community composition of the klipfish was significantly influenced by water temperature and parasite life cycle. These results emphasise the importance of parasitological surveys including all parasite taxa in hosts from multiple localities and seasons, to better comprehend their ecological role.

HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.

Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive read mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC.

Factors affecting soil invertebrate biodiversity in agroecosystems of the Po Plain area (Italy)

Soil is a fundamental component of the biosphere, whose properties and quality are affected by human activities, such as agriculture. Soil health is fundamental for different ecosystem services and soil biota has a crucial role in maintaining it. Elucidating how different crops and agricultural practices affect soil invertebrates communities is of relevance. In the present study, a DNA metabarcoding approach was adopted to evaluate the effects of different biotic and abiotic factors, including agricultural practices, on the composition and diversity of soil invertebrate communities of different agro-ecosystems (Po Plain-Italy). At this aim, the DNA markers and the more effective primers in retrieving soil metazoan communities were established. Bulk soil samples from different agro-ecosystems (i.e., cornfield, alfalfa, paddy fields, vineyard, stable meadow, woodland) were collected and, processed for obtaining 18S rRNA and coi sequences (raw reads analyzed using QIIME2 and R). Soil physical and chemical parameters were measured for each soil sample (e.g., pH, carbon-nitrogen ratio, texture, porosity) and metadata on farms management were retrieved. The most efficient primer pairs in recovering soil metazoans were M620F/M1260R for 18S rRNA, and mlCOIintF/jgHCO2198R for coi gene. Soil communities resulted dominated by Nematoda, Arthropoda, Annelida, Rotifera and Tardigrada. The most diverse invertebrate communities have been found in the soil of stable meadows and woodlands, while cornfields showed the lowest level of diversity. The diversity of soil invertebrate communities (Hill numbers) was positively correlated with the level of porosity and carbon-nitrogen ratio, while it was negatively correlated with the phosphate abundance. This pattern probably reflects the negative effect of excessive fertilization with phosphates on soil fauna, while the abundance of organic matter and microhabitats were found to enhance the presence of more complex communities. Other soil properties were correlated only with specific taxa (e.g., pH was negatively correlated with the diversity of Annelida and Rotifera).

Generalists and specialists decomposing labile and aromatic biochar compounds and sequestering carbon in soil

Biochar plays an important role in soil carbon (C) sequestration, while the effectiveness of sequestration is mostly determined by microbial preferences to utilize the different biochar components (i.e. labile substances or fused aromatic backbone). Thus, it is important to investigate the responses of the bacterial community and specific taxa, and associated C metabolic functions to biochar labile C (i.e. easily mineralizable C) or aromatic backbone (i.e. persistent C). Here, we separated the biochar components into labile C and aromatic backbone, and used the 16S sequencing in conjunction with the addition of an internal standard to quantify the absolute copy number of various bacterial taxa. The aromatic backbone decreased microbial metabolic quotient by 47 %, incorporating more C into biomass and contributing to C sequestration rather than releasing it into the atmosphere, while the labile C caused the opposite trends. The bacterial generalists utilizing aromatic backbone and labile C were mainly from Oxalobacteraceae (Proteobacteria) and Sporosarcina (Firmicutes). The bacterial specialists responsive for aromatic backbone were from Myxococcaceae and Flavisolibacter, while those responsive to labile C were from Ktedonobacteraceae and Bradyrhizobiaceae. Microbial abundance of specialists responsive to labile C was 3.3 times larger than those responsive to aromatic backbone, indicating the preferences of labile C specialists for energy sources and aromatic C specialists for slow utilization of persistent C in versatile habitats. Our work revealed microbial strategies for utilization of organic substances of very contrast availability, and their contributions to soil C sequestration depending on biochar components.

A geometric morphometric evaluation of equid tooth shape at Natural Trap Cave, Wyoming

Natural Trap Cave is an enigmatic site in Wyoming that has been accumulating fossils for tens of thousands of years from animals falling into it. One of the more common taxa present at this site are horses. North American equids have been separated into two main groups: caballine “stout legged” horses, which include the modern Equus ferus caballus; and the extinct non-caballine so-called “New World Stilt Legged” horses, which possess more gracile distal limb elements than modern horses. Genetic evidence has shown that both taxa are present at the Natural Trap Cave site. While post-cranial elements of both have been found, the most common horse specimens recovered have been isolated teeth, which have historically been difficult to identify to a specific taxon, though recent studies have been successful using geometric morphometrics on the occlusal surfaces of cheek teeth to differentiate equid taxa and populations. This study also uses geometric morphometrics to attempt to differentiate upper cheek tooth specimens between caballine and non-caballine stilt legged horses from Natural Trap Cave. Two landmark schemes were employed, one with fewer landmarks, and one with greater coverage, including sliding semi-landmarks. These schemes were used first on a dataset of only known specimens that had been taxonomically identified, and then unknown specimens from Natural Trap Cave were added. These analyses showed that the two taxa do indeed occupy statistically significant different areas of morphospace, as do premolars and molars. Surprisingly, the smaller landmark scheme produced better resolution on the Principal Components Analysis plots, possibly because the larger landmark scheme introduced ontogenetic variation due to different levels of tooth wear. While definitive identification does not seem advisable with this methodology, the unknown specimens grouped more with the known stilt legged specimens, suggesting that this taxon was more prevalent at Natural Trap Cave than the caballine Equus.

Testing microbiome associations with survival times at both the community and individual taxon levels.

Finding microbiome associations with possibly censored survival times is an important problem, especially as specific taxa could serve as biomarkers for disease prognosis or as targets for therapeutic interventions. The two existing methods for survival outcomes, MiRKAT-S and OMiSA, are restricted to testing associations at the community level and do not provide results at the individual taxon level. An ad hoc approach testing each taxon with a survival outcome using the Cox proportional hazard model may not perform well in the microbiome setting with sparse count data and small sample sizes. We have previously developed the linear decomposition model (LDM) for testing continuous or discrete outcomes that unifies community-level and taxon-level tests into one framework. Here we extend the LDM to test survival outcomes. We propose to use the Martingale residuals or the deviance residuals obtained from the Cox model as continuous covariates in the LDM. We further construct tests that combine the results of analyzing each set of residuals separately. Finally, we extend PERMANOVA, the most commonly used distance-based method for testing community-level hypotheses, to handle survival outcomes in a similar manner. Using simulated data, we showed that the LDM-based tests preserved the false discovery rate for testing individual taxa and had good sensitivity. The LDM-based community-level tests and PERMANOVA-based tests had comparable or better power than MiRKAT-S and OMiSA. An analysis of data on the association of the gut microbiome and the time to acute graft-versus-host disease revealed several dozen associated taxa that would not have been achievable by any community-level test, as well as improved community-level tests by the LDM and PERMANOVA over those obtained using MiRKAT-S and OMiSA. Unlike existing methods, our new methods are capable of discovering individual taxa that are associated with survival times, which could be of important use in clinical settings.