Changes In Relative Abundance Research Articles

ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs

Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridisation (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. ARTseq-FISH reveals relative changes in both abundance and localisation of mRNAs and (phospho-)proteins during the first 48 hours of exit from pluripotency. We confirm these changes by conventional immunofluorescence and time-lapse microscopy. Chemical labelling, immunofluorescence, and single-cell time-lapse microscopy further show that cells closer to the edge of the micropattern exhibit increased proliferation compared to cells at the centre. Together these data suggest that while gene expression is still highly heterogeneous position-dependent differences in mRNA and protein levels emerge as early as 12 hours after LIF withdrawal.

Prospective manipulation of the gut microbiome with microbial ecosystem therapeutic 4 (MET4) in HPV-related locoregionally-advanced oropharyngeal cancer squamous cell carcinoma (LA-OPSCC) undergoing primary chemoradiation: ROMA2 study.

Gut microbiome modulation to boost antitumor immune responses is under investigation. ROMA-2 evaluated the microbial ecosystem therapeutic (MET)-4 oral consortia, a mixture of cultured human stool-derived immune-responsiveness associated bacteria, given with chemoradiation (CRT) in HPV-related oropharyngeal cancer patients. Co-primary endpoints were safety and changes in stool cumulative MET-4 taxa relative abundance (RA) by 16SRNA sequencing. Stools and plasma were collected pre/post-MET-4 intervention for microbiome and metabolome analysis. Twenty-nine patients received ≥1 dose of MET-4 and were evaluable for safety: drug-related adverse events (AEs) occurred in 13/29 patients: all grade 1-2 except one grade 3 (diarrhea). MET-4 was discontinued early in 7/29 patients due to CRT-induced toxicity, and in 1/29 due to MET-4 AEs. Twenty patients were evaluable for ecological endpoints: there was no increase in stool MET-4 RA post-intervention but trended to increase in stage III patients (p = 0.06). MET-4 RA was higher in stage III vs I-II patients at week 4 (p = 0.03) and 2-month follow-up (p = 0.01), which correlated with changes in plasma and stool targeted metabolomics. ROMA-2 did not meet its primary ecologic endpoint, as no engraftment was observed in the overall cohort. Exploratory findings of engraftment in stage III patients warrants further investigation of microbiome interventions in this subgroup.

Yarrowia lipolytica yeast as a dietary supplement for rainbow trout (Oncorhynchus mykiss): Effects on gut microbiota, health and immunity

This study evaluated the effect of whole and autolysed Yarrowia lipolytica CBS 7504 strain on growth performance, gut immunity and gut microbiota composition in juvenile rainbow trout (Oncorhynchus mykiss). Fish were fed diets containing 2% and 5% whole or autolysed Y. lipolytica (WY and AY) in a 45-day trial, with a no-yeast diet as control. Log2 fold change analysis of Y. lipolytica diets showed relative change in abundance and association of certain microbial taxa with respect to control such as a correlation between the relative abundance of Desulfovibrionaceae in diets with WY. Moreover, diets at 5% and 2% levels demonstrated a synergistic association with relative levels of Sphingobacteriaceae and Rhodobacteraceae, respectively. However, the overall analyses showed little/no impact of Y. lipolytica supplementation on overall intestinal microbial composition, growth parameters and body indices. Gene expression analysis of the intestine revealed significant elevation in expression of immune-related genes of the complement pathway (c3 and c-type lectin), membrane receptor pathway (tlr2 and tlr5), mucosal innate immune pathway (muc-2), cytokines (tnf-α) and adaptive immune pathway (igt and cd4) in 5% WY. In conclusion, it can be inferred that dietary Y. lipolytica can be a useful functional feed supplement for rainbow trout when used as whole yeast at a 5% inclusion level since it can modulate gut microbial communities and act as a potential immunostimulant for the host.

Host influence on the eukaryotic virome of sympatric mosquitoes and abundance of diverse viruses with a broad host range.

Mosquitoes harbor a large diversity of eukaryotic viruses. Those viromes probably influence mosquito physiology and the transmission of human pathogens. Nevertheless, their ecology remains largely unstudied. Here, we address two key questions in virome ecology. First, we assessed the influence of mosquito species on virome taxonomic diversity and relative abundance. Contrary to most previous studies, the potential effect of the habitat was explicitly included. Thousands of individuals of Culex poicilipes and Culex tritaeniorhynchus, two vectors of viral diseases, were concomitantly sampled in three habitats over two years. A total of 95 viral taxa from 25 families were identified with meta-transcriptomics, with 75% of taxa shared by both mosquitoes. Viromes significantly differed by mosquito species but not by habitat. Differences were largely due to changes in relative abundance of shared taxa. Then, we studied the diversity of viruses with a broad host range. We searched for viral taxa shared by the two Culex species and Aedes vexans, another disease vector, present in one of the habitats. Twenty-six out of the 163 viral taxa were found in the three mosquitoes. These taxa encompassed 14 families. A database analysis supported broad host ranges for many of those viruses, as well as a widespread geographical distribution. Thus, the viromes of mosquitoes from the same genera mainly differed in the relative abundance of shared taxa, whereas differences in viral diversity dominated between mosquito genera. Whether this new model of virome diversity and structure applies to other mosquito communities remains to be determined.

The endophytic microbiome response patterns of Juglans regia to two pathogenic fungi.

The endophytic microbial community reassembles to participate in plant immune balance when the host plants are stressed by pathogens. However, it remains unclear whether this assembly is pathogen-specific and how regulatory pathways are coordinated in multi-pathogens. In order to investigate the effects of infection with Colletotrichum gloeosporioides (Cg treatment) and Fusarium proliferatum (Fp treatment) on walnut leaf endophytic microbiome in their assembly, co-occurrence pattern, and on comprehensive chemical function of the internal environment of leaf, an interaction system of the walnut-pathogenic fungi was constructed using seed embryo tissue culture technology. The study showed differences in the assembly of endophytic microbial communities in walnut trees across three groups (control group, Ck; Cg; Fp) after Cg and Fp treatments. Despite changes in relative abundances, the dominant communities in phyla and genera remained comparable during the infection of the two pathogens. Endophyte fungi were more sensitive to the pathogen challenge than endophyte bacteria. Both promoted the enrichment of beneficial bacteria such as Bacillus and Pseudomonas, changed the modularity of the community, and reduced the stability and complexity of the endophyte community. Pathogenic fungi infection mainly affects the metabolism of porphyrin and chlorophyll, purine metabolism, phenylpropane metabolism, and amino acid metabolism. However, there was no significant difference in the secondary metabolites for the different susceptible plants. By screening endogenous antagonistic bacteria, we further verified that Pseudomonas psychrotolerans and Bacillus subtilis had inhibitory effects on the two pathogenic fungi and participated in the interaction between the leaves and pathogenic fungi. The antibacterial substances may be 1-methylnaphthalene, 1,3-butadiene, 2,3-butanediol, and toluene aldehyde.

Proteomic biomarkers in seminal plasma as predictors of reproductive potential in azoospermic men.

Azoospermia, characterized by an absence of sperm in the ejaculate, represents the most severe form of male infertility. While surgical sperm retrieval in obstructive azoospermia (OA) is successful in the majority of cases, patients with non-obstructive azoospermia (NOA) show retrieval rates of only about 50% and thus frequently have unnecessary surgery. Surgical intervention could be avoided if patients without preserved spermatogenesis are identified preoperatively. This prospective study aimed to discover biomarkers in seminal plasma that could be employed for a non-invasive differential diagnosis of OA/NOA in order to rationalize surgery recommendations and improve success rates. All patients signed written informed consent, underwent comprehensive andrological evaluation, received human genetics to exclude relevant pathologies, and patients with azoospermia underwent surgical sperm retrieval. Using label-free LC-MS/MS, we compared the proteomes of seminal plasma samples from fertile men (healthy controls (HC), n=8) and infertile men diagnosed with 1) OA (n=7), 2) NOA with successful sperm retrieval (mixed testicular atrophy (MTA), n=8), and 3) NOA without sperm retrieval (Sertoli cell-only phenotype (SCO), n=7). Relative abundance changes of two candidate markers of sperm retrieval, HSPA2 and LDHC, were confirmed by Western Blot. We found the protein expression levels of 42 proteins to be significantly down-regulated (p ≤ 0.05) in seminal plasma from SCO NOA patients relative to HC whereas only one protein was down-regulated in seminal plasma from MTA patients. Analysis of tissue and cell expression suggested that the testis-specific proteins LDHC, PGK2, DPEP3, and germ-cell enriched heat-shock proteins HSPA2 and HSPA4L are promising biomarkers of spermatogenic function. Western blotting revealed a significantly lower abundance of LDHC and HSPA2 in the seminal plasma of men with NOA (SCO and MTA) compared to controls. The results indicate that certain testis-specific proteins when measured in seminal plasma, could serve as indicators of the presence of sperm in the testis and predict the success of sperm retrieval. Used in conjunction with conventional clinical assessments, these proteomic biomarkers may assist in the non-invasive diagnosis of idiopathic male infertility.

Environmental DNA based biomonitoring for hatchery-raised fish in riverine habitats before and after recordable flood event

It is reported that the magnitudes of flood events in riverine systems have been increasing due to global climate change. Because flood events could displace fish species downstream and/or increase the mortality of fish, it is important to know how the increased floods can affect fish in river networks. In this study, we focused a hatchery-raised amphidromous fish, Ayu Plecoglossus altivelis altivelis in a mainstem-tributary network in Japan and examined the relative fish abundance changes before and after the recordable massive flood using the environmental DNA (eDNA) analysis. We also examined the spatiotemporal patterns of the Ayu eDNA concentrations and the relationships with tributary discharge, width, and depth to examine if the relative abundance changes could be related to tributary size. Our results indicated that Ayu tended to inhabit large, deep tributaries more than small, shallow tributaries even after the flood event. Further, the eDNA concentrations of Ayu have decreased in most study sites after the flood; however, the eDNA concentrations in certain tributaries with lower tributary size have increased during the study period. These results suggest that (1) the habitat conditions could be important for the maintenance of Ayu populations before and after flood events, (2) increase in flood magnitude along climate changes could have impacts on Ayu populations, and (3) not only large tributary, but also small tributaries could be important habitats for the target species to avoid flood disturbances.

460 Changes in Lipid Profiles with Progression of Pregnancy in Black Women

OBJECTIVES/GOALS: Pregnant African American (Black women) have higher rates of adverse pregnancy outcomes compared to other races and routine monitoring of lipid levels is not currently in practice in prenatal care. We hypothesized that lipid profiles would show variation across pregnancy indicative of specific requirements during gestation and fetal development. METHODS/STUDY POPULATION: We used an untargeted lipidome analysis approach to investigate lipid metabolism with the progression of pregnancy. Pregnant Black women were recruited at prenatal clinics in Midwest (Metro Detroit, Michigan and Columbus, Ohio), women under 18 or above 45 years of age were not enrolled due to metabolic changes associated with these age groups. Women signed the consent forms and plasma samples were collected at 8-18 weeks at (T1), 22-29 weeks (T2) and 30-36 weeks (T3) of pregnancy. Samples from sixty-three women (mean age 27.41 ± 5.61 years) who had term birth (completed 37 weeks of pregnancy) were subjected to “shotgun” Orbitrap high resolution/ accurate mass spectrometry. Mixed-effects models were used to quantify systematic changes in relative lipid abundances over time using R lme4 and ggplot2 packages. RESULTS/ANTICIPATED RESULTS: Total lipids and some major lipid classes showed a significant increase with the progression of pregnancy. Phospholipids and glycerolipids exhibited a gradual increase throughout pregnancy, while sphingolipids and total sterol lipids displayed a more pronounced increase at the T3 timepoint. Acylcarnitines, hydroxy acylcarnitines and Lyso phospholipids levels significantly decrease from T1 to T3. One of the interesting finding was that non-esterified fatty acids decreased from T1 to T2 and increased again from T2 to T3, suggesting a possible role for these lipids during the later stages of pregnancy. The fatty acids showing this trend included key fatty acids- Linoleic Acid, Arachidonic Acid, Alpha-linolenic acid, Eicosapentaenoic acid, Docosapentaenoic acid, Docosahexaenoic acid. DISCUSSION/SIGNIFICANCE: Mapping lipid trends during pregnancy could lend support to a precision health approach to reduce perinatal health disparities among pregnant Black women. The findings from this study will be used to identify biomarkers and study associations with social and environmental factors responsible for adverse perinatal outcome in pregnant Black women.

Using plant functional types to predict the influence of fire on species relative abundance

Fire influences plant survival, reproduction, and establishment. Consequently, plants exhibit fire-related traits. Grouping species with similar traits into Plant Functional Types (PFTs) enables predictions of fire–related change based on ecological mechanisms. However, if PFTs are to advance conservation decision-making, we must know if predictions are robust. We developed a PFT approach to predict how species relative abundance changes as a function of time since fire, and tested predictions empirically. First, we used trait databases and ecological knowledge to assign species into PFTs based on fire-related mechanisms. Second, we developed graphical predictions of fire-related change in relative abundance. Third, we collected data on species relative abundance at 57 sites, across an 81–year post–fire chronosequence. Finally, we tested predictions using non–linear regression models. Predictions of the direction of changes in relative abundance (increase or decrease from 0 to 81 years since fire) were correct for 18 of 24 species modelled. Predictions of the shape of changes in relative abundance were not as accurate, but still useful: 13 out of 24 species showed ‘excellent’ conformity with shape predictions, 7 ‘good’ conformity, and 4 ‘poor’. Broader functional groupings commonly used in ecology, such as facultative resprouter, inadequately captured changes in relative abundance. An advance of this study is that the direction and trajectory of changes in species relative abundance can be predicted using deductive PFTs that represent population processes. This suggests PFTs can be used to generalize fire responses across species that share similar traits, and thus inform biodiversity conservation and management.

Intraoperative Evaluation of Breast Tissues During Breast Cancer Operations Using the MasSpec Pen

Surgery with complete tumor resection remains the main treatment option for patients with breast cancer. Yet, current technologies are limited in providing accurate assessment of breast tissue in vivo, warranting development of new technologies for surgical guidance. To evaluate the performance of the MasSpec Pen for accurate intraoperative assessment of breast tissues and surgical margins based on metabolic and lipid information. In this diagnostic study conducted between February 23, 2017, and August 19, 2021, the mass spectrometry-based device was used to analyze healthy breast and invasive ductal carcinoma (IDC) banked tissue samples from adult patients undergoing breast surgery for ductal carcinomas or nonmalignant conditions. Fresh-frozen tissue samples and touch imprints were analyzed in a laboratory. Intraoperative in vivo and ex vivo breast tissue analyses were performed by surgical staff in operating rooms (ORs) within 2 different hospitals at the Texas Medical Center. Molecular data were used to build statistical classifiers. Prediction results of tissue analyses from classification models were compared with gross assessment, frozen section analysis, and/or final postoperative pathology to assess accuracy. All data acquired from the 143 banked tissue samples, including 79 healthy breast and 64 IDC tissues, were included in the statistical analysis. Data presented rich molecular profiles of healthy and IDC banked tissue samples, with significant changes in relative abundances observed for several metabolic species. Statistical classifiers yielded accuracies of 95.6%, 95.5%, and 90.6% for training, validation, and independent test sets, respectively. A total of 25 participants enrolled in the clinical, intraoperative study; all were female, and the median age was 58 years (IQR, 44-66 years). Intraoperative testing of the technology was successfully performed by surgical staff during 25 breast operations. Of 273 intraoperative analyses performed during 25 surgical cases, 147 analyses from 22 cases were subjected to statistical classification. Testing of the classifiers on 147 intraoperative mass spectra yielded 95.9% agreement with postoperative pathology results. The findings of this diagnostic study suggest that the mass spectrometry-based system could be clinically valuable to surgeons and patients by enabling fast molecular-based intraoperative assessment of in vivo and ex vivo breast tissue samples and surgical margins.

Forest types outpaced tree species in centroid-based range shifts under global change

IntroductionMounting evidence suggests that geographic ranges of tree species worldwide are shifting under global environmental changes. Little is known, however, about if and how these species’ range shifts may trigger the range shifts of various types of forests. Markowitz’s portfolio theory of investment and its broad application in ecology suggest that the range shift of a forest type could differ substantially from the range shifts of its constituent tree species.MethodsHere, we tested this hypothesis by comparing the range shifts of forest types and the mean of their constituent species between 1970–1999 and 2000–2019 across Alaska, Canada, and the contiguous United States using continent-wide forest inventory data. We first identified forest types in each period using autoencoder neural networks and K-means cluster analysis. For each of the 43 forest types that were identified in both periods, we systematically compared historical range shifts of the forest type and the mean of its constituent tree species based on the geographic centroids of interpolated distribution maps.ResultsWe found that forest types shifted at 86.5 km·decade-1 on average, more than three times as fast as the average of constituent tree species (28.8 km·decade-1). We showed that a predominantly positive covariance of the species range and the change of species relative abundance triggers this marked difference.DiscussionOur findings provide an important scientific basis for adaptive forest management and conservation, which primarily depend on individual species assessment, in mitigating the impacts of rapid forest transformation under climate change.

Stability of fecal microbiota during degradation in ex situ cheetahs in the USA

Objective Gut health and its relationship to gut microbiota is an important consideration in the care and well-being of managed endangered species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal sampling as a proxy for gut microbiota is preferred and collecting fresh fecal samples is the current gold standard. Unfortunately, even in managed facilities, collecting fresh samples from difficult to observe or dangerous animals is challenging. Therefore, we conducted a study to determine the terminal collection timepoint for fecal microbial studies in the cheetah. Methods We longitudinally sampled eight freshly deposited fecals every 24 h for 5 days and assessed bacterial relative abundance, diversity, and composition changes over time. Results Our data indicated that fecal samples up to 24 h post defecation provided accurate representations of the fresh fecal microbiome. After 24 h, major changes in community composition began to occur. By 72 h, individual cheetah fecal microbiota signatures were lost. Conclusion Our findings suggest that cheetah fecal samples should be collected within 24 h of defecation in humid environments, especially if precipitation occurs, in order to provide a more biologically accurate representation of the gut microbiome, and we provide visual characteristics that can aid researchers in approximating time since defecation. Significance statement Data from this study provides guidelines for researchers investigating cheetah and other large felids and carnivores where the ability to collect fresh fecal deposits is limited.

Early Succession of Community Structures and Biotic Interactions of Gut Microbes in Eriocheir sinensis Megalopa after Desalination.

As an enduring Chinese freshwater aquaculture product, the Eriocheir sinensis has a high economic value and is characterized by a catadromous life style that undergoes seawater-freshwater migration. However, little is known about their gut microbial status as they move from saltwater to freshwater acclimatization. Here, we sampled and cultivated Eriocheir sinensis megalopa from three aquaculture desalination ponds and investigated their gut microbiota diversity, community structures and biotic interactions from megalopa stage to the first juvenile stage after desalination for 9 days. Our results revealed that during the transition from megalopa to the first juvenile in Eriocheir sinensis, a significant change in gut microbial composition was observed (for instance, changes in relative abundance of dominant phyla), which was, however, not influenced by different sampling sites. The species diversity (such as the richness) of the gut microbiota showed a hump-shaped pattern along the succession. However, the compositional differences of the gut microbes showed constantly increasing patterns during the succession after freshwater adaption for all three sampling sites. Further co-occurrence analysis also showed that the complexity of the ecological networks in gut microbes was significantly enhanced during the development, such as increasing numbers of network links, connectivity and modularity, and was confirmed by decreasing average path length and proportions of negative links. Taken together, the differences in community structures and biological interactions of gut microorganisms were more pronounced in Eriocheir sinensis megalopa during desalination than in diversity and species compositions. This implies that the gut microbes of Eriocheir sinensis megalopa would become more robust and adaptive during the developmental process.

Changes in Relative Abundance of Giant Silkworm and Royal Moths (Saturniidae) in Megalopolises, with Special Reference to Antheraea polyphemus

Changes in Relative Abundance of Giant Silkworm and Royal Moths (Saturniidae) in Megalopolises, with Special Reference to Antheraea polyphemus

Gut microbiota-derived 5-hydroxyindoleacetic acid from pumpkin polysaccharides supplementation alleviates colitis via MAPKs-PPARγ/NF-κB inhibition

Polysaccharides from Pumpkin (Cucurbita moschata Duchesne) (PPs) have many pharmacological activities, including anti-oxidant, immune, and intestinal microbiota regulation. These activities have provided some reminders of its potential therapeutic effect on ulcerative colitis (UC), but this has not yet been confirmed. This study preliminarily confirmed its significant anti-UC activity superior to Salicylazosulfapyridine. The average molecular weight of PPs was 3.10 × 105 Da, and PPs mainly comprised Mannose, Rhamnose, Galacturonic acid, Galactosamine, Glucose, and Xylose with molar ratios of 1.58:3.51:34.54:1.00:3.25:3.02. PPs (50, 100 mg/kg) could significantly resist dextran sodium sulfate induced UC on C57BL/6 mice by improving gut microbiota dysbiosis, such as the changes of relative abundance of Bacteroides, Culturomica, Mucispirillum, Escherichia-Shigella, Alistipes and Helicobacter. PPs also reverse the abnormal inflammatory reaction, including abnormal level changes of TNF-α, IFN-γ, IL-1β, IL-4, IL-6, IL-10, and IL-18. Metabolomic profiling showed that PPs supplementation resulted in the participation of PPAR and MAPK pathways, as well as the increase of 5-hydroxyindole acetic acid (5-HIAA) level. 5-HIAA also exhibited individual and synergistic anti-UC activities in vivo. Furthermore, combination of PPs and 5-HIAA could also elevate the levels of PPARγ in nuclear and inhibit MAPK/NF-ĸB pathway in the colon. This study revealed that PPs and endogenous metabolite 5-HIAA might be developed to treat UC.

Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.

The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.

A Randomized, Double-Blind, Phase 3 Safety and Efficacy Study of Ridinilazole Versus Vancomycin for Treatment of Clostridioides difficile Infection: Clinical Outcomes With Microbiome and Metabolome Correlates of Response.

Exposure to antibiotics predisposes to dysbiosis and Clostridioides difficile infection (CDI) that can be severe, recurrent (rCDI), and life-threatening. Nonselective drugs that treat CDI and perpetuate dysbiosis are associated with rCDI, in part due to loss of microbiome-derived secondary bile acid (SBA) production. Ridinilazole is a highly selective drug designed to treat CDI and prevent rCDI. In this phase 3 superiority trial, adults with CDI, confirmed with a stool toxin test, were randomized to receive 10 days of ridinilazole (200 mg twice daily) or vancomycin (125 mg 4 times daily). The primary endpoint was sustained clinical response (SCR), defined as clinical response and no rCDI through 30 days after end of treatment. Secondary endpoints included rCDI and change in relative abundance of SBAs. Ridinilazole and vancomycin achieved an SCR rate of 73% versus 70.7%, respectively, a treatment difference of 2.2% (95% CI: -4.2%, 8.6%). Ridinilazole resulted in a 53% reduction in recurrence compared with vancomycin (8.1% vs 17.3%; 95% CI: -14.1%, -4.5%; P = .0002). Subgroup analyses revealed consistent ridinilazole benefit for reduction in rCDI across subgroups. Ridinilazole preserved microbiota diversity, increased SBAs, and did not increase the resistome. Conversely, vancomycin worsened CDI-associated dysbiosis, decreased SBAs, increased Proteobacteria abundance (∼3.5-fold), and increased the resistome. Although ridinilazole did not meet superiority in SCR, ridinilazole greatly reduced rCDI and preserved microbiome diversity and SBAs compared with vancomycin. These findings suggest that treatment of CDI with ridinilazole results in an earlier recovery of gut microbiome health. Clinical Trials Registration.Ri-CoDIFy 1 and 2: NCT03595553 and NCT03595566.

Light-dark cycles may influence insitu soil bacterial networks and diurnally-sensitive taxa.

Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities insitu over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils insitu across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities insitu and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.

THE MODULATORY EFFECT OF PREBIOTIC INULIN-TYPE FRUCTANS ON THE MICROBIOME PROFILE OF CHILDREN WITH INFLAMMATORY BOWEL DISEASE: A DOUBLE-BLIND RANDOMIZED CONTROLLED TRIAL

Abstract OBJECTIVE The intestinal microbiota plays a pivotal role in the inflammation associated with inflammatory bowel disease (IBD) through their interaction with the mucosal immune system. Prebiotic interventions using inulin-type fructans increase faecal and mucosal bifidobacteria as well as butyrate producing bacteria in healthy volunteers. The aim of this study was to assess the effect of a two-month oligofructose-enriched inulin (OI) supplementation on the microbiome composition, metabolome of children with IBD with subclinical disease activity. DESIGN We performed a single-center, double-blind, placebo-controlled trial at the Children’s Hospital of Philadelphia. Participants included children, 6–21 years old, with subclinical active colonic IBD as defined by a fecal calprotectin level between 50 and 500 μg/g and clinical remission. Participants were randomly assigned 1:1 to consume prebiotic OI or maltodextrin placebo for 8 weeks. Fecal and rectal swabs samples were collected at baseline, week 4, 8 and 16 for fecal calprotectin, microbiome profiling (shotgun metagenomic sequencing) and matching metabolomics (liquid chromatography tandem mass spectrometry). RESULTS The study randomized 68 patients, and 59 were included in the efficacy analyses. The global fecal and mucosal microbiome composition was significantly altered by prebiotic intake and specific inulin-induced increase in relative abundance of Bifidobacterium and Anaerostipes in the fecal samples were identified at week 4 (Figure 1). Two months after discontinuation of OI, the microbial composition of both groups returned to baseline levels. Fecal metabolite profiles were not altered during the 8-week intervention. A negative correlation was observed between calprotectin levels and the relative abundance of Bifidobacterium [q=0.08] and butyrate producer Anaerostipes [q=0.017] (Figure 2). Outcome analysis of inulin-induced change in calprotectin level during the intervention is pending. CONCLUSIONS Dietary intervention with prebiotic OI causes short term alterations in the microbiome of children with IBD characterized by an enrichment of Bifidobacterium and butyrate producer Anaerostipes. These results open new perspectives for development of microbiome-targeted dietary interventions in pediatric IBD. JB received the Crohn’s and Colitis Foundation Career Development Award # 693867 for this study. Figure 1 Selective effect of prebiotic supplementation on microbiome composition Figure 2 Correlation between calprotectin level and inulin-induced microbiome shift A negative correlation between fecal calprotectin level and inulin-induced change in relative abundance of Bifidobacterium [q= 0.08] and Anaerostipes [q=0.017] was observed during the 8-week intervention.

Bird atlas in action: using citizen science data to generate population trend alerts in Hessequa, South Africa

Citizen science data are rapidly transforming the conservation landscape. Targeted participatory citizen science initiatives generate nuanced data capable of monitoring trends in populations and generating early warnings for species and habitats experiencing significant declines. In the Hessequa Atlasing Area, Western Cape, South Africa, citizen science 'atlasers' involved with the Second Southern African Bird Atlas Project (SABAP2) have worked with scientific leadership since 2014 to improve the quality of bird atlas data in their region for species monitoring. In this study, we used reporting rates from SABAP2 checklists in the Hessequa Atlasing Area to calculate changes in range size and relative abundance for the 165 most commonly reported species in the region. We used a seven-tier alert system and broad habitat categories to sort species by priority for conservation action. Our results showed that wetland and marine associated species are experiencing the greatest declines in range and relative abundance in the Hessequa Atlasing Area, whilst urban and grassland associated species are largely increasing. We discuss how observed changes in populations may be used to guide conservation action and provide recommendations for scientists and non-scientific community members on engaging with and responding to the changes highlighted in each of the seven alert levels provided.