Permutational Multivariate Analysis Research Articles

C‐section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice

In humans and animal models, Cesarean section (C‐section) has been associated with alterations in the taxonomic structure of the gut microbiome. These changes in microbiota populations are hypothesized to impact immune, metabolic, and behavioral/neurologic systems and others. It is not clear if birth mode inherently changes the microbiome, or if C‐section effects are context‐specific and involve interactions with environmental and other factors. To address this and control for potential confounders, cecal microbiota from ~3 week old mice born by C‐section (n = 16) versus natural birth (n = 23) were compared under matched conditions for housing, cross‐fostering, diet, sex, and genetic strain. A total of 601 unique species were detected across all samples. Alpha diversity richness (i.e., how many species within sample; Chao1) and evenness/dominance (i.e., Shannon, Simpson, Inverse Simpson) metrics revealed no significant differences by birth mode. Beta diversity (i.e., differences between samples), as estimated with Bray‐Curtis dissimilarities and Aitchison distances (using log[x + 1]‐transformed counts), was also not significantly different (Permutational Multivariate ANOVA [PERMANOVA]). Only the abundance of Lachnoclostridium [Clostridium] scindens was found to differ using a combination of statistical methods (ALDEx2, DESeq2), being significantly higher in C‐section mice. This microbe has been implicated in secondary bile acid production and regulation of glucocorticoid metabolism to androgens. From our results and the extant literature we conclude that C‐section does not inherently lead to large‐scale shifts in gut microbiota populations, but birth mode could modulate select bacteria in a context‐specific manner: For example, involving factors associated with pre‐, peri‐, and postpartum environments, diet or host genetics.

Regional and local environment drive biogeographic patterns in intertidal microorganisms

AbstractAimUnderstanding large‐scale spatial distribution patterns is not only a central goal of ecology but is also essential for conservation planning. Nevertheless, the biogeographical patterns of diversity and composition remain unclear for microorganisms and the role of various factors in structuring their assemblages is still poorly known. Here, we tested whether the diversity and community structure of ciliates are driven by both local environmental and regional dispersal‐related processes.LocationCoasts of China.TaxonBenthic ciliates.MethodsWe sampled ciliates at 30 sandy beaches covering a latitudinal range of over 2500 km from October to November 2020. We first used generalized linear models to examine the most important predictors of ciliate alpha diversity. Then, distance‐based linear models (DistLM) were used to identify the relative importance of local and regional variables in explaining community structure variability. We further used nonmetric multidimensional scaling (NMDS) and permutational multivariate analysis of variance (PERMANOVA) to reveal patterns in community structure.ResultsWe found that local environmental factors including beach index (BI), salinity and mean particle size (MPS) were more important in shaping ciliate alpha diversity than latitude. However, the Shannon alpha diversity index decreased with latitude, perhaps due to anthropogenic disturbances. DistLM analysis emphasized regional processes in shaping community structure. Both NMDS and PERMANOVA supported a clear separation among the three clusters matching with the ecoregional delineations suggested for macroorganisms. We also note that community trait composition was partially explained by a local factor, i.e. the maximum spring tide range of beaches.Main conclusionsCiliate communities were driven by both local environmental and regional factors. We suggest that these biogeographic patterns may have stemmed from large‐scale environmental filtering related to the outflow of Yangtze River, rather than from dispersal limitation or historical events. The current study provides a new understanding of the biogeographic patterns and underlying mechanisms of marine microorganisms, thus helping improve their management and conservation in the face of future global change.

Multiple surface runoff and soil loss responses by sandstone morphologies to land-use and precipitation regimes changes in the Loess Plateau, China

In this research, a long-term (2014–2020) approach to quantify surface runoff and soil loss generated by different land use and precipitation regimes on Pisha sandstone hillslopes from the Loess Plateau, China was carried out. Using the K-means clustering algorithm, 50 precipitation events were classified into three different regime types based on depth, duration, and maximum 30-minute intensity. Permutational multivariate analysis of variance (PERMANOVA) and Principal component analysis (PCA) were used to test clustering rationality. Our results suggest that runoff coefficient (RC) and soil loss (SL) exhibited significant differences depending on precipitation regimes: heavy storms (precipitation regime II) were found to induce the largest surface runoff and soil loss, followed by precipitation regimes I and III. RC and SL were also found with significant differences (p < 0.05) related to different land-use types. Mean RC and erosion rates among the six land-use types analyzed varied as bare land > cropland > artificial grassland > native grassland > shrubland > forestland. Results of this study suggest more attention should be paid to vegetation selection and land-use type depending on precipitation regimes in Pisha sandstone morphologies. Accordingly, forestland and shrubland should be the first choices to control soil erosion when land-use conversion is implemented, whereas bare land, croplands, or artificial grassland (e.g., alfalfa) should be carefully considered and future vegetation restoration policies should assess the proper re-vegetation type before any action may be initiated.

Abstract 720: Comparison of the gut microbiome between children with solid tumor receiving chemotherapy and healthy children

Abstract Background: Chemotherapy is commonly used for children with cancer. Intensive chemotherapy can disturb the gut microbiome, which may be associated with treatment-related toxicities. This study aimed to compare profiles of the gut microbiome in children with solid tumors pre- and post-chemotherapy with those of healthy children. Methods: A case-control study was conducted in 44 children (21 with solid tumors and 23 healthy). Children aged 7-18 years with solid tumors receiving chemotherapy were recruited from Children’s Healthcare of Atlanta (CHOA); healthy children were recruited by e-news in CHOA. The gut microbiome was measured using stool specimens that were collected pre cycle 2 chemotherapy and post the completion of all chemotherapy for cancers, and only once for healthy controls. Demographics and clinical variables (e.g., race and use of antibiotics) were reported by parents. Bacterial 16S rRNA gene V4 region was amplified and sequenced. Bacterial taxonomies were assigned using the Silva reference via QIIME 2. Permutational multivariate analysis of variance, analysis of composition of microbiomes, and linear discriminant analysis effect size were used to compare the gut microbiome between cancer and healthy children. Results: Children with solid tumors and healthy controls showed no differences in age, race, and BMI; more boys were enrolled in the solid tumor group than the healthy group (p=0.009). Both groups were dominated by phyla Firmicutes and Bacteroidetes. Compared to healthy children, children with solid tumors had significantly lower α-diversity metrics: Shannon p=0.042 and Chao1 p=0.015; children pre- (Shannon p=0.021; Chao1 p=0.024) and post-chemotherapy (Shannon p=0.011; Chao1 p=0.025) showed lower α-diversity metrics than healthy children; and difference was not significant between children pre- and post-chemotherapy. The β-diversity analysis (Bray-Curtis distance) showed that study group (p=0.008), gender (p=0.017), race (p=0.009), and cancer type (p=0.001) impacted the gut microbiome dissimilarities. Children with solid tumors had a lower abundance of phylum Verrucomicrobiotaand a higher abundance of genus Acidaminoccous than healthy controls; healthy children had a higher abundance of beneficial genera Prevotella and Akkermansia. Children with solid tumors had enriched in pathogenic oropportunistically pathogenic genera Clostridioides and Enterococcus. Children post all chemotherapy had enriched genera Blautia and CAG-352 associated with gut-brain axis. Conclusions: Children with solid tumors suggested different diversity profiles of the gut microbiome and a higher abundance of pathogenic taxa than healthy children. These different gut microbial profiles may be associated with treatment toxicities. Additional studies are needed to further corroborate these associations in children with cancer and reveal the underlying mechanisms. Citation Format: Jinbing Bai, Kumru Kocaman, Julia Slack, Melissa Martin, Christie Powell, Kathryn S. Sutton, Bradley George, Thomas Olson, Konstantinos T. Konstantinidis, Deborah W. Bruner. Comparison of the gut microbiome between children with solid tumor receiving chemotherapy and healthy children [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 720.

Microbial community diversity changes during voltage reversal repair in a 12-unit microbial fuel cell

Microbial fuel cell stacks (MFC-Stack) are often confronted with voltage reversals, likely due to an interplay between microbial community dynamics and insufficient electric circuit balancing. Herein, we provide new insight into voltage reversals by examining the microbiomes of twelve MFC units of a 12-liter Pilot-MFC-Stack during repair. Different biofilm repair methods (self-healing, electrostimulation, and re-acclimatization upon cross-inoculation) were used to evaluate the microbial community response. In addition, MFC-Stack simulation was performed based on Kirchhoff’s Second Law to predict values for source potentials and post-evaluate internal resistances. Analysis of the 16S rRNA amplicon sequencing data suggests that the biofilm repair methods could slowly heal damaged biofilms. Notably, severely voltage reversed MFC units had low electrogen relative abundances (18%) and positive anode potentials, while strong bioanodes and contained more than 50% electrogens and had negative anode potentials. Between-community analyses (beta diversity ordination and multinomial regression) of the voltage reversed MFC units revealed differences among biofilms in contrast to healthy/strong MFC units. Permutational multivariate analysis of variance (PERMANOVA) confirmed that reversed biofilms were, indeed, significantly (p < 0.05) different from stronger ones. Overall, these analyses demonstrated the utility of combining electrotechnical and microbial community analyses, especially beta diversity ordination and multinomial regression, to understand problematic MFC units and the potential success of a biofilm repair method. Finally, thicker biofilms were usually healthier and stronger, although thickness was no guarantee for proper structure and power function as all factors were interdependent. There was an evolutionary trend that strong anodes became stronger/healthier and others weaker. This spontaneous trend has to be considered to avoid irreversible voltage reversals and to repair electrogenic biofilms in an MFC-Stack.

Diet-Associated Variability in the Elderly Gut Microbiome

ObjectivesThe gut microbiome adapts to diet variations, which contribute to interindividual variability in human host metabolism and environmental factors. Microbe-diet studies have largely focused on specific diets (e.g., high-fat Western, Mediterranean-style) in American and European populations, with limited studies on compositionally-different diets in Asian populations. This study aimed to understand how diet composition modulates the gut microbiome in a Singapore multi-ethnic population.MethodsWe performed metagenomic sequencing of faecal samples from 118 healthy individuals (66 ± 5 years old), and estimated their food and nutrient intakes from 3-day food records (IRB-2018–01-011). Multivariate associations between microbial composition (species) and functional potentials (pathways, enzymes) with diet variables were analysed using linear mixed models with Benjamin-Hochberg correction, and adjusted for age, sex, BMI, physical activity, energy intake and medications. Permutational multivariate analysis of variance, based on Bray-Curtis dissimilarity metric, was applied to quantify variance within the microbiome that is explained by diet variables.ResultsWe found gut microbes (5 phyla, >100 species) significantly associated with one of four observed dietary patterns (P < 0.05), various food groups and nutrients (q < 0.1). The microbiome was driven by intake and diversity of plant-based foods. Parabacteroides and Blautia species, and microbial metabolism of energy, carbohydrate and glycan were associated with increased intakes of white rice and noodles. Prevotella species were associated with increased intakes of legumes, wholegrains and plant protein. Lachnospira, Clostridiumand Fournierella species, and microbial lipid metabolism were associated with energy-dense diet. Lastly, Firmicutes, Eubacterium, Ruminococcus and Roseburia species as well as microbial regulation of amino acid metabolism were associated with high-fibre diet.ConclusionsThis study provides new insights into gut microbial variations by distinct Asian dietary composition, supporting the feasibility of intervening habitual diets to reshape the gut microbiome for better health.Funding SourcesThis project was funded by LKC, CONIC and ARISE, NTU, and NTU-CSIRO Precision Health and Technologies Seed Fund.

Four Dietary Patterns Observed Within an Elderly Asian Cohort

ObjectivesDietary indices are largely established in American and European populations to measure diet quality based on the predominant food type and quantity consumed in those countries. However, applying these dietary indices to Asian or South Asian populations is complicated by diverse region-specific eating patterns, cultures and food availability. A challenge exists to identify a more relevant dietary index that agrees with distinct dietary patterns within the multi-ethnic Singapore context and what measures of dietary quality are appropriate for the unique food availability. This study aimed to characterise dietary patterns and quality in older Singapore individuals.MethodsDaily energy, food and nutrient intakes were estimated from 2 sets of 3-day food records (IRB-2018–01-011)using an in-house and public databases (Singapore Food and Nutrient Composition database, and Phenol-Explorer). Diet composition was categorised into 33 food groups and hierarchical clustering (Ward's method) was performed to characterise habitual dietary patterns based on energy intake. Adherence to Healthy Eating Index (HEI) and MEDI-LITE score were assessed. Differences in energy, food groups and nutrients were analysed using Kruskal-Wallis test and permutational multivariate analysis of variance.ResultsWe observed four distinct dietary patterns- i) noodle/rice-based diet, ii) highly refined diet, iii) energy-dense diet and iv) high-fibre diet consumed by 21%, 27%, 36% and 16% of the cohort, respectively (66 ± 5 years old, 1640–1874 kcal/day). Two patterns comprised high intakes of refined foods (i.e., white rice, bread, noodles), differed substantially from Western or Mediterranean diets and were characterised by higher visceral trunk fat. In contrast, the high-fibre pattern had favourable cardiometabolic risk markers and reduced body fat. These dietary patterns did not fit with HEI and MEDI-LITE score, considering the preference for rice, noodles and spices in Asian diets, and reduced preference for cereals, olive oil and red wine (emphasised in MEDI-LITE score).ConclusionsStudying populations exposed to regionally diverse food components challenge the relevance of applying previously established diet indices.Funding SourcesThis project was funded by LKC, CONIC and ARISE, NTU, and NTU-CSIRO Precision Health and Technologies Seed Fund.

Advances on Permutation Multivariate Analysis of Variance for big data

Abstract In many applications of the multivariate analyses of variance, the classic parametric solutions for testing hypotheses of equality in population means or multisample and multivariate location problems might not be suitable for various reasons. Multivariate multisample location problems lack a comparative study of the power behaviour of the most important combined permutation tests as the number of variables diverges. In particular, it is useful to know under which conditions each of the different tests is preferable in terms of power, how the power of each test increases when the number of variables under the alternative hypothesis diverges, and the power behaviour of each test as the function of the proportion of true alternative hypotheses. The purpose of this paper is to fill the gap in the literature about combined permutation tests, in particular for big data with a large number of variables. A Monte Carlo simulation study was carried out to investigate the power behaviour of the tests, and the application to a real case study was performed to show the utility of the method.

Assessing the catch efficiency of predators in the presence of prey using experimental gillnets in a temperate estuary

Fishery-independent sampling is designed to representatively sample faunal communities based on the effort-standardized catch rates of individual gears. In estuaries, experimental gillnets are widely used due to their ability to passively sample mobile fish communities with multiple panels of decreasing mesh sizes. To test if concurrently collected prey in experimental gillnets create a trophic-related sampling bias for predatory or scavenging (hereafter, predators) species, we set large mesh gillnets comprising two treatments, baited (n = 80) and unbaited (n = 78), using a paired design in Back Sound, North Carolina. Furthermore, we analyzed data from the North Carolina Division of Marine Fisheries (NC DMF) estuarine gillnet monitoring program with boosted regression tree models to correlate estuarine predator occurrence with environmental factors (salinity, temperature), habitat presence, and families of common prey species as predictor variables. In our experimental manipulation, neither total catch nor community composition statistically varied between treatments, determined using permutational multivariate analysis of variance (PERMANOVA). However, species richness estimated using species accumulation curves was higher in baited gillnets, with one frequently caught species (Atlantic sharpnose sharks) collected exclusively in baited gillnets. In NC DMF surveys, prey group variables were more important (average model importance; 10% ± 8.8% SD) than habitat composition (2% ± 1.7%) to the presence of predators, but less than abiotic environmental variables (21.1% ± 13.1%). This combined manipulative and mensurative study revealed mixed evidence towards increased catch efficiency of predatory fish collected in widely used experimental gillnets. These results should be considered in refining abundance estimations for estuarine predators, as catch efficiency for some piscivorous predators may vary in relation to the abundance and catch efficiency of prey.

Composition and structure of the parasitic fauna of Hypostomus spp. (Loricariidae: Hypostominae) from a Neotropical river in Brazil.

Hypostomus are abundant in Brazilian rivers and streams. In the Ivaí River, the loricariids represent 20.3% of the total species of the basin. Of these 13 species belong to Hypostomus. However, to date, there are no studies on these fish parasitic fauna. Thus, this research aimed to analyze the distribution of the parasitic infracommunity of six species of Hypostomus from the Ivaí River and investigate how the infracommunity is structured in these hosts. One hundred and twenty-eight fish were analyzed, belonging to six sympatric species of Hypostomus (Hypostomus hermanni, H. cochliodon, H. albopunctatus, H. regani, Hypostomus sp.1, and Hypostomus sp.2); of these, 92.9% were parasitized with at least one taxon, totaling 1478 specimens of parasites. The parasitic fauna was composed of the ectoparasites Trinigyrus anthus, T. carvalhoi, Unilatus unilatus (monogeneans), and Placobdella spp. (hirudinea), and the endoparasites Austrodiplostomum compactum (digenean) and Procamallanus annipetterae (nematode). The parasites exhibited similar patterns of infection in all hosts, including a low number of species, low diversity, and numerical dominance of a group of parasites. However, permutational multivariate analysis of variance (PERMANOVA) showed different parasite species compositions among the hosts. Hypostomus cochliodon and H. regani had the highest parasite richness, while Hypostomus sp.1 and Hypostomus sp.2 showed low abundance and intensity of parasitic infections. However, Hypostomus sp.1 showed the highest values of evenness, although the parasite composition in both species did not differ. The results presented herein contribute to increasing the knowledge about the parasitic fauna of Hypostomus spp. from the Ivaí River by presenting new hosts and locality records.

Nutrient Control of Phytoplankton Abundance and Biomass, and Microplankton Assemblage Structure in the Lower Columbia River (Vancouver, Washington, USA)

Nutrient limitation of phytoplankton is common but by no means universal in large temperate rivers. Previous field studies in the Columbia River, USA, are suggestive of nutrient limitations of phytoplankton, especially during summer, but this has never been tested experimentally. We therefore undertook monthly 5-day nutrient amendment incubation experiments from May–September 2018 using Columbia River water collected at Vancouver, Washington, USA. We compared replicate treatment bottles containing natural microplankton assemblages and amended nutrients (NO3, PO4 and SiO4 in combination) with replicate control bottles containing natural microplankton assemblages and ambient nutrients. Phytoplankton abundance and biomass were compared between treatments and controls on each day of each experiment, and microplankton assemblage structure was evaluated using Permutational Multivariate Analysis of Variance and Non-Metric Multi-Dimensional Scaling ordination on Day 0 (ambient) and Day 5 of each experiment. Nutrient amendment significantly affected phytoplankton abundance and biomass, particularly in June–August, although this varied between taxa (e.g., cyanobacteria, dinoflagellates, flagellates and ciliates showed more frequent positive responses than chlorophytes and diatoms did). Abundance-based microplankton assemblage structure was significantly correlated with PO4, SiO4 and NO3 concentrations, and BIOENV procedure in R revealed that the best subset of explanatory variables included SiO4 and NO3 concentrations. Biomass-based assemblage structure was significantly correlated with SiO4 and NO3, although BIOENV explanatory variables included only SiO4. These results are suggestive of summertime nutrient control of phytoplankton abundance and biomass, as well as microplankton composition, in the lower Columbia River, at least during some months. Since eutrophication is increasing in the watershed, this could have important implications for higher level consumers (e.g., zooplankton and out-migrating juvenile salmon).

Associations of Blautia Genus With Early-Life Events and Later Phenotype in the NutriHS.

IntroductionEarly-life events are associated with the risk of obesity and comorbidities later in life. The gut microbiota—whose composition is influenced by genetics and environmental factors—could be involved. Since the microbiota affects metabolism and fat storage, early-life insults could contribute to the occurrence of obesity driven, in part, by microbiota composition. We examined associations of gut bacteria with early-life events, nutritional status, and body composition in the Nutritionist’s Health Study (NutriHS).MethodsA cross-sectional study of 114 female participants examining early-life data, body composition, and biological samples was conducted. Fecal microbiota structure was determined targeting the V4 region of the 16S rRNA gene. Principal coordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) were used to test the impact of variables on microbial diversity. Profiles were identified using the Jensen-Shannon divergence matrix and Calinski–Harabasz index. Differential abundance between the categories of exclusive breastfeeding duration and nutritional status was tested using DESeq2.ResultsIn the sample [median age 28 years and body mass index (BMI) 24.5 kg/m2], 2 microbiota profiles driven by the Blautia or Prevotella genus were identified. An estimated 9.1% of the variation was explained by the profiles (p < 0.001), 2.1% by nutritional status (p = 0.004), and 1.8% by exclusive breastfeeding (p = 0.012). The proportion of participants with BMI <25 kg/m2 and who were breastfed for at least 6 months was higher in the Blautia profile (p < 0.05).ConclusionFindings in a Blautia-driven profile of healthy women reinforce that early-life events play a role in defining gut microbiota composition, confirming the importance of exclusive breastfeeding for infant gut colonization in establishing a protective profile against adiposity-related outcomes in adulthood.

Peripheral B-cell dysregulation is associated with relapse after long-term quiescence in patients with multiple sclerosis.

B cells play a major role in multiple sclerosis (MS), with many successful therapeutics capable of removing them from circulation. One such therapy, alemtuzumab, is thought to reset the immune system without the need for ongoing therapy in a proportion of patients. The exact cells contributing to disease pathogenesis and quiescence remain to be identified. We utilized mass cytometry to analyze B cells from the blood of patients with relapse‐remitting MS (RRMS) before and after alemtuzumab treatment, and during relapse. A complementary RRMS cohort was analyzed by single‐cell RNA sequencing. The R package “Spectre” was used to analyze these data, incorporating FlowSOM clustering, sparse partial least squares‐discriminant analysis and permutational multivariate analysis of variance. Immunoglobulin (Ig)A+ and IgG1 + B‐cell numbers were altered, including higher IgG1 + B cells during relapse. B‐cell linker protein (BLNK), CD40 and CD210 expression by B cells was lower in patients with RRMS compared with non‐MS controls, with similar results at the transcriptomic level. Finally, alemtuzumab restored BLNK, CD40 and CD210 expression by IgA+ and IgG1 + B cells, which was altered again during relapse. These data suggest that impairment of IgA+ and IgG1 + B cells may contribute to MS pathogenesis, which can be restored by alemtuzumab.

The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat

BackgroundDespite well-known effects of diet on gut microbiota diversity, relatively little is known about how maternal diet quality shapes the longitudinal maturation of gut microbiota in offspring. To investigate, we fed female rats standard chow (Chow) or a western-style, high-choice cafeteria diet (Caf) prior to and during mating, gestation and lactation. At weaning (3 weeks), male and female offspring were either maintained on their mother’s diet (ChowChow, CafCaf groups) or switched to the other diet (ChowCaf, CafChow). Fecal microbial composition was assessed in dams and longitudinally in offspring at 3, 7 and 14 weeks of age.ResultsThe effect of maternal diet on maturation of offspring gut microbiota was assessed by α- and β-diversities, Deseq2/LEfSe, and SourceTracker analyses. Weanling gut microbiota composition was characterised by reduced α- and β-diversity profiles that clustered away from dams and older siblings. After weaning, offspring gut microbiota came to resemble an adult-like gut microbiota, with increased α-diversity and reduced dissimilarity of β-diversity. Similarly, Deseq2/LEfSe analyses found fewer numbers of altered operational taxonomic units (OTUs) between groups from weaning to adulthood. SourceTracker analyses indicated a greater overall contribution of Caf mothers’ microbial community (up to 20%) to that of their offspring than the contribution of Chow mothers (up to 8%). Groups maintained on the maternal diet (ChowChow, CafCaf), versus those switched to the other diet (ChowCaf, CafChow) post-weaning significantly differed from each other at 14 weeks (Permutational Multivariate Analysis of Variance), indicating interactive effects of maternal and post-weaning diet on offspring gut microbiota maturation. Nevertheless, this developmental trajectory was unaffected by sex and appeared consistent between ChowChow, CafCaf, ChowCaf and CafChow groups.ConclusionsIntroducing solid food at weaning triggered the maturation of offspring gut microbiota to an adult-like profile in rats, in line with previous human studies. Postweaning Caf diet exposure had the largest impact on offspring gut microbiota, but this was modulated by maternal diet history. An unhealthy maternal Caf diet did not alter the developmental trajectory of offspring gut microbiota towards an adult-like profile, insofar as it did not prevent the age-associated increase in α-diversity and reduction in β-diversity dissimilarity.

Reversal of temperature responses to methylone mediated through bi-directional fecal microbiota transplantation between hyperthermic tolerant and naïve rats

ABSTRACT The synthetic cathinone (“bath salt”) methylone induces a hyperthermia response and with chronic administration tolerance to this hyperthermia has been reported. The microbiome-gut-brain axis has been implicated in multiple bodily systems and pathologies, and intentional manipulation of the gut-microbiome has yielded clinically significant results. Here, we examined the effects of bi-directional Fecal Microbiota Transplantation (FMT) between methylone-induced hyperthermic tolerant (MHT) and methylone-naïve (MN) rats. Rats treated with methylone once per week developed tolerance to methylone-induced hyperthermia by the fourth week. Once tolerant, daily bi-directional FMT between the two groups were performed for seven days prior to the next methylone treatment. The FMT abated the developed tolerance in the MHT group. When treated with methylone for the first time following FMT, recipient MN rats displayed significant tolerance to hyperthermia despite it being their initial drug treatment. Post-FMT, MHT rats displayed elevations in norepinephrine and expression of UCP1, UCP3 and TGR5 in brown adipose tissue, with reductions in expression of TGR5 and UCP3 in skeletal muscle. The pre- and post-FMT methylone tolerance phenotypes of transplant recipients are concurrent with changes in the relative abundance of several classes of Proteobacteria, most evident for Gammaproteobacteria and Alphaproteobacteria. MHT recipients demonstrated a marked increase in the relative proportion of the Firmicutes class Erysipelotrichia. These findings suggest that transplantation of gut-microbiomes can confer phenotypic responses to a drug and that the microbiome may be playing a major role in sympathomimetic-mediated hyperthermia. Abbreviations: 3,4-methylenedioxymethamphetamine (MDMA); methylone-induced hyperthermic tolerant (MHT); methylone-naïve (MN); fecal microbiota transplantation (FMT); uncoupling protein (UCP); subcutaneous (sc); intraperitoneal (ip); brown adipose tissue (BAT); skeletal muscle (SKM); sympathetic nervous system (SNS); norepinephrine (NE); quantitative PCR (qRT-PCR); quantification cycle (Cq); High Performance Liquid Chromatography-Electrochemical Detection (HPLC-EC); amplicon sequence variants (ASVs); principal coordinates analysis (PCoA); permutational multivariate analysis (PERMANOVA)

Time after time: detecting annual patterns in stream bacterial biofilm communities.

SummaryTo quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

Effects of drying and orientation to perennial refuges on aquatic biodiversity across two basins differing in aridity

AbstractIntermittent streams are globally distributed, comprise over half the length of the global river network, and are expected to become more prevalent. However, most studies of intermittent streams are conducted at extremes of scale, are limited in taxonomic and temporal scope, and focus exclusively on drying patterns. Here, we assessed how both flow intermittency and orientation to perennial refuges affect aquatic invertebrates and aquatic and semiaquatic vertebrates across 2 years within two intermittent river basins differing in their aridity. We used loggers to characterize flow intermittency and wet–dry mapping to determine orientation to perennial refuges of reaches. In winter and summer 2015 and 2016, we collected and identified invertebrates and visually surveyed vertebrates. Using permutational multivariate analyses of variance with distance matrices, we found distinct invertebrate communities by basin, flow class (perennial or intermittent), and season, and distinct vertebrate communities by basin, and between flow classes and seasons in the more arid basin. Invertebrate communities had higher beta diversity in the more arid than mesic basin, whereas the opposite was true for vertebrates. We identified indicator species for all combinations of basin and flow class, perennial reaches combined from both basins, each basin, and some combinations of flow class and season within basins. Flow intermittency and orientation to perennial refuge predictors correlated well with both invertebrate and vertebrate communities. However, we did not find nestedness of communities that differed significantly from that expected by chance in response to increasing flow intermittency or distance to refuges. Lastly, basin, flow intermittency, and orientation to perennial refuge predictors were generally important for modeling taxon richness and densities, and richness and densities decreased with increasing flow intermittency and distance to perennial refuges. Collectively, our data suggest that intermittent streams harbor unique biodiversity, but also that some taxa have context‐dependent responses to intermittency and orientation to perennial refuges. These findings also suggest that future increases in stream drying are likely to lead to changes to stream communities with high potential for the loss of aquatic biodiversity.

Association Between Long-Term Regular Exercise and Gut Microbiota Among Middle-Aged and Older Urban Chinese.

Increasing evidence has suggested that physical activity may modulate gut microbiome composition. We investigated associations of long-term regular exercise with gut microbiota among middle-aged and older urban Chinese individuals. Gut microbiota was assessed using 16S ribosomal ribonucleic acid gene sequencing of stool samples from 2,151 participants from the Shanghai Women's Health Study and Shanghai Men's Health Study. Participants were free of cancer, diabetes, and cardiovascular diseases at the time of stool sample collection. Physical activity was assessed in repeat surveys between 1996 and 2015 using validated questionnaires. Regular exercise was defined as any type of leisure-time physical activity with a standard metabolic equivalent score >3.0. Stool samples were collected using the 95% ethanol method between 2015 and 2018 with an average of 3.0 years (SD = 0.9) after the latest exposure assessment. General linear regression and permutational multivariate analysis of variance were carried out to evaluate associations of microbial α- and β-diversity with regular exercise participation. Logistic regression and linear regression models were used to evaluate the prevalence and relative abundance of individual taxa in association with regular exercise. Regular exercise was significantly associated with β-diversity (Bray-Curtis and Jaccard dissimilarities, both false discovery rates = 0.03%, 0.12% and 0.09% variance explained, respectively) but not with α-diversity. Relative abundance of genus Ruminococcus was significantly lower among regular exercisers compared with nonexercisers (median relative abundance: 0.64% vs. 0.81%, false discovery rate <0.10). Further studies are needed to validate the findings from this study and evaluate health benefits of regular exercise on gut microbiota.

Three‐dimensional distribution of mesoplankton assemblages in the Central Atlantic

AbstractAimMesoplankton distribution depends on many factors including depth, hydrological parameters, trophic conditions, etc. Recent studies show a link between mesoplankton biomass and trophic factors in the deep sea, whereas relationships between deep‐sea mesoplankton structure/composition and trophic factors remain unknown.LocationCentral Atlantic, between 32°S and 42°N, 14°W and 46°W.Time periodSeptember–November 2012, 2013, 2016.Major taxa studiedAll mesoplankton taxa.MethodsWe linked composition of mesoplankton assemblages to trophic conditions: surface chlorophyll a (Chl) concentration and particulate organic carbon (POC) flux at different depths—the epipelagic (0–200 m), mesopelagic (200–800/1000 m), upper (800/1000–1500 m), and lower (1500–3000 m) bathypelagic. We collected 146 samples at 40 stations from corresponding depths with Bogorov–Rass plankton net (opening 1.0 m2, mesh 500 µm). The effect of trophic conditions on mesoplankton composition was analysed in horizontal and vertical dimensions using linear mixed‐effects models and canonical correspondence analyses (CCAs). Non‐transformed and transformed data matrices were processed using the Bray–Curtis similarity index, permutational multivariate analysis of variance (PERMANOVA), similarity profiles permutation (SIMPROF) and Kruskal–Wallis tests, and Dunn’s post‐hoc comparisons. Diversity was estimated using the Shannon–Wiener and Hurlbert rarefaction indices.ResultsWe identified 118 zooplankton taxa including 90 copepods. The depth effect (vertical dimension of the trophic factor) was greater than the horizontal effect of Chl and POC distribution. The epi‐, meso‐, upper, and lower bathypelagic mesoplankton were further analysed separately. Five assemblages linked to Chl and POC were identified; two of them (an oligotrophic one in the Southern or Northern Gyre and a mesotrophic one in the Equatorial Atlantic) were recorded at all depths.Main conclusionsWe found a link between structure/composition of mesoplankton assemblages and trophic factors enabling projections of mesoplankton taxonomic structure throughout the water column using Chl and POC maps, respectively. These results will contribute to the development of ecological research methodology and to better understanding of carbon transport in the deep sea.

Responses of Nitrogen-Fixing Bacteria Communities to Elevation, Season, and Slope Aspect Variations in Subtropical Forests of Yunnan, China

Nitrogen-fixing bacteria play a significant role in tropical forest ecosystems. However, little is known about the comprehensive effects of altitude gradient (1000–2600 m), seasons (October, January, April, and July), and slope aspects (east and west) on the abundance and diversity of nitrogen-fixing bacteria in subtropical forest. Q-PCR and PCR-DGGE methods were performed to explore the abundance and diversity of nitrogen-fixing bacteria, respectively, in the Ailao Mountain subtropical forest. Our results showed that the abundance of nitrogen-fixing bacteria was highest in October and December, whereas it was lowest in April and July. Moreover, there was no difference in the total number of soil nitrogen-fixing bacteria on the eastern and western slopes. The diversity of soil nitrogen-fixing bacteria is higher at low and medium altitudes, but lower at high and medium altitudes with increasing altitude, and similar variation in the eastern and western slopes as well. Moreover, the most influential factors affecting the abundance of nitrogen-fixing bacteria was NH4+-N and herbal coverage, while those most affecting the diversity of nitrogen-fixing bacteria were NH4+-N and NO3−-N. In addition, permutational multivariate analysis demonstrated that the season had the greatest effects on the abundance of nitrogen-fixing, whereas altitude had the greatest effects on the diversity of nitrogen-fixing bacteria. These findings provide evidence that the variation in nitrogen-fixing bacteria is affected by multiple factors (altitudes, seasons and slope aspects) in the subtropical forests of Yunnan, China.