Chao1 Diversity Indices Research Articles

Ammonia nitrogen stress induces dysbiosis of the intestinal bacterial community and facilitates the enrichment of pathogenic bacteria in intestines of shrimp

Environmental stress can disrupt the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to elucidate the dynamic changes in the bacterial community within shrimp intestines under short-term ammonia nitrogen stress and investigate the subsequent ecological risks associated with it. Our findings revealed a significant reduction in the Chao1 diversity index within shrimp intestines of the ammonia nitrogen stress group compared to the Control group. Furthermore, distinct disparities in the bacterial community structures were observed between the two groups at 72 h and 120 h post-stress. Additionally, ammonia nitrogen stress significantly altered the abundances of specific bacterial taxa within shrimp intestines. Specifically, the abundance of Bacillus subtilis increased while that of Lactococcus garvieae decreased in the intestine under stress at 72 h. Additionally, Roseivivax jejudonensis exhibited an increase, whereas uncultured_o_Saccharimonadales and Hyphomicrobium sp. showed a decrease at 120 h. Notably, opportunistic pathogens such as Vibrio parahaemolyticus experienced a significant increase at 72 h post-stress, potentially due to a substantial contribution from stochastic processes in shaping the assembly of the intestinal community. Additionally, the intestinal bacterial community of shrimp displayed a noticeable decrease in complexity of bacterial co-association networks under stress conditions. Thus, short-term exposure to ammonia nitrogen disrupts the integrity of shrimp's intestinal community, indicating potential ecological risks within their microhabitat. Confirmatively, we conducted the immersion challenge experiment of V. parahaemolyticus on shrimp post community disturbance under stress, and observed a significantly higher copy numbers of V. parahaemolyticus in host intestines of stressed compared to control shrimp. These findings can provide novel insights into the interactions among ammonia nitrogen stress, intestinal microbiota and host health of aquatic animals, and guide the practices for shrimp healthy culture.

Effects of forest fire smoke deposition on soil physico-chemical properties and bacterial community

The number of forest fires has increased globally, together with considerable smoke emission that significantly impacts the atmospheric environment and associated ecosystems. Most current studies have focused on the in situ effects of fire on the forest ecosystem. However, the mechanisms by which smoke particles affect adjacent ecosystems are largely unexplored. In this study, a simulated forest fire combustion system was developed to evaluate the effect of different smoke concentrations (control, low and high) on soil physico-chemical properties of adjacent farmland at two soil depths. The abundance and diversity of bacterial community were also determined. The results showed that smoke deposition increased the contents of total carbon (TC), total nitrogen (TN), and total phosphorus (TP) in the 0–10 cm soil layer; however, no significant changes in soil water content (SWC) and pH values was observed. The ACE(Abundance Coverage-based Fastimator) and Chao1 diversity indices of bacterial community generally showed a downward trend whereas the PD_whole_ tree diversity index increased after 180 d of smoke deposition. The relative abundance of Proteobacteria remained stable, while abundance of Firmicutes in soil decreased after 180 d of smoke deposition. Smoke deposition slightly affected the physical and chemical properties of the 10–20 cm soil, but the range of variation of the relative abundance and diversity dominant bacteria exceeded that of the 0–10 cm soil. A significant positive correlation was found between the soil properties and the alpha diversity indices during the first 30 d after smoke deposition; the correlation then decreased gradually. Redundancy analysis revealed that Proteobacteria, Firmicutes, and Actinobacteria were generally positively correlated with TC, TN, and SWC. As a whole, the study reveals that the effects of smoke deposition on soil physico-chemical properties and bacterial community depends on smoke concentration where relatively low concentration appears to be beneficial to soil bacterial community.

Differential effects of cow dung and its biochar on Populus euphratica soil phosphorus effectiveness, bacterial community diversity and functional genes for phosphorus conversion.

Continuous monoculture leading to soil nutrient depletion may cause a decline in plantation productivity. Cow dung is typically used as a cheap renewable resource to improve soil nutrient status. In this study, our purpose was to compare the effects of different cow dung return methods (direct return and carbonization return) on soil microbial communities and phosphorus availability in the root zone (rhizosphere soil and non-rhizosphere soil) of P.euphratica seedlings in forest gardens and to explore possible chemical and microbial mechanisms. Field experiments were conducted. Two-year-old P.euphratica seedlings were planted in the soil together with 7.5 t hm-2 of cow dung and biochar made from the same amount of cow dung. Our findings indicated that the available phosphorus content in soil subjected to biochar treatment was considerably greater than that directly treated with cow dung, leading to an increase in the phosphorus level of both aboveground and underground components of P.euphratica seedlings. The content of Olsen-P in rhizosphere and non-rhizosphere soil increased by 134% and 110%, respectively.This was primarily a result of the direct and indirect impact of biochar on soil characteristics. Biochar increased the biodiversity of rhizosphere and non-rhizosphere soil bacteria compared with the direct return of cow dung. The Shannon diversity index of carbonized cow manure returning to field is 1.11 times and 1.10 times of that of direct cow manure returning to field and control, and the Chao1 diversity index is 1.20 times and 1.15 times of that of direct cow manure returning to field and control.Compared to the direct addition of cow dung, the addition of biochar increased the copy number of the phosphorus functional genes phoC and pqqc in the rhizosphere soil. In the biochar treatment, the abundance of the phosphate-solubilizing bacteria Sphingomonas and Lactobacillus was significantly higher than that in the other treatments, it is relative abundance was 4.83% and 2.62%, respectively, which indirectly improved soil phosphorus availability. The results indicated that different cow dung return methods may exert different effects on phosphorus availability in rhizosphere and non-rhizosphere soils via chemical and microbial pathways. These findings indicated that, compared to the direct return of cow dung, biochar return may exert a more significant impact on the availability of phosphorus in both rhizosphere and non-rhizosphere soils, as well as on the growth of P.euphratica seedlings and the microbial community.

Metagenomic analysis of mycobiome in wild and captivity Sumatran orangutans (Pongo abelii).

This study analyzes the mycobiome in wild and captive Sumatran orangutans. Nine orangutan feces samples from the wild and nine from captivity were divided into three repeats from 11- to 15-year-olds in good health. The Illumina platform for analysis of ITS bioinformatics was used according to the Qiime2 and CCMetagen approaches. Wild Sumatran orangutans include 53% Ascomycota, 38% uncultured fungi, and 4% Basidiomycota. Orangutans in captivity are 57% Ascomycota, 26% uncultured fungi, and 2% Basidiomycota. Based on genus level, uncultured Neurospora (31%), Penicillium (10%), Aspergillus (3%), Fusarium (3%), Candida (2%), Cutaneotrichosporon (2%), and Limonomyces (2%) are found in wild orangutans. The most prevalent genus among captivity orangutans is Aspergillus (32%), followed by fungal sp. (11%), Lasiodiplodia (18%), Devriesia (2%), and Sordariomycetes (2%). According to the Chao1 diversity index and Shannon and Simpson, there was no significant difference between wild and captive Sumatran orangutans. Neurospora is unique to wild Sumatran orangutans, although Aspergillus predominates in captive orangutans. We hypothesize that the gut mycobiome of wild orangutans will resemble that of orangutans in captivity. The excellent range of food sources in the forest does not result in the prevalence of fungi in the typical gut microbiome.

Macrofungal Diversity and Distribution Patterns in the Primary Forests of the Shaluli Mountains.

The Shaluli Mountains are located in the southeastern part of the Tibetan Plateau at an elevation of 2500-5000 m. They are characterized by a typical vertical distribution of climate and vegetation and are considered a global biodiversity hotspot. We selected ten vegetation types at different elevation gradients representing distinct forests in the Shaluli Mountains to assess the macrofungal diversity, including subalpine shrub, Pinus spp., Populus spp., Pinus spp. and Quercus spp., Quercus spp., Abies spp., Picea spp. and Abies spp., Picea spp., Juniperus spp., and alpine meadow. In total, 1654 macrofungal specimens were collected. All specimens were distinguished by morphology and DNA barcoding, resulting in the identification of 766 species belonging to 177 genera in two phyla, eight classes, 22 orders, and 72 families. Macrofungal species composition varied widely among vegetation types, but ectomycorrhizal fungi were predominant. In this study, the analysis of observed species richness, the Chao1 diversity index, the invsimpson diversity index, and the Shannon diversity index revealed that the vegetation types with higher macrofungal alpha diversity in the Shaluli Mountains were composed of Abies, Picea, and Quercus. The vegetation types with lower macrofungal alpha diversity were subalpine shrub, Pinus spp., Juniperus spp., and alpine meadow. The results of curve-fitting regression analysis showed that macrofungal diversity in the Shaluli Mountains was closely related to elevation, with a trend of increasing and then decreasing with rising elevation. This distribution of diversity is consistent with the hump-shaped pattern. Constrained principal coordinate analysis based on Bray-Curtis distances indicated that macrofungal community composition was similar among vegetation types at similar elevations, while vegetation types with large differences in elevation differed significantly in macrofungal community composition. This suggests that large changes in elevation increase macrofungal community turnover. This study is the first investigation of the distribution pattern of macrofungal diversity under different vegetation types in high-altitude areas, providing a scientific basis for the conservation of macrofungal resources.

A198 THE LONG-TERM IMPACT OF ENVIRONMENTAL EXPOSURES ON HOST HEALTH AND THE RISK FACTORS OF CROHN'S DISEASE

Abstract Background Several environmental factors are associated with Crohn’s disease (CD) in large case-control studies; however, it is not clear how these factors maybe be influenced by age of exposure and if they are related to alterations in pre-disease biological markers of CD risk. Purpose To investigate the association between environmental factors in different age groups with future risk of CD onset and assess their relation to other pre-disease biomarkers. Method We used an environmental risk assessment questionnaire (ERA) to collect information from healthy first-degree relatives(FDR) of CD enrolled in the CCC-GEM project. ERA was a multi-item questionnaire querying 69 questions under 7 section headings: background, cultural/ethnic, smoking history, medical history, family history, environmental history and pet history. For the environmental and pet sections, current and historical (<1, 2-4, 5-15 years old) data was captured at the time of recruitment. We used Cox proportional hazard models to identify exposures associated with future CD onset. Next, we used regression models to identify the relationship of exposures with biological factors associated with CD risk previously identified by our group i.e.: i) intestinal permeability using urinary fractional excretion of lactulose to mannitol ratio (LMR) with LMR≥0.025 defined as abnormal; ii) subclinical inflammation using fecal calprotectin (FCP) with FCP≥100µg/g; and iii) fecal microbiome composition and diversity using 16S rDNA sequencing. Two-sided p<0.05 (or false discovery rate corrected p<0.05) were considered significant. Result(s) A total of 4289 FDRs were recruited, 47% were male, median recruitment age was 17.0 years[6-35]. After a median follow-up of 5.6-years (IQR=3.42-8.67), 86 FDRs developed CD. Living with a dog between age 5-15 (Hazard Ratio (HR)=0.61; 95% confidence interval (CI)=0.39-0.95), and a large family size (>3) in the first year of life (HR=0.41; 95% CI=0.22-0.89) were protective against CD onset. Conversely, having a bird at time of survey (HR=2.84; CI=1.37-5.90), and having a sibling with CD (HR=2.07; 95% CI=1.18-3.63) were risk factors for CD onset. We found that owning a dog between age of 5-15 (Odd Ratio(OR)=0.77, 95% CI=0.65-0.90) was significantly associated with LMR, nine taxa bacterial and higher chao1 diversity index. Having a bird at time of survey was significantly associated with FCP (OR=2.04, 95% CI=1.33-3.11). There was no association between large family size and having a CD sibling with gut microbiome, FCP or LMR. Conclusion(s) The study identified four environmental factors associated with future development of CD. Among them, exposure to dogs during early life was protective against CD onset and might be explained by its association with normal gut permeability and microbiome. We also identified that having a bird at recruitment increased risk of CD onset which might be mediated by an increase in subclinical inflammation. Submitted on behalf of the CCC-GEM consortium Disclosure of Interest None Declared

A healthy dietary pattern is associated with microbiome diversity in bipolar patients: the Bipolar Netherlands Cohort (BINCO) study

IntroductionThe gut microbiome is one of our most prominent surfaces interacting with the outside world through the food we eat. It is influenced in terms of composition and diversity by our diets and life style habits and, in turn, affects us through the ‘gut-brain axis’. Cardiovascular risk, which is one of the main causes of death in Bipolar Disorder (BD), is affected by diet. The association between diet and microbiome in BD patients has not been studied.ObjectivesWe aimed to assess whether [1] dietary quality is associated with the microbiome’s diversity, and [2] what changes and interactions occur during in both the dietary quality and microbiome diversity during the subsequent year of onset BD.Methods39 recently diagnosed patients with BD of the ‘Bipolair Nederlands Cohort’ (BINCO) (mean age 36 years, 61.5% female) were included. Food Frequency Questionnaires (FFQ) and corresponding Dutch Healthy index (DHD-15) were analyzed at baseline and one year follow-up. Feces samples corresponding to the FFQ were analyzed using 16S rDNA gene amplicon sequencing to attain the Shannon Diversity index and the Chao1 diversity index. Multivariate regression analyses were performed.ResultsThe Shannon diversity index significantly correlated to the DHD-15 total score after adjusting for sex and age (beta = 0.451; P = 0.004). The Chao1 index showed the same trend, but did not reach significance (beta = 0.264; P = 0.11). These positive correlations seemed to be driven by the positive effect of fish, beans, coffee, fruits and nuts. There was neither a significant change in DHD-15 index nor in the diversity measures after one year.Image:Image 2:ConclusionsDiversity of the microbiome is positively associated with a healthy and varied diet in BD patients, which could have consequences on mood episodes and cardiovascular risk.Disclosure of InterestNone Declared

Effect of drip irrigation on richness, abundance and diversity of soil arthropods

Arthropods maintain soil ecosystem in variety of ways like breaking down the plant debris and broadcasting the microorganisms. The human induced changes in the agricultural land (i.e., irrigation methods, tillage practices and land use changes) have profound impacts on the richness, diversity and abundance of arthropods. The present study was carried out to assess the effect of drip irrigation on the richness, abundance and diversity of soil arthropods at three different Tehsils of District Bahawalpur i.e. Bahawalpur, Khairpur and Ahmedpur East. At each location, one flood and one drip irrigated guava orchard was selected. Weekly data of soil arthropods was recorded using 10 pitfall traps (at least 50 feet apart) in each orchard during April and May, 2022. The species richness, abundance, dominance and evenness of soil arthropods were slightly higher in flood irrigation orchards. However, Simpson, Shannon-wiener and chao-1 diversity indices did not vary significantly. Rank abundance curves showed that in all the drip and flood irrigated orchards, there was still some possibility of finding new species with the increasing sample size. Only one ant species Camponotus compressus (Hymenoptera: Formicidae) constituted the major proportion of arthropods abundance in all the orchards whereas most of the species were very low in abundance. The results suggest that the soil arthropod diversity is not significantly affected with the flood and drip irrigation methods. Therefore, keeping in view the proven economic and water conservation advantages, the drip irrigation system can be adopted without harming soil arthropods diversity.

Influence of dietary oils rich in omega-6 or omega-3 fatty acids on rumen microbiome of dairy cows.

The objective of this study was to compare the effect of supplementing dairy cow diets with contrasting sources of omega-6 (soybean oil) and omega-3 (fish oil) PUFA on rumen microbiome. For 63 d, 15 mid-lactating cows were fed a control diet (n = 5 cows; no fat supplement) or control diet supplemented with 2.9% dry matter (DM) of either soybean oil (SO; n = 5 cows) or fish oil (FO; n = 5 cows). Ruminal contents were collected on days 0, 21, 42, and 63 for 16S rRNA gene sequencing. Beta diversity and Shannon, Simpson and Chao1 diversity indices were not affected by dietary treatments. In terms of core microbiome, Succiniclasticum, Prevotella, Rikenellaceae_RC9_gut_group, and NK4A214_group were the most prevalent taxa regardless of treatments. Bifidobacterium was absent in SO diet, Acetitomaculum was absent in FO, and Sharpea was only detected in SO. Overall, results showed that at 2.9% DM supplementation of either SO or FO over 63 days in dairy cow diets does not cause major impact on bacterial community composition and thus is recommended as feeding practice.

How to Maintain a Healthy Gut Microbiome in Children with Cancer? Gut Microbiome Association with Diet in Children with Solid Tumors Postchemotherapy.

Malnutrition is a common complication in children with cancer. Cancer treatment and malnutrition can disrupt gut microbiome diversity and composition. The gut microbiome is of broad interest to better understand the mechanisms of malnutrition in cancer therapy. This study aimed to compare the gut microbiome between children with solid tumors postchemotherapy and healthy controls, and investigated the association of the putative microbiome differences with diet. Study participants were 27 children (7-18 years) with solid tumors within the first year after the completion of chemotherapy and 22 healthy controls. The study groups did not have a statistically significant difference in age, race, sex, and body mass index. At study intake, the participants completed the Block Kids Food Screener for dietary intakes in the past week. Fecal specimens were collected and analyzed for the gut microbiome. The cancer and control groups differed in gut microbial β-diversity and abundance analyses. The macronutrient intakes such as carbohydrates, fiber, beta-carotene, and vitamin B6 were positively associated with α-diversity. Children with adequate vitamin B6 had a higher Chao1 diversity index than children with inadequate or excessive intake (p = 0.0004). Children with excessive selenium intake had a trend for higher Pielou's_e index than children with inadequate intake (p = 0.091). Maintaining a healthy gut microbiome is critical among children with cancer. This study provides new insights on the linkages between dietary intakes and the gut microbiome in children with solid tumors postchemotherapy. These findings, if replicated in future independent studies, may help anticipate malnutrition and plan for personalized nutrition approaches during chemotherapy in pediatric cancers.

Fungi Occurring in Norway Spruce Wood Decayed by Heterobasidion parviporum in Puszcza Borecka Stands (Northeastern Poland)

In many spruce stands, trees are frequently attacked by the pathogen Heterobasidion parviporum, albeit without visible symptoms in the crown. In the present work, the results of the presence of stem rot, assessed by PICUS Sonic Tomography, and the fungal biota on trees and stumps in eight plots in the Puszcza Borecka Forest are described. The plots were located in stands on original forest soil (4) and on post-agricultural soil (4), where around a stump with H. parviporum symptoms (signs of internal rot and basidiocarps), 30 trees were selected and examined for internal rot. Wood samples were collected from two selected trees for fungal molecular analysis. A total of 79 fungal taxa were found, including 57 taxa in plots on post-agricultural soil and 45 on forest soil. There were 395 fungal records on stumps and 22 records on trees, therein, from the inner parts of felled trunks. Significant differences in the Chao-1 diversity index indicate that the origin of the soil—post-agricultural or forest soil—influenced the alpha diversity of the fungal communities in the forests studied. The values of the Shannon and Simpson indices show that the two communities were similar in terms of species numbers. The presence of basidiomata of H. parviporum and two species of Armillaria (mainly A. cepistipes) in samples on all plots is striking, although Armillaria spp. was detected more frequently. Most of the species identified were typical saprotrophs, although rare species were also found, such as Entoloma byssisedum, Onnia tomentosa, Physisporinus vitreus, Postia ptychogaster, and Ramaria apiculata. The presence of H. parviporum in the inner woody parts was confirmed by PCR analysis, and decay was detected even up to a stem height of 6 m. Armillaria was the dominant genus in the studied stands and plays a significant and underestimated role in heartwood decay of old spruce trees in Puszcza Borecka Forest.

Dynamic variability of soil diazotrophs in bulk‐rhizosphere and phenological stages under long‐term mulching in an eroded area in the Loess Plateau

AbstractFree‐living diazotrophs play a significant role in the process of soil biological nitrogen fixation. Long‐term field management has a cumulative effect on soil microbial communities. However, after long‐term mulching measures in erosion areas, the stability difference in diazotrophs in bulk‐rhizosphere soil and the temporal dynamic changes remain unclear. In this study, we analysed the dynamic variability of soil diazotrophic community structures using high‐throughput sequencing. The result of Chao1 diversity index showed that mulching effectively increased the richness of soil diazotrophs. Combining the community composition, it was found that the diversity level of the soil diazotrophic community under mulching decreased more drastically along the development stages compared with no‐tillage, and Bradyrhizobium played a major role in nitrogen fixation. In rhizosphere soil, mulching promoted the relative abundances of Azohydromonas, Bradyrhizobium, and Skermanella. Co‐occurrence network analysis indicated that mulching measures strengthened the connection between the dominant components to improve the aggregation of the network. The partial least squares‐path model showed that the richness of diazotrophs in rhizosphere soil had an indirect effect on mulching through the available carbon and nitrogen nutrients of bulk soil, thereby improving the response rate to environmental variables. Overall, our findings showed that under long‐term mulching, the richness and aggregation of dominant components of the soil diazotrophic community increased with the phenological period and distance from roots, revealing the importance of mulching in eroded areas to improve farmland soil nitrogen fixation capacity. This study provides a theoretical reference for microecology to effectively improve soil fertility in similar areas.

The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls

Introduction: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers. Objective: To compare the gut microbiome composition between adult AR sufferers and controls. Methods: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences. Results: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG. Conclusion: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.

Diversity of Planktonic Bacteria in Durgun and Taishir Reservoirs (Western Mongolia)

This is the first report on the application of high-throughput sequencing of the 16S rRNA gene fragments for investigation of bacterioplankton diversity in two largest and relatively young reservoirs of Mongolia—Taishir, formed on the Zavkhan River, and Durgun, formed on the Chono Harayh Channel. A total of 145 phylotypes (with a cluster distance of 0.03) belonging to 18 phyla were identified in the communities. The share of OTUs that were not identified at the phylum level varied in the range of 0.6–3.0%. According to the ACE and CHAO1 diversity indices, bacterioplankton species richness was highest in the hypertrophic section of the Chono Harayh channel below the dam of the Durgun Hydropower Station and lowest in the mesotrophic section of the Zavkhan River above the Taishir Reservoir. According to the Shannon and Simpson indices, the species abundance of different species in the community characterized the mesotrophic and eutrophic pelagic zones of the Taishir and Durgun reservoirs, respectively, as areas with the most equality. The reservoir systems differed significantly in taxonomic diversity, as evidenced by the ratio of common and unique OTUs, but their representation was not uniform along the rivers.

Fungal diversity in the brown coniferous forest soils of Daxing'anling Mountains, Northeast China

To explore the distribution of fungal community in soil of brown coniferous forest in Daxing'anling and its relationship with soil characteristics, soil fungal community structure and diversity in three forest types, light brown coniferous forest, grass brown coniferous forest, and typical brown coniferous forest, were analyzed by high-throughput sequencing technology. The relationship between soil fungal community and soil characteristics was analyzed by R and SPSS 17.0 software. The results showed that soil physical and chemical characteristics differed significantly across the three brown coniferous forests. A total of 111 species belonged to six phyla, 23 class, 46 orders, 74 families and 88 genera were recorded in this study. Ascomycetes and basidiomycetes were dominant phyla. There were significant differences in relative abundance of phyla among three forest types. There was no significant difference in the Ace and Chao1 diversity indices among three brown coniferous forests, whereas there were significant differences in the Shannon and Simpson indices. Results from canonical correlation analysis and correlation analysis showed that both α and β diversity were significantly correlated with soil moisture, soil pH, soil organic matter, soil total nitrogen, and soil total potassium. The results indicated that soil characteristics were important factors affecting soil fungal diversity of brown coniferous forest in Xing'an larch forest in Daxing'anling.

Urinary fungi associated with urinary symptom severity among women with interstitial cystitis/bladder pain syndrome (IC/BPS).

To correlate the presence of fungi with symptom flares, pain and urinary severity in a prospective, longitudinal study of women with IC/BPS enrolled in the MAPP Research Network. Flare status, pelvic pain, urinary severity, and midstream urine were collected at baseline, 6 and 12months from female IC/BPS participants with at least one flare and age-matched participants with no reported flares. Multilocus PCR coupled with electrospray ionization/mass spectrometry was used for identification of fungal species and genus. Associations between "mycobiome" (species/genus presence, relative abundance, Shannon's/Chao1 diversity indices) and current flare status, pain, urinary severity were evaluated using generalized linear mixed models, permutational multivariate analysis of variance, Wilcoxon's rank-sum test. The most specific analysis detected 13 fungal species from 8 genera in 504 urine samples from 202 females. A more sensitive analysis detected 43 genera. No overall differences were observed in fungal species/genus composition or diversity by flare status or pain severity. Longitudinal analyses suggested greater fungal diversity (Chao1 Mean Ratio 3.8, 95% CI 1.3-11.2, p = 0.02) and a significantly greater likelihood of detecting any fungal species (OR = 5.26, 95% CI 1.1-25.8, p = 0.04) in high vs low urinary severity participants. Individual taxa analysis showed a trend toward increased presence and relative abundance of Candida (OR = 6.63, 95% CI 0.8-58.5, p = 0.088) and Malassezia (only identified in 'high' urinary severity phenotype) for high vs low urinary symptoms. This analysis suggests the possibility that greater urinary symptom severity is associated with the urinary mycobiome urine in some females with IC/BPS.

High-Throughput Sequencing Analysis Reveals Correlations between Host Phylogeny, Gut Microbiota, and Habitat of Wild Frogs from a Mountainous Area

Gut microbiota of vertebrate hosts play crucial roles for the host they inhabit. In this study, we compared the composition and predicted functions of gut microbiota of female individuals belonging to four frog species from different habitats using bacterial 16S rRNA gene sequencing. Our results showed that the gut microbiota of the examined frog species were dominated by the phyla Firmicutes, Proteobacteria, Bacteriodetes, Verrucomicrobia, and Fusobacteria. There were significant differences in the relative abundance of dominant phyla among the four species, although the relative abundance of dominant phyla in the microbiota of individuals of Odorrana tormota was more evenly balanced (ranged from 10.45% for Fusobacteria to 27.21% for Bacteroidetes). The alpha diversity patterns varied depending on the microbial taxon level. At the phylum level, the Chao1 diversity was positively associated with body weight, with the diversity index scores of O. tormota and Amolops wuyiensis markedly lower than those of Odorrana schmackeri and Polypedates megacephalus. At the genus level, Chao1 diversity was associated with evolutionary relationships among species, with the Chao1 diversity index score for P. megacephalus of distant evolutionary relationships being significantly higher than the scores for frogs with close evolutionary relationships. Moreover, permutational multivariate analysis of variance revealed significant differences in the gut bacterial community structure among species (R2 = 0.510, P = 0.001). Further, the predicted functions of the gut microbiota were similar for species with close evolutionary relationships but differed with distant evolutionary relationships. Taken together, our results indicate that wild frogs have species-specific microbial communities and provide insight into the ecological and evolutionary dynamics of host–microbe interactions.

Pilot study: Gut microbiome and intestinal barrier in anorexia nervosa

Recent research has shown changes of the intestinal flora in anorexia nervosa (AN) patients. Alpha diversity (AD) represents the number of different bacterial species in the gut. Reduced AD and a leaky gut (zonulin) lead to inflammation and changes in nutrient absorption. AD was calculated from stool samples of 18 AN patients and 20 normal weight controls (NC) after 16S ribosomal RNA sequencing. Furthermore, Zonulin as an indicator of gut barrier function and inflammation parameters were investigated. AN patients had significantly lower AD compared to NC (number of observed species p=0.042, Chao1 Diversity Index p=0.043). Zonulin was not significantly altered in AN patients compared to NC. There were no significant correlations of serum parameters and AD. Regardless of gut permeability, AN patients showed significantly decreased AD compared to NC. Decreased AD can have an additional negative impact on calorie intake in AN. These results contribute to a better understanding of the illness and the development of new therapeutic options.

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil.

Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production

Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m3/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during water sample filtration or from DNA extraction protocols. Control measurements for sample contamination are important for clean water studies.