Relative Abundance Of Bacterial Taxa Research Articles

Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm (Elaeis guineensis) via High-Throughput Sequencing.

Simple SummaryBiological and physicochemical soil factors involved in the incidence of the basal stem rot (BSR) disease in an oil palm (Elaeis guineensis) plantation in Malaysia were characterized. Blenheim soil with a low BSR disease incidence and Bernam soil with high BSR disease incidence were analyzed and observed to have differences in composition and diversity of soil prokaryotic and eukaryotic communities. Blenheim soil with a high pH and calcium was shown to have higher prokaryotic and eukaryotic diversity compared to Bernam soil. High abundances of rare metabolically diverse and versatile bacterial taxa, bacterial taxa that increased with the introduction of biocontrol agents, potential disease-suppressive bacteria, and bacterivorous flagellates were observed in Blenheim soil. In contrast, Bernam soil was predominantly characterized by potential disease-inducible bacterial taxa. A combination of both abiotic and biotic elements might be essential in driving disease-suppressive soil microbiome toward Ganoderma BSR in Blenheim soil.Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.

Fusobacterium nucleatum in biopsied tissues from colorectal cancer patients and alcohol consumption in Korea

The roles of individual bacteria and their relationship in the development of colorectal cancer (CRC) remain unclear. We aimed to determine the prevalence of CRC-associated bacteria using quantitative real-time PCR (qPCR) or 16S rRNA analysis and the statistical correlations of patient demographics and clinical characteristics comprising alcohol consumption with CRC-associated bacteria. We determined the prevalence of five CRC-associated bacterial species in 38 CRC patients (39 samples) and 21 normal individuals using qPCR, and the relative abundance of bacterial taxa in the gut microbiome was assessed using 16S rRNA analysis. Fusobacterium nucleatum was the only bacterium that was significantly (P < 0.0001) more prevalent in the cancer tissue (82.1%) than in the normal tissue (0%) by qPCR. 16S rRNA analysis showed a significant correlation between six operational taxonomic units (OTUs), namely, the genera Fusobacterium, Peptostreptococcus, Collinsella, Prevotella, Parvimonas, and Gemella, in patients with CRC. An integrated analysis using 16S rRNA data and epidemiological characteristics showed that alcohol consumption was significantly correlated with the abundance of Fusobacterium OTUs. The correlation of alcohol consumption with the abundance of Fusobacterium OTUs in cancer tissue discovered using 16S rRNA analysis suggests a possible link between alcohol metabolism and subsequent tumorigenesis caused by F. nucleatum.

Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains

Productivity and sustainability of tropical forest plantations greatly rely on regulation of ecosystem functioning and nutrient cycling, i.e., the link between plant growth, nutrient availability, and the microbial community structure. So far, these interactions have never been evaluated in the Acacia and Eucalyptus forest planted on infertile soils in the Congolese coastal plains. In the present work, the soil bacterial community has been investigated by metabarcoding of the 16S rRNA bacterial gene in different stands of monoculture and mixed-species plantation to evaluate the potential of nitrogen-fixing trees on nutrient and bacterial structure. At the phylum level, the soil bacterial community was dominated by Actinobacteria, followed by Proteobacteria, Firmicutes, and Acidobacteria. A principal coordinate analysis revealed that bacterial communities from pure Eucalyptus, compared to those from plantations containing Acacia in pure and mixed-species stands, showed different community composition (beta-diversity). Regardless of the large variability of the studied soils, the prevalence of Firmicutes phylum, and lower bacterial richness and phylogenic diversity were reported in stands containing Acacia relative to the pure Eucalyptus. Distance-based redundancy analysis revealed a positive correlation of available phosphorus (P) and carbon/nitrogen (C/N) ratio with bacterial community structure. However, the Spearman correlation test revealed a broad correlation between the relative abundance of bacterial taxa and soil attributes, in particular with sulfur (S) and carbon (C), suggesting the important role of soil bacterial community in nutrient cycling in this type of forest management. Concerning mixed plantations, a shift in bacterial community structure was observed, probably linked to other changes, i.e., improvement in soil fertility (enhanced P and C dynamics in forest floor and soil, and increase in soil N status), and C sequestration in both soil and stand wood biomass with the great potential impact to mitigate climate change. Overall, our findings highlight the role of soil attributes, especially C, S, available P, and C/N ratio at a lesser extent, in driving the soil bacterial community in mixed-species plantations and its potential to improve soil fertility and to sustain Eucalyptus plantations established on the infertile and sandy soils of the Congolese coastal plains.

Relationships between root morphology, root exudate compounds and rhizosphere microbial community in durum wheat

A multidisciplinary approach was adopted to investigate multiple relationships between root morphology, rhizosphere soil exudates and soil microbial community in eight durum wheat [Triticum turgidum ssp. durum (Desf.)] cultivars previously characterized in terms of their ability to interact with mycorrhizal fungi. Six plants from each cultivar were grown to the five-leaf stage in a growth chamber. Root system architecture was characterized by root scans, root exudates were identified and quantified by gas chromatography–mass spectrometry (GC–MS), and the rhizosphere bacterial, archaeal and fungal community structure was assessed using terminal-restriction fragment length polymorphism (T-RFLP). Wheat cultivars were very different in terms of the morphological root traits. Cappelli, Grecale, Ofanto and PR22D89 cultivars showed the most developed root system. Root exudates included sugars, amino acids, polyalcohols and organic acids, with carbohydrates accounting for 87.3% of the whole data set. All the compounds showed significant differences among cultivars, with Grecale and Claudio showing the highest exudation ability of metabolites. T-RFLP profiles showed a greater relative abundance of bacterial taxa (55.8% on average) than those of archaea and fungi (35.6% and 8.6%, on average, respectively) in all cultivars, and responded positively to root exudation. Principal component analysis identified root dry weight, surface area and volume, carbohydrate exudation, bacterial and archaeal Shannon–Weaver diversity indices and the fungal evenness index as the traits that mainly contributed to the cultivar variability. A larger root system did not always promote a higher diversity of the rhizosphere microbial biomass. This then suggests complex interactions between traits, probably due to the differences in the quality and/or composition of the root exudates. Based on our results, we propose that durum wheat cultivars could be classified according to the different plant resource-use strategies employed, such as conservative (i.e. Cappelli, with a large root system but low exudation ability) and explorative/competitive (i.e. Grecale and Claudio, with a high exudation ability) cultivars. The results are discussed with reference to the complex relationships between the plant and the rhizospheric microorganisms in order to determine the best combinations that would enhance root efficiency.

Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota.

Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota. We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance. More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease. Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.

Aerosol microbial community structure analysis based on two different sequencing platforms

As the main biological components of the air ecosystem, airborne microorganisms play an important role in ecosystem function, and most existing studies focus on their health and environmental effects, while ignoring ecological effects. In this study, air microbial samples from two sampling points in the coastal city of Qingdao were collected by a large volume air sampler. The Illumina MiSeq and PacBio high-throughput sequencing methods were used to analyze the microbial community structure and diversity of the two sampling points. The results showed that there were significant differences in the number and relative abundances of microorganisms identified by the two platforms, and with the refinement of the sample classification, the differences in the community became increasingly significant. Proteobacteria and Firmicutes were the dominant bacterial phyla among the airborne microorganisms. MiSeq sequencing showed that the relative abundances of unidentified bacteria were as high as 8.03–16.42% in MiSeq sequencing, while they were almost undetected in PacBio sequencing. Based on the different sequencing platforms, Bacilli, Gammaproteobacteria and Alphaproteobacteria could be seen as significant gaps in the two sampling points. Betaproteobacteria showed differences only in the coastal area, while the other 14 classes were differentially abundant in the urban area. Pseudomonas was the main genus in the aerosol, followed by Lactococcus. The relative abundances of bacterial taxa displayed statistically significant differences in the different functional areas. There were more diverse microbes in the urban area than in the coastal area; moreover, the relative abundances of dominant genera showed significant differences, such as Variovorax and Deinococcus.

Effects of Smoking and Smoking Cessation on the Intestinal Microbiota.

We evaluated associations of smoking heaviness markers and the effects of smoking cessation on the intestinal microbiota and cardiovascular disease risk factors in current smokers undertaking a quit attempt. Participants were current smokers enrolled in a prospective randomized clinical trial of smoking cessation therapies with visits at baseline, 2, and 12 weeks. Genomic DNA was extracted from fecal samples followed by 16S rRNA gene sequencing and analysis using the QIIME2 software workflow. Relative abundances of bacterial taxa and alpha- and beta-diversity measures were used for comparisons. The 36 smokers were (mean (standard deviation)) 51.5 (11.1) years old (42% male) and smoked 15.1 (6.4) cigarettes per day for 22.7 (11.9) pack-years. Relative abundances of the phylum Actinobacteria correlated with pack-years (rho = −0.44, p = 0.008) and Cyanobacteria correlated with CO levels (rho = 0.39, p = 0.021). After 12 weeks, relative abundances of the phylum Bacteroidetes increased (pANCOVA = 0.048) and Firmicutes decreased (pANCOVA = 0.036) among abstainers compared to continuing smokers. Increases in alpha-diversity were associated with heart rates (rho = −0.59, p = 0.037), systolic blood pressures (rho = −0.58, p = 0.043), and C-reactive protein (rho = −0.60, p = 0.034). Smoking cessation led to minor changes in the intestinal microbiota. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota.

General Microbiota of the Soft Tick Ornithodoros turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico.

The general bacterial microbiota of the soft tick Ornithodoros turicata found on Bolson tortoises (Gopherus flavomarginatus) were analyzed using next generation sequencing. The main aims of the study were to establish the relative abundance of bacterial taxa in the tick, and to document the presence of potentially pathogenic species for this tortoise, other animals, and humans. The study was carried-out in the Mapimi Biosphere Reserve in the northern-arid part of Mexico. Bolson tortoises (n = 45) were inspected for the presence of soft ticks, from which 11 tortoises (24.4%) had ticks in low loads (1–3 ticks per individual). Tick pools (five adult ticks each) were analyzed through 16S rRNA V3–V4 region amplification in a MiSeq Illumina, using EzBioCloud as a taxonomical reference. The operational taxonomic units (OTUs) revealed 28 phyla, 84 classes, 165 orders, 342 families, 1013 genera, and 1326 species. The high number of taxa registered for O. turicata may be the result of the variety of hosts that this tick parasitizes as they live inside G. flavomarginatus burrows. While the most abundant phyla were Proteobacteria, Actinobacteria, and Firmicutes, the most abundant species were two endosymbionts of ticks (Midichloria-like and Coxiella-like). Two bacteria documented as pathogenic to Gopherus spp. were registered (Mycoplasma spp. and Pasteurella testudinis). The bovine and ovine tick-borne pathogens A. marginale and A. ovis, respectively, were recorded, as well as the zoonotic bacteria A. phagocytophilum, Coxiella burnetii, and Neoehrlichia sp. Tortoises parasitized with O. turicata did not show evident signs of disease, which could indicate a possible ecological role as a reservoir that has yet to be demonstrated. In fact, the defense mechanisms of this tortoise against the microorganisms transmitted by ticks during their feeding process are still unknown. Future studies on soft ticks should expand our knowledge about what components of the microbiota are notable across multiple host–microbe dynamics. Likewise, studies are required to better understand the host competence of this tortoise, considered the largest terrestrial reptile in North America distributed throughout the Chihuahuan Desert since the late Pleistocene.

Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L.

The plant microbiome influence plant health, yield and vigor and has attained a considerable attention in the present era. In the current study, native bacterial community composition and diversity colonizing Triticum aestivum L. rhizosphere at two distant geographical locations including Mirpur Azad Kashmir and Islamabad was elucidated. Based on IonS5™XL platform sequencing of respective samples targeting 16S rRNA gene that harbor V3-V4 conserved region revealed 1364 and 1254 microbial operational taxonomic units (OTUs) at ≥97% similarity and were classified into 23, 20 phyla; 70, 65 classes; 101, 87 orders; 189,180 families; 275, 271 genera and 94, 95 species. Respective predominant phyla accounting for 97.90% and 98.60% of bacterial community were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Gemmatimonadetes. Diversity indices revealed variations in relative abundance of bacterial taxa owing to distant geographical locations however predominant bacterial taxa at both locations were similar. These findings paved a way to dissect consequence of associated microbiota on future wheat production system.

Dysbiosis is not present in horses with fecal water syndrome when compared to controls in spring and autumn.

BackgroundFecal water syndrome (FWS) is long‐standing and common in horses, particularly in central Europe. No large epidemiological data sets exist, and the cause remains elusive. Dysbiosis could play a role in pathogenesis.ObjectivesTo evaluate whether dysbiosis is present in horses with FWS when compared to stable‐matched control horses in spring and autumn.AnimalsFecal samples were collected from horses with FWS (n = 16; 9 mares, 7 geldings) and controls (n = 15; 8 mares, 7 geldings).MethodsThe bacterial microbiome of samples collected in spring and autumn of 2016 was analyzed using high‐throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity, and beta diversity indices were assessed between horses with FWS and controls based on season.ResultsDifferences in microbial community composition based on time point and health status were not observed on any taxonomic level. Limited differences were seen on linear discriminant analysis effect size analysis. No difference in alpha diversity indices was observed including richness, diversity based on health status, or time point. No effect of health status on microbial community membership structure was observed.Conclusions and Clinical ImportanceLimited differences were found in the bacterial microbiota of horses with and without FWS, regardless of season. Further research is needed to elucidate the role of microbiota in the development of FWS.

Bacterial ecotoxicity and shifts in bacterial communities associated with the removal of ibuprofen, diclofenac and triclosan in biopurification systems

The proliferation and possible adverse effects of emerging contaminants such as pharmaceutical and personal care products (PPCPs) in waters and the environment is a cause for increasing concern. We investigated the dissipation of three PPCPs: ibuprofen (IBP), diclofenac (DCF) and triclosan (TCS), separately and in mixtures, in the ppm range in biopurification system (BPS) microcosms, paying special attention to their effect on bacterial ecotoxicity, as well as bacterial community structure and composition. The results reveal that BPS microcosms efficiently dissipate IBP and DCF with 90% removed after 45 and 84 days of incubation, respectively. However, removal of TCS required a longer incubation period of 127 days for 90% removal. Furthermore, dissipation of the PPCPs was slower when a mixture of all three was applied to BPS microcosms. TCS had an initial negative effect on bacterial viability by a decrease of 34–43% as measured by live bacterial cell counts using LIVE/DEAD® microscopy; however, this effect was mitigated when the three PPCPs were present simultaneously. The bacterial communities in BPS microcosms were more affected by incubation time than by the PPCPs used. Nonetheless, the PPCPs differentially affected the composition and relative abundance of bacterial taxa. IBP and DCF initially increased bacterial diversity and richness, while exposure to TCS generally provoked an opposite effect without full recovery at the end of the incubation period. TCS, which negatively affected the relative abundance of Acidobacteria, Methylophilales, and Legionellales, had the largest impact on bacterial groups. Biomarker OTUs were identified in the BPS microcosms which were constrained to higher concentrations of the PPCPs and thus are likely to harbour degradation and/or detoxification mechanisms. This study reveals for the first time the effect of PPCPs on bacterial ecotoxicity and diversity in biopurification system microcosms and also facilitates the design of further applications of biomixtures to eliminate PPCPs.

Effects of winter and summer conditions on Cd fractionation and bioavailability, bacterial communities and Cd phytoextraction potential of Brachiaria decumbens and Panicum maximum grown in a tropical soil

The interactions between soil properties, microorganisms, plant species and climate affect cadmium (Cd) availability in tropical soils. In this study, we investigated the effects of simulated summer and winter conditions on Cd fractionation and bacterial communities in Oxisols and on growth of two high biomass production-grasses (Brachiaria decumbens and Panicum maximum) that were evaluated for their Cd phytoextraction potential. We also assessed how these interactions could influence the availability of Cd and its possible phytoextraction by these grasses. The Cd fraction bound to carbonates was higher in the winter conditions, while Cd bound to Fe- and Mn oxides was higher in the summer conditions, which resulted in a higher Cd availability in winter compared to summer conditions. B. decumbens and P. maximum took up more Cd when grown in the winter conditions, but their biomasses were not affected by the higher Cd uptake. The occurrence and relative abundance of bacterial taxa in the bare soil differed from the soils cultivated with grasses, where the Gammaproteobacteria predominated. However, no positive correlations were observed between the rhizosphere bacterial community in the cultivated soils and Cd availability, irrespective of the season conditions.

Trash Your Agar Plates! Blood Stream Bacteria Are Now Quantified by in vivo Flow Cytometry.

© 2020 International Society for Advancement of Cytometry.

Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome.

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species.IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species' relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species' concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

Distinct successional patterns and processes of free‐living and particle‐attached bacterial communities throughout a phytoplankton bloom

Abstract Understanding the successional patterns of microbial communities during a phytoplankton bloom is crucial for predicting the compositional and functional stability of lake ecosystems in response to the disturbance of a bloom. Previous studies on bacterial communities associated with blooms have rarely studied the dynamics of these communities. The successional patterns of bacterial communities within different micro‐habitats (i.e. water column versus particles) and mechanisms that shape these communities that differ in composition and structure remain unclear. We selected a eutrophic urban lake to investigate the succession of bacterial communities during a bloom. We divided the bacterial communities into free‐living (FL) and particle‐attached (PA) groups based on their different lifestyles. The amplicon‐based 16S rRNA gene high‐throughput sequencing technology was used to obtain bacterial community composition and phylogenetic structure. Our study showed distinct successional patterns between FL and PA bacterial communities, and the two bacterial lifestyles showed different responses and resilience to the bloom, in terms of diversity and relative abundance of bacterial taxa. Alpha‐diversity of the PA bacterial community decreased during the bloom, whereas that of the FL bacterial community increased. More taxa in the FL bacterial community showed resilience after the disturbance than in the PA bacterial community. The influence of phytoplankton blooms on the assembly of the bacterial community can be viewed as niche selection that led to the decrease in the relative importance of stochastic processes in shaping both FL and PA bacterial communities. This study shows the ecological significance of the bacterial community response to bloom events in lakes. It also shows that assembly processes differ for bacterial communities that have different lifestyles in lake ecosystems disturbed by phytoplankton blooms.

Investigating the role of the gut microbiome as a trigger for arthritis development in individuals at risk of rheumatoid arthritis

Background: Rheumatoid arthritis (RA) is now recognised as the end point of a disease continuum. Anti-citrullinated peptide antibodies (ACPA) mark the presence of RA-related systemic autoimmunity, but the production of auto-antibodies alone is not sufficient to develop disease. Data on progression between the stages of RA disease are limited, but accumulating evidence suggests a microbial dysbiosis in the gut may trigger RA development. Using a prospective ‘at-risk’ cohort of ACPA positive individuals without arthritis, we investigated for the presence of a gut dysbiosis before the onset of RA. Materials/methods: Faecal samples from 25 ACPA-positive individuals, with non-specific musculoskeletal pain, were sequenced using16S rRNA gene. A control population was selected from publicly available data on the NCBI database, matched for rRNA V4 amplification region, sequencing technique, and approximately for age, gender, diet and ethnicity. Taxonomic analysis was performed using QIIME and MEGAN, and statistical analysis using R software. Results: Comparison of the ACPA-positive and control populations shows large clustering at bacterial family level. The ACPA population has an abundance of Lachnospiraceae, Helicobacteraceae, Ruminococcaceae, Erysipelotrichaceae and Bifidobacteriaceae, and a lower abundance of Bacteroidaceae, Barnesiellaceae, Methanobacteriaceae amongst others. The relative abundance of bacterial taxa between the ACPA positive and control population was significantly different (P value 0.01, permutation MANOVA). Conclusions: The gut microbiome of individuals ‘at-risk’ of developing RA is distinct from heathy controls. These pilot data can inform further studies, and are an important step in the attribution of causality to the gut microbiome in the development of RA.

Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.

Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.

A novel calcium-based magnetic biochar is effective in stabilization of arsenic and cadmium co-contamination in aerobic soils

This study developed a novel calcium-based magnetic biochar by pyrolysing rice straw mixed with calcium carbonate and iron oxide for stabilization of contamination of multiple metals. A 160-day incubation study was conducted to investigate its performance in stabilization of cadmium and arsenic co-contamination in soil. Both biochar and Ca-MBC treatments increased soil pH, decreased the bioavailability of cadmium. Ca-MBC decreased but biochar enhanced the bioavailability of arsenic. The BCR (European Community Bureau of Reference) sequential extraction confirmed Ca-MBC facilitated the transformation of the unstable fraction of arsenic to stable fractions. The stabilization mechanisms were explored through synchrotron-based micro X-ray fluorescence and X-ray absorption near edge structure. The results show that Ca-MBC remediated the dual contamination of arsenic and cadmium through (1) elevated pH and cation exchange capacity (for Cd); (2) the formation of bi-dentate chelate and ternary surface complexes on the surface of iron oxide; (3) enhanced adsorption ability of porous biochar. In addition, Ca-MBC increased the abundance and diversity of bacterial community, and modified the relative abundances of bacterial taxa, leading to a shift of the composition. These new insights provide valuable information for stabilization of co-contamination of arsenic and cadmium in soil using the potential material Ca-MBC.

Bacterial community composition in agricultural soils under long‐term organic and conventional management

AbstractOrganic row cropping systems utilize diverse management regimes, but share required practices, including biological fertility sources, diverse rotations, incorporation of organic matter, and lack of synthetic pesticides. The practices can alter the composition of functionally significant soil microbes relative to conventional practices. We used 16S rRNA sequencing to profile soil bacterial communities at five locations where long‐term organic and conventional row cropping were practiced in close proximity on the same underlying soil type. Location effects, reflecting soil characteristics, were stronger than effects of organic vs. conventional management or corn (Zea mays L.) vs. soybean [Glycine max (L.) Merr.] cropping on the relative abundance of bacterial taxa. A core subset of 1,300 operational taxonomic units (OTUs) were detected in all sampled soils. Firmicutes made up a smaller portion of core OTUs than total OTUs, indicating that taxa in this group were more likely to be found only in specific environments. Conversely, Actinobacteria OTUs were more highly represented in the core than the full OTU set, indicating wide distribution of these taxa across environments. The genus Streptomyces comprised a five‐fold–greater proportion of core OTUs than of total OTUs. We identified 303 OTUs whose abundance differed with management system. Of those, members of the phyla Bacteroidetes and Planctomycetes tended to be more abundant under organic management, whereas members of the Actinobacteria and Verrucomicrobia tended to be more abundant in conventional. This multi‐site study contributes to identification of bacterial community members most affected by organic practice adoption across soil types and practices.

Changes in the Bacterial Community Structure of Denitrifying Sludge from a Recirculating Aquaculture System (RAS) After Geosmin and 2-Methylisoborneol Enrichment.

The secondary metabolites geosmin and 2-methylisoborneol (MIB) are known to taint fish with an undesirable, earthy-muddy taste and odor. In an earlier study on a zero-discharge recirculating aquaculture system (RAS), it was found that geosmin and MIB were removed by microbial communities residing in sludge from the digestion basin of the system. In the present study, 16S amplicon sequencing was used to identify changes in relative abundances of bacterial taxa in geosmin and MIB-enriched crude sludge. The removal of geosmin and MIB by the sludge was accompanied by increased abundances of 12 operational taxonomic units (OTUs). The most prominent increase in abundances was recorded for OTUs affiliated with bacterial genera known to harbor denitrifiers. Among these were the Betaproteobacteria genera Thauera, which utilizes terpenes to fuel denitrification, and Comamonas, which was previously isolated from the digestion basin of the same system and is capable of growth on geosmin and MIB as sole carbon and energy sources. Thus far, denitrification has been associated with bacteria capable of utilizing terpenes other than geosmin and MIB. The significant increase in the abundance of denitrifying bacterial genera in sludge in which geosmin and MIB comprised only 0.06% of the total carbon content might indicate that such bacteria play a major role in the removal of these compounds in anoxic environments.