scholarly journals Straw-Based Biopurification Systems to Remove Ibuprofen, Diclofenac and Triclosan from Wastewaters: Dominant Microbial Communities

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1507
Author(s):  
Laura Delgado-Moreno ◽  
Pieter van Dillewijn ◽  
Rogelio Nogales ◽  
Esperanza Romero
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Point Source ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
Microbial Structure ◽  
Methyl Triclosan ◽  
Source Contamination ◽  
Biopurification Systems ◽  
Olive Mill

The continued discharge of pharmaceuticals and personal care products (PPCPs) into the environment due to their widespread use and the lack of effective systems for their removal from water is a global problem. In this study, the dissipation of ibuprofen, diclofenac and triclosan added simultaneously in biopurification systems (BPSs) with different compositions and their effect on the microbial community structure was analysed. Three BPSs, constituted by mixtures of soil (S), peat (P), or raw wet olive mill cake (A) or its vermicompost (V) and straw (S) were prepared (SPS, SAS and SVS). Sorption and degradation experiments were carried out. After 84 days of incubation, more than 85% of each PPCP applied had dissipated. Methyl-triclosan was determined to be highest in the SVS biomixture. Biomixtures with lower C/N ratio and higher alpha diversity were the most effective in the removal of PPCPs. Initially, the BPS biomixtures showed a different microbial structure dominated by Proteobacteria, Actinobacteria and Bacteroidetes but after addition of PPCPs, a similar pattern was observed in the relative abundance of the phylum Chloroflexi, the class Sphingobacteriia and the genus Brevundimonas. These biopurification systems can be useful to prevent point source contamination due to the disposal of PPCP-contaminated waters.

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

scholarly journals PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Poultry Production ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Madangchanok Imchen ◽  
Ranjith Kumavath
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Community ◽  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Mangrove Ecosystem ◽  
Mangrove Sediment ◽  
Mangrove Forests ◽  
Human Intervention ◽  
Shotgun Metagenomics

ABSTRACT Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.

scholarly journals Simulation-based approaches to characterize metagenome coverage as a function of sequencing effort and microbial community structure

2018 ◽  
Author(s):  
Taylor Royalty ◽  
Andrew D. Steen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Genome Size ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Software Tool ◽  
Individual Genome ◽  
Base Pairs ◽  
Simulation Based ◽  
Sequencing Experiment

AbstractWe applied simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short read sequences. An initial analysis evaluated the quantity, completion, and contamination of complete-metagenome-assembled genome (complete-MAG) equivalents, a bioinformatic-pipeline normalized metric for MAG quantity, as a function of sequencing effort, on four preexisting sequence read datasets taken from a maize soil, an estuarine sediment, the surface ocean, and the human gut. These datasets were subsampled to varying degrees of completeness in order to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A second analysis explored the theoretical relationship between sequencing effort and the proportion of available metagenomic DNA sequenced during a sequencing experiment as a function of community richness, evenness, and genome size. Simulations from this analysis demonstrated that while community richness and evenness influenced the amount of sequencing required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion was only dependent on the relative abundance of the corresponding organism and its genome size. A software tool, GRASE, was created to assist investigators further explore this relationship. Re-evaluation of the relationship between sequencing effort and binning success in the context of the relative abundance of genomes, as opposed to base pairs, provides a framework to design sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort.

scholarly journals Analysis of Microbial Community Structure Around Roots of Stipa Grandis

2021 ◽  
Author(s):  
Ai-Min Zhu ◽  
Guo-Dong Han ◽  
Hai-Li Liu ◽  
Yue-Hua Wang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Root Zone ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Microbial Structure ◽  
Root Epidermis ◽  
16S Rna

Abstract The root zone microbial structure is particularly complex for plants with rhizosheaths, which may play an important role in the future agricultural sustainable development. However, one of the important reasons for restricting our study of rhizosheath microbial structure is that there is no definite method for rhizosheath separation. The aim of this study was to explore the isolation methods of rhizosheath and the diversity and functional characteristics of microorganisms around the rhizosphere. In this study, we isolated the rhizosheath of Stipa grandis, a dominant species in desert steppe, and the microorganisms in the roots, root epidermis, rhizosheath, rhizosphere soil were extracted and sequenced by 16s RNA and ITS. The bacterial alpha diversity index was in the order rhizosphere soil > rhizosheath > root epidermis > endophytic, and the fungal alpha diversity index was rhizosphere soil and rhizosheath > root epidermis and endophytic. There were significant differences in bacterial community structure between the root epidermis and endophytic, rhizosheath, rhizosphere soil, and the sum of relative abundance of the dominant bacterial populations Actinobacteria and Proteobacteria was 73.9% in the root epidermis. Different from bacterial community structure, the community structure of root epidermis fungi was similar to endophytic, but significantly different from rhizosheath and rhizosphere soil. We suggest that the root epidermis can act as the interface between the host plant root and the external soil environment. This study will provide theoretical and technical guidance for the isolation of plant rhizosheath and the study of microorganisms in it.

Altered microbial community structure and metabolism in cow’s milk allergic mice treated with oral immunotherapy and fructo-oligosaccharides

2020 ◽  
Vol 11 (1) ◽  
pp. 19-32
Author(s):  
M.M. Vonk ◽  
P.A. Engen ◽  
A. Naqib ◽  
S.J. Green ◽  
A. Keshavarzian ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Propionic Acid ◽  
Butyric Acid ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Oral Immunotherapy ◽  
Cow’S Milk ◽  
Microbiota Composition ◽  
Faecal Samples

Previously, we showed enhanced efficacy of oral immunotherapy (OIT) using fructo-oligosaccharides (FOS, prebiotics) added to the diet of cow’s milk allergic mice indicated by a reduction in clinical symptoms and mast cell degranulation. Prebiotics are fermented by gut bacteria, affecting both bacterial composition and availability of metabolites (i.e. short-chain fatty acids (SCFA)). It is thus far unknown which microbial alterations are involved in successful outcomes of OIT with prebiotic supplementation for the treatment of food allergy. To explore potential changes in the microbiota composition and availability of SCFA induced by OIT+FOS. C3H/HeOuJ mice were sensitised and received OIT with or without a FOS supplemented diet. After three weeks, faecal samples were collected to analyse gut microbiota composition using 16S rRNA sequencing. SCFA concentrations were determined in cecum content. FOS supplementation in sensitised mice changed the overall microbial community structure in faecal samples compared to sensitised mice fed the control diet (P=0.03). In contrast, a high level of resemblance in bacterial community structure was observed between the non-sensitised control mice and the OIT+FOS treated mice. OIT mice showed an increased relative abundance of the dysbiosis-associated phylum Proteobacteria compared to the OIT+FOS mice. FOS supplementation increased the relative abundance of genus Allobaculum (Firmicutes), putative butyrate-producing bacteria. OIT+FOS reduced the abundances of the genera’s unclassified Rikenellaceae (Bacteroidetes, putative pro-inflammatory bacteria) and unclassified Clostridiales (Firmicutes) compared to sensitised controls and increased the abundance of Lactobacillus (Firmicutes, putative beneficial bacteria) compared to FOS. OIT+FOS mice had increased butyric acid and propionic acid concentrations. OIT+FOS induced a microbial profile closely linked to non-allergic mice and increased concentrations of butyric acid and propionic acid. Future research should confirm whether there is a causal relationship between microbial modulation and the reduction in acute allergic symptoms induced by OIT+FOS.

scholarly journals Fecal Microbial Diversity and Structure Are Associated with Diet Quality in the Multiethnic Cohort Adiposity Phenotype Study

2019 ◽  
Vol 149 (9) ◽  
pp. 1575-1584 ◽  
Author(s):  
Gertraud Maskarinec ◽  
Meredith A J Hullar ◽  
Kristine R Monroe ◽  
John A Shepherd ◽  
Jeani Hunt ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Healthy Eating ◽  
Diet Quality ◽  
Microbial Community Structure ◽  
Alpha Diversity ◽  
Clinic Visit ◽  
Healthy Eating Index ◽  
Dietary Index ◽  
Multiethnic Cohort

ABSTRACT Background Variation in gut microbial community structure is partly attributed to variations in diet. A priori dietary indexes capture diet quality and have been associated with chronic disease risk. Objectives The aim of this study was to examine the association of diet quality, as assessed by the Healthy Eating Index, Alternative Healthy Eating Index-2010, alternate Mediterranean Diet, and the Dietary Approaches to Stop Hypertension Trial, with measures of fecal microbial community structure assessed in the Adiposity Phenotype Study (APS), an ethnically diverse study population with varied food intakes. Methods Multiethnic Cohort Study members completed a validated quantitative food frequency questionnaire (QFFQ) at cohort entry (1993–1996) and, for the APS subset, at clinic visit (2013–2015), when they also provided a stool sample. DNA was extracted from stool, and the V1-V3 region of the 16S rRNA gene was amplified and sequenced. Dietary index scores were computed based on the QFFQ and an extensive nutritional database. Using linear regression adjusted for relevant covariates, we estimated associations of dietary quality with microbiome measures and computed adjusted mean values of microbial measures by tertiles of dietary index scores. Results The 858 men and 877 women of white, Japanese American, Latino, Native Hawaiian, and African American ancestry had a mean age of 69.2 years at stool collection. Alpha diversity according to the Shannon index increased by 1–2% across tertiles of all 4 diet indexes measured at clinic visit. The mean relative abundance of the phylum Actinobacteria was 13–19% lower with higher diet quality across all 4 indexes (difference between tertile 3 and tertile 1 divided by tertile 1). Of the 104 bacterial genera tested, 21 (primarily from the phylum Firmicutes) were positively associated with at least 1 index after Bonferroni adjustment. Conclusion Diet quality was strongly associated with fecal microbial alpha diversity and beta diversity and several genera previously associated with human health.

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