scholarly journals Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Taylor M. Royalty ◽  
Andrew D. Steen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Genome Size ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Data Sets ◽  
Short Read ◽  
Coupon Collector ◽  
Simulation Based ◽  
The Relationship

ABSTRACT We applied theoretical and 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. First, a coupon collector equation was proposed as an analytical model for predicting sequencing effort as a function of microbial community structure. Characterization was performed by varying community structure properties such as richness, evenness, and genome size. Simulations demonstrated that while community richness and evenness influenced the sequencing effort required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion depended only on the relative abundance of the genome and its genome size. A second analysis evaluated the quantity, completion, and contamination of metagenome-assembled genomes (MAGs) as a function of sequencing effort on four preexisting sequence read data sets from different environments. These data sets were subsampled to various degrees of completeness 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 software tool, Genome Relative Abundance to Sequencing Effort (GRASE), was created to assist investigators to further explore this relationship. Reevaluation of the relationship between sequencing effort and binning success in the context of genome relative abundance, as opposed to base pairs, provides a constraint on sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort. IMPORTANCE Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical framework for selecting sequencing effort as a function of genome relative abundance. As such, experimental goals in metagenome-assembled genome creation projects can select sequencing effort based on the rarest target genome as a constrained threshold. We hope that the results presented here, as well as GRASE, will be valuable to researchers planning sequencing experiments.

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 Microbial community structure and the relationship with soil carbon and nitrogen in an original Korean pine forest of Changbai Mountain, China

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Minghui Liu ◽  
Xin Sui ◽  
Yanbo Hu ◽  
Fujuan Feng
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Community Structure ◽  
Soil Microbes ◽  
Mixed Forest ◽  
Korean Pine ◽  
Soil Microbial ◽  
The Relationship ◽  
Main Factor

Abstract Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.

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.

Effect of pH on the Microbial Community Structure of SBBR Autotrophic Nitrogen Removal Process

2011 ◽  
Vol 378-379 ◽  
pp. 428-432
Author(s):  
Yu Qin ◽  
Jing Song Guo ◽  
Fang Fang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Nitrogen Removal ◽  
Microbial Community Structure ◽  
Anaerobic Bacteria ◽  
Biofilm Reactor ◽  
Active Sludge ◽  
Removal Process ◽  
The Relationship ◽  
Autotrophic Nitrogen Removal

PCR-DGGE was applied to analyze the relationship between pH and the microbial community structure of Sequence Batch Biofilm Reactor (SBBR) autotrophic nitrogen removal process. The reactor was possessed of a high nitrogen removal efficiency at pH=8.0 where the similarity of microbial community structure between active sludge and biofilm samples was the lowest about 84.6% and the richness of bacterial community was the most abundant in biofilm compared with other pH conditions. pH=7.0 was good for the microbes in active sludge but unfavorable for anaerobic bacteria. At pH=9.0, the effects were presented with both bacterial activities and microbial community structure and when pH=6.0 the amount of microbial types dramatically dropped

scholarly journals PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Peter Rubbens ◽  
Ruben Props ◽  
Frederiek-Maarten Kerckhof ◽  
Nico Boon ◽  
Willem Waegeman
Keyword(s):  
Flow Cytometry ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Gaussian Mixture Models ◽  
Gaussian Mixture ◽  
Community Diversity ◽  
Data Sets ◽  
Natural Ecosystems ◽  
Flow Cytometry Data

ABSTRACT Microbial flow cytometry can rapidly characterize the status of microbial communities. Upon measurement, large amounts of quantitative single-cell data are generated, which need to be analyzed appropriately. Cytometric fingerprinting approaches are often used for this purpose. Traditional approaches either require a manual annotation of regions of interest, do not fully consider the multivariate characteristics of the data, or result in many community-describing variables. To address these shortcomings, we propose an automated model-based fingerprinting approach based on Gaussian mixture models, which we call PhenoGMM. The method successfully quantifies changes in microbial community structure based on flow cytometry data, which can be expressed in terms of cytometric diversity. We evaluate the performance of PhenoGMM using data sets from both synthetic and natural ecosystems and compare the method with a generic binning fingerprinting approach. PhenoGMM supports the rapid and quantitative screening of microbial community structure and dynamics. IMPORTANCE Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Flow cytometry has been proposed as an alternative technology to characterize microbial community diversity and dynamics. The technology enables a fast measurement of optical properties of individual cells. So-called fingerprinting techniques are needed in order to describe microbial community diversity and dynamics based on flow cytometry data. In this work, we propose a more advanced fingerprinting strategy based on Gaussian mixture models. We evaluated our workflow on data sets from both synthetic and natural ecosystems, illustrating its general applicability for the analysis of microbial flow cytometry data. PhenoGMM supports a rapid and quantitative analysis of microbial community structure using flow cytometry.

scholarly journals Aquaculture Water Quality Improvement by Mixed Bacillus and Its Effects on Microbial Community Structure

2021 ◽  
Author(s):  
Xue Li ◽  
Tianie Wang ◽  
Baorong Fu ◽  
Xiyan Mu
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Relative Abundance ◽  
Bacillus Megaterium ◽  
Microbial Community Structure ◽  
Pathogenic Bacteria ◽  
Phosphorus Compounds ◽  
Nitrogen And Phosphorus ◽  
Aquaculture Water

Abstract Nutrients nitrogen and phosphorus pollution in aquaculture is one of the greatest challenges threatening the survival of aquatic organisms, which requires efficient and sustainable remediation approach. Microbial remediation, especially the application of probiotics, has recently gained popularity in improving the water quality and maintaining the health condition of aquatic animals. In the present study, two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0+BS) and Bacillus megaterium and Bacillus coagulans (A0+BC)) were applied to aquaculture system of Crucian carp to improve the treatment of nitrogenous and phosphorus compounds. The effects of mixed Bacillus on water quality, and the structure and function of microbial communities in aquaculture water were investigated. Our results showed that the improvement effect of mixed Bacillus A0+BS on water quality was better than that of A0+BC, and the NH4+-N, NO2--N, NO3--N and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of bacterial community and decreased the diversity of fungal community. Microbial community analysis showed that mixed Bacillus A0+BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, e.g., Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). The redundancy analysis showed that NH4+-N, NO2--N, and TP were primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the treatment groups were up-regulated, and all pathways in A0+BS group were richer than those in other groups. These results indicated that mixed Bacillus A0+BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.

scholarly journals Effects of Trichoderma asperellum 6S-2 on Apple Tree Growth and Replanted Soil Microbial Environment

2022 ◽  
Vol 8 (1) ◽  
pp. 63
Author(s):  
Haiyan Wang ◽  
Rong Zhang ◽  
Yunfei Mao ◽  
Weitao Jiang ◽  
Xuesen Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Gene Copy ◽  
Available Phosphorus ◽  
Trichoderma Asperellum ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Trichoderma asperellum strain 6S-2 with biocontrol effects and potential growth-promoting properties was made into a fungal fertilizer for the prevention of apple replant disease (ARD). 6S-2 fertilizer not only promoted the growth of Malus hupehensis Rehd seedlings in greenhouse and pot experiments, but also increased the branch elongation growth of young apple trees. The soil microbial community structure changed significantly after the application of 6S-2 fertilizer: the relative abundance of Trichoderma increased significantly, the relative abundance of Fusarium (especially the gene copy numbers of four Fusarium species) and Cryptococcus decreased, and the relative abundance of Bacillus and Streptomyces increased. The bacteria/fungi and soil enzyme activities increased significantly after the application of 6S-2 fertilizer. The relative contents of alkenes, ethyl ethers, and citrullines increased in root exudates of M. hupehensis Rehd treated with 6S-2 fertilizer and were positively correlated with the abundance of Trichoderma. The relative contents of aldehydes, nitriles, and naphthalenes decreased, and they were positively correlated with the relative abundance of Fusarium. In addition, levels of ammonium nitrogen (NH4-N), nitrate nitrogen (NO3-N), available phosphorus (AP), available potassium (AK), organic matter (SOM), and pH in rhizosphere soil were also significantly related to changes in the microbial community structure. In summary, the application of 6S-2 fertilizer was effective in alleviating some aspects of ARD by promoting plant growth and optimizing the soil microbial community structure.

scholarly journals Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation

2019 ◽  
Author(s):  
Chol Gyu Lee ◽  
Eriko Kunitomo ◽  
Toshiya Iida ◽  
Kazuhiro Nakaho ◽  
Moriya Ohkuma
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Soil Disinfestation ◽  
Chain Reactions ◽  
Anaerobic Soil Disinfestation ◽  
Polymerase Chain Reactions ◽  
Operational Taxonomic Units ◽  
The Relationship

AbstractAnaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. To this end, we investigated changes in the microbial community and pathogen density during a period of ASD under field conditions for 14 days in a greenhouse using three different substrates. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions, prokaryotic community analysis was conducted using unidirectional pyrosequencing, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14, but the rate of decrease differed among the substrates. The microbial communities became altered after 3 days and recovered to their original state on day 14. The dipyridyl reaction, microbial diversity, richness, and community structure were not correlated with pathogen density. The most negatively correlated operational taxonomic units with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. These results suggested that the growth of specific microbes, but not the changes in microbial community structure, might be important for ASD disinfestation efficiency.

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