Biology subjects

Antonopoulos, D. A.

Publications and source records attributed to Antonopoulos, D. A..

7 recordsLinked to original sources

bioRxiv2023

Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential

Chemicals involved in plutonium uranium reduction extraction (PUREX) have the potential to be released from nuclear reprocessing facilities and accumulate in the environment. In order to understand how soil microbial communities respond to contamination by PUREX chemicals, we carried out a series of microcosm experiments, exposing chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. We tested 4 PUREX chemicals, and 5 soil types using 16S rRNA amplicon sequencing, determining that responses of microbial communities are dependent on the soil type in which they reside, and that tributyl phosphate exposure appears to generate the most reproducible and detectable shifts in microbial communities. We identified a number of key taxa that are consistently enriched in soils exposed to tributyl phosphate. These key taxa are either in the family Rhizobiaceae or genus Pseudomonas. The relative abundance of these key taxa is concentration dependent, and their abundance remains elevated at least 100 days post initial exposure. Using whole-shotgun metagenomic sequencing, we reconstructed the genomes of these key taxa and find a number of putative phosphotriesterase genes found only in Rhizobiaceae. We find the abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. These phosphotriesterase genes, which degrade tributyl phosphate into dibutyl phosphate and butanol, may serve as effective biomarkers for tributyl phosphate contaminated soil, as well as a method for future bioremediation. ImportanceNuclear materials reprocessing facilities have the capacity to release toxic chemicals during normal operations or accidents. This study examines the ways in which chemicals involved with nuclear materials reprocessing impact microorganisms in the soil. Our intention was to understand the consequences of the release of these chemicals on ecosystems that may surround these reprocessing facilities. We find soil microbial communities change in response to some chemicals but not others, and that tributyl phosphate appears to generate the most reproducible and detectable shifts in microbial communities. Microorganisms in the family Rhizobiaceae increase in abundance in response to the addition of tributyl phosphate, and an examination of the genomes of these microbes suggest they may be able to break down tributyl phosphate to access the phosphosphate present in this chemical. Overall, this work demonstrates that changes in soil microbial communities in response to contamination with chemicals from nuclear materials reprocessing facilities may be predictable, and these responses could be leveraged to remediate contamination.

microbiology↗

bioRxiv2022

A microbial community growth model for dynamic phenotype predictions

1Microbial communities are increasingly recognized as key drivers in animal health, agricultural productivity, industrial operations, and ecological systems. The abundance of chemical interactions in these complex communities, however, can complicate or evade experimental studies, which hinders basic understanding and limits efforts to rationally design communities for applications in the aforementioned fields. Numerous computational approaches have been proposed to deduce these metabolic interactions - notably including flux balance analysis (FBA) and systems of ordinary differential equations (ODEs) - yet, these methods either fail to capture the dynamic phenotype expression of community members or lack the abstractions required to fit or explain the diverse experimental omics data that can be acquired today. We therefore developed a dynamic model (CommPhitting) that deduces phenotype abundances and growth kinetics for each community member, concurrent with metabolic concentrations, by coupling flux profiles for each phenotype with experimental growth and -omics data of the community. These data are captured as variables and coefficients within a mixed integer linear optimization problem (MILP) designed to represent the associated biological processes. This problem finds the globally optimized fit to all experimental data of a trial, thereby most accurately computing aspects of the community: (1) species and phenotype abundances over time; (2) a linearized growth kinetic constant for each phenotype; and (3) metabolite concentrations over time. We exemplify CommPhitting by applying it to study batch growth of an idealized two-member community of the model organisms (Escherichia coli and Pseudomonas flourescens) that exhibits cross-feeding in maltose media. Measurements of this community from our accompanying experimental studies - including total biomass, species biomass, and metabolite abundances over time - were parameterized into a CommPhitting simulation. The resultant kinetics constants and biomass proportions for each member phenotype would be difficult to ascertain experimentally, yet are important for understanding community responses to environmental perturbations and therefore engineering applications: e.g. for bioproduction. We believe that CommPhitting - which is generalized for a diversity of data types and formats, and is further available and amply documented as a Python API - will augment basic understanding of microbial communities and will accelerate the engineering of synthetic communities for diverse applications in medicine, agriculture, industry, and ecology.

systems biology↗

bioRxiv2022

Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine

Several pyridine derivatives including the pesticide nitrapyrin [2-chloro-6-(trichloromethyl) pyridine] are strong inhibitors of methane monooxygenase, a key enzyme of aerobic methane (CH4) oxidation. In this study we examined the effects of 2-chloro-6-methylpyridine (2C6MP) concentration on aerobic CH4 oxidation and the development of populations of putative methanotrophs in sediment from Old Woman Creek, a freshwater estuary in Huron Co., Ohio. Experimental systems were prepared in serum bottles containing minimal medium with a headspace containing 20% O2 and 10% CH4. The microcosms were spiked with 2C6MP to achieve concentrations of 0, 0.1, 1, or 10 mM and inoculated with sediment. When headspace CH4 concentrations decreased from 10% to < 2%, subsamples were taken for DNA extraction and sequencing of 16S rRNA gene amplicons. There was minimal effect of 2C6MP on CH4 oxidation at concentrations of 0.1, and 1 mM, but complete inhibition for > 20 months was observed at 10 mM. ANOSIM of weighted UniFrac distances between groups of triplicate samples supported a primary distinction of the inoculum relative to the enrichments (R=0.999) and a secondary distinction between bottles containing 2C6MP versus those without (R=0.464 [0.1 mM]; R=0.894 [1 mM]). The inoculum was dominated by members of the Proteobacteria (49.9{+/-}1.5%), and to a lesser extent by Bacteroidetes (8.8{+/-}0.2%), Acidobacteria (8.9{+/-}0.4%), and Verrucomicrobia (4.4{+/-}0.3%). In enrichments with or without 2C6MP, Proteobacteria expanded to comprise 65-70% of the total. In the absence of inhibitor, members of the Methylococcaceae and Methylophilaceae increased in relative abundance from < 0.1% of the inoculum to 8.5{+/-}1.0% and 13.4{+/-}2.3%, of the total community respectively. At both 0.1 and 1 mM concentrations of the inhibitor, the Methylococcaceae were much less abundant, representing 3.3{+/-}0.5% and 2.8{+/-}3.3% respectively. No inhibition of the Methylophilaceae was seen at the lower concentration of 2C6MP, but at the higher concentration this taxon was only 7.8{+/-}1.1% of the total. In contrast, members of the Crenotrichaceae, another group of methane oxidizers, increased in relative abundance with greater amounts of inhibitor, representing 8.6{+/-}3.6% of the total at 0.1 mM and 12.0{+/-}4.5% at 1 mM, compared to only 4.1{+/-}0.4% when no inhibitor was present. These results clearly show changes in the populations of putative aerobic methanotrophs relative to the amount of 2C6MP present.

microbiology↗

bioRxiv2020

Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model

Background & AimsInflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts. MethodsUsing the IL-10 gene-deficient (IL-10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone, CPZ) treated dams vertically-transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes. ResultsCompared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership both in bacteriome and mycobiome that were associated with alterations in specific functional subsystems. Furthermore, among IL-10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome. ConclusionsOur findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD. SynopsisCurrently, predictive markers for the development and course of inflammatory bowel diseases (IBD) are not available. This study supports the notion that gut microbiome metagenomic profiles could be developed into a useful tool to assess risk and manage human IBD.

microbiology↗

bioRxiv2020

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

Perturbations in the early life gut microbiome are associated with increased risk to complex immune disorder like inflammatory bowel diseases. We previously showed maternal antibiotic-induced gut dysbiosis vertically passed to offspring increases experimental colitis risk in IL-10 gene deficient (IL-10-/-) mice. While this could arise from emergence of pathobionts or loss/lack of essential microbes needed for appropriate immunological education, our findings suggest the latter. A dominant Bacteroides strain absent following antibiotic-induced perturbation was cultivated from murine fecal samples. Addition of this strain into mice with antibiotic-induced dysbiosis significantly promoted immune tolerance and reduced incidence of colitis in IL-10-/- mice, but only if engrafted early in life, and not during adulthood. Thus, key members of the gut microbiome are essential for development of immune tolerance to commensal microbes in early life and their addition in presence of gut dysbiosis during this period can reduce colitis risk in genetically prone hosts. HighlightsO_LISpecific gut microbes promote early life immune tolerance to key commensal microbes C_LIO_LILoss of early life keystone microbes increases colitis risk in genetically prone hosts C_LIO_LIEmergence of absent commensal microbes late in life worsened colitis outcome C_LIO_LIEarly life exposure to a missing keystone Bacteroides strain reduced colitis risk C_LI

microbiology↗

bioRxiv2017

Community dynamics in parallelized, aerobic, single carbon-source enrichments

Here we seek to test the extent to which laboratory enrichments mimic natural community processes and the degree to which the initial structure of a community determines its response to a press disturbance via the addition of environmentally-relevant carbon compounds. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from 6 different classes of organic compound (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 hours, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still is strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g. Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g. Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Niche selection therefore seems to play a strong role in shaping the communities in the substrate arrays, although some stochasticity is seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to a changing environment.

microbiology↗

bioRxiv2016

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. Here we used shotgun metagenomics to reconstruct 97 metagenome-assembled genomes (MAGs) from fecal samples of a single donor and followed their distribution in two FMT recipients to identify microbial populations with different colonization properties. Our analysis of the occurrence and distribution patterns post-FMT revealed that 22% of the MAGs transferred from the donor to both recipients and remained abundant in their guts for at least eight weeks. Most MAGs that successfully colonized the recipient gut belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales and colonization success was negatively correlated with the number of genes related to sporulation. Although our dataset showed a link between taxonomy and the ability of a MAG to colonize the recipient gut, we also identified MAGs with different colonization properties that belong to the same taxon, highlighting the importance of genome-resolved approaches to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems for mechanistic insights.

microbiology↗