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Fracking
Crohn’s Disease
Oil Spill
Diet
Combined Sewer Overflow
Soil

The Response of Freshwater Aquatic Microbial Communities to Marcellus Shale Natural Gas Extraction

Caroline Solomon (1), Ryan Trexel (1), Regina Lamendella (1)

(1) Juniata College

Marcellus Shale natural gas extraction has increased dramatically in Pennsylvania over the past six years. Due to accelerating exploration rates, the combination of horizontal drilling and hydraulic fracturing may potentially lead to environmental pollution through a variety of pathways. Because microbial communities can shift dramatically in response to changes in environmental parameters, they can be used as biomarkers to assess ensuing environmental threats. The purpose of our study is to compare the microbial community structure of Marcellus Shale impacted and non-impacted headwater stream ecosystems. Water, sediment, bryophyte, and biofilm samples were collected from 26 forested headwater streams and genomic DNA was extracted from a total of 59 samples. In order to determine bacterial community structure, 16S rRNA gene libraries were created and sequenced using the Illumina MiSeq Platform. Metadata including stream temperature, pH, conductivity, salinity, total dissolved solids, and dissolved and particulate total and methyl mercury were collected from each site. Additionally, biodiversity information has been collected using macroinvertabrates and Salvelinus fontinalis brook trout. Approximately 4.5 million, 16S rRNA gene sequences were analyzed using the QIIME. Alpha and beta diversity statistics, and multivariate statistics showed significant changes in abiotic parameters, including pH and temperature in sites impacted by documented spills and contamination events. Pearson correlation of abiotic parameters to microbial community structure showed that pH was the most highly correlated factor to microbial community structure. Microbial community structure was statistically significantly different between impacted and non-impacted sites. For example, changes in Methanobacterium, Magnetospirillum, and Sterolibacterium spp. correlate with samples collected from watersheds potentially impacted by fracking activities. To our knowledge, the response of microbial communities to natural gas exploration in the Marcellus Shale formation has not yet been studied. Our data suggest that by studying bacterial shifts in response to natural gas extraction we can identify bacterial groups relevant to environmental remediation and long-term environmental stewardship.

Shifts in the Gut Microbiota of Inflammatory Bowel Disease Patients in a Longitudinal Study

Erin McClure (1), Mitchell Dunklebarger (1), Kent Li (2), Jonas Halfvarsson (3), Curt Tysk (3), Daniel McDonald (4), Yoshiki Vázquez Baeza (4), William Walters (4), Rob Knight (4), Janet K. Jansson (2,5), Regina Lamendella (1,2)

(1) Juniata College, Huntingdon, PA; (2) Lawrence Berkeley National Laboratory, Berkeley, CA; (3) Orebro University Hospital, Orebro, SE; (4) University of Colorado Boulder; Boulder, CO; (5) Joint Genome Institute, Walnut Creek, CA

Background:The incidence of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, has been increasing in industrialized nations. Ulcerative colitis (UC) and Crohn’s disease (CD) are the two main subtypes of IBD. The etiology of IBD is unknown, however dysbiosis, or a shift, in the gut microbial community structure has been observed in IBD patients. A dysregulated immune response to the commensal gut microbiota has been implicated in IBD pathogenesis. It remains unknown whether this dysbiosis causes or is a result of this aberrant immune response. The aim of this study is to track the microbial community dynamics of IBD patients over multiple time points to better correlate disease condition with the status of the gut microbiota.
Methods:This is the first longitudinal study of dysbiosis in IBD patients, with a total of 692 samples taken from a cohort of IBD patients and healthy controls. Samples from between four and six timepoints were taken from 74 members of the IBD cohort (5 healthy controls, 43 UC, 3 collagenous colitis, 1 lymphocytic colitis, 11 colonic CD, 6 terminal CD, and 6 ileal CD) to yield 363 samples. The QIIME pipeline was used to analyze the 250 million 16S rRNA reads obtained using the Illumina iTAG sequencing platform. Sequences were clustered with Uclust Ref and annotated using the Greengenes database. The cumulative abundance of top 20 phyla and families were determined for each sample, and the data were clustered by non-metric multidimensional scaling (nMDS) in PC-ORD. Temporal barcharts were created to visualize dysbiosis overtime.
Results: Prevotellaecae dominate the gut microbiota in healthy individuals. Temporal shifts in the relative abundance of Bacteroides have been observed in some CD patients with multiple time points. Overall instability is seen in CD patients compared to UC and healthy controls. The nMDS shows a possible spectrum of dysbiosis in IBD, as healthy timepoints clustered with predicted non-flare up timepoints in IBD.

Genome Sequencing of Hydrocarbon Degrading Bacteria Isolated from Biotrap Amended Beads in the Gulf of Mexico

Steven Strutt, Regina Lamendella

Juniata College

The Deepwater Horizon Spill represents one of the worst natural disasters in oil-spill history. The influx of nearly 5 million barrels of crude oil has had untold effects on marine microbial environments. Novel organisms adjacent to the site of oil irruption were isolated and PCR analyses revealed homology to members of Oceanospirillales and Rhodobacterales. Genome sequencing data will be analyzed for genes involved in hydrocarbon degradation. Correlating hydrocarbon degradation data from microcosm experiments with genomic data, we aim to understand the potential of autochthonous organisms for in situ oil degradation.

Impact of Resistant Starch Diets on Gut Microbial Community Dynamics

Andrew Maul (1), Keiko Sing (1), Janet Jannson (2), Robert Knight (3), Ronald Krauss (4), and Regina Lamendella (1,2)

(1)Juniata College, (2)Lawrence Berkeley National Lab, (3) University of Colorado at Boulder, (4) Children’s Hospital Oakland Research Institute

Over the past decade, the prevalence of obesity and its associated health issues have become an issue at the forefront of global health. Understanding the composition of the gut microbiome as it relates to obesity may lead to the development of novel treatments for the disease. The impacts of a resistant starch diet on the gut microbiome and physiological conditions have not been thoroughly investigated. In order to determine these effects, a DNA library that specifically targeted the 16S rRNA gene was generated from 94 fecal samples collected from 39 patients who participated in a 56 day, two-phase study. The DNA collected from the samples was PCR amplified and sequenced on the Illumina HiSeq2000 platform. The generated library was then combined with physiological metadata obtained from each of the patients and uploaded to the QIIME database. Statistical analysis of the metadata was executed through the use of non-metric multidimensional scaling (nMDS) and analysis of variance (ANOVA). Preliminary results of nMDS showed little correlation between the high and low resistant starch diets and the composition of the gut microbiome. ANOVA tests showed that insulin, glucose, and certain components of triglycerides were significantly correlated to the high resistant starch diet. These results suggest that the resistant starch diet does impact physiological variables, but further statistical analysis is needed. Future results of this study may provide novel biomarkers for obesity as well as insight on potential gut microbes that may be targeted for use in pre- and probiotic therapies for management of obesity related health issues.

Determination of Microbial Makeup of Combined Sewer Overflow by Genomic Fragment Enrichment

Wilbert Beachy and Regina Lamendella

Juniata College

Distinguishing what microbial species make up a microbial community near a combined sewer overflow (CSO) can provide valuable information as to which harmful species have entered the watershed. Currently isolating rare pathogenic species remains a prohibitively expensive and laborious process. Through the use of a novel competitive hybridization procedure called Genomic Fragment Enrichment (GFE) species unique to a specific environmental sample will be isolated to demonstrate a cost effective model for visualizing these rare members. GFE may provide a possible model for identifying low level virulence genes in an environment sample, and creating specie PCR primers to track these species. GFE will be applied to CSO sediment samples and sediment samples from up and down river of the CSO to visualize rare members in each of these communities. DNA from one of the communities will be utilized as a blocker DNA in an initial hybridization, whereas a later competitive hybridization with terminally tagged DNA from the non-blocking sample will bind with microbial members who are unique to this sample. These community members will then be separated and selectively amplified by targeting the terminal sequence tag. The result will give a picture of community member that are unique to the particular environmental sample as well and a rough estimate of the relative abundance of these species in the microbial community.

Correlation of Metageonmics and Metaproteomics Datasets to Predict Carbon-Cycle Capacity in Great Prairie Soil Microbiome

Coming soon