Meeting Report: The 2nd Annual Argonne Soils Workshop, Argonne National Laboratory, Chicago Illinois, USA, October 6-8, 2010

This report summarizes the proceedings of the 2nd Annual Argonne Soils Workshop held at Argonne National Laboratory October 6–8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was “designing ecologically meaningful soil metagenomics research”, which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools

Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen

Peer reviewedPublisher PD

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

Abstract Background The indigenous gut microbiota are thought to play a crucial role in the development and maintenance of the abnormal inflammatory responses that are the hallmark of inflammatory bowel disease. Direct tests of the role of the gut microbiome in these disorders are typically limited by the fact that sampling of the microbiota generally occurs once disease has become manifest. This limitation could potentially be circumvented by studying patients who undergo total proctocolectomy with ileal pouch anal anastomosis (IPAA) for the definitive treatment of ulcerative colitis. A subset of patients who undergo IPAA develops an inflammatory condition known as pouchitis, which is thought to mirror the pathogenesis of ulcerative colitis. Following the development of the microbiome of the pouch would allow characterization of the microbial community that predates the development of overt disease. Results We monitored the development of the pouch microbiota in four patients who underwent IPAA. Mucosal and luminal samples were obtained prior to takedown of the diverting ileostomy and compared to samples obtained 2, 4 and 8 weeks after intestinal continuity had been restored. Through the combined analysis of 16S rRNA-encoding gene amplicons, targeted 16S amplification and microbial cultivation, we observed major changes in structure and function of the pouch microbiota following ileostomy. There is a relative increase in anaerobic microorganisms with the capacity for fermentation of complex carbohydrates, which corresponds to the physical stasis of intestinal contents in the ileal pouch. Compared to the microbiome structure encountered in the colonic mucosa of healthy individuals, the pouch microbial community in three of the four individuals was quite distinct. In the fourth patient, a community that was much like that seen in a healthy colon was established, and this patient also had the most benign clinical course of the four patients, without the development of pouchitis 2 years after IPAA. Conclusions The microbiota that inhabit the ileal-anal pouch of patients who undergo IPAA for treatment of ulcerative colitis demonstrate significant structural and functional changes related to the restoration of fecal flow. Our preliminary results suggest once the pouch has assumed the physiologic role previously played by the intact colon, the precise structure and function of the pouch microbiome, relative to a normal colonic microbiota, will determine if there is establishment of a stable, healthy mucosal environment or the reinitiation of the pathogenic cascade that results in intestinal inflammation.http://deepblue.lib.umich.edu/bitstream/2027.42/112442/1/40168_2012_Article_10.pd

Comparative Gene-Centric Metagenomics of the Rumen Microbiome

149 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009.The complex microbiome of the rumen functions as an exceptionally effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases including hydrogen and methane. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels from lignocellulose. Since a majority of this complex microbiome has yet to be fully cultivated and explored, uncharacterized microbial populations may alter their physiological profile and possess critical enzymatic components essential for the breakdown of fiber-based feeds. The objectives of this research were to provide information pertaining to the physiological ecology of both of the rumen community and of specialist fiber-degraders. We proposed to use culture-independent metagenomic approaches that addressed the differences in the rumen microbial community and, more importantly, described and linked their metabolic potential. Our hypothesis was that the most important organisms and their gene sets involved in the most efficient hydrolysis of plant cell walls are associated with the fiber portion of the rumen digesta. Therefore, we used a cadre of metagenomic approaches to analyze the phylogenetic and genomic content of the fiber-associated rumen communities. This approach allowed us to not only identify the fiber-associated microbial community at great phylogenetic depth but also multiple functional gene sets responsible for efficient fiber degradation. Additionally, we were able to identify one specific gene cluster that may be an indicator of intra-species diversity within fiber-degrading specialists.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment.

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of FeIII reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory FeIII-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly "sulfate-reducing" phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions

Diversity of Bacteria at Healthy Human Conjunctiva

This pilot study explored the true diversity of human ocular surface bacteria using next generation sequencing and 16S rRNA gene-based phylogenetic reconstruction. The analysis identified an unexpectedly diverse microbial community with a core subset of genera ubiquitously present across all analyzed samples

Synchrotron-based X-ray diffraction (XRD) patterns of the solids in the incubations at 124 d after incubation (top) and reference patterns of select minerals (bottom).

<p>Synchrotron-based X-ray diffraction (XRD) patterns of the solids in the incubations at 124 d after incubation (top) and reference patterns of select minerals (bottom).</p