Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis

Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.

Role of the Gut Microbiome in Obstructive Sleep Apnea-Induced Hypertension

Individuals suffering from obstructive sleep apnea (OSA) are at increased risk for systemic hypertension. The importance of a healthy gut microbiota, and detriment of a dysbiotic microbiota, on host physiology is becoming increasingly evident. We tested the hypothesis that gut dysbiosis contributes to hypertension observed with OSA. OSA was modeled in rats by inflating a tracheal balloon during the sleep cycle (10-s inflations, 60 per hour). On normal chow diet, OSA had no effect on blood pressure; however, in rats fed a high-fat diet, blood pressure increased 24 and 29 mm Hg after 7 and 14 days of OSA, respectively (P<0.05 each). Bacterial community characterization was performed on fecal pellets isolated before and after 14 days of OSA in chow and high-fat fed rats. High-fat diet and OSA led to significant alterations of the gut microbiota, including decreases in bacterial taxa known to produce the short chain fatty acid butyrate (P<0.05). Finally, transplant of dysbiotic cecal contents from hypertensive OSA rats on high-fat diet into OSA recipient rats on normal chow diet (shown to be normotensive) resulted in hypertension similar to that of the donor (increased 14 and 32 mm Hg after 7 and 14 days of OSA, respectively; P<0.05). These studies demonstrate a causal relationship between gut dysbiosis and hypertension, and suggest that manipulation of the microbiota may be a viable treatment for OSA-induced, and possibly other forms of, hypertension.

Abstract PL01-01: Meet your microbiome: An introduction to the who, what, and how of mixed microbial communities

The human microbiome is comprised of the bacteria, archaea, fungi, protists, and viruses that live in and on our bodies. It is estimated that the microbial cells that comprise your individual microbiome outnumber your own cells by a factor of 10 and that their collective gene content outnumbers your own by a factor of 100. Although scientists and physicians have appreciated the diversity of our “fellow travelers” for decades, our ability to count, study, and categorize our microbes was long limited by the challenges associated with their culture in the laboratory. The utilization of high-throughput sequencing platforms, development of new and improved bioinformatics resources, and the introduction of other ‘omics technologies have shed new light on the composition and function of the human microbiome. The NIH-sponsored Human Microbiome Project characterized the microbial communities of hundreds of healthy individuals in an attempt to define the “healthy” microbiome at various sites throughout the body, and other projects have examined the human microbiome under varying states of disease and health. Microbiome and metagenomic studies have revealed that microbes may contribute to metabolic disorders, inflammatory bowel disease, heart disease, and cancer; and emerging evidence from mouse models suggests a strong link between gut microbiome composition and brain development and behavior. Microbiome and metagenomic studies have also demonstrated that our microbiota may confer protective or beneficial effects, and the depletion or loss of these “good” microbes may leave us susceptible to disease or infection. This talk will introduce the concept of the human microbiome, discuss the techniques that are used to characterize the structure and function of mixed microbial communities, and highlight recent findings from the literature.

Citation Format: Emily B. Hollister. Meet your microbiome: An introduction to the who, what, and how of mixed microbial communities. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr PL01-01.

Structure and function of the healthy pre-adolescent pediatric gut microbiome

BACKGROUND

The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA).

RESULTS

Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity.

CONCLUSIONS

Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome

BACKGROUND

A low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet can ameliorate symptoms in adult irritable bowel syndrome (IBS) within 48 h.

AIM

To determine the efficacy of a low FODMAP diet in childhood IBS and whether gut microbial composition and/or metabolic capacity are associated with its efficacy.

METHODS

In a double-blind, crossover trial, children with Rome III IBS completed a 1-week baseline period. They then were randomised to a low FODMAP diet or typical American childhood diet (TACD), followed by a 5-day washout period before crossing over to the other diet. GI symptoms were assessed with abdominal pain frequency being the primary outcome. Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. Metagenomic biomarker discovery (LEfSe) compared Responders (≥50% decrease in abdominal pain frequency on low FODMAP diet only) vs. Nonresponders (no improvement during either intervention).

RESULTS

Thirty-three children completed the study. Less abdominal pain occurred during the low FODMAP diet vs. TACD [1.1 ± 0.2 (SEM) episodes/day vs. 1.7 ± 0.4, P < 0.05]. Compared to baseline (1.4 ± 0.2), children had fewer daily abdominal pain episodes during the low FODMAP diet (P < 0.01) but more episodes during the TACD (P < 0.01). Responders were enriched at baseline in taxa with known greater saccharolytic metabolic capacity (e.g. Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism.

CONCLUSIONS

In childhood IBS, a low FODMAP diet decreases abdominal pain frequency. Gut microbiome biomarkers may be associated with low FODMAP diet efficacy. ClinicalTrials.gov identifier: NCT01339117.

The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome

BACKGROUND

Changes in the intestinal microbiome of patients with short bowel syndrome (SBS) are thought to significantly affect clinical outcome. These changes may not only delay enteral diet advancement but may also predispose patients to bacterial translocation, bacteremia, and liver disease. Patients with SBS are thought to be more susceptible to changes in gut microbial communities due to intestinal dysmotility and/or lack of anatomic safeguards such as the ileocecal valve.

MATERIALS AND METHODS

We analyzed the bacterial composition of 21 fecal specimens from 9 children with SBS and 8 healthy children ages 4 months to 8 years by 16S ribosomal RNA gene sequencing. The sequences were quality filtered and analyzed using QIIME, the Ribosomal Database Project Classifier, and the randomForest supervised learning algorithm.

RESULTS

The fecal microbiome of patients with SBS is different from that of healthy controls. Stool from patients with SBS had a significantly greater abundance of the bacterial classes Gammaproteobacteria and Bacilli. Stool from patients with SBS who experienced increased stool frequency tended to have increased abundance of Lactobacillus (P = .057) and decreased abundance of Ruminococcus.

CONCLUSION

This study shows that the fecal microbiome of patients with SBS is significantly different from that of healthy controls when analyzed by 16S metagenomics. Differences in the composition and function of gut microbiomes in children with SBS may affect bowel physiology, and these findings may provide new opportunities for intestinal rehabilitation and clinical management.

The Microbiome, Intestinal Function, and Arginine Metabolism of Healthy Indian Women Are Different from Those of American and Jamaican Women

BACKGROUND

Indian women have slower arginine flux during pregnancy compared with American and Jamaican women. Arginine is a semi-essential amino acid that becomes essential during periods of rapid lean tissue deposition. It is synthesized only from citrulline, a nondietary amino acid produced mainly in the gut. The gut is therefore a key site of arginine and citrulline metabolism, and gut microbiota may affect their metabolism.

OBJECTIVE

The objective of this study was to identify differences in the gut microbiota of nonpregnant American, Indian, and Jamaican women and characterize the relations between the gut microbiota, gut function, and citrulline and arginine metabolism.

METHODS

Thirty healthy American, Indian, and Jamaican women (n = 10/group), aged 28.3 ± 0.8 y, were infused intravenously with [guanidino-15N2]arginine, [5,5-2H2]citrulline, and [15N2]ornithine and given oral [U-13C6]arginine in the fasting and postprandial states. Fecal bacterial communities were characterized by 16S rRNA gene sequencing.

RESULTS

In the fasting state, Indian women had lower citrulline flux than did American and Jamaican women [7.0 ± 0.4 compared with 9.1 ± 0.4 and 8.9 ± 0.2 μmol ⋅ kg fat-free mass (FFM)-1 ⋅ h-1, P = 0.01] and greater enteral arginine conversion to ornithine than did American women (1.4 ± 0.11 compared with 1.0 ± 0.08 μmol ⋅ kg FFM-1 ⋅ h-1, P = 0.04). They also had lower mannitol excretion than American and Jamaican women (154 ± 37.1 compared with 372 ± 51.8 and 410 ± 39.6 mg/6 h, P < 0.01). Three dominant stool community types characterized by increased abundances of the genera Prevotella, Bacteroides, and Bacteroides with Clostridium were identified. Indian women had increased mean relative abundances of Prevotella (42%) compared to American and Jamaican women (7% and < 1%, P = 0.03) which were associated with diet, impaired intestinal absorptive capacity, and arginine flux.

CONCLUSIONS

These findings suggest that dysregulated intestinal function and a unique gut microbiome may contribute to altered arginine metabolism in Indian women.

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation

The meals from many oilseed crops have potential for biofumigation due to their release of biocidal compounds such as isothiocyanates (ITCs). Various ITCs are known to inhibit numerous pathogens; however, much less is known about how the soil microbial community responds to the different types of ITCs released from oilseed meals (SMs). To simulate applying ITC-releasing SMs to soil, we amended soil with 1% flax SM (contains no biocidal chemicals) along with four types of ITCs (allyl, butyl, phenyl, and benzyl ITC) in order to determine their effects on soil fungal and bacterial communities in a replicated microcosm study. Microbial communities were analyzed based on the ITS region for fungi and 16S rRNA gene for bacteria using qPCR and tag-pyrosequencing with 454 GS FLX titanium technology. A dramatic decrease in fungal populations (~85% reduction) was observed after allyl ITC addition. Fungal community compositions also shifted following ITC amendments (e.g., Humicola increased in allyl and Mortierella in butyl ITC amendments). Bacterial populations were less impacted by ITCs, although there was a transient increase in the proportion of Firmicutes, related to bacteria know to be antagonistic to plant pathogens, following amendment with allyl ITC. Our results indicate that the type of ITC released from SMs can result in differential impacts on soil microorganisms. This information will aid selection and breeding of plants for biofumigation-based control of soil-borne pathogens while minimizing the impacts on non-target microorganisms.

From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions

The vertebrate gut symbiont Lactobacillus reuteri has diversified into separate clades reflecting host origin. Strains show evidence of host adaptation, but how host–microbe coevolution influences microbial-derived effects on hosts is poorly understood. Emphasizing human-derived strains of L. reuteri, we combined comparative genomic analyses with functional assays to examine variations in host interaction among genetically distinct ecotypes. Within clade II or VI, the genomes of human-derived L. reuteri strains are highly conserved in gene content and at the nucleotide level. Nevertheless, they share only 70–90% of total gene content, indicating differences in functional capacity. Human-associated lineages are distinguished by genes related to bacteriophages, vitamin biosynthesis, antimicrobial production, and immunomodulation. Differential production of reuterin, histamine, and folate by 23 clade II and VI strains was demonstrated. These strains also differed with respect to their ability to modulate human cytokine production (tumor necrosis factor, monocyte chemoattractant protein-1, interleukin [IL]-1β, IL-5, IL-7, IL-12, and IL-13) by myeloid cells. Microarray analysis of representative clade II and clade VI strains revealed global regulation of genes within the reuterin, vitamin B₁₂, folate, and arginine catabolism gene clusters by the AraC family transcriptional regulator, PocR. Thus, human-derived L. reuteri clade II and VI strains are genetically distinct and their differences affect their functional repertoires and probiotic features. These findings highlight the biological impact of microbe:host coevolution and illustrate the functional significance of subspecies differences in the human microbiome. Consideration of host origin and functional differences at the subspecies level may have major impacts on probiotic strain selection and considerations of microbial ecology in mammalian species.

Compositional and functional features of the gastrointestinal microbiome and their effects on human health

The human gastrointestinal tract contains distinct microbial communities that differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host. We describe the bacterial taxa present in different locations of the GI tract, and their specific metabolic features. The distinct features of these specific microbial communities might affect human health and disease. Several bacterial taxa and metabolic modules (biochemical functions) have been associated with human health and the absence of disease. Core features of the healthy microbiome might be defined and targeted to prevent disease and optimize human health.

Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome

We sought to determine whether a low fermentable substrate diet (LFSD) decreases abdominal pain frequency in children with irritable bowel syndrome (IBS) and to identify potential microbial factors related to diet efficacy. Pain symptoms, stooling characteristics, breath hydrogen and methane, whole intestinal transit time, stool microbiome, and metabolite composition were collected and/or documented in eight children with IBS at baseline and during one week of an LFSD intervention. Pain frequency (P<0.05), pain severity (P<0.05), and pain-related interference with activities (P<0.05) decreased in the subjects while on the LFSD. Responders vs. non-responders: four children (50%) were identified as responders (> 50% decrease in abdominal pain frequency while on the LFSD). There were no differences between responders and non-responders with respect to hydrogen production, methane production, stooling characteristics, or gut transit time. Responders were characterized by increased pre-LFSD abundance of bacterial taxa belonging to the genera Sporobacter (P<0.05) and Subdoligranulum (P<0.02) and decreased abundance of taxa belonging to Bacteroides (P<0.05) relative to non-responders. In parallel, stool metabolites differed between responders and non-responders and were associated with differences in microbiome composition. These pilot study results suggest that an LFSD may be effective in decreasing GI symptoms in children with IBS. Microbial factors such as gut microbiome composition and stool metabolites while on the diet may relate to LFSD efficacy.

Evaluating the performance of carboxylate platform fermentations across diverse inocula originating as sediments from extreme environments

To test the hypothesis that microbial communities from saline and thermal sediment environments are pre-adapted to exhibit superior fermentation performances, 501 saline and thermal samples were collected from a wide geographic range. Each sediment sample was screened as inoculum in a 30-day batch fermentation. Using multivariate statistics, the capacity of each community was assessed to determine its ability to degrade a cellulosic substrate and produce carboxylic acids in the context of the inoculum sediment chemistry. Conductance of soils was positively associated with production of particular acids, but negatively associated with conversion efficiency. In situ sediment temperature and conversion efficiency were consistently positively related. Because inoculum characteristics influence carboxylate platform productivity, optimization of the inoculum is an important and realistic goal.

Cellulose supplementation early in life ameliorates colitis in adult mice

Decreased consumption of dietary fibers, such as cellulose, has been proposed to promote the emergence of inflammatory bowel diseases (IBD: Crohn disease [CD] and ulcerative colitis [UC]) where intestinal microbes are recognized to play an etiologic role. However, it is not known if transient fiber consumption during critical developmental periods may prevent consecutive intestinal inflammation. The incidence of IBD peaks in young adulthood indicating that pediatric environmental exposures may be important in the etiology of this disease group. We studied the effects of transient dietary cellulose supplementation on dextran sulfate sodium (DSS) colitis susceptibility during the pediatric period in mice. Cellulose supplementation stimulated substantial shifts in the colonic mucosal microbiome. Several bacterial taxa decreased in relative abundance (e.g., Coriobacteriaceae [p = 0.001]), and other taxa increased in abundance (e.g., Peptostreptococcaceae [p = 0.008] and Clostridiaceae [p = 0.048]). Some of these shifts persisted for 10 days following the cessation of cellulose supplementation. The changes in the gut microbiome were associated with transient trophic and anticolitic effects 10 days following the cessation of a cellulose-enriched diet, but these changes diminished by 40 days following reversal to a low cellulose diet. These findings emphasize the transient protective effect of dietary cellulose in the mammalian large bowel and highlight the potential role of dietary fibers in amelioration of intestinal inflammation.

Differential impacts of brassicaceous and nonbrassicaceous oilseed meals on soil bacterial and fungal communities

Demand for alternative fuels has sparked renewed interest in the production of biodiesel from oil-rich seeds. Oilseed meals are a byproduct of this process, and given their relatively high nutrient content, land application represents a potential value-added use. In this microcosm-based study, soil microbial community responses to amendments of a glucosinolate-containing brassicaceous oilseed meal (Brassica juncea, mustard), a non-glucosinolate-containing, nonbrassicaceous oilseed meal (Linum usitatissimum, flax), and a nonoilseed biomass (Sorghum bicolor) were characterized using a 28-day time series of replicated 16S rRNA gene and fungal ITS gene sequence libraries. We hypothesized that biomass type and glucosinolate content would alter community composition but that effects would diminish over time. Distinct separation occurred by amendment type, with mustard inducing large increases in the abundance of bacterial taxa associated with fungal disease suppression (e.g. Bacillus, Pseudomonas, and Streptomyces spp.). Dramatic shifts were seen among the fungi, too, with phylotype richness decreasing by > 60% following mustard addition. Changes in bacterial and fungal community composition were rapid, and distinct community types persisted throughout the study. Oilseed amendment, and mustard in particular, has the potential to alter soil microbial community structure substantially, and such changes are likely to be important in the context of ecosystem health.

Comparison of mixed-acid fermentations inoculated with six different mixed cultures

The MixAlco™ process biologically converts biomass to carboxylate salts that may be converted to a variety of chemicals and fuels. This study examines the fermentation performance of six different mixed cultures, and how the performance was affected by the bacterial composition of each community. All six countercurrent fermentations had very similar performance, but were dissimilar in microbial community composition. The acid concentrations varied by only 12% between fermentation trains and the conversions varied only by 6%. The microbial communities were profiled using 16S rRNA tag-pyrosequencing, which revealed the presence of dynamic communities that were dominated by bacteria resembling Clostridia, but they shared few taxa in common. Yue-Clayton similarity calculations of the communities revealed that they were extremely different. The presence of different but functionally similar microbial communities in this study suggests that it is the operating parameters that determine the fermentation end-products.

Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion

The carboxylate platform is a flexible, cost-effective means of converting lignocellulosic materials into chemicals and liquid fuels. Although the platform's chemistry and engineering are well studied, relatively little is known about the mixed microbial communities underlying its conversion processes. In this study, we examined the metagenomes of two actively fermenting platform communities incubated under contrasting temperature conditions (mesophilic 40°C; thermophilic 55 °C), but utilizing the same inoculum and lignocellulosic feedstock. Community composition segregated by temperature. The thermophilic community harbored genes affiliated with Clostridia, Bacilli, and a Thermoanaerobacterium sp, whereas the mesophilic community metagenome was composed of genes affiliated with other Clostridia and Bacilli, Bacteriodia, γ-Proteobacteria, and Actinobacteria. Although both communities were able to metabolize cellulosic materials and shared many core functions, significant differences were detected with respect to the abundances of multiple Pfams, COGs, and enzyme families. The mesophilic metagenome was enriched in genes related to the degradation of arabinose and other hemicellulose-derived oligosaccharides, and the production of valerate and caproate. In contrast, the thermophilic community was enriched in genes related to the uptake of cellobiose and the transfer of genetic material. Functions assigned to taxonomic bins indicated that multiple community members at either temperature had the potential to degrade cellulose, cellobiose, or xylose and produce acetate, ethanol, and propionate. The results of this study suggest that both metabolic flexibility and functional redundancy contribute to the platform's ability to process lignocellulosic substrates and are likely to provide a degree of stability to the platform's fermentation processes.

Impacts of Cropping Systems and Long-Term Tillage on Soil Microbial Population Levels and Community Composition in Dryland Agricultural Setting

Few studies have used molecular methods to correlate the abundance of specific microbial taxonomic groups with changes in soil properties impacted by long-term agriculture. Community qPCR with 16S rRNA gene sequencing to examine the effects of long-term crop-management practices (no-till vs. conventional tillage, and continuous wheat (Triticum aestivum L.) vs. sorghum-wheat-soybean rotation (Sorghum bicolor L. Moench-Triticum aestivum L.-Glycine max L. Merr) on bacterial and fungal relative abundances and identify the dominant members of the soil microbial community. The qPCR assays revealed that crop rotation decreased bacterial copy numbers, but no-till practices did not significantly alter bacteria or fungi relative to conventional tillage. Cyanobacteria were more abundant while Actinobacteria were less numerous under continuous wheat. Acidobacteria and Planctomycetes were positively correlated with soil microbial biomass C and N. This study highlights ways cropping systems affect microbial communities and aids the development of sustainable agriculture.

Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments

Rice cultivated on arsenic (As) contaminated-soils will accumulate variable grain-As concentrations, as impacted by varietal differences, soil variables, and crop management. A field-scale experiment was conducted to study the impact of intermittent and continuous flooding on As speciation and microbial populations in rice rhizosphere compartments of soils that were either historically amended with As pesticide or unamended with As. Rhizosphere-soil, root-plaque, pore-water and grain As were quantified and speciated, and microbial populations in rhizosphere soil and root-plaque were characterized. Total-As concentrations in rhizosphere and grain were significantly lower in intermittently flooded compared to the continuously flooded plots (86% lower in pore-water, 55% lower in root-plaque and 41% lower in grain samples). iAs(V), iAs(III), and DMAs(V) were the predominant As species detected in rhizosphere-soil and root-plaque, pore-water and grain samples, respectively. Relative proportions of Archaea and iron-reducing bacteria (FeRB) were higher in rhizosphere soil compared to root-plaque. In rhizosphere soil, the relative abundance of FeRB was lower in intermittently flooded compared to continuously flooded plots, but there were no differences between root-plaque samples. This study has demonstrated that reductions in dissolved As concentrations in the rhizosphere and subsequent decreases in grain-As concentration can be attained through water management.

Investigation of intermittent air exposure on four-stage and one-stage anaerobic semi-continuous mixed-acid fermentations

This study evaluated anaerobic mixed-acid countercurrent fermentations in both strict S (minimal oxygen) and relaxed R (high oxygen) conditions. In relaxed fermentations, filter solids and liquids were exposed to air for 90 min every 56 h. The total acid concentrations for four-stage trains were 23.0 (4S) and 22.1 (4R) g/L(Liq), and for one-stage trains were 17.2 (1S) and 18.4 (1R) g/L(Liq). The strict and relaxed trains had statistically similar exit yields. The strict trains had significantly more high-molecular-weight carboxylic acids. The relaxed trains had slightly higher conversion and slightly lower selectivity, but not significantly. Air exposure had no significant effect on the bacterial profiles of the strict and relaxed fermentations. For all fermentations, the most abundant bacterial genus was Prevotella, a strict anaerobe. This study shows that the mixed-culture community is oxygen tolerant because it maintains fermentation performance during oxygen-induced stress.

Microbial community composition and dynamics in a semi-industrial-scale facility operating under the MixAlco™ bioconversion platform

AIMS

To monitor microbial community dynamics in a semi-industrial-scale lignocellulosic biofuel reactor system and to improve our understanding of the microbial communities involved in the MixAlco™ biomass conversion process.

METHODS AND RESULTS

Reactor microbial communities were characterized at six time points over the course of an 80-day, mesophilic, semi-industrial-scale fermentation using community qPCR and 16S rRNA tag-pyrosequencing. We found the communities to be dynamic, bacterially dominated consortia capable of changing quickly in response to reactor conditions. Clostridia- and Bacteroidetes-like organisms dominated the reactor communities, but ultimately the communities established consortia containing complementary functional capacities for the degradation of lignocellulosic materials. Eighteen operational taxonomic units were found to share strong correlations with reactor acid concentration and may represent taxa integral to fermentor performance.

CONCLUSIONS

The results of this study indicate that the emergence of complementary functional classes within the fermentor consortia may be a trait that is consistent across scales, and they suggest that there may be flexibility with respect to the specific identities of the organisms involved in the fermentor's degradation and fermentation processes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides new information regarding the composition, dynamics and potential flexibility of the microbial communities associated with the MixAlco™ process and is likely to inform the improvement of this and other applications that employ mixed microbial communities.

Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets

The existing chimera detection programs are not specifically designed for "next generation" sequence data. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduction of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs of basic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequencing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept files containing large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. The graphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screening software the B2C2 performed as well or better while dramatically decreasing the amount of time required generating and screening results. Even average computer users are able to interact with the Windows .Net GUI-based application and define the stringency to which the analysis should be done. B2C2 may be downloaded from http://www.researchandtesting.com/B2C2.

Effects of repeated glyphosate applications on soil microbial community composition and the mineralization of glyphosate

BACKGROUND

Repeated applications may have a greater impact on the soil microbial community than a single application of glyphosate. Experiments were conducted to study the effect of one, two, three, four or five applications of glyphosate on soil microbial community composition and glyphosate mineralization and distribution of (14)C residues in soil.

RESULTS

Fatty acid methyl esters (FAMEs) common to gram-negative bacteria were present in higher concentrations following five applications relative to one, two, three or four applications both 7 and 14 days after application (DAA). Additionally, sequencing of 16S rRNA bacterial genes indicated that the abundance of the gram-negative Burkholderia spp. was increased following the application of glyphosate. The cumulative percentage (14)C mineralized 14 DAA was reduced when glyphosate was applied 4 or 5 times relative to the amount of (14)C mineralized following one, two or three applications. Incorporation of (14)C residues into soil microbial biomass was greater following five glyphosate applications than following the first application 3 and 7 DAA.

CONCLUSION

These studies suggest that the changes in the dissipation or distribution of glyphosate following repeated applications of glyphosate may be related to shifts in the soil microbial community composition.