Invited Oral Abstract Presentation
Linking intracellular metabolism to microbial ecosystem dynamics in structured environments.
William Harcombe, University of Minnesota, St Paul, MN, USA
2017 SIMB Annual Meeting and Exhibition
The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion in a structured environment. Our computational approach provides quantitatively accurate predictions of how species ratios fluctuate in synthetic 2 and 3-species communities. We further used the modeling approach to elucidate how location mediates interactions between colonies of Escherichia coli or Salmonella enterica grown on different carbon sources. Interestingly, we find that geometry, not distance, is the best predictor of microbial interactions. Our work highlights that location is an important determinant of microbial interactions. Further we demonstrate that models of intracellular metabolism can quantitatively predict ecological interactions, and microbial community dynamics in complex structured environments.
Invited Oral Abstract Presentation
The microbial metabolic response to drought and implications for carbon cycling in tropical forest soils.
Nicholas Bouskill, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
2017 SIMB Annual Meeting and Exhibition
Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of microbial trait distribution, however, the feedback between changes in metabolic functional potential and ecosystem properties related to carbon cycling are poorly understood. Herein I leverage a year long drought experiment in a tropical forest to demonstrate that drought-induced shifts in microbial metabolic traits and activity shape, and are shaped by, the composition of dissolved and soil-associated carbon. Shifts in metabolic traits toward osmolyte and hygroscopic compounds subsequently suppress the efflux of carbon dioxide following soil rewetting. Furthermore, this metabolic response to drought appears to condition (biologically and physically) the soil matrix, notably through the production of polysaccharides, particularly in experimental soils pre-exposed to drought. In this talk I will expand on the findings of this study with further discussion as to the importance of microbial metabolic traits in the formation and evolution of soil organic matter. I will conclude by discussing how these traits can, in part, determine the vulnerability of soil carbon to future climate change.
Invited Oral Abstract Presentation
Linking phylogenetic identity and biogeochemical function of uncultivated marine microbes with novel mass spectrometry techniques
Ryan Mueller1, Sam Bryson1, Zhou Li2, Dr. Jennifer Pett-Ridge3, Robert L. Hettich2, Chongle Pan2 and Xavier Mayali3, (1)Oregon State University, Corvallis, OR, USA, (2)Oak Ridge National Lab, Oak Ridge, TN, USA, (3)Lawrence Livermore National Lab, Livermore, CA, USA
2017 SIMB Annual Meeting and Exhibition
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying partitioning patterns among diverse populations in natural environments, thereby characterizing functional guilds within the complex communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (proteomic SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to concurrently characterize the assimilation a variety of stable isotope labeled substrates, and to define overall changes in communities collected from coastal marine environments. Interestingly, observed increases and decreases in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. Use of these complementary SIP approaches revealed differential assimilation of substrates into protein and ribonucleotide biomass among taxa, indicating distinct metabolic routing of substrates that is not apparent by genome sequence data alone. Substrate assimilation trends indicated significantly conserved resource preferences among populations, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. Additionally, clear differences were observed in the functions expressed and in the types of enzymes synthesized de novo by distinct taxa in these communities, indicating divergent environmental growth strategies of these populations. By integrating ‘omics methods with stable isotope probing, we have developed a high-throughput and sensitive approach to define the niches of organisms in situ and to characterize the functional responses of individual populations to competitive interactions, allowing deeper insight into how communities as a whole adapt to environmental change.
Invited Oral Abstract Presentation
Break
2017 SIMB Annual Meeting and Exhibition
Invited Oral Abstract Presentation
Comparative metagenomics clarifies the gut microbiome’s functional association with health and evolution
Thomas Sharpton, Oregon State University, Corvallis, OR, USA
2017 SIMB Annual Meeting and Exhibition
The gut microbiome contributes to animal health and homeostasis. Unfortunately, the precise mechanisms through which the gut microbiome operates to influence animal physiology remain elusive, which consequently challenges the development of disease diagnostics and therapeutics. We recently conducted a series of comparative metagenomic investigations to uncover potential mechanisms through which the gut microbiome interacts with its animal host to influence physiology. First, we analyzed over 2,000 gut metagenomes from a variety of human clinical populations to statistically model how the metabolic pathways encoded in the microbiome associate with health. This analysis revealed aspects of microbiome metabolism that are perturbed in diseased humans, many of which are common to multiple disease types. Second, we compared microbiome samples spanning many vertebrate species to quantify how the microbiome may have diversified over evolutionary timescales. Our analysis reveals properties of the microbiome that are relatively conserved across host species, which indicates that they may have been anciently integrated into the gut microbiome and subsequently retained, potentially because they promote host fitness. Collectively, these investigations clarify the aspects of the gut microbiome that may yield disease when perturbed and implicate their potential interaction with host physiology.
Invited Oral Abstract Presentation
The role of gut microbiota in obesity among pregnant women and children
Maggie Stanislawski1, Dana Dabelea1, Brandie Wagner1, Marci Sontag1, Nina Iszatt1, Cecilie Dahl2, Catherine Lozupone3 and Merete Eggesbø2, (1)University of Colorado, Aurora, CO, USA, (2)Norwegian Institute of Public Health, Oslo, Norway, (3)University of Colorado Denver, Aurora, CO, USA
2017 SIMB Annual Meeting and Exhibition
Recent research suggests that gut microbiota may play a key role in obesity and metabolic diseases; less is known about what role it plays in the development of these conditions in children. Using a large Norwegian observational cohort, we have investigated the relationships between obesity and the gut microbiota of pregnant women and their infants. We explored gut microbial characteristics as a potential mechanism to explain the association between maternal overweight and the development of obesity in offspring. We found differences in the maternal gut microbiota at the time of delivery with both pre-pregnancy overweight/obesity (OW/OB) and with excessive GWG. The infant gut microbiota was predictive of BMI at age 12; strikingly, the microbiota at 2 years of age predicted 53% of the variation in BMI at age 12 even though the infants who became OW/OB at age 12 did not significantly differ in BMI z-scores at this age. Maternal OW/OB also showed consistent associations with the infant gut microbiota taxa predictive of childhood BMI. The findings of this research could have implications for public health efforts to prevent obesity because the gut microbiota of pregnant women and children are alterable through non-invasive means, such as diet, prebiotics, and probiotics. Furthermore, our results suggest that the gut microbiota may also offer potential as an early biomarker for obesity, which could help to target prevention efforts more effectively.
Invited Oral Abstract Presentation
Functional and spatial characterization of diverse microbiomes by activity-based protein profiling
Aaron T. Wright, Natalie Sadler, Christopher Whidbey, Joshua Rosnow, Lindsey Anderson, Pavlo Bohutskyi and Bryan Killinger, Pacific Northwest National Laboratory, Richland, WA, USA
2017 SIMB Annual Meeting and Exhibition
Within microbes and microbial communities, from host-associated to those occurring within terrestrial, aquatic, or other environments, nutrient allocation and utilization is a key factor driving microbiome interactions and functions. We have developed chemical activity-based probes based upon B vitamins, or as mechanism-based inhibitors of metabolic enzyme families such as cellulases, glucuronidases, and proteases. By employing these chemical probes, we capture extracellular enzymes involved in polymeric carbon metabolism, nutrient transporters and intracellular protein interactions. In mammalian gut microbiomes we use probes to isolate distinct functional subpopulations of microbes, that are subsequently sequenced. Our complement of probes is enabling a functional analysis in live microbiomes of nutrient scavenging and utilization. Our results are identifying new enzymes, proteins, and regulators playing pivotal roles in the control of cell growth, response to stress, and other activities that potentially are leading to coordination of cell behavior in complex multicellular systems.