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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Irene Garcia Newton

Photo of Irene Garcia Newton
Research Images
Research photo by Irene Garcia Newton

Bacterial diversity found in the honey bee gut based on 16S rRNA clone libraries.

Research photo by Irene Garcia Newton

Prevalence of potential pathogens (y axis) in honey bee colonies is inversely correlated with that of Bifidobacterium, a known probiotic genus.

Assistant Professor of Biology
Contact Information
By telephone: 812-855-3883
By fax: 812-855-6705
JH 221C

Newton lab website

Program
Microbiology
Research Areas
  • Genomics and Bioinformatics
  • Microbial Cell Biology and Environmental Responses
  • Microbial Interactions and Pathogenesis
Education

Ph.D., Harvard University, 2008
Postdoctoral Fellow, Tufts University, 2008-2010 

Awards

Woodrow Wilson Foundation Fellow

Research Description

My research interests span the areas of microbiology, genomics, and evolution. A common thread in my research is the following question: What is the molecular basis of interactions between bacteria and eukaryotes and ultimately, how do these interactions affect the diversity, population structure, and genomic evolution of bacteria? In order to answer these questions we use a series of molecular and bioinformatic techniques including functional genomics, computational evolutionary analyses, and genetic screens. We currently focus on two groups of insect-associated organisms: the ubiquitous reproductive parasite Wolbachia pipientis and the microbiota of honey bees. In the first project we're exploring the molecular interaction between Wolbachia and its insect hosts and how these interactions affect genomic evolution. In the second project, we work to understand how host genetic diversity affects bacterial diversity in the context of Apis mellifera, the honey bee. Details can be found below:

Wolbachia pipientis - reproductive parasite extraordinaire

Wolbachia pipientis is an extraordinarily widespread bacterial infection found in insects, isopods, and filarial nematodes. In insects, it is famous for causing so-called "reproductive effects" such as parthenogenesis induction, male-killing, feminization, and cytoplasmic incompatibility. It is estimated that 20-60% of all insect species are infected with the bacterium making Wolbachia a globally important organism. More recently, Wolbachia has been used to control the arthropod vectors for both Dengue and Malaria, increasing its relevance to public health. Importantly, Wolbachia are a persistent infection in these hosts -- they are transmitted via the gametes to the next generation and persist in most tissues although their numbers are greatest in the reproductive organs.

Investigating the function of Wolbachia pipientis type IV effectors

The fitness effects of Wolbachia vary depending on the host and the situation. However, all intracellular bacteria, regardless of fitness outcome to the host, must be able to promote uptake, prevent phago-lysozome degradation, acquire nutrients from the host cytoplasm in order to replicate, and disseminate to other host cells. For many intracellular bacteria, these events are orchestrated, in part, through the secretion of protein substrates into the eukaryotic cell. These so-called "effectors" are proteins of bacterial origin that have evolved to function in a eukaryotic context to modify host cellular processes. Wolbachia harbor a type IV secretion system that can be used to secrete effectors into host cells. From the genomic sequencing of various Wolbachia strains, we know that these bacterial symbionts encode a type IV secretion system. This secretion system is complete, homologous to the type IV - 1A system of Agrobacterium, and expressed in the natural host.

Most obligately intracellular organisms are genetically intractable -- we cannot modify them directly. Because of this, we have developed a yeast genetic system to identify and initially characterize Wolbachia type IV effectors. In this large-scale functional genomic screen we express candidate Wolbachia effectors in Saccharomyces. Bacterial effectors often target core cellular processes and they find those conserved processes in the yeast cell and cause growth defects when expressed. We can then further functionally characterize these candidates in the context of the eukaryotic cell by using yeast deletion strains, drugs, and various growth conditions. Candidates that are most interesting are then transferred to Drosophila for expression where we can monitor the effects on the natural host in the context of the symbiosis. Our experiments have identified the first known interactions between Wolbachia proteins and the host cell, including modifications of the cytoskeleton. Identification of proteins translocated by Wolbachia will allow us to better understand the basic biology of infection, and perhaps also how this organism induces the reproductive effects for which it is infamous.

The Apis mellifera Microbiota

Recent challenges to honey bee health, including dramatic colony losses attributable to Colony Collapse Disorder (CCD) and the introduction of pests and pathogens into managed colonies, have devastated honey bee stocks worldwide. However, a causative agent has yet to be identified and new ideas about factors that might explain a decline in the health of honey bee colonies are still emerging. At present, honey bee researchers view these alarming losses as a likely product of multiple honey bee pathogens overlapped with chronic stressors, including poor nutrition and a lack of genetic diversity among colonies' work forces. One factor that is likely shaped by colony genotype and is critical for easing nutritional stress-but has not yet been fully characterized-is the composition and function of honey bee microbiotas. The breadth of bacterial flora (and other microbes) that are found in honey bee colonies may play a role in the health and vitality of these organisms, much as they do in our own bodies. Host-associated microorganisms contribute enormously to the development of their host's immune system, digestion, and general well being.

Our lab explores the links between colony health, genetic diversity, and nutrition. We aim to describe the active bacterial microbiotas that are associated with honey bee colonies and their food products and their functional role within the colony. Additionally, we explore the effects of within-colony genetic diversity on the colony microbiotas. To answer these questions, we utilize next-generation sequencing technologies to sample the bacterial mRNA as well as rRNA (for classification). Our initial results are that genetically diverse colonies host broader and more healthful microbiota than genetically uniform ones. We are now investigating the source of this genetic diversity through a series of ecological experiments.

Select Publications
Lee FJ, Rusch D, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental Microbiology. In press.  DOI: 10.1111/1462-2920.12526  [article]
Newton, I.L.G. K. B. Sheehan,  F. Lee, M. Horton, R. Hicks. 2013. Invertebrate systems for hypothesis-driven microbiome research. Microbiome Science and Medicine. 1:1-9
Newton RR, Newton ILG. 2013. PhyBin: binning trees by topologyPeerJ 1:e187http://dx.doi.org/10.7717/peerj.187
Newton, I.L.G. and G. Roeselers. 2012. The effect of training set on the classification of honey bee gut microbiota using the Naive Bayesian Classifier. BMC Microbiology 12:221 doi:10.1186/1471-2180-12-221

Roeselers, G and ILG Newton. 2012. On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves.  Applied Microbiology and Biotechnology DOI 10.1007/s00253-011-3819-9

Mattila, H.R., D.Rios, V.E. Walker-Sperling, G. Roeselers, and ILG Newton. 2012. Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962. DOI:10.1371/journal.pone.0032962
Kent, B.N., L. Salichoss, J.G. Gibbons, A. Rokas, I.L.G. Newton, M.E Clark and S.R. Bordenstein. 2011. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biology 3:209-218.
Newton, I.L.G. and S.R. Bordenstein. 2010. Correlations between bacterial ecology and mobile DNA. Current Microbiology 62:198-208.
Roeselers, G., I.L.G. Newton, T. Woyke, T.A. Auchtung, G.F. Dilly, R.J. Dutton, M.C. Fisher, K.M. Fontanez, E. Lau, F.J. Stewart, P.M. Richardson, K.W. Barry, E. Saunders, J.C. Detter, D. Wu, J.A. Eisen, C.M. Cavanaugh. 2010. The complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomic Sciences 3:163-173.
Guss, A.M., Roeslers, G., I.L.G. Newton, C.R. Young, V. Klepac-Ceraj, S. Lory and C.M. Cavanaugh. 2010. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. The ISME Journal. 5:20-29.
Newton, I.L.G., P.R. Girguis, C.M. Cavanaugh. 2008. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts. BMC Genomics 9:585.
Newton, I.L.G., T. Woyke, T.A. Auchtung, G.F. Dilly, R.J. Dutton, M.C. Fisher, K.M. Fontanez, E. Lau, F.J. Stewart, P.M. Richardson, K.W. Barry, E. Saunders, J.C. Detter, D. Wu, J.A. Eisen, C.M. Cavanaugh. 2006. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 315: 998-1000.
Cavanaugh, C.M. McKiness, Z., Newton, I.L.G. and F.Stewart. 2005. Marine Chemosynthetic Symbioses. The Prokaryotes, A handbook on the biology of bacteria, 3rd Edition, M. Dworkin et al., ed.
Stewart, F., Newton, I.L.G. and C.M. Cavanaugh. 2005. Chemosynthetic endosymbioses: adaptations to oxicanoxic interfaces. Trends in Microbiology 13: 439-448.  [article]

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