My consulting services can help you provide a microbial perspective for scientific discovery in biomedicine and agriculture

Here are some of the research questions I can help you answer.  Each topic contains references to my relevant work.  

Please email me for a copy of any reference, or for discussion of services and pay rates.

Microbiome

  • Which microbes live in sample type X?
  • How do the microbes living in sample type X compare to those living in sample type Y?
  • Do particular microbes change in abundance after treatments of interest (e.g., exposures to drugs or different environments)?
  • Why is the taxonomy of my bacterial group of interest so confusing? 
  • How do I characterize and/or culture a new microbe found in my sample of interest?
  • How can I quantify bacterial gene expression in my sample of interest?
    1. Azad, M.B., T. Konya, H. Maughan, D.S. Guttman, C.J. Field, M.R. Sears, A.B. Becker, J.A. Scott, A.L. Kozyrskyj, and CHILD Study Investigators. 2013. Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy, Asthma & Clinical Immunology 9:15
    2. Azad, M.B., T. Konya, H. Maughan, D.S. Guttman, C.J. Field, R.S. Chari, M.R. Sears, A.B. Becker, J.A. Scott, A.L. Kozyrskyj, and CHILD Study Investigators. 2013. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185:385
    3. Maughan, H., P.W. Wang, J. Diaz-Caballero, P. Fung, Y. Gong, S.L. Donaldson, L. Yuan, S. Keshavjee, Y. Zhang, Y.C.W. Yau, V.J. Waters, D.E. Tullis, D.M. Hwang, and D.S. Guttman. 2012. Analysis of the Cystic Fibrosis lung microbiota via Serial Illumina Sequencing of bacterial 16S rRNA hypervariable regions. PLoS ONE 7(10):e45791.
    4. Maughan, H., K.S. Cunningham, P.W. Wang, Y. Zhang, M. Cypel, et al. 2012. Pulmonary bacterial communities in surgically resected noncystic fibrosis bronchiectasis lungs are similar to those in cystic fibrosis. Pulmonary Medicine, vol. 2012, Article ID 746358, 9 pages, 2012. doi:10.1155/2012/746358
    5. Lee, S.-J., J. Lee, K. K. Li, D. Holland, H. Maughan, D.S. Guttman, B. Yusta, and D.J. Drucker. 2012. Disruption of the Murine Glp2r Impairs Paneth Cell Function and Increases Susceptibility to Small Bowel Enteritis. Endocrinology 153:1141—1151
    6. Maughan, H. and G. Van der Auwera. 2011. Bacillus taxonomy in the genomic era finds phenotypes essential though misleading. Infect. Genet. Evol. 11:789—797.

Bacterial evolution and genomics

  • How do I assemble millions of DNA sequence reads into something I can use? 
  • How are my favorite bacterial strains or species related?
  • Which genes are shared among these bacterial genomes?  Which genes are unique to particular genomes? 
  • What is the best way to select for my trait of interest in laboratory cultures of bacteria?
    1. Maughan, H. and W.L. Nicholson. 2011. Increased fitness and alteration of metabolic pathways during Bacillus subtilis evolution in the laboratory. Appl. Environ. Microbiol. 77:4105—4018.
    2. Maughan, H. and G. Van der Auwera. 2011. Bacillus taxonomy in the genomic era finds phenotypes essential though misleading. Infect. Genet. Evol. 11:789—797.
    3. Maughan, H. and R. J. Redfield. 2009.  Tracing the evolution of competence in Haemophilus influenzae.  PLoS ONE 4: e5854.
    4. Maughan, H. and R. J. Redfield. 2009. Extensive variation in natural competence in Haemophilus influenzae.  Evolution 63: 1852—1866.
    5. Maughan, H., C. W. Birky, Jr., and W. L. Nicholson. 2009. Transcriptome divergence and the loss of plasticity in Bacillus subtilis after 6,000 generations of evolution under relaxed selection for sporulation.  J. Bacteriol. 191: 428—433.
    6. Maughan, H., and W.L. Nicholson. 2004. Stochastic processes influence stationary phase decisions in Bacillus subtilis. J. Bact. 186:2212-2214

Bacteriology

  • How do I characterize and/or culture a new microbe found in my sample of interest?
  • How can I measure different traits in laboratory cultures of bacteria?
  • Why is the taxonomy of my bacterial group of interest so confusing? 
  • How can I quantify gene expression in my bacterial culture?
    1. Maughan, H. and G. Van der Auwera. 2011. Bacillus taxonomy in the genomic era finds phenotypes essential though misleading. Infect. Genet. Evol. 11:789—797.
    2. Maughan, H., J. Masel, C. W. Birky, Jr., and W.L. Nicholson. 2007. The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis. Genetics 177: 1—12 
    3. Maughan, H., V. Callicotte, A. Hancock, C.W. Birky, Jr,, W.L. Nicholson, and J. Masel. 2006. The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis. Evolution 60: 686-695
    4. Maughan, H., B. Galeano, and W.L. Nicholson. 2004. Novel rpoB mutations conferring rifampicin resistance on Bacillus subtilis: global effects on growth, competence, sporulation, and germination.  J. Bact. 186:228-2486
    5. Nicholson, W.L., and H. Maughan. 2002.  The spectrum of spontaneous rifampicin resistance mutations in the rpoB gene of Bacillus subtilis 168 spores differs from vegetative cells and resembles that of Mycobacterium tuberculosis.  J Bact. 184: 4936-4940.

Phylogenomics

  • Is my gene of interest related to another gene with a known function?
  • How has my gene of interest evolved in different organisms?
    1. Maughan, H. and R. J. Redfield. 2009.  Tracing the evolution of competence in Haemophilus influenzae.  PLoS ONE 4: e5854
    2. Maughan, H., C.W. Birky, Jr., W.L. Nicholson, W.D. Rosenzweig, and R.H. Vreeland.  2002. The paradox of the “ancient” bacterium which contains “modern” protein-coding genes.  Mol. Biol. Evol. 19: 1637-1639.