The Science

In depth understanding of microbiome by coupling DNA sequencing with artificial intelligence and machine learning assisted bioinformatics.

Overview

Biology is increasingly data rich, especially when capturing the complex interactions between plants, animals, microbes, and their environments. Effectively analyzing these data can provide meaningful insights into the health, productivity, and functional profile of client samples. At Metagenom, we specialize in the data-driven analysis of the microbiome through species surveys, metagenomics, and genomics.

Through a variety of data and analytics products as well as custom bioinformatics services we can ensure clients receive actionable information from their data. Our analytics platform enables a comprehensive investigation of microbial community membership and functional roles. Metagenom also provides custom solutions for your bioinformatics and analysis needs, including workflow design and implementation. This promotes faster, more reliable analysis and reproducible research within your organization.

Process Pipeline


With our diverse library of tools, proprietary methodology, consulting expertise, and experienced team, we help our clients by simplifying the understanding of complex microbiome data and focus on providing actionable results for their projects.

Publications


Our services have supported many studies. Here is a list.

Asemaninejad, A., Munford, K., Watmough, S., Campbell, D., Glasauere, S., Basiliko, N., and Mykytczuk, N. 2020. Structure of microbial communities in amended and unamended acid-generating mine wastes along gradients of soil amelioration and revegetation. Agric., Ecosyst. Environ., Appl. Soil Ecol. 155: 103645. https://doi.org/10.1016/j.apsoil.2020.103645.

Lobb, B., Hodgson, R., Lynch, M.D.J., Mansfield, M.J., Cheng, J., Charles, T.C., Neufeld, J.D., Craig, P.M.,  Doxey, A.C. 2020. Time series resolution of the fish necrobiome reveals a decomposer succession involving toxigenic bacterial pathogens. mSystems 5 (2) e00145-20 https://doi.org/10.1128/mSystems.00145-20.

Donovan M, Lynch MDJ, Mackey CS, Platt GN, Washburn BK, Vera DL, Trickey DJ, Charles TC, Wang Z, Jones KM. 2020. Metagenome-assembled genome sequences of five strains from the Microtus ochrogaster (prairie vole) fecal microbiome. Microbiology Resource Announcements 9:e01310-19. https://doi.org/10.1128/MRA.01310-19.

Chik, A.H.S., Emelko, M.B., Anderson, W. B., O’Sullivan, K.E., Savio, D., Farnleitner, A.H., Blaschke, A.P., and Schijven, J.F. 2020. Evaluation of groundwater bacterial community composition to inform waterborne pathogen vulnerability assessments. Sci. Total Environ. 140472. https://doi:10.1016/j.scitotenv.2020.140472.

Douglas, A.J., Hug, L.A. & Katzenback, B.A. 2020. Composition of the north american wood frog (Rana sylvatica) bacterial skin microbiome and seasonal variation in community Structure. Microb Ecol. https://doi.org/10.1007/s00248-020-01550-5.

Erdozain, M., Emilson, C. E., Kreutzweiser, D. P., Kidd, K. A., Mykytczuk, N., and Sibley, P. K.. 2020. Forest management influences the effects of streamside wet areas on stream ecosystems. Ecol Appl. 30(4): e02077. https://doi.org/10.1002/eap.2077.x

Franco-Lopez J., Duplessis, M., Bui, A., Reymond, C., Poisson, W., Blais, L., Chong, J., Gervais, R., Rico, D.E., Cue, R.I., Girard, C.L., and Ronholm, J.. 2020. Correlations between the composition of the bovine microbiota and vitamin B12 abundance. mSystems 5:e00107-20. https://doi.org/10.1128/mSystems.00107-20.

Gupta, V. 2020. A systematic study of interaction effects between plants, microbes, and metals in a model constructed wetland system treating mining influenced waters. PhD thesis, Laurentian University, Sudbury, Ontario. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3506

Gupta, V., Courtemanche, J., Gunn, J., and Mykytczuk, N. 2020. Shallow floating treatment wetland capable of sulfate reduction in acid mine drainage impacted waters in a northern climate. J. Environ. Manage. 263: 110351. https://doi:10.1016/j.jenvman.2020.110351.

Ordonez, P.A.C. 2020. Frequency of soybean in rotation and persistence of Rhizobia in Manitoba soils. MSc thesis, University of Manitoba, Manitoba, Winnipeg. Retrieved from: http://hdl.handle.net/1993/34649

Pakostova, E., Johnson, D.B., Bao, Z., MacKenzie, P.M., Ptacek, C.J., and Blowes, D.W. 2020. Bacterial and Archaeal Diversity in Sulfide-Bearing Waste Rock at Faro Mine Complex, Yukon Territory, Canada, Geomicrobiol. J. 37(6): 511-519, https://doi.org/10.1080/01490451.2020.1731020.

Pakostova, E., Schmall, A. J., Holland, S. P., White, H., Ptacek, C. J., and Blowes, D. W. 2020. Performance of a geosynthetic clay-liner cover system at a Cu/Zn mine tailings impoundment: microbiological characterization. Appl. Environ. Microbiol. https://doi.org/10.1128/aem.02846-19

Rullo, J., Far, P.M., Quinn, M. Sharma, N., Bae, S., Irrcher, I., and Sharma, S. 2020. Local oral and nasal microbiome diversity in age-related macular degeneration. Sci. Rep. 10: 3862 https://doi.org/10.1038/s41598-020-60674-3.

van Leeuwen, P., Mykytczuk, N., Mastromonaco, G.F., and Schulte‐Hostedde, A.I. 2020. Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice. Ecol. Evol. 10: 4677– 4690. https://doi.org/10.1002/ece3.6221

Bieniek, A.K. 2019. A metagenomic analysis of tailings microbial communities from both cold and hot environments. MSc thesis, Laurentian University, Sudbury, Ontario. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3370.

Martinez, A.R., Heil, J.R., Charles, T.C. 2019. An engineered GFP fluorescent bacterial biosensor for detecting and quantifying silver and copper ions. Biometals 32: 265-272.  https://doi.org/10.1007/s10534-019-00179-3.

Carson, M.A., Bräuer, S., and Basiliko, N. 2019. Enrichment of peat yields novel methanogens: approaches for obtaining uncultured organisms in the age of rapid sequencing. FEMS Microbiol. Ecol. 95(2): fiz001. https://doi.org/10.1093/femsec/fiz001.

Dart, M.M. 2019. The impacts of environmental changes on peatland microbial community structure and function. MSc thesis, Laurentian University, Sudbury, Ontario. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3348. 

Jones, J.M.C., Webb, E.A., Lynch, M.D.J., Charles, T.C., Antunes, P.M., and Guinel, F.C. 2019. Does a carbonatite deposit influence its surrounding ecosystem?. FACETS 4: 389–406. https://doi.org/10.1139/facets-2018-0029.

Kirkwood, A.H. 2019. Microbial community and C cycling across permafrost peatlands in the Hudson Bay Lowlands: feedbacks to in-situ degradation and simulated warming. MSc thesis, Laurentian University, Sudbury, Ontario. Retrieved from:  https://zone.biblio.laurentian.ca/handle/10219/3388.

Mullins, N. R., and Daugulis, A. J. 2019. The biological treatment of synthetic fracking fluid in an extractive membrane bioreactor: selective transport and biodegradation of hydrophobic and hydrophilic contaminants. J. Hazard. Mater. https://doi.org/10.1016/j.jhazmat.2019.01.003.

Schmidt, E., Mykytczuk, N., and Schulte-Hostedde, A.I. 2019. Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). ISME J. 13: 1293–1305. https://doi.org/10.1038/s41396-019-0345-8.

Stothart, M.R., Palme, R., and Newman, A.E.M. 2019. It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal. Proc. R. Soc. B. 286: 20192111. https://doi.org/10.1098/rspb.2019.2111.

Asemaninejad, A., Arteaga, J., Spiers, G., Beckett, P., McGarry, S., Mykytczuk, N., & Basiliko, N. 2018. Blended pulp mill, forest humus and mine residual material Technosols for mine reclamation: A growth-chamber study to explore the role of physiochemical properties of substrates and microbial inoculation on plant growth. J. Environ. Manage., 228: 93–102. https://doi.org/10.1016/j.jenvman.2018.08.114

Principe, E. 2018. Evaluating mineralogical, geochemical and microbial relationships within sulfur-bearing mine wastes; a multianalytical and multivariate statistical approach. MSc thesis, Laurentian University, Sudbury, Ontario. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3179

Schmidt, E.A. 2018. Environment-microbe-host interactions: understanding the relationship between the external environment, gut microbiome diversity, and host immunocompetence. MSc thesis. Laurentian University. Sudbury. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3004.

Emilson, E.J.S., Carson, M.A., Yakimovich, K.M., Osterholz, H., Dittmar, T., Gunn, J.M., Mykytczuk, N.C.S., Basiliko, N., Tanentzap, A.J. 2018. Climate-driven shifts in sediment chemistry enhance methane production in northern lakes. Nat. Commun. 9:1801. https://doi.org/10.1038/s41467-018-04236-2.

Valiquette, N.L. 2018. Genomic insights into the psychrotrophic microbial leaching of low sulfide waste rock in kinetic testing systems. MSc thesis. Laurentian University. Sudbury. Retrieved from: https://zone.biblio.laurentian.ca/handle/10219/3224

Xiong, Z., Hussain, A., Lee, J., and Lee, H.-S. 2018. Food waste fermentation in a leach bed reactor: reactor performance, and microbial ecology and dynamics. Bioresour. Technol. 274: 153-161. https://doi.org/10.1016/j.biortech.2018.11.066

Yakimovich, K.M., Emilson, E.J.S., Carson, M.A., Tanentzap, A.J., Basiliko, N., and Mykytczuk, N.C.S. 2018. Plant litter type dictates microbial communities responsible for greenhouse gas production in amended lake sediments. Front. Microbiol. 9: 2662. https://doi.org/10.3389/fmicb.2018.02662.

Bobbie, C.B., Mykytczuk, N.C.S., and Schulte-Hostedde, A.I. 2017. Temporal variation of the microbiome is dependent on body region in a wild mammal (Tamiasciurus hudsonicus). FEMS Microbiol. Ecol. 93(7): fix081. https://doi.org/10.1093/femsec/fix081.

Heil, J.R., Lynch, M.D.J., Cheng, J., Matysiakiewicz, D’Alessio, M., Charles, T.C. 2017. The completed PacBio Single-Molecule Real-Time sequence of Methylosinus trichosporium strain OB3b reveals the presence of a third large plasmid. Genome Announcements: 5:e01349-17; https://doi.org/10.1128/genomeA.01349-17.

Stothart, M.R., Bobbie, C.B.., Schulte-Hostedde, A.I., Boonstra, R., Palme, R., Mykytczuk N.C.S., and Newman, A.E.M. 2016. Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels. Biol. Lett. 12: 20150875. https://doi.org/10.1098/rsbl.2015.0875.