ZymoBIOMICS Services

Bullman et al. used the ZymoBIOMICS Targeted Sequencing Service to show that Fusobacterium and other pathogenic microbes are frequently found in both the primary and distant metastatic sites of the most aggressive and deadliest colon cancers. The authors demonstrated the potential for antibiotics to help fight Fusobacterium-positive metastatic colon cancer in a mouse model containing patient-derived xenografts.

Bullman, S., Pedamallu, C.S., Sicinska, E., Clancy, T.E., Zhang, X., Cai, D., … Meyerson, M. (2017). Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science, 358(6369), 1443-1448. doi: 10.1126/science.aal5240

Akyol et al. performed 16S and 18S analysis of anaerobic digestates using the ZymoBIOMICS Targeted Sequencing Service to assess microbial diversity in lignocellulose-rich digestates. The most abundant bacterial and fungal genera were consistent across digestate samples.

Akyol, Ç., Ince, O., and Ince, B. (2019). Crop-based composting of lignocellulosic digestates: Focus on bacterial and fungal diversity. Bioresour. Technol., 121549. doi: 10.1016/j.biortech.2019.121549

The authors investigated the role of the mucosal immune system, the commensal gut microbiota, and the intestinal epithelium in the loss of intestinal homeostasis that drives inflammatory bowel disease (IBD). The ZymoBIOMICS Targeted Sequencing Service was used to determine altered microbiome diversity in mice with different types of inflammation and to demonstrate that rapamycin, the drug used to inhibit mTOR signaling in mice in vivo, did not affect the commensal gut microbiota.

Lyons, J., Ghazi, P.C., Starchenko, A., Tovaglieri, A., Baldwin, K.R., Poulin, E.J., … Haigis, K.M. (2018). The colonic epithelium plays an active role in promoting colitis by shaping the tissue cytokine profile. PLOS Biology, 16(3), e2002417. doi: 10.1371

Improving the methane production and energy yield of biogas reactors by fungal bioaugmentation was investigated in this research. Results from testing with the ZymoBIOMICS Targeted Sequencing Service revealed that both fungal bioaugmentation and the different use of either whole crop or crop residues influenced the composition of the bacterial community in the reactors, with several taxa only identified in the bioaugmented samples, but that neither factor influence the methanogenic archaea composition, even though the methane yield in bioaugmented samples increased by 15-33%.

Akyol, Ç., Ince, O., Bozan, M., Ozbayram, E.G., and Ince, B. (2019). Fungal bioaugmentation of anaerobic digesters fed with lignocellulosic biomass: What to expect from anaerobic fungus Orpinomyces sp. Bioresour. Technol., 277, 1-10. doi: 10.1016/j.biortec

The authors investigated the microbial pools associated with landfill reactors that are impacted by nanomaterials. Using the ZymoBIOMICS Targeted Sequencing Service, they discovered that the bacterial communities were similar between control reactors and nanomaterial-containing reactors, but the archaea communities were highly different.

Akyol, Ç., Ozbayram, E.G., Demirel, B., Onay, T.T., Ince, O., and Ince, B. (2019). Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations. Environ Sci Pollut Res. doi: 10.1007/s11356-019-04906-8

This study investigated how varying interchange ratios in wastewater treatment affects microbial community composition. Sample analysis via the ZymoBIOMICS Targeted Sequencing Service demonstrated that the relative abundance of the phyla Proteobacteria, Acidobacteria, and Bacteroidetes varied according to the interchange ratio and that the species of Thiothrix were highly abundant in all samples, revealing their potential importance to wastewater treatment processes.

Karlikanovaite-Balikci, A., Ozbayram, E.G., Yagci, N., and Ince, O. (2019). Microbial community shifts in the oxic-settling-anoxic process in response to changes to sludge interchange ratio. Heliyon, 5(4), e01517. doi: 10.1016/j.heliyon.2019.e01517

This study is the first to investigate the bacterial community of the egg parasitoid Telenomus tridentatus. Using the ZymoBIOMICS Targeted Sequencing Service, Ramírez-Ahuja et al. showed the gut bacterial community of this parasitoid wasp is dominated by Proteobacteria and Actinobacteria and lay the groundwork for future studies regarding the role of bacterial communities in wasp species.

Ramírez-Ahuja, M.D.L., Gómez-Govea, M.A., Lugo-Trampe, A., Borrego-Soto, G., Delgado-Enciso, I., Ponce-Garcia, G., ... Rodríguez-Sanchez, I.P. (2019). Microbiota of Telenomus tridentatus (Platygastroida: Scelionidae): An unwanted parasitoid. J Appl Entomol