Haneef, M. et al. Advanced materials from fungal mycelium: fabrication and tuning of physical properties. Sci. Rep. 7, 41292 (2017).
Google Scholar
Jones, M., Mautner, A., Luenco, S., Bismarck, A. & John, S. Engineered mycelium composite construction materials from fungal biorefineries: a critical review. Mater. Des. 187, 108397 (2020).
Google Scholar
Elsacker, E. et al. A comprehensive framework for the production of mycelium-based lignocellulosic composites. Sci. Total Environ. 725, 138431 (2020).
Google Scholar
Silverman, J., Cao, H. T. & Cobb, K. Development of mushroom mycelium composites for footwear products. Cloth. Text. Res. J. 38, 119–133 (2020).
Attias, N. et al. Mycelium bio-composites in industrial design and architecture: comparative review and experimental analysis. J. Clean. Prod. 246, 119037 (2020).
Gilbert, C. & Ellis, T. Biological engineered living materials: growing functional materials with genetically programmable properties. ACS Synth. Biol. 8, 1–15 (2019).
Google Scholar
Nguyen, P. Q., Courchesne, N. M. D., Duraj-Thatte, A., Praveschotinunt, P. & Joshi, N. S. Engineered living materials: prospects and challenges for using biological systems to direct the assembly of smart materials. Adv. Mater. 30, e1704847 (2018).
Townsend-Nicholson, A. & Jayasinghe, S. N. Cell electrospinning: a unique biotechnique for encapsulating living organisms for generating active biological microthreads/scaffolds. Biomacromolecules 7, 3364–3369 (2006).
Google Scholar
Gonzalez, L. M., Mukhitov, N. & Voigt, C. A. Resilient living materials built by printing bacterial spores. Nat. Chem. Biol. 16, 126–133 (2020).
Google Scholar
Charrier, M. et al. Engineering the S-layer of Caulobacter crescentus as a foundation for stable, high-density, 2D living materials. ACS Synth. Biol. 8, 181–190 (2019).
Google Scholar
Nguyen, P. Q., Botyanszki, Z., Tay, P. K. R. & Joshi, N. S. Programmable biofilm-based materials from engineered curli nanofibres. Nat. Commun. 5, 4945 (2014).
Google Scholar
Chen, A. Y. et al. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater. 13, 515–523 (2014).
Google Scholar
Walker, K. T., Goosens, V. J., Das, A., Graham, A. E. & Ellis, T. Engineered cell-to-cell signalling within growing bacterial cellulose pellicles. Microb. Biotechnol. 12, 611–619 (2019).
Google Scholar
Caro-Astorga, J., Walker, K. T., Herrera, N., Lee, K.-Y. & Ellis, T. Bacterial cellulose spheroids as building blocks for 3D and patterned living materials and for regeneration. Nat. Commun. 12, 5027 (2021).
Google Scholar
Gerber, L. C., Koehler, F. M., Grass, R. N. & Stark, W. J. Incorporation of penicillin-producing fungi into living materials to provide chemically active and antibiotic-releasing surfaces. Angew. Chem. Int. Ed. 51, 11293–11296 (2012).
Google Scholar
Seker, U. O., Chen, A. Y., Citorik, R. J. & Lu, T. K. Synthetic biogenesis of bacterial amyloid nanomaterials with tunable inorganic–organic interfaces and electrical conductivity. ACS Synth. Biol. 6, 266–275 (2017).
Google Scholar
Tay, P. K. R., Nguyen, P. Q. & Joshi, N. S. A synthetic circuit for mercury bioremediation using self assembling functional amyloids. ACS Synth. Biol. 6, 1841–1850 (2017).
Liu, X. et al. Stretchable living materials and devices with hydrogel–elastomer hybrids hosting programmed cells. Proc. Natl Acad. Sci. USA 114, 2200–2205 (2017).
Google Scholar
Chen, X., Mahadevan, L., Driks, A. & Sahin, O. Bacillus spores as building blocks for stimuli-responsive materials and nanogenerators. Nat. Nanotechnol. 9, 137–141 (2014).
Google Scholar
Cheng, H. P., Wang, P. M., Chen, J. W. & Wu, W. T. Cultivation of Acetobacter xylinum for bacterial cellulose production in a modified airlift reactor. Biotechnol. Appl. Biochem. 35, 125–132 (2002).
Google Scholar
Dorval Courchesne, N.-M., Duraj-Thatte, A., Tay, P. K. R., Nguyen, P. Q. & Joshi, N. S. Scalable production of genetically engineered nanofibrous macroscopic materials via filtration. ACS Biomater. Sci. Eng. 3, 733–741 (2016).
Heveran, C. M. et al. Biomineralization and successive regeneration of engineered living building materials. Matter 2, 481–494 (2020).
Castro-Alonso, M. J. et al. Microbially induced calcium carbonate precipitation (MICP) and its potential in bioconcrete: microbiological and molecular concepts. Front. Mater. 6, 126 (2019).
BioMASON https://biomason.com (2020).
Botusharova, S., Gardner, D. & Harbottle, M. Augmenting microbially induced carbonate precipitation of soil with the capability to self-heal. J. Geotech. Geoenviron. Eng. 146, 04020010 (2020).
Google Scholar
Chen, Y., Peng, R. & You, Z. Origami of thick panels. Science 349, 396–400 (2015).
Google Scholar
Pinto, P. A. et al. Influence of ligninolytic enzymes on straw saccharification during fungal pretreatment. Bioresour. Technol. 111, 261–267 (2012).
Google Scholar
Walterson, A. M. & Stavrinides, J. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol. Rev. 39, 968–984 (2015).
Google Scholar
Sheth, R. U., Cabral, V., Chen, S. P. & Wang, H. H. Manipulating bacterial communities by in situ microbiome engineering. Trends Genet. 32, 189–200 (2016).
Google Scholar
McKenzie, G. J. & Craig, N. L. Fast, easy and efficient: site-specific insertion of transgenes into Enterobacterial chromosomes using Tn7 without need for selection of the insertion event. BMC Microbiol. 6, 39 (2006).
Furubayashi, M. et al. A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes. Nat. Commun. 6, 7534 (2015).
Google Scholar
Ji, B. W. et al. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nat. Methods 16, 731–736 (2019).
Google Scholar
Dong, Y. H., Xu, J. L., Li, X. Z. & Zhang, L. H. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl Acad. Sci. USA 97, 3526–3531 (2000).
Google Scholar
Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358, 1457–1461 (2017).
Google Scholar
Lee, J. W., Chan, C. T. Y., Slomovic, S. & Collins, J. J. Next-generation biocontainment systems for engineered organisms. Nat. Chem. Biol. 14, 530–537 (2018).
Google Scholar
Martinez, L. M., Martinez, A. & Gosset, G. Production of melanins with recombinant microorganisms. Front. Bioeng. Biotechnol. 7, 285 (2019).
Google Scholar
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Callahan, B. Silva taxonomic training data formatted for DADA2. Silva v.132. Zenodo https://doi.org/10.5281/zenodo.1172783 (2018).
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Google Scholar
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Google Scholar
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Google Scholar
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
Google Scholar
Ronda, C., Chen, S. P., Cabral, V., Yaung, S. J. & Wang, H. H. Metagenomic engineering of the mammalian gut microbiome in situ. Nat. Methods 16, 167–170 (2019).
Google Scholar
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Yoon, S. H., Ha, S. M., Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Ant. Van Leeuw. 110, 1281–1286 (2017).
Google Scholar
Blin, K. et al. The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 47, D625–D630 (2019).
Google Scholar
Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101 (2018).
Google Scholar
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517–D525 (2020).
Google Scholar
Johns, N. I. et al. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nat. Methods 15, 323–329 (2018).
Google Scholar
