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PERSPECTIVE e0134752(2015) 39. 21) .toL.Adandngtehighhroughptieninationoftie 389-39 (2014 .Mol 45. 308,191 920(2005 g3tcusgn9yoponuiptrhetnge 6L79.3770-377812013 48.Wilm f plant biomas 49- 5016092o16 for m 1) EDITOR SUMMARY lanet lar n and collea eview the development of microbiome the past decade.and comment on the future potential of this fast-moving field 台 NATURE PROTOCOLS VOL.11 NO.11 2016 2053NATURE PROTOCOLS | VOL.11 NO.11 | 2016 | 2053 PERSPECTIVE e0134752 (2015). 44. Huang, E.L. et al. The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environ. Microbiol. Rep. 6, 389–395 (2014). 45. Burnum, K.E. et al. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J. 5, 161–164 (2011). 46. Verberkmoes, N.C. et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179–189 (2009). 47. Handley, K.M. et al. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J. 7, 800–816 (2013). 48. Wilmes, P., Heintz-Buschart, A. & Bond, P.L. A decade of metaproteomics: where we stand and what the future holds. Proteomics 15, 3409–3417 (2015). 49. Jansson, J.K. & Baker, E.S. A multi-omic future for microbiome studies. Nat. Microbiol. 1, 16049 (2016). 38. Kelly, R.T., Tolmachev, A.V., Page, J.S., Tang, K. & Smith, R.D. The ion funnel: theory, implementations, and applications. Mass Spectrom. Rev. 29, 294–312 (2010). 39. Baker, E.S. et al. Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry. Mol. Cell. Proteomics 13, 1119–1127 (2014). 40. Baker, E.S. et al. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics 15, 2766–2776 (2015). 41. Ram, R.J. et al. Community proteomics of a natural microbial biofilm. Science 308, 1915–1920 (2005). 42. Aylward, F.O. et al. Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl. Environ. Microbiol. 79, 3770–3778 (2013). 43. Aylward, F.O. et al. Enrichment and broad representation of plant biomass￾degrading enzymes in the specialized hyphal swellings of Leucoagaricus gongylophorus, the fungal symbiont of leaf-cutter ants. PLoS One 10, EDITOR SUMMARY In this Perspective, Janet Jansson and colleagues review the development of microbiome analysis technologies over the past decade, and comment on the future potential of this fast-moving field. npg © 2016 Nature America, Inc. All rights reserved
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