Toward personalized control of human gut bacterial communities

mSystems

Volumn 3, Issue 2, 2018, Pages

  David, Lawrence A ^a,b  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

Human microbiome; Microbiome engineering; Systems biology

Indexed keywords

ARTICLE; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; NONHUMAN; PERSONALIZED MEDICINE; PRIORITY JOURNAL;

EID: 85045203795     PISSN: None     EISSN: 23795077     Source Type: Journal    
DOI: 10.1128/mSystems.00165-17     Document Type: Article

References (14)

1. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium. 2015. MICROBIOME. A unified initiative to harness Earth’s microbiomes. Science 350:507–508. https://doi.org/10.1126/science.aac8480.
2. Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, Sonnenburg JL. 2013. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502:96–99. https://doi.org/10.1038/nature12503.
3. Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. 2016. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 352:586–589. https://doi.org/10.1126/science.aad8852.
4. Dyson FJ. 2012. History of science. Is science mostly driven by ideas or by tools? Science 338:1426–1427. https://doi.org/10.1126/science.1232773.
5. Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. 2015. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161:1202–1214. https://doi.org/10.1016/j.cell.2015.05.002.
6. Terekhov SS, Smirnov IV, Stepanova AV, Bobik TV, Mokrushina YA, Ponomarenko NA, Belogurov AA, Jr, Rubtsova MP, Kartseva OV, Gomzikova MO, Moskovtsev AA, Bukatin AS, Dubina MV, Kostryukova ES, Babenko VV, Vakhitova MT, Manolov AI, Malakhova MV, Kornienko MA, Tyakht AV, Vanyushkina AA, Ilina EN, Masson P, Gabibov AG, Altman S. 2017. Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity. Proc Natl Acad Sci U S A 114:2550–2555. https://doi.org/10.1073/pnas.1621226114.
7. McDonald JA, Schroeter K, Fuentes S, Heikamp-Dejong I, Khursigara CM, de Vos WM, Allen-Vercoe E. 2013. Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemo-stat model. J Microbiol Methods 95:167–174. https://doi.org/10.1016/j.mimet.2013.08.008.
8. Silverman JD, Washburne AD, Mukherjee S, David LA. 2017. A phylogenetic transform enhances analysis of compositional microbiota data. Elife 6:e21887. https://doi.org/10.7554/eLife.21887.
9. Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, Fierer N, David LA. 2017. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ 5:e2969. https://doi.org/10.7717/peerj.2969.
10. West M, Harrison J. 1997. Bayesian forecasting and dynamic models, 2nd ed. Springer-Verlag, New York, NY.
11. Lieb CW. 1929. The effects on human beings of a twelve months’ exclusive meat diet—based on intensive studies on two Arctic explorers living under average conditions in a New York climate. J Am Med Assoc 96:20–22.
12. David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ. 2014. Host lifestyle affects human microbiota on daily timescales. Genome Biol 15:R89. https://doi.org/10.1186/gb-2014-15-7-r89.
13. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563. https://doi.org/10.1038/nature12820.
14. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5:220–230. https://doi.org/10.1038/ismej.2010.118.