When: January 21, 2016, 1:30 PM
Location: Auditorium, Genetics-Biotechnology Center Building
Jack Gilbert, PhD., Principal Investigator, Argonne Lab-BioScience Division
Little is known about how microbial (e.g. bacteria, Archaea and fungi) organisms are transmitted around built infrastructure. Here we will discuss our continued exploration of the home and hospital microbiome. The Home Microbiome Project has identified forensic level capabilities for tracking microbial and host interaction in the building space. The Hospital Microbiome Project is characterizing the microbial taxonomic and functional composition of surface-, air-, water-, and human-associated communities to monitor changes in community structure following the introduction of patients and hospital staff. The goal of the hospital study is to determine the influence of numerous factors on the rate and nature of microbial community succession in these hospitals including: human population demographics, how these demographics interface with a space, and the building materials, environmental conditions, and building operational characteristics used to create and maintain that space. A total of 10,000 samples were collected using sterile swabs from patients, staff, rooms, common areas, water, and air filters over 365 time points prior to and following the official opening of the hospital. Absolute microbial abundance (plate counts and qPCR) and building environmental measurements (ventilation rates, temperature, relative humidity, light intensity, and human occupancy) were combined with relative taxonomic and functional gene abundance via amplicon sequencing (16S/ITS) and shotgun metagenomics. The microbial assemblage trends towards increased diversity with the introduction of patients and staff, and an increased human microbiome presence. A total of 70,000 bacterial taxa that call the hospital home are exploiting novel transmission routes that may influence building design and operation.
Recent publications (selected)
A simple novel device for air sampling by electrokinetic capture.Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J, Gilbert JA. Microbiome. 2015 Dec 27;3(1):79. doi: 10.1186/s40168-015-0141-2.
Tools for the Microbiome: Nano and Beyond. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD. ACS Nano. 2015 Dec 22. [Epub ahead of print]
Microbial community assembly and metabolic function during mammalian corpse decomposition. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. Science. 2015 Dec 10. pii: aad2646. [Epub ahead of print]
Microbial diversity-exploration of natural ecosystems and microbiomes. Gibbons SM, Gilbert JA. Curr Opin Genet Dev. 2015 Dec;35:66-72. doi: 10.1016/j.gde.2015.10.003. Epub 2015 Nov 18. Review.
MICROBIOME. A unified initiative to harness Earth’s microbiomes. 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. Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. No abstract available.
16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. Perisin M, Vetter M, Gilbert JA, Bergelson J. ISME J. 2015 Sep 11. doi: 10.1038/ismej.2015.161. [Epub ahead of print]
Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? Gilbert JA, Alverdy J. Gut. 2016 Jan;65(1):1-2. doi: 10.1136/gutjnl-2015-310043. Epub 2015 Jul 17.
Athletic equipment microbiota are shaped by interactions with human skin. Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT. Microbiome. 2015 Jun 19;3:25. doi: 10.1186/s40168-015-0088-3. eCollection 2015.
Lifestyle evolution in cyanobacterial symbionts of sponges. Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. MBio. 2015 Jun 2;6(3):e00391-15. doi: 10.1128/mBio.00391-15.
Our unique microbial identity. Gilbert JA. Genome Biol. 2015 May 14;16:97. doi: 10.1186/s13059-015-0664-7.
Development of the preterm infant gut microbiome: a research priority. Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. Microbiome. 2014 Oct 13;2:38. doi: 10.1186/2049-2618-2-38. eCollection 2014. Review.
Longitudinal analysis of microbial interaction between humans and the indoor environment. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.
Satellite remote sensing data can be used to model marine microbial metabolite turnover. Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, Gilbert JA. ISME J. 2015 Jan;9(1):166-79. doi: 10.1038/ismej.2014.107. Epub 2014 Jul 29.