Welcome to the McLean Lab


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Jeffrey Scott McLean, PhD

Associate Professor

Dr. McLean’s research career began at the Pacific Northwest National Laboratory in Richland, WA (2000-2007). He then established a research program at the non-profit J. Craig Venter Institute in San Diego, CA in 2007. He moved to the University of Washington School of Dentistry in 2014 and is a tenured Associate Professor in the Department of Periodontics at the School of Dentistry with a joint appointment in Oral Health Sciences as well as an adjunct position in the Department of Microbiology at UW. For the past 21 years, his research has been primarily devoted to developing innovative methodologies, tools and new genomic based approaches to study microbial interactions within biofilm communities. Dr. McLean received his MSc at the University of Guelph in Canada and PhD at the University of Southern California. Currently, he is funded as a PI on multiple NIH awards to characterize the microbial processes that lead to oral diseases and maintain the health of the human oral microbiome.

The goal of the research in the McLean lab has been to gain an understanding for the molecular basis of bacteria-bacteria as well as bacteria-host interactions and further develop innovative methodologies, tools and integrated “omic” based approaches combined with wet-lab cultivation work on oral communities to ultimately translate this fundamental knowledge to the overall benefit of human health. His lab has extensive experience in next generation sequencing and combining omic approaches such as temporal resolved metatranscriptomic analysis (gene expression of all the microbes at once) in parallel with measuring global metabolites to reveal the homeostatic mechanisms of oral microbial communities. The lab tracks oral microbiome community assembly and maturation both in vitro and in vivo, capturing the temporal taxonomic and expression dynamics of key disease related species in direct association with the clinical host responses. Recent work of the team on the variation in human inflammatory responses to oral plaque bacteria leading to gum disease (gingivitis and chronic periodontitis) has links to overall systemic health.

Full Bio

Recent News

Humans are inhabited by a broad diversity of nano-sized bacteria with tiny genomes.

McLean, J.S., Bor, B., Kerns, K.A., Liu, Q., To, T.T., Solden, L., Hendrickson, E.L., Wrighton, K., Shi, W., and He, X. (2020). Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Reports 32.

Starvation Study Shows Bacteria’s Survival Skills


In their paper published on Thursday, researchers including Dr. Jeffrey McLean of the UW School of Dentistry describe their discovery that three closely related species of bacteria of the family Enterobacteriaceae outlived all other oral bacteria in a long-term starvation or “doomsday” experiment. To create a battle of bacteria, researchers placed a community of oral bacteria, derived from human saliva, into a mixture of sterilized saliva and saline solution. The bacteria, which are accustomed to living in the nutrient-rich mouth, were starved in their new environment. Every few days, scientists checked the samples to see which bacteria were still alive. The techniques employed in this research are key to illuminating the ecological dynamics of bacterial communities. Read more about what species survived at PNAS.


A Review of Saccharibacteria (TM7) in the Human Oral Microbiome


 figure The recent cultivation and characterization of Nanosynbacter lyticus type strain TM7x (HMT_952)—the first Saccharibacteria strain co-isolated as an ultra-small obligate parasite with its bacterial host from the human oral cavity—provide a rare glimpse into the novel symbiotic lifestyle of these enigmatic human-associated bacteria. TM7x is unique among all bacteria: it has an ultra-small size and lives on the surface of its host bacterium. Here, we review the current knowledge on the diversity and unique biology of this recently uncovered group of ultra-small bacteria within the human oral microbiome.

UW researchers help take major step in study of elusive bacteria


Two University of Washington researchers and their colleagues have helped take a significant step forward in the study of especially tiny bacteria that may be linked to gum disease.

Dr. Jeffrey McLean

Dr. Jeffrey McLean

Dr. Jeffrey McLean and Dr. Thao (Jenny) To of the UW School of Dentistry and their cohorts at the Forsyth Institute in Cambridge, Mass., have been studying a group of microbes known as TM7, which is considered microbial “dark matter.” This term alludes to the extreme difficulty such bacteria have posed to researchers trying to cultivate them in the lab. Dr. McLean is Associate Professor of Periodontics at the UW and Dr. To is a senior postdoctoral fellow in his lab.

TM7 is found in a number of environments, including the mouth, and may play a role in gum disease, scientists believe. In 2015, Dr. Xuesong He of Forsyth and Dr. McLean co-wrote and published a paper telling how they had cultured TM7 for the first time in a test tube and sequenced the complete genome. They discovered that it is an ultra-small bacterial parasite with a tiny genome that lives and feeds on other bacteria, which makes it difficult to isolate and examine. This was considered a major step toward understanding the human oral microbiome, or the collection of bacteria that live in the mouth.

Now, in a paper published recently in the journal Proceedings of the National Academy of SciencesDr. Batbileg Bor, a senior postdoctoral fellow in microbiology at Forsyth, said that he and the team have been able to isolate TM7 bacteria from their host and count them individually, and then add the bacteria back to their host cultures.

This has allowed the researchers to see not only how TM7 infects and parasitizes its hosts, but also to uncover the mechanism TM7 uses to establish a long-term parasitic relationship with those hosts. The finding may also explain why TM7 bacteria persist for so long in the human mouth.

The system the researchers developed could be used to study other types of ultra-small bacteria, as well, Dr. He said. TM7 is still relatively new to scientists, and it took Dr. Bor nearly three years to develop the new method of studying it.

“We are continuing to learn about how this TM7 species and other ultra-small bacteria like them are able to survive and find other cells to live on, since they are in found in every human body and increase in number within certain oral diseases,” Dr. McLean said.

Other collaborators on the study included Drs. Wenyuan Shi, Floyd E. Dewhirst, and Lujia Cen from the Forsyth Institute, and Kevin R. Foster from the University of Oxford.

PNAS Article: https://www.pnas.org/content/115/48/12277


Combined metatranscriptomic metabolomic study of homeostasis within oral microbiome tinyurl.com/nzathxt pic.twitter.com/HsOStR7ted

Anna Edlund, Youngik Yang, Shibu Yooseph, Adam P. Hall, Don D. Nguyen, Pieter C. Dorrestein, Karen E. Nelson, Xuesong He, Renate Lux, Wenyuan Shi, Jeffrey S. McLean. Meta-Omics Uncover Temporal Regulation of Pathways Across Oral Microbiome Genera During in vitro Sugar Metabolism. (2105)  International Society for Microbial Ecology Journal (ISME) http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201572a.html (OPEN ACCESS)

Fig 3. ORFS on KEGG map comined_png_3_0509_embed_2.jpgFig-1_ISMEJ

TWiM #109: Precision killing

Created on Thursday, 06 August 2015 05:37 Hosts: Vincent RacanielloMichael Schmidt, Elio Schaechter and Michele Swanson.

The TWiM cohort discusses the use of antimicrobial peptides to target specific bacteria in the microbiome, and how the intracellular bacterium Wolbachia selectively kills male hosts.

MicrobeWorld – This Week in Microbiology

Right click to download TWiM#109 (50 MB .mp3, 69 minutes).

Elusive ‘dark matter’ from human microbiome is revealed (HSNewsBeat)

Tm7 cover