Laboratory of Host Immunity and Microbiome (LHIM)

Yasmine Belkaid, Ph.D., Chief

The vision of the Laboratory of Host Immunity and Microbiome (LHIM), led by Dr. Yasmine Belkaid, is to comprehensively examine the factors controlling immunity and inflammation, whether they are host intrinsic (e.g., tissue-specific or the consequence of tissue-tissue communication) or extrinsic (e.g., involving the microbiota, nutrition, or infection). One major goal of the laboratory is to assess the consequences of environmental stress, such as infection, nutrition, and pollution, on host immunity and predisposition to inflammatory disorders in the context of fetal development, early life, and in adults. The laboratory also seeks to explore novel microbiota-mediated and immunotherapeutic approaches to combat the increasing threat of antimicrobial resistance. The laboratory is built upon strong clinical-basic research foundations and partnership with the NIH Clinical Center and the NIAID Microbiome Program. 

LHIM has been specifically organized to maximize the capacity of its investigators to conduct cutting edge research. It is home to the NIAID Microbiome Program, which supports microbiome-related research through gnotobiotic, microbiology, and genomic core services. To help foster a rich local intellectual and technological environment, LHIM has also developed a close partnership with the adjacent Laboratory of Immune System Biology,  including shared resources for single cell analysis, proteomics, genomics, and advanced imaging. A major emphasis of LHIM is to promote collaborations between the laboratories within NIAID, as well as with the larger NIH (including the larger NIH immunology community), and extramural scientific communities. LHIM also has a strong emphasis on mentorship and on fostering increased diversity in the next generation of scientific leaders.

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Major Areas of Research

LHIM utilizes transdisciplinary approaches in the exploration of host-microbe, tissue-tissue, and host-environment interactions. Areas of research focus include:

  • Immunology (e.g., human immunology, immunometabolism, nutritional immunology)
  • Microbiology (e.g., microbial ecology, antimicrobial resistance)
  • Chemistry (e.g., microbiota-derived natural products)
  • Neuroscience (e.g., gut/brain axis)
  • Genomics

In these latter cases, the lab has a particular interest in how such studies would enhance our understanding of host immunity.


The Laboratory of Host Immunity and Microbiome (LHIM) includes the following principal investigators, staff scientists, and/or staff clinicians:


  • The NIAID Microbiome Program is a collaborative effort to explore the metaorganism. The Program supports microbiome-related research through gnotobiotic, microbiology, and genomic core services.
  • The Center for Human Immunology (CHI) is a trans-NIH initiative  to achieve an integrated understanding of human immunity and the microbiome in health and disease.

Major Accomplishments

  • Defined the role of defined nutrients in the induction of immunity and immunoregulation
  • Defined the role for the microbiota in the control of host immunity
  • Defined the role of defined acute infections in tissue physiology and inflammation
  • Defined the role of infection in the optimization of antimicrobial function of the microbiota
  • Developed approaches to optimize host immunity via dietary intervention


Stacy A, Andrade-Oliveira V, McCulloch JA, Hild B, Oh JH, Perez-Chaparro PJ, Sim CK, Lim AI, Link VM, Enamorado M, Trinchieri G, Segre JA, Rehermann B, Belkaid Y. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell. 2021 Feb;184(3):615-627.e17.

Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y. Host variables confound gut microbiota studies of human disease. Nature. 2020 Nov;587(7834):448-454.

Constantinides MG, Link VM, Tamoutounour S, Wong AC, Perez-Chaparro PJ, Han SJ, Chen YE, Li K, Farhat S, Weckel A, Krishnamurthy SR, Vujkovic-Cvijin I, Linehan JL, Bouladoux N, Merrill ED, Roy S, Cua DJ, Adams EJ, Bhandoola A, Scharschmidt TC, Aubé J, Fischbach MA, Belkaid Y. MAIT cells are imprinted by the microbiota in early life and promote tissue repair. Science. 2019 Oct;366(6464):eaax6624.

Collins N, Han SJ, Enamorado M, Link VM, Huang B, Moseman EA, Kishton RJ, Shannon JP, Dixit D, Schwab SR, Hickman HD, Restifo NP, McGavern DB, Schwartzberg PL, Belkaid Y. The Bone Marrow Protects and Optimizes Immunological Memory during Dietary Restriction. Cell. 2019 Aug;178(5):1088-1101.e15.

Harrison OJ, Linehan JL, Shih HY, Bouladoux N, Han SJ, Smelkinson M, Sen SK, Byrd AL, Enamorado M, Yao C, Tamoutounour S, Van Laethem F, Hurabielle C, Collins N, Paun A, Salcedo R, O'Shea JJ, Belkaid Y. Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury. Science. 2019 Jan;363(6422):eaat6280.

Linehan JL, Harrison OJ, Han SJ, Byrd AL, Vujkovic-Cvijin I, Villarino AV, Sen SK, Shaik J, Smelkinson M, Tamoutounour S, Collins N, Bouladoux N, Dzutsev A, Rosshart SP, Arbuckle JH, Wang CR, Kristie TM, Rehermann B, Trinchieri G, Brenchley JM, O'Shea JJ, Belkaid Y. Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair. Cell. 2018 Feb;172(4):784-796.e18.

Images of Host Immunity and Microbiome (LHIM)

Laboratory of Host Immunity and Microbiome (LHIM) images

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