Chronic Diseases + The Microbiome

​Microbiome research has revealed that the bacteria, viruses and fungi that cohabit our bodies influence not only digestion, but also brain development and immune system function. Research into the human microbiome is an exciting new pathway to advance our understanding of the role that over a trillion microorganisms play in our body in health and in the development of disease. The CII is addressing these challenges through rigorous research into the following chronic conditions:



Chronic Fatigue Syndrome

Chronic fatigue syndrome, also known as myalgic encephalomyelitis or ME/CFS is a complex illness that affects as many as 2 percent of adults in the U.S. While ME/CFS is characterized by a severe debilitating fatigue, individuals with ME/CFS also report cognitive, sleep and musculoskeletal pain disturbances, and symptoms similar to those of infectious diseases.  

In 2015, CII published two groundbreaking studies providing insights into the causes and mechanisms of the disease, including the first robust physical evidence that ME/CFS is a biological illness as opposed to a psychological disorder, and the first evidence that the disease has distinct stages. The findings could help improve diagnosis and identify treatment options for the disabling disorder. CII researchers also identified a unique pattern of immune molecules in the cerebrospinal fluid of people with ME/CFS that provides insights into the basis for cognitive dysfunction—frequently described by patients as “brain fog.” 

Going forward, CII is embarking on studies of human microbiome as it relates to ME/CFS to determine how bacteria, fungi, viruses and toxins—and the immune response to them—contribute to ME/CFS. Discoveries in these areas may point us toward treatment strategies that reduce vulnerability through exclusion diets, probiotics, or drugs.

A dedicated group of CFS patients have formed a unique crowdfunding campaign called the Microbe Discovery Project to assist in the Center's fundraising efforts.

CLICK HERE to donate now to support Chronic Fatigue Syndrome research. 


Autism and Neuropsychiatric Disorders


As one of the world’s largest and most advanced academic centers for basic and translational research in microbe surveillance, discovery and diagnosis, CII has the equipment and expertise required to determine how the microbiome, the immune system, and environmental toxins contribute to autism and related disorders.

Research through the Autism Birth Cohort—one of the largest and most comprehensive prospective birth cohorts devoted to the investigation of genetic and environmental interactions in autism and related disorders—has shown that children with autism and gastrointestinal problems have an altered microbiome, providing new insights into gastrointestinal disturbances that develop in children with autism. Ongoing research is examining how bacteria, fungi, and viruses in the microbiome contribute to autism spectrum disorders.

With suggestive evidence that inflammation and abnormal immune responses contribute to autism spectrum disorders, CII has recently embarked upon a project to determine the frequency of abnormal immune responses in autistic children and their mothers as well as the environmental triggers of those responses. Another line of research is looking at the role of chemicals in autism spectrum disorders—either directly by those produced by industry or indirectly by the metabolism of these agents by microflora in the intestinal tract.

Neuropsychiatric Disorders

Infection may contribute to several neuropsychiatric diseases, including autism spectrum disorders (ASDs), attention deficit hyperactivity disorder (ADHD), mood disorders, schizophrenia, and obsessive-compulsive disorder (OCD). CII researchers have developed animal models to test how viruses and bacteria affect the developing brain in relation to ASD, ADHD, and pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS).


PANDAS is an autoimmune condition that describes a subset of children with features of OCD or tic disorders, including Tourette's Syndrome. Symptoms begin and may worsen with infections with the bacterium Group A beta-hemolytic streptococcus (GABHS) that can range from a strep throat to scarlet fever. Children with PANDAS may also be hyperactive or exhibit abnormal movements, ADHD, anxiety, mood disturbance, sleep problems, daytime urinary frequency, changes in motor capacity, joint pains, and anorexia. 

CII researchers developed an animal model to assess if strep infections cause changes in the brain that could lead to PANDAS. Understanding the link between strep infection and neurodevelopmental damage may also illuminate the mechanisms underlying other neurodevelopmental disorders, including autism spectrum disorders, schizophrenia, and ADHD. Researchers have identified several neurological pathways—endoplasmic reticulum stress, zinc dysregulation, poly(ADP) ribosylation, and caspase activation— that may allow viruses to damage  to viral injury in the maturing central nervous system.



ADHD is a behavioral disorder characterized by a chronic and varied combination of features of inattention and hyperactivity, causing social, academic, and other functional impairments. 

CII scientists have developed animal models to test whether immune responses to viruses and exposure to toxins affect normal neurological development, resulting in disorders like ADHD. Research focuses on the three-dimensional relationship between genetic vulnerabilities, the temporal framework of brain development, and exposure to environmental toxins, pathogens and psychosocial stressors. Applying genetic, immunologic, microbial, toxicologic, and imaging approaches over the course of development, CII seeks to enhance public understanding of the development of various types of ADHD and uncover opportunities to develop better therapies.