Microbes
Microbes, short for microorganisms, are tiny living organisms that are ubiquitous in the environment, including on and inside the human body. They play a crucial role in human health and disease, functioning within complex ecosystems in various parts of the body, such as the skin, mouth, gut, and respiratory tract. The human microbiome, which is […]
Microbiome Signatures identifies and validates condition-specific microbiome shifts and interventions to accelerate clinical translation. Our multidisciplinary team supports clinicians, researchers, and innovators in turning microbiome science into actionable medicine.
Karen Pendergrass
Overview Microbes, short for microorganisms, are tiny living organisms that are ubiquitous in the environment, including on and inside the human body. They play a crucial role in human health and disease, functioning within complex ecosystems in various parts of the body, such as the skin, mouth, gut, and respiratory tract. The human microbiome, which is the collective genome of all these microorganisms, is essential for maintaining health by aiding in digestion, producing vitamins, and protecting against pathogenic microorganisms. However, microbes can also cause a wide range of diseases when the balance of these communities is disturbed or when pathogenic microbes invade the body.
Microbes are categorized into several major types, each with distinct characteristics, roles, and implications for human health. The table below summarizes the main types of microbes relevant to human health and disease:
Overview
Types of Microbes
| Type of Microbe | Characteristics | Examples | Role in Human Health | Role in Disease |
|---|---|---|---|---|
| Bacteria | Single-celled organisms without a nucleus. Can be beneficial or harmful. | Escherichia coli, Staphylococcus aureus | Some species are part of the normal flora, aiding in digestion and nutrient absorption. Can also synthesize vitamins. | Can cause infections such as strep throat, urinary tract infections, and tuberculosis. Antibiotic resistance is a growing concern. |
| Viruses | Tiny, non-living particles that require a host cell to replicate. Consist of DNA or RNA within a protein coat. | Influenza virus, Human immunodeficiency virus (HIV) | Some viruses can be beneficial by infecting and killing harmful bacteria. | Cause diseases ranging from the common cold to AIDS. Antiviral resistance is an issue. |
| Fungi | Include yeasts, molds, and mushrooms. Some are single-celled, while others are complex multicellular organisms. | Candida albicans, Aspergillus spp. | Some fungi are used in food production and biotechnology. A small number are part of the normal flora. | Can cause infections like thrush and athlete’s foot. Invasive fungal infections can be life-threatening, especially in immunocompromised individuals. |
| Protozoa | Single-celled organisms with complex cell structures. Most are free-living, but some are parasitic. | Plasmodium falciparum, Giardia lamblia | Some protozoa in the gut can help in digestion and nutrient synthesis. | Cause diseases such as malaria and giardiasis. Can be waterborne or transmitted by vectors. |
| Archaea | Single-celled organisms similar to bacteria but genetically distinct. Known for thriving in extreme environments. | Methanobrevibacter smithii (in the human gut) | Some archaea in the human gut may play a role in digestion and metabolism. | Currently, archaea are not known to cause diseases in humans, but research is ongoing to fully understand their role. |
Microbes interact with the human body in complex ways, contributing to health in numerous beneficial ways but posing threats when pathogenic species invade or when the balance of microbial communities is disrupted. The study of microbes and their relationship with human health and disease is a vast and rapidly advancing field, highlighting the need for continued research and development of new therapeutic and diagnostic approaches.
Pathogenic Bacteria
The World Health Organization (WHO) has identified a list of bacteria that pose the greatest threat to human health due to antibiotic resistance. The WHO Global Priority Pathogens List (GPL) of antibiotic-resistant bacteria is designed to guide research, discovery, and development of new antibiotics as part of a broader effort to combat the growing threat of antimicrobial resistance (AMR). This list categorizes bacteria based on the urgency of the need for new antibiotics: Critical, High, and Medium priority.
| Priority Level | Bacteria | Reason for Concern |
|---|---|---|
| Critical | Acinetobacter baumannii, carbapenem-resistant | Difficult to treat due to resistance to multiple antibiotics, including last-resort drugs. |
| Critical | Pseudomonas aeruginosa, carbapenem-resistant | Known for causing severe infections, especially in hospitalized patients, with limited treatment options. |
| Critical | Enterobacteriaceae, carbapenem-resistant, ESBL-producing | Includes common pathogens like E. coli and K. pneumoniae, resistant to a broad range of antibiotics. |
| High | Enterococcus faecium, vancomycin-resistant | Causes infections that are difficult to treat due to vancomycin resistance, a last-resort antibiotic. |
| High | Staphylococcus aureus, methicillin-resistant, vancomycin-intermediate and resistant | A major cause of hospital and community-acquired infections that are increasingly difficult to treat. |
| High | Helicobacter pylori, clarithromycin-resistant | Resistance complicates treatment of ulcers and gastric cancer. |
| High | Campylobacter spp., fluoroquinolone-resistant | Resistance makes gastroenteritis more difficult to treat. |
| High | Salmonellae, fluoroquinolone-resistant | Complicates treatment of severe salmonellosis, including typhoid fever. |
| High | Neisseria gonorrhoeae, cephalosporin-resistant, fluoroquinolone-resistant | Growing resistance threatens control of gonorrhea, a major sexually transmitted infection. |
| Medium | Streptococcus pneumoniae, penicillin-non-susceptible | A leading cause of bacterial pneumonia and meningitis, with resistance impacting treatment efficacy. |
| Medium | Haemophilus influenzae, ampicillin-resistant | Resistance affects treatment options for respiratory tract infections and meningitis. |
| Medium | Shigella spp., fluoroquinolone-resistant | Resistance complicates treatment of shigellosis, an important cause of diarrheal disease globally. |
The bacteria listed above are of concern due to their high levels of resistance to existing antibiotics, leading to increased morbidity, mortality, and healthcare costs. This list underscores the urgent need for the development of new treatment modalities and antimicrobial stewardship to combat the growing threat of antibiotic resistance.
Commensal Bacteria
Numerous bacterial species have been extensively studied for their contributions to human health, especially in the gut microbiome, skin, oral cavity, and other parts of the human body. These bacteria are recognized for their roles in maintaining health through various mechanisms, including nutrient synthesis, protection against pathogens, and immune system modulation. The following table lists some of the most significant commensal bacteria and their known health contributions:
| Rank | Bacteria Name | Contribution to Human Health |
|---|---|---|
| 1 | Bifidobacterium longum | Supports gut health, aids in digesting fiber, and produces vitamins and other important chemicals. |
| 2 | Lactobacillus rhamnosus | Enhances the gut barrier, has potential anti-inflammatory effects, and supports immune function. |
| 3 | Lactobacillus acidophilus | Aids in lactose digestion and contributes to a healthy vaginal microbiota. |
| 4 | Bifidobacterium bifidum | Important for digesting dietary fiber, supports the production of vitamins and inhibits pathogens. |
| 5 | Lactobacillus reuteri | Produces reuterin, which has antimicrobial properties, and supports oral and gut health. |
| 6 | Lactobacillus casei | Influences the immune system and aids in the digestion of dairy in lactose-intolerant individuals. |
| 7 | Lactobacillus plantarum | Offers anti-inflammatory benefits and supports gut barrier integrity. |
| 8 | Bifidobacterium breve | Helps digest plant fibers and may reduce intestinal irritation. |
| 9 | Lactobacillus fermentum | Offers antioxidant properties and supports vaginal and gut health. |
| 10 | Bifidobacterium adolescentis | Breaks down body waste and aids in the absorption of food. |
| 11 | Staphylococcus epidermidis | Protects skin by producing antimicrobial peptides and inhibiting pathogen colonization. |
| 12 | Faecalibacterium prausnitzii | Produces butyrate, an important short-chain fatty acid for colon health and anti-inflammatory effects. |
| 13 | Roseburia intestinalis | Involved in butyrate production and supports a healthy gut lining. |
| 14 | Eubacterium hallii | Contributes to metabolic health by producing butyrate and converting lactate to butyrate. |
| 15 | Akkermansia muciniphila | Promotes a healthy mucosal layer in the gut and has been associated with metabolic health. |
| 16 | Streptococcus salivarius | Prominent in the oral microbiome, supports oral health by inhibiting pathogenic bacteria. |
| 17 | Streptococcus thermophilus | Used in yogurt and cheese production, supports lactose digestion. |
| 18 | Clostridium butyricum | Produces butyrate, supporting gut health and potentially enhancing immune function. |
| 19 | Neisseria mucosa | Part of the healthy oral and respiratory microbiota, may play a role in immune regulation. |
| 20 | Prevotella copri | Linked to the metabolism of complex polysaccharides and may influence the immune system. |
This table provides an overview of diverse commensal bacteria that benefit human health, highlighting their roles in nutrition, immunity, and disease prevention. It’s important to note that the balance and effects of these bacteria can vary significantly among individuals, influenced by factors such as diet, lifestyle, and genetics. The ongoing research continues to uncover the complex interactions between commensal bacteria and their human hosts, offering promising avenues for improving health and treating diseases.
Viruses
Pathogenic Viruses
The World Health Organization (WHO) was particularly concerned about several viruses due to their potential to cause epidemics or pandemics, their impact on global health, and the lack of effective treatments or vaccines for some of them. The WHO continuously monitors and responds to outbreaks of viral diseases around the world. The level of concern for specific viruses can change over time as new information becomes available, outbreaks occur, or vaccines and treatments are developed. Below are some of the viruses that have been of significant concern:
| Virus Name | Reason for Concern |
|---|---|
| COVID-19 (SARS-CoV-2) | Global pandemic causing significant morbidity, mortality, and societal disruption. |
| Influenza | Potential for causing pandemics; seasonal strains impact global health annually. |
| Ebola Virus Disease | Causes severe hemorrhagic fever with high fatality rates; outbreaks mainly in Africa. |
| Zika Virus | Linked to birth defects and neurological complications; outbreaks in various regions. |
| HIV/AIDS | Ongoing global pandemic affecting millions, with research focused on vaccines and treatments. |
| Hepatitis B and C | Major causes of liver disease and liver cancer, with ongoing efforts for better vaccination and treatment. |
| Dengue Fever | Causes severe flu-like illness and, in severe cases, hemorrhagic fever; widespread in tropical areas. |
| Rabies | Almost always fatal once symptoms appear but preventable through vaccination. |
| Measles | Highly contagious virus with outbreaks in areas of low vaccination coverage. |
| Poliovirus | Subject of a global eradication initiative, with cases now limited but requiring continued efforts. |
| Crimean-Congo Hemorrhagic Fever (CCHF) | Causes severe hemorrhagic fever outbreaks; transmitted by ticks or contact with infected animal blood. |
| Marburg Virus Disease | Similar to Ebola, causes severe hemorrhagic fever with high fatality rates; rare but lethal. |
| Lassa Fever | Endemic in West Africa, causes hemorrhagic fever with varied symptoms; transmitted by rodents. |
| Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS) | Coronaviruses causing severe respiratory infections with significant fatality rates. |
| Nipah and Henipaviral Diseases | Causes severe respiratory and neurological disease; high fatality rates and no vaccines or treatments. |
| Rift Valley Fever | Affects animals and humans; can cause severe disease including hemorrhagic fever in humans. |
Beneficial Viruses
While the focus here is on phages due to their clear applications and benefits, ongoing research continues to explore the roles and therapeutic potential of other types of viruses, indicating a broadening understanding of viruses as entities that can have positive as well as negative impacts on human health and the environment. Focusing on their applications to human health and other beneficial roles, beneficial viruses primarily highlight bacteriophages due to their well-documented potential.
| Beneficial Virus | Application | Description |
|---|---|---|
| Bacteriophages | Phage Therapy | Used to target and kill antibiotic-resistant bacteria, offering a potential treatment for bacterial infections. |
| Bacteriophages | Food Safety | Applied to food products or surfaces to eliminate pathogenic bacteria, improving food safety. |
| Bacteriophages | Agriculture | Used to control bacterial diseases in crops, reducing the need for chemical pesticides. |
| Bacteriophages | Aquaculture | Employed as biocontrol agents to combat bacterial infections in fish and other marine organisms. |
| Bacteriophages | Gut Health | May influence the human gut microbiome’s composition and health by controlling bacterial populations. |
| Bacteriophages | Biotechnology and Research | Utilized in molecular biology for genetic engineering, phage display technologies, and the development of novel therapeutics. |
Fungi
Pathogenic
Fungi play diverse roles in human health, with some species being pathogenic and causing diseases, while others offer beneficial effects. Below are two tables: one for clinically investigated pathogenic fungi responsible for human diseases, and another for fungi that have been investigated for their beneficial impacts on human health.
| Pathogenic Fungus | Associated Conditions | Description |
|---|---|---|
| Candida albicans | Candidiasis, thrush, systemic infections | A common cause of fungal infections, which can range from superficial skin infections to systemic diseases in immunocompromised individuals. |
| Aspergillus fumigatus | Aspergillosis, lung infections | Primarily affects the respiratory system, can cause severe complications in people with weakened immune systems. |
| Cryptococcus neoformans | Cryptococcal meningitis | A significant cause of meningitis in immunocompromised patients, particularly those with HIV/AIDS. |
| Histoplasma capsulatum | Histoplasmosis | Causes lung infections, and can disseminate to other organs in severe cases, particularly in immunocompromised hosts. |
| Pneumocystis jirovecii | Pneumocystis pneumonia (PCP) | Primarily affects individuals with weakened immune systems, such as those with HIV/AIDS, causing severe pneumonia. |
| Dermatophytes (e.g., Trichophyton, Microsporum) | Dermatophytosis (ringworm), athlete’s foot, onychomycosis | Infects skin, hair, and nails, causing a range of superficial mycoses. |
Beneficial
| Beneficial Fungus | Application | Description |
|---|---|---|
| Saccharomyces boulardii | Probiotic supplement | Used to treat and prevent diarrhea, including antibiotic-associated diarrhea, and other gastrointestinal disorders. |
| Penicillium chrysogenum | Source of Penicillin | The original source of penicillin, transforming the treatment of bacterial infections. |
| Aspergillus oryzae | Fermentation | Used in the production of fermented foods and beverages, enhancing flavor, preservation, and nutritional value. |
| Saccharomyces cerevisiae | Brewing, baking, biotechnology | Baker’s or brewer’s yeast; essential in baking, brewing, and as a model organism in scientific research. |
| Trichoderma reesei | Enzyme production | Produces cellulases and other enzymes for industrial applications, including in the textile, paper, and biofuel industries. |
| Ganoderma lucidum (Reishi) | Immunomodulation, anti-tumorigenic | Known for its immune-boosting and anti-cancer properties. Studies suggest it can inhibit tumor growth and modulate the immune system. |
| Cordyceps sinensis | Anti-tumorigenic, anti-viral | Traditionally used for enhancing stamina and reducing fatigue. Research indicates potential anti-cancer and anti-viral activities. |
| Grifola frondosa (Maitake) | Immunomodulation, anti-tumorigenic | Demonstrates immune system support and potential anti-cancer effects in clinical studies. |
The table encapsulates the diverse roles and applications of various fungi in promoting human health and their utilization in food production, biotechnology, and medicine. This collection showcases the significant potential of fungi in enhancing human health through various traditional and innovative applications.
These two tables highlight the dual nature of fungi: while some species are harmful and can cause significant health issues, others are invaluable for their contributions to medicine, food, and industry.
Protozoa
Pathogenic
Below is a table summarizing key information about several notable diseases caused by protozoa, including their causative agents, primary symptoms, and modes of transmission:
| Disease | Causative Agent | Primary Symptoms | Mode of Transmission |
|---|---|---|---|
| Malaria | Plasmodium spp. | Fever, chills, flu-like symptoms | Bite of infected Anopheles mosquitoes |
| Amoebiasis | Entamoeba histolytica | Diarrhea, liver abscesses | Contaminated water or food |
| Giardiasis | Giardia lamblia | Gastrointestinal symptoms | Contaminated water |
| Toxoplasmosis | Toxoplasma gondii | Severe problems in fetuses and immunocompromised individuals | Cat feces, undercooked meat |
| Leishmaniasis | Leishmania spp. | Affects skin, mucous membranes, internal organs | Bites of infected sandflies |
| Trypanosomiasis | Trypanosoma cruzi, Trypanosoma brucei | Chagas disease: heart and digestive system disorders; African sleeping sickness: fever, headaches, joint pains | Insect vectors (kissing bug for Chagas disease, tsetse fly for African sleeping sickness) |
This table encapsulates diseases caused by various protozoa, highlighting the diversity of these pathogens and the range of health issues they can induce. Malaria, transmitted by Anopheles mosquitoes, remains one of the most significant parasitic diseases globally. Amoebiasis and giardiasis are primarily waterborne diseases leading to gastrointestinal symptoms. Toxoplasmosis, though often asymptomatic in healthy individuals, poses a severe risk to fetuses and immunocompromised people. Leishmaniasis and trypanosomiasis are vector-borne diseases causing significant morbidity and mortality, transmitted through the bites of sandflies and tsetse flies, respectively. These diseases underscore the importance of prevention, control measures, and the need for ongoing research to find effective treatments.
Beneficial
In the human body, the role of protozoa is more commonly associated with pathogenic effects rather than beneficial ones. Unlike the gut microbiome, which consists mainly of beneficial bacteria and fungi that contribute to health in various ways, the presence of protozoa in humans is often indicative of parasitic infections rather than mutualistic or commensal relationships.
To date, there are no protozoa known to play a directly beneficial role in human health akin to the beneficial bacteria found in the human gut microbiome. However, research into the human microbiome is continually evolving, and our understanding of the microorganisms living in and on the human body is expanding. It’s conceivable that future research may uncover specific protozoa or protozoal communities that have neutral or potentially beneficial effects on human health, possibly through interactions with the human immune system or by influencing the bacterial microbiome in beneficial ways.
Archaea
In the human microbiome, archaea have been identified, particularly in the gut, skin, and oral cavity. The most studied archaeon in humans is Methanobrevibacter smithii, which is involved in the digestion process by consuming hydrogen and producing methane, thereby affecting the gut’s overall efficiency and microbial ecosystem. While these interactions are crucial for understanding human health and disease, Methanobrevibacter smithii and other archaea in the human body have not been classified as pathogenic in the same clear-cut manner as certain bacteria, viruses, or fungi.
The current understanding is that archaea might play roles in human health and disease that are more subtle and complex than direct pathogenicity. For example, they may influence the balance of other microbes in the gut microbiome, which can impact health conditions like obesity, inflammatory bowel disease (IBD), and colon cancer. However, these effects are part of broader microbial community interactions rather than the result of direct infection or disease causation by archaea.
To date, no archaea have been definitively identified as pathogenic in the same sense as many bacteria, viruses, and fungi. Research into the human microbiome and the role of archaea in health and disease is ongoing, and future discoveries may further elucidate the complex interactions between archaea and their human hosts. The absence of known pathogenic archaea highlights the unique nature of these microorganisms and their distinct evolutionary path from bacteria and eukaryotes.