HUMAN MICROBIOTA AND THE HUMAN MICROBIOME

What is microbiota, what is a microbiome—and why is it important information for nurses? Our understanding and management of health and disease is a work in progress. Variations of past models from ancient civilizations to today taught us that disease is mainly caused by germs or pathogenic microorganisms that infect our bodies. While the models of how some diseases occur still hold true in many cases (i.e., infectious diseases), the causes of disease are also strongly rooted in genetics. Research has revealed that in addition to our own human genes, microorganisms and their genes also have a significant affect on our health.

As new editions of this manual have been written, study content related to the genetic basis for disease and the impact of genomics on human health, patient care, and patient education has been added to assist nurses in incorporating information regarding genetics into their practice. The microbiome (MB) appendix has been prepared in order to review some terminology regarding genetics and molecular test methods used to gather genetic information. Mainly, this appendix is intended to provide some basic information regarding the human MB, how it affects our health, and potential nursing implications. The role of the human MB is an ever-evolving scientific inquiry with findings that may contradict traditional beliefs and even provide contradictory data between similar studies. Some of the relatable changes brought about by research on this topic have had and will continue to have a major impact on moving the needle of the information burden for nurses in practice, nursing students, and nursing instructors. The implications stand at multiple points across the age continuum and across all nursing subspecialties. Nurses need to be comfortable with this information as it will affect the way patient care and patient education are delivered and could affect the way test results are generated and interpreted in the future, including the ability to

• Learn new specimen collection protocols for microbial gene sequencing studies, in addition to the collection of traditional culture specimens.
• Make observations, assessments, and feedback that will require an understanding of linkages between the MB and diseases by body site (e.g., reviewing site-specific culture result reports, therapeutic drug levels, patient response to therapy, interventions required to restore good health).
• Learn new strategies to prevent and manage health-care-associated infections (HAI; e.g., related to the results of laboratory testing—genetic and traditional microbiology reports that identify organisms, provide antimicrobial sensitivity data, or indicate the presence of sequence variations that confer antimicrobial resistance).
• Actively participate/expand role in antibiotic stewardship (e.g., feedback to the health-care provider [HCP] or pharmacist regarding the patient’s response to antimicrobial therapy).
• Provide updated education for patients and families (e.g., to explain our current understanding of the numerous ways human disease occurs to include infection, genetics, genomics, dysbiosis of the microbiome); our understanding of how diet specifically affects our bodies on a micro-basis (rather than the teaching about traditional macronutrients such as fat, protein, carbohydrates), how crucial an individual’s diet is in maintaining health and support for their microbiota, new/experimental therapies (as relate to traditional and emerging laboratory testing for human genetic sequence variations and microbiome panels).
• Strengthen interdepartmental communication regarding specimen collection, results reporting, results interpretation, and referrals to specialists or consultants.

Every environment has its own biome or community. Examples of well-studied biomes include soil, water, plants, animals, and more recently, humans. The term microbiota refers to all types of the trillions of microorganisms that live on and inside humans to include bacteria, viruses, fungi, and archaea. Microbiome (MB) refers to the microbiota and all of its genetic material. Consider the human body a biome consisting of multiple, separate communities of microbiota populating specific body sites. The composition of our microbiota evolves throughout our entire life span, from a newborn to an older adult.

• Bacteria comprise as much as 90% of the MB and include
• Symbionts—beneficial bacteria that live in harmony with their human hosts. They provide essential functions for good health; examples include the metabolism of indigestible complex carbohydrates into energy, the production of vitamins, and provision of immune support. Symbionts like Bifidobacterium and Lactobacillus perform important functions as probiotics to support gut health.
• Commensals—bacteria that are usually harmless but can become opportunistic pathogens when circumstances favor an imbalance in the normal microbiota (i.e., commensals can become pathogenic in one host and be harmless to another).
• Pathogens—the bacteria that cause disease.

Genes are the basic units of heredity. They are organized in the DNA of our chromosomes—every person inherits a set of 23 chromosomes from each parent, and so two copies of every gene have the potential to contribute to our unique physical and functional characteristics. About 1% of human DNA contains genes that code for proteins. Noncoding DNA is believed to carry out crucial functions such as activating or shutting down expression of other genes, providing instructions for the formation of certain kinds of RNA molecules, and contributing to structural functions of the chromosome itself (e.g., DNA sequences at the ends of chromosomes form telomeres, which protect the ends of chromosomes from being damaged during cell replication, when a copy of the cell’s genetic material is made, prior to cell division). How did we come to study human microbiota and the MB? The Human Microbiome Project (HMP), launched by the National Institutes of Health in 2007, is a natural and logical extension of the Human Genome Project (HGP), which began in 1990 and was completed in 2003. Research brought forth by the HGP has pointed to how our genes affect our health and even further how the interaction between our genes, environmental factors, and lifestyle choices can influence and inform whether we were predisposed or, in some cases, predestined to experience poor health. Goals of the HGP:

• Define the human genome (identify the genes in human DNA and map the nucleic acid sequence of human DNA)
• Determine the role of the human genome in health and disease

• Development of automated DNA sequencing methods (Sanger sequencing)
• Estimation of the size of the human genome; approximated at 20,000 to 25,000 genes
• Mapping of the entire sequence of nucleic acid base pairs in human DNA
• Precursor of precision molecular medicine to better diagnose disease, provide earlier detection of some diseases, and use gene therapy to design more effective, condition-specific drugs
• Precursor of genomics (human and microbial); predisposition to disease affected by external factors

• Describe the essential characteristics of the human microbiome and determine its role in health and disease.
• Establish a DNA sequence database and develop calculations for a reliable model to characterize the MB in populations of healthy individuals and people with MB-associated diseases.
• Conduct studies of healthy individuals over time to gain greater understanding of the role of the human MB in health and disease. The HMP focused on studying the microbes residing in/on five body sites: colon, mouth, nose, skin, and vagina.

• Development of less costly, more rapid sequencing methods, using smaller sample sizes; next-generation sequencing (NGS) has largely replaced Sanger sequencing methods. NGS methods developed and used in the HGP provided the ability to discover and identify microorganisms independent of traditional techniques. NGS methods are used in many clinical applications in addition to those relating to microorganisms.
• Development of the 16S rRNA targeted sequencing method for bacterial identification, which overcame obstacles encountered with traditional microbiological techniques.
• Creation of a microbial reference database for future comparison and classification; a database that continues to grow.

How are we studying the human MB today? Historically, bacteria have been identified and classified phenotypically (i.e., based on observable characteristics such as biochemical reactions, staining characteristics, and culture results). Obstacles to accurate and complete bacterial identifications included the inability to culture certain fastidious organisms, complications related to studying mixed bacterial populations with different individual growth characteristics, inability to obtain specimens from body sites of interest other than by invasive methods, and the lack of a complete reference database. 16S ribosomal RNA sequencing, more commonly known as 16S rRNA sequencing, is a method that permits a relatively rapid, simple, and valid alternative to traditional techniques. 16S rRNA sequencing reveals bacterial genotype or the exact arrangement of nucleotides in a gene. The 16S rRNA gene codes for a ribosomal subunit that is shared among bacteria. Alleles are forms of the same gene with small differences in their sequence of nucleotide bases. These small differences contribute to the expression of unique features. Hypervariable regions are distributed between the shared regions of its sequence. The shared regions help identify the microorganism as bacterial; the hypervariable regions are unique to each bacterial species, providing a means for further classification.

Diversity in the MB: Alpha diversity refers to the number of different microbiota in a specific site (e.g., such as the colon or the vagina); beta diversity refers to the number of different communities in one individual compared to another individual (e.g., individual 1 colon vs individual 2 colon) or the number of different communities in one geographic location compared to a different location (e.g., rural communities vs urban communities).

What are the most commonly studied body sites? Microbial communities are specific to various body sites. Of the five sites selected for the HMP, the colon and vagina have been studied the most.

Colon

• Choice of the colon as a body site suitable for MB study has to do with ease of accessibility (low level of invasiveness) for specimen collection and reliable availability of stool samples. An important consideration is that stool does not reflect the MB inhabiting the entire gastrointestinal (GI) tract (e.g., those attached to the intestinal mucosa or those found in the small intestine are not represented).
• Size and diversity of the GI or gut MB: The GI MB has been shown to contain the greatest total number of microorganisms, most of which are located in the colon. The gut MB is one of the least diversified with the majority of bacteria belonging to two major phyla: Bacteriodetes and Firmicutes.
• Significant functions of the colon MB:
  1. Energy harvesting whereby the bacteria metabolize the undigestible fiber available in the colon and convert it to an energy substrate either used directly by colon cells or absorbed into the bloodstream in the form of short-chain fatty acids (SCFAs).
  2. Synthesis of essential nutrients for use by epithelial cells in the colon such as biotin, vitamin B₁₂, and vitamin K.
  3. Promoting host immunity: growth of new colon epithelial cells is promoted with nutrients supplied by the microbiota to maintain the integrity of the intestinal membrane. The new cells create a physical barrier that protects the membrane from invasion by pathogenic bacteria. SCFAs along the surface of the membrane also bind to cell receptors and act as immune modulators. They are believed to reduce inflammation (e.g., as seen with Crohn disease) and provide antitumor protection against invasive cancer cells.
• Nutritional requirements of the gut microbiota: The foods we eat are a significant determinant in maintaining the normal diversity and healthy functioning of the gut MB. The two categories of natural dietary ingredients most closely aligned with studies of healthy gut MB are prebiotics and probiotics. Both have been found to promote beneficial effects during the process of digestion, and studies often highlight the importance of including both in the daily diet. Prebiotics are the indigestible ingredients naturally present in foods such as almonds, apples, artichokes, asparagus, bananas, beetroot, bran, chickpeas, dates, fennel, figs, garlic, grapefruit, green peas, leeks, lentils, nectarines, onions, peaches, pomegranites, plums, savoy cabbage, snow peas, tomatoes, watermelon, and zucchini; foods that selectively promote the growth and beneficial metabolic activities of a limited number of the bacterial species normally found in the gut. Probiotics are live microorganisms, usually bacteria capable of metabolizing substrates by fermentation; they also provide a health benefit for the gut. The most commonly recommended probiotics include Bifidobacterium, Lactobacillus, or Streptococcus bacteria because they are capable of resisting destruction during digestion while assisting in the natural digestive process, restoring imbalance in the healthy gut MB, and regulating the immune system. They are found in cultured dairy products such as acidophilus milk, buttermilk, fermented cheeses, kafir, fermented cabbage (e.g., sauerkraut), sour cream, and yogurt. The probiotic bacteria are ineffective if not ingested in sufficient quality and quantity. Products purchased in the typical grocery store will state whether the product contains a live culture, and some will list the type and quantity of live organisms; live cultures are best.
• Disruption of the normal bacterial community (dysbiosis) occurs when there is an imbalance in the MB (i.e., its normal functions are adversely affected by external factors such as poor diet, stress, infections, and medications, e.g., some antibiotics modify the composition of the gut MB; the changes can be lasting and possibly incompletely reversible). Gut dysbiosis is associated with conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and cancer. Recent studies have also demonstrated a potential neurological link between gut dysbiosis and Alzheimer disease, anxiety, autism, depression, and obesity.

Vagina

• Choice of vagina as a body site suitable for MB study: While the MB of the colon is probably the most studied of the body sites, the origin of every human being’s individualized gut MB is now believed to begin during the process of birth, with the most significant colonization occurring in the vagina.
• Size and diversity:
  1. Neonates—Colonization of the GI tract begins at birth and evolves as we grow. The mode of delivery, physical environment in which the delivery takes place, and how the newborn is fed from the third day forward (human milk vs formula, patient vs other caregiver) affect the size and composition of the neonate’s gut microbiota. The skin of a newborn delivered vaginally is quickly colonized by microorganisms from the patient’s vagina, skin, and breast. Skin microbiota of newborns delivered by cesarean section begin with less diverse communities composed of skin bacteria presumed to be transferred during postpartum handling by HCPs (e.g., nurses, midwives, physicians, etc.) and contact with surfaces in the delivery environment itself; direct parental contact and breastfeeding are delayed while the patient recovers from the C-section surgery.
  2. Adults—Lactobacillus species are the most abundant bacterial community found in the vaginal site.
• Significant functions of the vaginal MB over the course of the life cycle: 16S rRNA targeted gene profile studies have demonstrated that the vaginal microbiota changes in response to hormonal influences during puberty, pregnancy, and menopause.
  1. Prevention of infection: Lactobacilli prevent infection by secreting lactic acid and other bacteriocins, which prevent other bacteria from binding to and infecting epithelial cells in the vagina. The lactic acid creates an acidic environment (pH 3.5 to 4.5) that kills or inhibits the growth of other harmful bacteria. Lactic acid also induces autophagy, a process in which the body directs infected epithelial cells to degrade intracellular microorganisms, which promotes a return to homeostasis. Homeostasis is a state of balance or stability. Lactobacilli prevent infection without inducing inflammation.
  2. Neonatal GI tract colonization: Scientists believe that the vagina is where newborns are given their most significant innoculation of microbiota as they pass through the birth canal.
  3. Disruption of the normal bacterial community (dysbiosis): An example of dysbiosis in the vaginal MB is bacterial vaginosis (BV). While BV is a fairly common infection during the reproductive years, there is no specific associated bacterial profile related to increased predisposition. However, vaginal pH greater than 5 and decreased presence of Lactobacilli are usually characteristic.

PATIENT CARE APPLICATIONS: THE AGE CONTINUUM—NURSING IMPLICATIONS

Human beings are now known to be born with certain bacteria, archaea, and viruses that live as symbiotic, commensal, or pathogenic organisms, sharing our bodies throughout our life span. The gut MB is formed early in life and is influenced at birth by many factors, including parental health. Development of the gut MB continues until age 2 to 3 yr with 90% of the community composed of Bacteriodetes and Firmicutes. Development of the MB stabilizes between the ages of 30 and 70 yr. After age 70 yr, the MB becomes less diverse and less stable.

Newborn and Pediatric Considerations Potential Nursing Interventions and Opportunities for Patient Education

• Preparing for delivery: Perinatal nurses should understand that common practices during labor and delivery can alter the composition of the vaginal microbiota; the effects of which might result in suboptimal colonization of the vaginally delivered newborn. Potential interventions might include minimizing the number of vaginal examinations during labor using lubricants. In situations where the patient has been given antibiotics, the nurse may have discussions with the patient about the benefits of breastfeeding the newborn as early after birth as possible and the importance of continuing to breastfeed for as long as the patient wants in order to help the baby develop a healthy MB.
• Mode of delivery: The GI tract of cesarean-born infants is different than that of vaginally born infants; mode of delivery by C-section has a greater correlation with neonatal development of conditions such as allergic rhinitis, asthma, celiac disease, IBD, obesity, and type I diabetes than vaginal delivery. Research also suggests the MB contributes significantly to the development of the immune system and normal physical growth. Potential interventions might include discussions with the patient about the importance of breastfeeding the newborn as early after birth as possible and, if indicated, discussions with the patient’s HCP regarding the administration of prebiotics and probiotics to the newborn.
• Skin-to-skin care (SSC) is a practice used in some facilities where infants are clothed only in a diaper and are held upright against the chest of the parent, caregiver, or nurse. The benefit from this care is attributed to the transfer of microbes, which further promotes bacterial innoculation of the newborn. Potential interventions might include explaining that transferring good microbes from the parents’ skin to the baby’s skin is beneficial; therefore, SSC from both parents should be encouraged.
• Feeding method: The immunological benefits of colostrum are well known; breastfeeding reduces upper and lower respiratory tract infections and enhances immune system development. Human milk contains important prebiotics (e.g., caseins, human milk oligosaccharides) and probiotics (e.g., Bifidobacterium bifidum). Potential interventions might include recommending consultation with a lactation specialist to answer questions and providing information about breastfeeding, encouraging patients to begin breastfeeding immediately after birth and continue using fresh human milk whenever possible. Proper nutrition for children is a huge global issue. Poor nutrition in developing children results in significant adverse effects (e.g., delayed or stunted physical growth and development, chronic infections).
• Exposure to the environment: Potential interventions might include discussing topics such as good hygiene in the home environment, involvement of siblings in welcoming the new baby, introducing pets to the new baby, and teaching how environmental exposure impacts the baby’s developing MB.
• Medications: Antibiotic use has been implicated in changes in gut microbiota and weight gain, especially in children. Potential interventions might include participation in the facility’s Antimicrobial Stewardship Best Practices Program to achieve appropriate, shorter administration of antibiotics and encourage breastfeeding, especially when the patient or neonate is receiving antimicrobial medications. Teach parents about the connection between antibiotic use and adverse effects on the child’s MB; instill the idea that antibiotics are not the “cure-all,” and other nonmedication options can be explored with the HCP to avoid the adverse effects antibiotics have on the MB.

Adult and Older Adult Considerations

• Females of reproductive potential: A number of modifiable factors contribute to vaginal dysbiosis—these should be discussed with the patient who presents with bacterial vaginosis (BV). The use of vaginal lubricants and the practice of douching should be discouraged as both are associated with development of BV. Intercourse with numerous sexual partners is also associated with development of BV. Potential interventions might include providing education regarding hygienic practices that should be avoided with an explanation of why they result in infection. A discussion of high-risk sexual behaviors accompanied by information regarding safe sex practices would also be appropriate.
• Older adults: Providing health care for older adults requires special considerations; the health status of older adults is often complex, and sometimes health issues present atypically. Age-related changes in immune status are associated with a decrease in the diversity and stability of the MB. Physical location also influences the composition of the MB; facilities like nursing homes are associated with a high incidence of C. difficile and multidrug resistant organisms (MDROs). Potential interventions might include consideration of nutritional interventions (prebiotic and probiotic food sources) because many of the critical metabolic pathways carried out by the MB decrease in functionality with age. Malnurished older adults cannot support a healthy MB; dysbiosis with replacement by pathogens begins to take its toll in the form of recurrent infections. Teaching and administering mouth care is another important way to improve appetite and support the health of the oral MB—gateway to the gut MB. Actually, good mouth care is essential for people of all ages to maintain good health.

Summary: What Affects the MB?

• Age
• Diet
• Exposure to the external environment (e.g., skin MB has the highest beta diversity with a lower alpha diversity, most likely reflecting the result of environmental effects)
• Environmental toxins
• Medical interventions (e.g., colonoscopy, insertion of a central line)
• Medication use, especially antibiotics
• Method of initial “innoculation” or colonization
• Physical location/environment (e.g., rural vs urban, nursing home vs independent community living)

Summary: What Has MB Research Revealed?

• The human MB is diverse and dynamic in its composition. In other words, because the types and amounts of microbiota vary between individuals, there is no standard definition of what comprises a healthy human MB.
• Linkage exists between the MB and human disease (brain–gut, heart–gut, gut, lung, vagina, mouth, etc.).
• Areas of the body previously thought to be sterile are now believed to contain microbiota (e.g., blood, lungs). We now know that many of the bacteria inhabiting various sites of the body were undetected because they are difficult to easily obtain and too fastidious or difficult to grow by traditional culture methods.
• 16S ribosomal RNA (rRNA) targeted gene amplification is the most common molecular method used to study the human MB because the 16S rRNA gene is found in all types of bacteria. The 16S rRNA gene also has areas that vary between different bacterial species, making it capable of identifying bacteria we never knew existed or reclassifying bacteria that were misidentified by traditional methods.
• Different sampling and sample preparation techniques, laboratory methods, and analysis models do not yield similar results.
• Reference microbial databases are incomplete at this point.

There has been an explosion of continuing research regarding the human MB and its role in human disease. Examples include investigations into the use of prebiotics, probiotics, and fecal transplantation to prevent and treat diseases. What is certain is that patient care will continue to evolve as we continue to better understand how our bodies work and how nursing interventions that have been taught throughout the years continue to support the health of the human MB.

Potential Applications for Future Nursing Practice

• Colon/gut—Across the age continuum The role of the gut MB across the life span continues to be fertile ground for scientific research, the results of which portend far-reaching implications. Maternal-newborn-child health studies have demonstrated the importance of the birthing process in the establishment of the gut MB and the negative effects of birth by C-section on the development of the gut MB. Other studies in this patient population have focused on the negative effects associated with the administration of antibiotics. Fecal microbiota transplantation (FMT) is a good example of how gut MB research has been applied to therapeutic treatments with good success; many are performed on pediatric and young adult patients. Studies of older adults’ gut MB have shown improvements over time following dietary adjustments and nutritional supplementation with vitamins and minerals. Improvements occurred in physical function and in emotional well-being, evidenced by decreased levels of depression and anxiety. MB profiling may provide a reliable way to individualize diets using prebiotics and probiotics to support a healthy MB.
• Colon/gut Regarding patient education, there is a movement away from the medical or nutritional explanation of diet in terms of macronutrients (carbohydrates, fat, protein) and toward identifying foods (and their nutritional properties) that will assist in supporting the MB and decreasing systemic inflammation.
• Multisite Changing the approach to antibiotic use. Excessive use of (broad-spectrum) antibiotics negatively affects the human MB. Various studies demonstrate that the MB does not quickly rebound and may possibly never fully recover in some cases because the normal microbiota are replaced by antibiotic-resistant organisms.
• Multisite Regarding patient education, there is a shift away from explanations that characterize microorganisms (e.g., bacteria, viruses) as bad germs and instead toward the perception that our MB is necessary for good health; our MB make mostly good, sometimes essential contributions to our health; disease is likely to occur in situations where there is an unhealthy disturbance of the normal MB.
• Multisite HAIs continue to be important issues in clinical microbiology and epidemiology. Identification of pathogens, especially those resistant to antibiotics, is necessary for appropriate antibiotic stewardship. Culture methods are typically used to identify pathogenic bacteria, but treatment with broad-spectrum antibiotics is often begun prior to identification because of the lag in time between culture growth and results reporting. 16S rRNA targeted sequencing is a more rapid method of identifying pathogens. Although the technology is not commonly used in most clinical facilities at this point in time, it is available in some of the state department of health laboratories and in national reference laboratories. It is highly likely to become more easily accessible in the coming years as the urgency for its availability increases in the event of pandemic outbreaks.
• Multisite The investigation of linkages between different body systems has been slow to gain traction. Previous models of human health have created the perception of the human body as a series of semi-isolated systems (e.g., cardiovascular, neurological, respiratory, etc.). Science is beginning to demonstrate findings that point to definite communication between organs and the MB. An unusual and interesting area for research is the connection believed to take place between the gut MB and the brain; it is believed that there is bidirectional communication between the gut MB and the brain such that significant changes in the gut MB are believed to trigger changes in brain structure and function.