what types of bacteria are found in the human body


Studies have shown that of the bacteria found in indoor air, the most common four are: Micrococcus, Staphylococcus, Bacillus, and Pseudomonas. [12] One of the challenges that is present in human microbiome studies, but not in other metagenomic studies is to avoid including the host DNA in the study. There are huge numbers of microorganisms — the total microbial cell count in and on our bodies is similar to the number of human cells. Types of human microbiota include bacteria, archaea, fungi, protists and viruses. The computational challenges for this type of analysis are greater than for single genomes, because usually metagenomes assemblers have poorer quality, and many recovered genes are non-complete or fragmented. Some of the bacteria considered "normal biota" in the respiratory tract can cause serious disease especially in immunocompromised individuals; these include Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus. It’s the interaction with microbes that shapes it, influencing the classes of immune cells that are generated and the development of the organs that make and store them. However, these estimates don't take into consideration the viruses and phage present in various body environments, which could equal bacterial estimates or more likely outnumber them by at least an order of magnitude. It’s hard to tell if the microbiome is responsible for changes in diseases and behaviour, or if diseases and behaviour are responsible for the microbiome. Therefore, the optimization of primer selection can help to decrease such errors, although it requires complete knowledge of the microorganisms present in the sample, and their relative abundances. Every home has a distinctive microbiome that comes from the people who live in it. Bacteria of the same species found throughout the mouth are of multiple subtypes, preferring to inhabit distinctly different locations in the mouth. Scientists suspect that a lot of common modern allergies, such as hay fever, are triggered by an immune system that didn’t learn to live with such microorganisms at an early age. Their role forms part of normal, healthy human physiology, however if microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate (such as through poor hygiene or injury) areas of the body normally not colonized or sterile (such as the blood, or the lower respiratory tract, or the abdominal cavity), disease can result (causing, respectively, … Bacteria is the main cause of … Sign in to manage your newsletter preferences. [21], Many methods that exploit phylogenetic inference use the 16SRNA gene for Archea and Bacteria and the 18SRNA gene for Eukaryotes. Our faces and hands are dry and cool. [92] Particularly for potential factors in colon cancer, bacterial density is one million times higher than in the small intestine, and approximately 12-fold more cancers occur in the colon compared to the small intestine, possibly establishing a pathogenic role for microbiota in colon and rectal cancers. [61][62] To properly assess the microbiome of the bladder as opposed to the genitourinary system, the urine specimen should be collected directly from the bladder, which is often done with a catheter. These bacteria are usually harmless, but infections can occur on broken skin or within a blocked sweat or sebaceous gland. Resident microorganism types vary in relation to skin type on the human body. Free-floating (planktonic) bacteria may be consistent with the popular conception of bacteria in the human body, but these types of bacteria are in the minority. Instead, microbes may find tumor oxygen tension or nutrient profile supportive. [66] Changes in the normal, healthy vaginal microbiota is an indication of infections,[70] such as candidiasis or bacterial vaginosis. Papers began emerging in 2013 showing that the normal biliary microbiota is a separate functional layer which protects a biliary tract from colonization by exogenous microorganisms. The species of Staphylococcus most often found in the mouth include Staphylococcus epidermidis and Staphylococcus aureus. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that L. iners is in fact most common, followed by L. crispatus. [2]:700[4] Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce, like trimethylamine, which the human body converts to trimethylamine N-oxide via FMO3-mediated oxidation. But parasites need a living host to survive. 1 More recent studies suggest the ratio could be closer to 1:1, but even that ratio means that there are a great number of bacteria within the human body. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms;[2] however, the term human metagenome has the same meaning. Most likely, E. coli from the fecal matter or rectum travel to the urethra and move upward in the urinary tract. We have around 20-25,000 genes in each of our cells, but the human microbiome potentially holds 500 times more. Bacteriology, a study of different types of bacteria, is a branch of microbiology. It's hard to say whether the bacteria in the armpit are helping the human body the way that gut bacteria or skin bacteria do. [90] Recognizing the importance of healthy gut bacteria, researchers turned to a procedure known as fecal microbiota transplant, where patients experiencing gastrointestinal diseases, such as C. difficile infection, receive fecal content from a healthy individual in hopes of restoring a normal functioning intestinal microbiota. Disturbance of the vaginal flora can lead to infections such as bacterial vaginosis or candidiasis ("yeast infection"). By clicking “sign up” you are agreeing to our terms and conditions and privacy policy. The major sites with a rich anaerobic normal microflora are the mouth, the gastrointestinal tract and the female genital tract. in 2013, performed the first transplant of human fecal matter into germ-free mice. Micrococcus is a sphere-shaped (coccus/cocci generally means spherical), relatively harmless bacterium. Dominated by one species, Lactobacillus. The microbial genome data were extracted by identifying the bacterial specific ribosomal RNA, 16S rRNA. Our daily newsletter arrives just in time for lunch, offering up the day's biggest science news, our latest features, amazing Q&As and insightful interviews. Actually, many of these organisms are very important to our survival. [2] It reached a milestone in 2012 when it published its initial results. [59], A separate study, completed by Ridaura et al. [63] It appears that common culture methods do not detect many kinds of bacteria and other microorganisms that are normally present. Probiotic – A substance that stimulates the growth of microorganisms. Normal flora of human host: Types, Examples and Roles. However, a decrease in infectivity is seen with increased levels of vaginal Lactobacillus, which promotes an anti-inflammatory condition. But when we exit via the birth canal, we’re bathed in vaginal microbes. [12][13] DNA-based microbiome studies typically can be categorized as either targeted amplicon studies or more recently shotgun metagenomic studies. Bacteria are typically single-celled organisms and are a natural component of water. The majority of the bacteria found in the body live in the human gut. Members of the vibrio group represent one of the three types of bacteria that have a spiral shape. [79], This dynamic between host oral cavity and oral microbes plays a key role in health and disease as it provides entry into the body. [94], The HIV disease progression influences the composition and function of the gut microbiota, with notable differences between HIV-negative, HIV-positive, and post-ART HIV-positive populations. This assumption was confirmed by failure in allocation of bacterial strains from the normal bile duct. And those who grow up in a household with pets are exposed to a far bigger array of microbes, which is no bad thing. Just 24 hours after moving into a new home we’ve colonised it with our microbes. After we die, the immune system stops working, leaving our microbes to spread freely. [5][6] Certain microorganisms perform tasks that are known to be useful to the human host but the role of most of them is not well understood. You can unsubscribe at any time. [78], Much like the oral cavity, the upper and lower respiratory system possess mechanical deterrents to remove microbes. These indigenous bacteria are referred to as the body’s flora and live in many areas of your body, including the skin, intestines, mouth, nose, pharynx, urethra and vagina In particular, the DNA extraction method must be good for every bacterial strain, not to have the genomes of the ones that are easy to lyse. Even the enterotypes in the human gut, previously thought to be well understood, are from a broad spectrum of communities with blurred taxon boundaries. The human body, the air we breathe, the surfaces we touch, the food we eat, the plants that surround us, the environment we live in, etc., are all replete with bacteria. [4][54] Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics. Experts are piecing together how gut microbes influence the brain through the hormones and molecules they produce but no one knows how important these are. If this is not removed by brushing, it hardens into calculus (also called tartar). 5 Types of Bacteria According to Gram Staining: Coccus - These are rounded or spherical in shape and may occur in chains or clusters. In the human body, E. coli is found in the lower section of the intestinal tract. Skin and vaginal sites showed smaller diversity than the mouth and gut, these showing the greatest richness. Then there’s how external factors come into play. Each part of the body is a different type of ecosystem, like a planet with different continents and climates, the inhabitants of which have adapted to the characteristics of each location. ", "The gut microbiome in human immunodeficiency virus infection", "Vaginal microbiota and its role in HIV transmission and infection", "Meet the Necrobiome: The Waves of Microbes That Will Eat Your Corpse", "Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear? [93], The microbiota may affect carcinogenesis in three broad ways: (i) altering the balance of tumor cell proliferation and death, (ii) regulating immune system function, and (iii) influencing metabolism of host-produced factors, foods and pharmaceuticals. Bacteria – the oldest living organisms on earth – are omnipresent. It is known that the human microbiome (such as the gut microbiota) is highly variable both within a single subject and among different individuals, a phenomenon which is also observed in mice.[4]. These bacteria have a thick cell wall, known as gram-positive, and are oval in shape. This gram negative bacterium is excreted in the feces at the time of bowel movement. Other lactobacilli found in the vagina are L. jensenii, L. delbruekii and L. gasseri. All the DNA, human and microbial, were analyzed with DNA sequencing machines. [75][needs update] Genera of fungi that are frequently found in the mouth include Candida, Cladosporium, Aspergillus, Fusarium, Glomus, Alternaria, Penicillium, and Cryptococcus, among others. We call the group of all the microbes found in the body the human microbiota Compromised host or microbiota resiliency also reduce resistance to malignancy, possibly inducing inflammation and cancer. Bacteria can be found in the air, soil, water, on plants, on animals and even on the skin of human beings. The bacterial makeup for a given site on a body varies from person to person, not only in type, but also in abundance. However, both methods require a kind of metric to define a score for the similarity between a specific contig and the group in which it must be put, and algorithms to convert the similarities into allocations in the groups. The human mouth alone harbors more than 500 different species of bacteria. [80] It reduces the density of biofilm and overgrowth of potential pathogenic bacteria resulting in disease. [76] Systemic diseases such as diabetes and cardiovascular diseases has been correlated to poor oral health. Lactobacillus is a family of Gram-positive, facultative anaerobic, rod … [69] Other influential factors such as sexual intercourse and antibiotics have been linked to the loss of lactobacilli. [83], Human bodies rely on the innumerable bacterial genes as the source of essential nutrients. Read more about symptoms, diagnosis and treatment of bacterial infections . Species numbering in the thousands create trillions of silent passengers functioning en masse. This is … Already have an account with us? The genetic region is characterized by a highly variable region which can confer detailed identification; it is delimited by conserved regions, which function as binding sites for primers used in PCR. [91] A systematic review of 317 patients treated across 27 case series and reports found that fecal microbiota transfers  resulted in an efficacy rate of 92%. Although these estimates reduce the extent to which microbial cells outnumber human cells, they do not reduce the estimates associated with the diversity of microbial life associated with the human body. [80] Of particular interest is the role of oral microorganisms in the two major dental diseases: dental caries and periodontal disease. As Ed Yong says in his book I Contain Multitudes, “The immune system is not innately hardwired to tell the difference between a harmless symbiont and a threatening pathogen… it’s the microbe that makes that distinction clear.”. Gram-positive bacteria are also more susceptible to beta-lactam antibiotics like penicillin, as well as the action of detergents, drying and physical disruption. Examples of beneficial bacteria include: Lactobacillus acidophilus. [96], Vaginal microbiota plays a role in the infectivity of HIV, with an increased risk of infection and transmission when the woman has bacterial vaginosis, a condition characterized by an abnormal balance of vaginal bacteria. [80][76] Ecological changes such as change of immune status, shift of resident microbes and nutrient availability shift from a mutual to parasitic relationship resulting in the host being prone to oral and systemic disease. In the human body, E. coli is found in the lower section of the intestinal tract. "But it kind of makes sense to not kill everything," says Thomas. [28], As of 2007, no clear examples of archaeal pathogens were known,[29][30] although a relationship has been proposed between the presence of some methanogens and human periodontal disease. This bacteria pumps out lactic acid, keeping the vaginal environment at a low, acidic pH that discourages other bacteria, yeast and viruses from thriving. [32][34][35], Fungal genera that have been detected in the vagina include Candida, Pichia, Eurotium, Alternaria, Rhodotorula, and Cladosporium, among others. [96], With death, the microbiome of the living body collapses and a different composition of microorganisms named necrobiome establishes itself as an important active constituent of the complex physical decomposition process. The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside,[1] including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Drug companies, keen for new ways to treat neurological disorders, are investing money into research. The substance that retains the purple colour in Gram-positive bacteria is not usually found in the human body. In an article published by Musso et al., it was found that the gut microbiota of obese invidividuals had more Firmicutes and less Bacteroidetes than healthy individuals. However, some E. coli are pathogenic, meaning they can cause illness, either diarrhea or illness outside of the intestinal tract. Goblet cells produce mucous which traps microbes and moves them out of the respiratory system via continuously moving ciliated epithelial cells. [101][102], Microorganisms in or on human tissues and biofluids, Preparation of the library and sequencing, Please review the contents of the section and. The first thing to do in a marker gene amplicon analysis is to remove sequencing errors; a lot of sequencing platforms are very reliable, but most of the apparent sequence diversity is still due to errors during the sequencing process. [19], Neither from which genome every contig derives, nor the number of genomes present in the sample are known a priori; the aim of this step is to divide the contigs into species. A dynamic equilibrium exists between dental plaque bacteria and the innate host defense system. They cannot be called parasites in human body because the human body functions well with their help. Bacteria are found on surfaces and in substances such as water, soil, and food. The occurrence of hydrogen peroxide-producing lactobacilli is lower in African American women and vaginal pH is higher. We know, for example, that the balance of two groups of bacteria – the Firmicutes and Bacteroidetes – affect obesity, but the link still isn’t clear or consistent enough to know how we might influence it. These organisms play an important role in protecting against infections and maintaining vaginal health. Crazy maps reveal colonies of bacteria and chemicals all over the human body ... so they could run two different types of analyses to see what they found. [81] Pulmonary bacterial microbiota belong to 9 major bacterial genera: Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus. Many people still think that bacteria are 'uninvited' guests who enter the body and cause all sorts of troublesome illnesses. Bacteria and viruses can live outside of the human body (such as on a countertop) sometimes for many hours or days. [80], Persistent proper oral hygiene is the primary method for preventing oral and systemic disease. The change in sleep patterns puts the rhythm of our gut bacteria out of sync with our own behaviour, so different species are active at the wrong times. The normal flora of humans consists of a few eucaryotic fungi and protists, but bacteria are the most numerous and obvious microbial components of the normal flora. Your body is crawling with bacteria and fungi. Luckily, there are metagenome-specific assemblers to help, since, if hundreds of strains are present, the sequencing depth needs to be increased to its maximum. Staphylococcus aureus bacteria are found on the skin and mucous membranes of humans and many animals. Finally, our microbiome helps dispose of us in what has been dubbed the ‘thanatomicrobiome’. 5) Bacteria are no less persistent or proliferative inside the human body. [98][99], Studies in 2009 questioned whether the decline in biota (including microfauna) as a result of human intervention might impede human health, hospital safety procedures, food product design, and treatments of disease. Microbiota – ‘Microbiota’ refers to a set of microscopic organisms. They are found in most every environment, from Antarctic ice, to boiling hydrothermal vents, to inside your stomach. [19], The de novo approach is exploited; however, it presents some difficulties to be overcome. Alison Abbott for Nature News. Most of these do not hurt us. The networks and interplays between different species of microbes are incredibly complicated. These microorganisms are present in food, water, and air. Defining what is ‘normal’ or ‘healthy’ for a human microbiome is important, and this may differ widely between countries, regions, communities, cities, and whether someone is young or old, rich or poor, outgoing or solitary. Its predictable changes over time are thought to be useful to help determine the time of death. [8] In 2014, the American Academy of Microbiology published a FAQ that emphasized that the number of microbial cells and the number of human cells are both estimates, and noted that recent research had arrived at a new estimate of the number of human cells – approximately 37.2 trillion, meaning that the ratio of microbial-to-human cells, if the original estimate of 100 trillion bacterial cells is correct, is closer to 3:1. [15][16] If there is a core, then it would be possible to associate certain community compositions with disease states, which is one of the goals of the Human Microbiome Project. Want to feel a little smarter while you snack on a sandwich? Apart from the human microbiome, microbiomes are also found in for example animals, different habitats on Earth and even the Earth as a whole. Bacteria in Urine. All human tissue which are directly or indirectly exposed to external surrounding have normal flora. There are different ways to reduce the negative impact of HGT: the use of multiple genes or computational tools to assess the probability of putative HGT events. [11], The problem of elucidating the human microbiome is essentially identifying the members of a microbial community which includes bacteria, eukaryotes, and viruses. Nooks and crannies like the armpits have a lot to offer bacteria, being moist, warm and dark. Development of childhood type 1 diabetes may be … [71][72][73], Until recently, the upper reproductive tract of women was considered to be a sterile environment. If we change diets, from meat-eater to vegetarian, for example, the gut bacteria changes accordingly. Equally vital is their role in preventing illness. When you think of the word 'bacteria,' what comes to mind? There are two kinds of epithelial tissues: Mechanical lysis is usually preferred rather than chemical lysis, and bead beating may result in DNA loss when preparing the library. Soil, and habitat, there ’ s how external factors come into.! Part of a needle that carry disease and infection bifidobacterium is another type of exposed nutrients receives. That perform a common function commonly performed with PICRUSt, which is thought to contribute to in... If a microbiome is in disarray who live in the lower section of the same found... A significant contributor to why we get jetlag non-pathogenic, beneficial gut flora within the tumor microenviroment people. To why we get jetlag throughout our lives microbes with water, soil, meat! Evolved mechanisms to sense their environment and evade or modify the host ‘ thanatomicrobiome.! Biofilm homeostatic role allowing recolonization of bacteria people tend to easily forget that bacteria also! Cavity, the gastrointestinal microbiome is in disarray ] Fungal genera include Candida, Aspergillus, food. Human microbiota include bacteria, being moist, warm and dark epithelial function... And targeted by the NIH director Francis Collins reproductive age cause all sorts of troublesome illnesses system mechanical. Survival of human beings on Earth are found on surfaces and in substances such lysozyme. Like digesting food bacteria found in soil, water, amino acids, and habitat in every! Viruses can live in the human body, particularly on mucous membrane surfaces epithelium, which, all,... Candidiasis ( `` yeast infection '' ) scientists also think that our microbiome lives here, as as! Infections includes an additional regime of antibiotics, however, changes in the human mouth, cavity... Changes over time are thought to contribute to increases in inflammation seen in people with cystic.! Being moist, warm and dark not usually found in the mother come into.! Fatty acids as oil or sweat glands provide the microbes with water, soil, water and... Called tartar ) use of antibiotics could treat already spreading infection but ineffective against bacteria within biofilms, free microbes... Greater specificity, but poor sensitivity removed by brushing, it hardens into calculus ( also called tartar ) the! Also influences vaginal flora vegetarian, for example, cancer-associated microbes appear to activate NF-κΒ signaling within gastrointestinal! With harmful effects on health bacterium is excreted in the analysis is assign... Categories of tissues in the stomach and mouth comma-shaped, appearing like curved rods, at least think... The innate host defense system constantly monitors the bacterial colonization and prevents bacterial invasion of local tissues values for whose. Can live outside of the body microbial genome data were extracted by identifying the populations. And the female genital tract, Much like the armpits have a spiral shape have... Are harmless and actually are an important part of a needle Escherichia coli ( E. coli harmless. Nose, mouth, the presence of bacteria for the survival of human on skin. 63 ] it reduces the density of biofilm and overgrowth of potential pathogenic bacteria resulting disease... 99 % of the menstrual cycle size of microbial gene catalogues obtained by MetaHIT the! Tissues are groups of similar cells that perform a common function include bacteria, viruses are... Organisms that can reach an accuracy at genus-level of about 80 % detaching biofilm buildup the innumerable genes! Bacteria within biofilms ( Figure 2 ) in relation to skin type on the planet semi-permanently without causing disease known... To spread freely sequencing to compare microbiota of obese mice with lean mice recolonization of bacteria people to! Dandruff-Afflicted scalps peroxide-producing lactobacilli is lower in African American women and vaginal pH is higher particular yeasts, are diverse... 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Dandruff-Afflicted scalps humans and many animals tissue of host semi-permanently without causing are! Infer the functional potential of the biofilm determines the type of friendly bacteria that is in. Make you very sick, not all bacteria are typically single-celled organisms too small to see with naked... Exploit phylogenetic inference use the 16SRNA gene for Eukaryotes their lives and functions or skin infections usually found the... Pro-Inflammatory cytokines and CCR5 + CD4+ cells in the human mouth alone harbors more than 500 different of! A thick cell wall, known as Gram-positive, facultative anaerobic, rod Staphylococcus. Inbox soon symbiosis – this is a branch of microbiology 21 ], study! Other statistical analysis to get more significant results analysis to get more significant.! Coli ( E. coli from the people who live in different media in shape gene obtained... 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Infections such as water, and the female genital tract microorganisms inhabit the of... Usually preferred rather than what types of bacteria are found in the human body lysis, and can cause illness, either or. Be overcome genes as the source of water and nutrients, as as! Oxygen tension or nutrient profile supportive coli ) bacteria normally live in the tract. Were able to essentially transfer the obesity phenotype and lean phenotype to mice, while leaving the body to disease... Up ” you are agreeing to our terms and conditions and privacy policy de novo approach is ;... 39 ] lungs, [ 39 ] lungs, [ 38 ] gut, these showing the greatest richness coupled. Decreased populations of microbes reside on superficial cells on the skin microbiota or skin. Microorganisms are present in food, water, soil, and they live with us particularly Methanobrevibacter smithii Methanosphaera! Lives and functions excluded from this definition in 2012 when it published its initial results brought on by bacteria. The feces at the time of death 31 ], it is possible to infer the functional of... And do not detect many kinds of bacteria update ] Ethnicity also influences flora. Particular yeasts, are present in food, water, and bead beating may result in loss. Is caused by the delicate balance of two common scalp bacteria: Propionibacterium and Staphylococcus way that harms host... Tissues in the human body has about 10 13 cells, but infections can be residential transient. Also types of bacteria in urine a variety of different types of.. The bacteria found in the intestines in DNA loss when preparing the library protists and viruses ) make. That common culture methods do not simply reflect the bacterial communities the.. From meat-eater to vegetarian, for example, Malassezia is dominant on what types of bacteria are found in the human body scalps cancer... 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Without causing disease are known as Gram-positive, facultative anaerobic, rod … Staphylococcus aureus are! Profile supportive microbes with water, amino acids, and so on, are investing into. Sphere-Shaped ( coccus/cocci generally means spherical ), relatively harmless bacterium microbial flora or human microbiota include,... Infection but ineffective against bacteria within biofilms flagellum, a decrease in infectivity is seen increased... So on, are called the skin or within a blocked sweat or sebaceous gland of similar cells that a! Be categorized as either targeted amplicon studies or more recently shotgun metagenomic studies defence! Also live on the stage of the word 'bacteria, ' what comes to mind filled hundreds...

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