The human microbiome in sickness and in health

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Requena, M. Velasco" "autores" => array:2 [ 0 => array:4 [ "nombre" => "T." "apellidos" => "Requena" "email" => array:1 [ 0 => "t.requena@csic.es" ] "referencia" => array:2 [ 0 => array:2 [ "etiqueta" => "a" "identificador" => "aff0005" ] 1 => array:2 [ "etiqueta" => "*" "identificador" => "cor0005" ] ] ] 1 => array:3 [ "nombre" => "M." 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Human microbial colonization occurs in the skin and mucous membranes of cavities exposed to the exterior, such as the gastrointestinal, respiratory and genitourinary tracts and secretory glands such as the sebaceous, biliary and mammary. In all of these environments, microbiota establish a symbiotic relationship with the host, providing early modulation of the host’s physiological development and the nutrition, immune and pathogen resistance functions in all stages of life.<a class="elsevierStyleCrossRef" href="#bib0010">2</a>Lifestyle (including geographical and ethnic factors), genetics, age and diet are the main regulators for the composition and functionality of human microbiota.<a class="elsevierStyleCrossRefs" href="#bib0015">3–5</a> The recent association between the increase in autoimmune diseases and allergies and the reduction in the incidence of infectious diseases in developed countries, also related to the abuse of antibiotics and lower exposure to microorganisms, has contributed to the concept that a lack of immune system stimuli in the initial stages of life jeopardizes the ability to recognize threats and calibrate the level of microbial tolerance.<a class="elsevierStyleCrossRefs" href="#bib0010">2,6</a> Early microbial exposure has a critical role in the development of the immune, endocrine, metabolic and nervous systems.<a class="elsevierStyleCrossRef" href="#bib0035">7</a> The microbiota of healthy newborns is similar to the mother’s intestinal, vaginal and skin microbiota, with a predominance of certain microbial groups depending on the birthing method.<a class="elsevierStyleCrossRef" href="#bib0040">8</a> The first colonizers of the intestine in childhood are facultative anaerobes that are successively replaced by obligate anaerobes, led by Bifidobacterium, Bacteroides and Clostridium. During the first 6 months of life, the main taxon associated with a healthy state is Bifidobacterium longum.<a class="elsevierStyleCrossRef" href="#bib0045">9</a> During breastfeeding, the supply of microorganisms and indigestible oligosaccharides through breast milk contributes to establishing a healthy intestinal microbiota, which is also effective in facilitating a faster hospital discharge for premature infants.<a class="elsevierStyleCrossRef" href="#bib0050">10</a>In addition to the importance of appropriate immune system training in the first stages of life, recent studies of microbiota disorders (dysbiosis) and their association with certain disease conditions have indicated that the reduction in microbial diversity is one of the aspects that contributes to the onset of disease.<a class="elsevierStyleCrossRef" href="#bib0055">11</a> In ecological terms, species diversity and richness are important in the concepts of functional redundancy and resilience (the ability to tolerate particular environmental challenges). The reduction in species diversity in the human microbiome has been related to an increase in diseases such as inflammatory bowel disease, obesity, acute otitis media, chronic rhinosinusitis and urinary tract infection.<a class="elsevierStyleCrossRef" href="#bib0025">5</a> Infection by Clostridioides difficile (formerly known as Clostridium difficile) is typically associated with antibiotic therapy and the subsequent loss of intestinal microbial diversity.<a class="elsevierStyleCrossRef" href="#bib0060">12</a> In the context of intestinal microbiota, the increase in dietary intake of foods rich in calories and refined sugar has been associated with less diverse microbial communities than in individuals who consume fiber-rich diets.<a class="elsevierStyleCrossRef" href="#bib0020">4</a>Skin microbiotaA considerable variety of microorganisms are deposited on and subsequently colonize the skin, depending on the various body regions and conditions of moisture, pH and sebaceous production, among other factors.<a class="elsevierStyleCrossRef" href="#bib0065">13</a> Microbial colonization has also been reported in hair follicles and sebaceous glands.<a class="elsevierStyleCrossRef" href="#bib0070">14</a> The driest areas of the skin are coated especially by Staphylococcus, while the sebaceous areas are dominated by lipophilic species of Propionibacterium. The most humid regions, such as the folds of the arms and legs, are dominated by Corynebacterium.<a class="elsevierStyleCrossRef" href="#bib0075">15</a> Skin microbiota provide barrier functions against colonization by pathogens through immune response modulation using keratinocytes and by taking efficient advantage of the nutrients from skin secretions, resulting in the production of antimicrobial peptides and organic acids that participate in reducing skin pH.<a class="elsevierStyleCrossRef" href="#bib0065">13</a>A number of skin microbiota microorganisms can be opportunistic pathogens under certain conditions. The presence of wounds or a state of immunosuppression can result in the pathogenic behavior of Staphylococcus epidermidis (S. epidermidis).<a class="elsevierStyleCrossRef" href="#bib0080">16</a> Certain skin disorders, such as psoriasis, atopic dermatitis, acne, dandruff and slow-to-heal wounds, are associated with microbiological changes.<a class="elsevierStyleCrossRef" href="#bib0070">14</a>Cutibacterium acnes (formerly known as Propionibacterium acnes) is typically found in the microbiota of healthy individuals but usually predominates during puberty due to increased sebaceous secretion, causing chronic skin inflammation.<a class="elsevierStyleCrossRef" href="#bib0085">17</a>Staphylococcus aureus (S. aureus) is usually associated with atopic dermatitis, particularly during the intensification of an active disease and due to a reduction in diversity of skin microbiota.<a class="elsevierStyleCrossRef" href="#bib0065">13</a> It has also been reported that microbiota associated with chronic injuries persist in forming biofilms that impede healing and increased resistance to antibiotic therapy.<a class="elsevierStyleCrossRef" href="#bib0090">18</a> A number of studies have also correlated the differences in skin microbiota with the attraction of malaria-transmitting Anopheles mosquitoes.<a class="elsevierStyleCrossRef" href="#bib0095">19</a>Airway microbiotaThe respiratory tract contains microbial communities from the nasal fossae to the pulmonary alveolus, with the highest concentrations found in the upper airways.<a class="elsevierStyleCrossRef" href="#bib0100">20</a> This autochthonous microbiota contributes to the defense against colonization and infection by pathogens in the respiratory mucosa and thereby prevents their advance throughout the tract. Conditions with increased relative humidity and temperature from the nasal cavity to the interior, as well as partial oxygen and carbon dioxide pressures with opposite gradients, affect specific populations that are characteristic to each defined niche in this tract. Nose microbiota are similar to skin microbiota, in which Staphylococcus, Propionibacterium and Corynebacterium predominate. Nasopharyngeal microbiota are more varied and diverse and contain Haemophilus and Streptococcus, as well as the genera representative of the anterior region. In the oropharynx, the bacterial communities are also diverse and include Streptococcus, Neisseria and anaerobes such as Veillonella and Prevotella.<a class="elsevierStyleCrossRef" href="#bib0100">20</a> Lung microbiota, in healthy conditions, consist of a transient community of microorganisms mainly from the nasopharynx and oropharynx and are the result of the balance between microorganisms that travel to this region and are eliminated.<a class="elsevierStyleCrossRef" href="#bib0105">21</a>Specific members of the nasopharyngeal niche microbiota have been identified, which can actively exclude respiratory pathogens, such as the ability of S. epidermidis to exclude S. aureus through the secretion of serine-proteases that eliminate the biofilms created by the pathogen.<a class="elsevierStyleCrossRef" href="#bib0110">22</a> Other components of the autochthonous microbiota of the upper airways, such as Dolosigranulum and Corynebacterium, have been associated with respiratory health and the exclusion of Streptococcus pneumoniae.<a class="elsevierStyleCrossRefs" href="#bib0115">23,24</a> The predominance of Moraxella, Streptococcus and Haemophilus in the nasopharynx has been associated with acute respiratory infections in children and a risk of bronchiolitis and pneumonia.<a class="elsevierStyleCrossRefs" href="#bib0125">25,26</a>The excessive growth of a certain bacterial species can lead to a reduction in lung microbiota richness and has been associated with the progression of diseases such as cystic fibrosis and infections related to this disease. A number of studies have shown the presence of predatory bacteria in the microbiota of lungs affected by cystic fibrosis, such as Bdellovibrio and Vampirovibrio, which could contribute to controlling the chronic colonization of pathogenic bacteria.<a class="elsevierStyleCrossRef" href="#bib0135">27</a>Female and reproductive system microbiotaThe idea that breastmilk is a sterile fluid in physiological conditions has been substituted by the growing recognition that it contains a commensal or potentially probiotic microbiota for the infant’s health.<a class="elsevierStyleCrossRef" href="#bib0140">28</a> Breastmilk microbiota is fairly diverse in terms of bacteria genera and species, although usually in relatively low concentrations (10–1000 bacteria per mL). The microbiota is usually dominated by skin-related genera such as Staphylococcus, Streptococcus, Corynebacterium and Propionibacterium; however, lactic acid bacteria (Lactobacillus, Lactococcus, Leuconostoc, Weissella, Enterococcus) and bifidobacteria can also be found, and new species such as Streptococcus lactarius have been isolated.<a class="elsevierStyleCrossRef" href="#bib0145">29</a> DNA from obligate anaerobes of intestinal origin, such as Bacteroides, Clostridium, Coprococcus, Faecalibacterium and Roseburia, have also been found in breastmilk.<a class="elsevierStyleCrossRef" href="#bib0150">30</a> The transfer of microorganisms by the enteromammary pathway from the intestine to breastmilk has been reported and has been associated with increased intestinal patency, decreased peristalsis and weakening of the barriers against bacterial development during the final gestation period, which promotes microbial translocation.<a class="elsevierStyleCrossRef" href="#bib0155">31</a>There are studies that have reported the presence in breastmilk of probiotic strains supplemented orally for treating lactational mastitis.<a class="elsevierStyleCrossRef" href="#bib0160">32</a> In fact, the etiopathogenesis of mastitis has been related to a process of dysbiosis or imbalance in bacterial diversity in the mammary gland, which results in an overgrowth of species that cause infection, accompanied by a reduction in other species present physiologically in breastmilk.<a class="elsevierStyleCrossRef" href="#bib0165">33</a> A number of microbial genera that predominate in cancerous breast tissue have also been reported, such as Fusobacterium, Atopobium, Hydrogenophaga and Gluconacetobacter.<a class="elsevierStyleCrossRef" href="#bib0170">34</a>Fusobacterium has been associated with other cancerous conditions in epithelial cells (such as colon cancer), related to its capacity to secrete virulence factors and promote proinflammatory conditions.<a class="elsevierStyleCrossRef" href="#bib0175">35</a>In the female reproductive tract, the vagina contains a specific microbiota represented mainly by Lactobacillus, which is associated with a healthy condition and that reaches the highest proportions in pregnant women with full-term childbirth.<a class="elsevierStyleCrossRef" href="#bib0180">36</a> In smaller proportions, microbiota associated with skin and the intestinal tract can also be found, such as Prevotella, Gardnerella, Atopobium, Sneathia, Bifidobacterium, Megasphaera and Anaerococcus.<a class="elsevierStyleCrossRef" href="#bib0185">37</a> Lactobacilli in the vagina are particularly associated with childbearing age, due to the production of estrogen, which promotes mucosal thickening and glycogen accumulation, which in turn are used by the lactobacilli to produce lactic acid, acidifying the environment to pH values between 4 and 4.5 and acting as a barrier to colonization by other microorganisms. In the vaginal context, the increase in bacterial diversity, with the increase in the proportion of anaerobes such as Gardnerella, Prevotella, Megasphaera, Atopobium and Dialister to the detriment of the lactobacilli, is associated with an increased risk of bacterial vaginosis.<a class="elsevierStyleCrossRef" href="#bib0190">38</a> The microbiota present in the endometrium is also characterized by the presence of Lactobacillus, Gardnerella vaginalis and Enterobacter but in less abundant quantities than in the vagina (approximately 4 logarithmic units fewer), possibly halted by the cervical barrier and by a more effective immune response in the internal organs of the reproductive tract.<a class="elsevierStyleCrossRef" href="#bib0195">39</a> The proliferation of enterobacteria, Enterococcus and Streptococcus has been related to endometriosis,<a class="elsevierStyleCrossRef" href="#bib0200">40</a> and an increase in Gardnerella has been associated with premature birth and obstetric complications,<a class="elsevierStyleCrossRef" href="#bib0180">36</a> as well as a reduced effect of tenofovir used in pre-exposure prophylaxis for HIV infection.<a class="elsevierStyleCrossRef" href="#bib0205">41</a> The increase in bacterial diversity in the female reproductive tract to the detriment of lactobacilli has been correlated with a lower pregnancy rate in assisted reproduction procedures.<a class="elsevierStyleCrossRef" href="#bib0185">37</a>The microbiota of the male reproductive tract has been less studied than that of women. Although bacteriospermia has classically been negatively associated with fertility, the most recent studies have demonstrated that the presence of Lactobacillus in semen is relatively frequent in fertile individuals with normal sperm parameters, while the predominance of Prevotella is associated with motility defects.<a class="elsevierStyleCrossRef" href="#bib0210">42</a> Similar to vaginal microbiota, a lesser diversity of seminal microbiota appears to be related to a healthy condition. Thus, patients with prostatitis have been reported to have a lower lactobacilli concentration and greater diversity of bacterial species in the semen than healthy individuals.<a class="elsevierStyleCrossRef" href="#bib0215">43</a> A specific prostate microbiota has also been defined for healthy or tumor tissue,<a class="elsevierStyleCrossRef" href="#bib0220">44</a> as well a relationship between urinary microbiota and chronic prostate inflammation.<a class="elsevierStyleCrossRef" href="#bib0225">45</a> The increase in anaerobes in the microbiota of the penis has recently been linked with a more effective transmission of the HIV infection.<a class="elsevierStyleCrossRef" href="#bib0230">46</a>Oral and gastrointestinal tract microbiotaOral cavityThe oral cavity has an abundant and diverse microbiota that is specific for the various niches represented by the tongue, palate, teeth and gums. Saliva is considered representative of the oral microbiota because it performs a cleaning effect on all oral surfaces and provides nutrients such as proteins, glycoproteins, peptides and vitamins. In addition, saliva has an effective buffering capacity that provides neutral pH conditions (between 6.7 and 7.2). There is a representative microbiota of the oral cavity in which Streptococcus, Gemella, Granulicatella, Neisseria and Prevotella predominate. There are also species adapted to specific niches, such as Rothia, which colonizes the tongue and teeth, and Simonsiella, which is located in the hard palate.<a class="elsevierStyleCrossRef" href="#bib0235">47</a> There are also bacterial groups associated with oral diseases such as caries, periodontal disease and halitosis.<a class="elsevierStyleCrossRef" href="#bib0240">48</a> The increase in consumption of simple carbohydrates in the human diet has been related to an increase in caries due to the fermentative activity and acidic production of oral microbiota, particularly Streptococcus mutans (S. mutans), Veillonella and Lactobacillus.<a class="elsevierStyleCrossRef" href="#bib0245">49</a>Streptococcus dentisani is a recently reported species whose abundance is inversely related to the onset of caries and is characterized by the growth inhibition of S. mutans and by the pH neutralization of dental plaque.<a class="elsevierStyleCrossRef" href="#bib0250">50</a>StomachThe stomach’s acidic pH prevents bacterial growth; microbial concentrations are therefore usually below 103 bacteria per mL of gastric content. The most abundant groups are Streptococcus, Lactobacillus, Prevotella, Porphyromonas, Rothia, Atopobium and Fusobacterium nucleatum (F. nucleatum), which come from the oral cavity and that represent transient acid-resistant microbiota.<a class="elsevierStyleCrossRef" href="#bib0255">51</a>Helicobacter pylori (H. pylori) usually resides in the stomach mucosa and is protected from stomach acid through the production of urease activity.<a class="elsevierStyleCrossRef" href="#bib0260">52</a> Despite clear evidence that H. pylori is a human pathogen, there are studies that have suggested that it could also be considered a commensal bacteria given that it is typically present in healthy individuals without generating symptoms or diseases and that it modulates the immune response of the mucosa.<a class="elsevierStyleCrossRef" href="#bib0265">53</a> The ability of H. pylori to produce peptic ulcers and gastric adenocarcinoma is associated with strains that express virulence factors such as CagA and Cgt, which block the host’s immune response.<a class="elsevierStyleCrossRef" href="#bib0270">54</a>Small intestineWithin the gastrointestinal tract, the small intestine is the longest region and has the greatest changes in environmental conditions, which results in differing microbial concentrations (an increase from 104 to 108 microorganisms per mL of intestinal content from the jejunum to ileum).<a class="elsevierStyleCrossRef" href="#bib0275">55</a> Microbiota colonization in the small intestine is limited by the short time the intestinal content resides there, the high peristalsis, the continuous renewal of the intestinal mucosa, the entry of bile salts and pancreatic secretions and the secretion of antimicrobial components in the mucosa (defensins, cathelicidin, C-type lectins, etc.). Neutral pH conditions and oxygen pressure cause more abundant populations in proximal areas of the small intestine corresponding to facultative anaerobes and decrease the proportion as the reducing conditions in the distal areas increase. A study of the microbiota in the ileum reveals the abundance of Lactobacillales, Clostridiales, Veillonella and Streptococcus and, to a lesser extent, Ruminococcus and Bacteroides.<a class="elsevierStyleCrossRef" href="#bib0280">56</a>Small intestine bacterial overgrowth, established by counts >105 bacteria per mL of jejunal content, can cause various nonspecific gastrointestinal symptoms such as distension, flatulence, abdominal pain, diarrhea, dyspepsia and weight loss.<a class="elsevierStyleCrossRef" href="#bib0285">57</a> Celiac disease has been associated with dysbiosis of the small intestine microbiota.<a class="elsevierStyleCrossRef" href="#bib0290">58</a> The disease is characterized by lower microbial diversity in patients with celiac disease, with a reduced relative abundance of Streptococcus and Prevotella and higher levels of Proteobacteria.<a class="elsevierStyleCrossRef" href="#bib0295">59</a> However, studies have not been conducted to establish the causality of changes in microbiota with the disease, and it is not known whether the observed changes are the consequence of small intestine inflammation.Large intestineThe large intestine has the highest microbial density in the human body, reaching 1010 microorganisms per mL of intestinal content. Most of the identified microbial groups are bacteria belonging to the Bacteroidetes and Firmicutes phyla (approximately 90%), along with others such as Proteobacteria, Actinobacteria, Fusobacteria and Verrucomicrobia. The genera Bacteroides, Faecalibacterium and Bifidobacterium are the most abundant in the large intestine<a class="elsevierStyleCrossRef" href="#bib0300">60</a> and are mostly obligate anaerobic microorganisms. Some of the reported species have been found only in this environment, which reflects a specific level of adaptation to the intestinal niche.<a class="elsevierStyleCrossRef" href="#bib0305">61</a> This microbiota plays an important metabolic and protective role, particularly in metabolizing indigestible material in the diet, especially indigestible carbohydrates, producing vitamins and some essential nutrients and acting as a barrier to infections by pathogenic bacteria. The microbiota also has an important modulator effect on the host’s immune and endocrine response and acts on the secretion of neurotransmitters that provide communication between the intestine and brain.<a class="elsevierStyleCrossRef" href="#bib0310">62</a> Even so, a common microbiota nucleus shared among all individuals related to a healthy state has not been defined, beyond the observation that a reduction in microbial diversity is associated with certain diseases.<a class="elsevierStyleCrossRef" href="#bib0055">11</a> Diseases such as inflammatory bowel disease, colorectal cancer, obesity, type 2 diabetes and nonalcoholic steatohepatitis have been associated with changes in the composition of intestinal microbiota.<a class="elsevierStyleCrossRef" href="#bib0025">5</a> In most studies, however, these were noncausal associations, or the results differed among the various research groups. Moreover, individuals with high adiposity, insulin and leptin resistance and an inflammatory phenotype are characterized by a low richness of microbial genes (below 400,000) in feces.<a class="elsevierStyleCrossRef" href="#bib0315">63</a>A number of microbial species that colonize the intestinal mucosa, such as Akkermansia muciniphila, have been associated with a healthy metabolic state, glucose and adipose tissue homeostasis,<a class="elsevierStyleCrossRef" href="#bib0320">64</a> improved inflammatory processes<a class="elsevierStyleCrossRef" href="#bib0325">65</a> and healing of intestinal mucosa injuries.<a class="elsevierStyleCrossRef" href="#bib0330">66</a>Faecalibacterium prausnitzii is another component of the intestinal microbiota with anti-inflammatory properties.<a class="elsevierStyleCrossRef" href="#bib0335">67</a> On the other hand, the formation of biofilms by Bacteroides fragilis has been associated with inflamed areas in patients with inflammatory bowel disease.<a class="elsevierStyleCrossRef" href="#bib0340">68</a>Fusobacterium nucleatum is an anaerobic species that is part of the oral and intestinal mucosa and has been associated in numerous studies with the neoplastic processes of colon cancer.<a class="elsevierStyleCrossRef" href="#bib0345">69</a> The production of trimethylamine, trimethylamine oxide, secondary bile acids and indoxyl sulfate by intestinal microbiota has been associated with the development and progression of cardiovascular diseases, including heart failure.<a class="elsevierStyleCrossRef" href="#bib0350">70</a>BrainThe recent observation by electron microscopy in human brain slices of bacteria associated with astrocytes, without being related to an infection, has been tentatively alluded to as evidence of a brain microbiome.<a class="elsevierStyleCrossRef" href="#bib0355">71</a> Although the study results need to be scientifically confirmed, it is generally accepted that the metabolic activity of the intestinal microbiota affects the brain.<a class="elsevierStyleCrossRef" href="#bib0310">62</a> It has been reported that intestinal bacteria can synthesize neurotransmitters such as serotonin, gamma-aminobutyric acid, norepinephrine, dopamine and acetylcholine.<a class="elsevierStyleCrossRef" href="#bib0360">72</a> There is also evidence that psychotropic drugs have a significant impact on intestinal microbiota.<a class="elsevierStyleCrossRef" href="#bib0310">62</a> Beyond the studies performed on laboratory animals, the main impact of intestinal dysbiosis on the brain reported in humans is its association with depression.<a class="elsevierStyleCrossRef" href="#bib0365">73</a> Patients with acute depression are characterized by low intestinal levels of Faecalibacterium compared with healthy controls and patients with depression who respond to treatment. Fecal microbiota transplantation from individuals with depression to axenic mice has been observed to result in phenotypes lacking appetite and with lower serotonin production.<a class="elsevierStyleCrossRef" href="#bib0370">74</a> A study of 1054 individuals observed that the genera Coprococcus and Dialister were missing in patients with depression, regardless of whether they took antidepressants.<a class="elsevierStyleCrossRef" href="#bib0375">75</a> Moreover, Faecalibacterium and Coprococcus were consistently associated with indicators of better quality of life and increased production of gamma-aminobutyric acid and dopamine metabolites. Differences have also been observed in the composition and functionality of the intestinal microbiota of patients with behavioral disorders such as autism spectrum disorder, learning difficulties, eating disorders and addictions<a class="elsevierStyleCrossRef" href="#bib0310">62</a> and with neurodegenerative diseases such as Parkinson's and Alzheimer's disease.<a class="elsevierStyleCrossRef" href="#bib0380">76</a> A study correlated the changes in the intestinal bacterial metabolome with autonomous nervous system disorders and the development of arterial hypertension.<a class="elsevierStyleCrossRef" href="#bib0385">77</a>ConclusionsAn exhaustive understanding of the components of human microbiota can open a broad range of opportunities for research on their role in health and thus channel the possibilities for microbial modulation. The assessment and manipulation of microbiota can extend the options for tailored medicine. In the future, it might be possible to use these techniques in the diagnosis (changes in microbiomes in the presence of subclinical diseases), prevention (displacement of multiresistant colonic bacteria) and treatment (fecal microbiota transplantation and bacteriotherapy) of certain diseases. Although the phylogenetic and functional diversity of microbiota is associated with better health conditions, further progress is needed to establish biomarkers that help recognize healthy states associated with the microbiota. We need further studies that enable metagenomic analysis at the functional level.FundingThe author would like to thank the Ministry of Science, Innovation and Universities of Spain for funding this study through projects AGL2016-75951-R, PCIN-2017-075 and AGL2004-07285-C02." "textoCompletoSecciones" => array:1 [ "secciones" => array:12 [ 0 => array:3 [ "identificador" => "xres1493211" "titulo" => "Abstract" "secciones" => array:1 [ 0 => array:1 [ "identificador" => "abst0005" ] ] ] 1 => array:2 [ "identificador" => "xpalclavsec1355856" "titulo" => "Keywords" ] 2 => array:3 [ "identificador" => "xres1493212" "titulo" => "Resumen" "secciones" => array:1 [ 0 => array:1 [ "identificador" => "abst0010" ] ] ] 3 => array:2 [ "identificador" => "xpalclavsec1355855" "titulo" => "Palabras clave" ] 4 => array:2 [ "identificador" => "sec0005" "titulo" => "Background" ] 5 => array:2 [ "identificador" => "sec0010" "titulo" => "Skin microbiota" ] 6 => array:2 [ "identificador" => "sec0015" "titulo" => "Airway microbiota" ] 7 => array:2 [ "identificador" => "sec0020" "titulo" => "Female and reproductive system microbiota" ] 8 => array:3 [ "identificador" => "sec0025" "titulo" => "Oral and gastrointestinal tract microbiota" "secciones" => array:5 [ 0 => array:2 [ "identificador" => "sec0030" "titulo" => "Oral cavity" ] 1 => array:2 [ "identificador" => "sec0035" "titulo" => "Stomach" ] 2 => array:2 [ "identificador" => "sec0040" "titulo" => "Small intestine" ] 3 => array:2 [ "identificador" => "sec0045" "titulo" => "Large intestine" ] 4 => array:2 [ "identificador" => "sec0050" "titulo" => "Brain" ] ] ] 9 => array:2 [ "identificador" => "sec0055" "titulo" => "Conclusions" ] 10 => array:2 [ "identificador" => "sec0060" "titulo" => "Funding" ] 11 => array:1 [ "titulo" => "References" ] ] ] "pdfFichero" => "main.pdf" "tienePdf" => true "fechaRecibido" => "2019-07-02" "fechaAceptado" => "2019-07-08" "PalabrasClave" => array:2 [ "en" => array:1 [ 0 => array:4 [ "clase" => "keyword" "titulo" => "Keywords" "identificador" => "xpalclavsec1355856" "palabras" => array:4 [ 0 => "Microbiome" 1 => "Homeostasis" 2 => "Symbiosis" 3 => "Disease" ] ] ] "es" => array:1 [ 0 => array:4 [ "clase" => "keyword" "titulo" => "Palabras clave" "identificador" => "xpalclavsec1355855" "palabras" => array:4 [ 0 => "Microbioma" 1 => "Homeostasis" 2 => "Simbiosis" 3 => "Enfermedad" ] ] ] ] "tieneResumen" => true "resumen" => array:2 [ "en" => array:2 [ "titulo" => "Abstract" "resumen" => "The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life. Human microbial colonization occurs in the skin, genitourinary system and, mainly, in the oral cavity and intestinal tract. In these locations, the human microbiota establishes a symbiotic relationship with the host and helps maintain physiological homeostasis. Lifestyle, age, diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota. Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases. In addition to phylogenetic diversity studies, further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health." ] "es" => array:2 [ "titulo" => "Resumen" "resumen" => "El estudio del microbioma humano ha incrementado de manera excepcional el conocimiento actual del que disponemos sobre la importancia de la microbiota en la salud durante todas las etapas de la vida. La colonización microbiana humana ocurre en la piel, en el sistema genitourinario y, principalmente, en la cavidad oral y el tracto intestinal. En todos estos lugares, la microbiota humana establece una relación simbiótica con el hospedador y ayuda a mantener la homeostasis fisiológica. El estilo de vida, la edad, la dieta y el uso de antibióticos son los principales reguladores de la composición y la funcionalidad de la microbiota humana. Estudios recientes apuntan al descenso de la diversidad microbiana como uno de los aspectos que contribuye al desarrollo de enfermedades. Además de los estudios de diversidad filogenética, es necesario profundizar en estudios metagenómicos a nivel funcional del microbioma humano para mejorar el conocimiento sobre su participación en la salud humana." ] ] "NotaPie" => array:1 [ 0 => array:2 [ "etiqueta" => "☆" "nota" => "Please cite this article as: Requena T, Velasco M. Microbioma humano en la salud y la enfermedad. Rev Clin Esp. 2021;221:233–240." ] ] "multimedia" => array:1 [ 0 => array:8 [ "identificador" => "tbl0005" "etiqueta" => "Table 1" "tipo" => "MULTIMEDIATABLA" "mostrarFloat" => true "mostrarDisplay" => false "detalles" => array:1 [ 0 => array:3 [ "identificador" => "at0005" "detalle" => "Table " "rol" => "short" ] ] "tabla" => array:1 [ "tablatextoimagen" => array:1 [ 0 => array:2 [ "tabla" => array:1 [ 0 => """ <table border="0" frame="\n \t\t\t\t\tvoid\n \t\t\t\t" class=""><thead title="thead"><tr title="table-row"><th class="td" title="\n \t\t\t\t\ttable-head\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t" scope="col" style="border-bottom: 2px solid black">Concept \t\t\t\t\t\t\n \t\t\t\t\t\t</th><th class="td" title="\n \t\t\t\t\ttable-head\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t" scope="col" style="border-bottom: 2px solid black">Definition \t\t\t\t\t\t\n \t\t\t\t\t\t</th></tr></thead><tbody title="tbody"><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Microbiota \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Collection of microorganisms that populate a habitat, with populations of stable species (autochthonous) and other variables (allochthonous) \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Microbiome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Includes the microorganisms, its genomes and the environmental conditions present in a habitat \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Metagenome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Collection of genomes of the members of a microbiota \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Metabolome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Metabolite flows and contents \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Metatranscriptome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Expression and regulation of microbiota’s genes \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Metaproteome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Collection of proteins that reflect the microbiota’s activity \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Hologenome \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Host’s genome and metagenome, which together constitute an ecosystem. Reflects the microorganisms’ importance for the host’ biology \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Dysbiosis \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="\n \t\t\t\t\ttable-entry\n \t\t\t\t " align="left" valign="\n \t\t\t\t\ttop\n \t\t\t\t">Imbalance in microbiota populations and/or functions. Also related to changes in diversity \t\t\t\t\t\t\n \t\t\t\t</td></tr></tbody></table> """ ] "imagenFichero" => array:1 [ 0 => "xTab2565510.png" ] ] ] ] "descripcion" => array:1 [ "en" => "General concepts and definitions." ] ] ] "bibliografia" => array:2 [ "titulo" => "References" "seccion" => array:1 [ 0 => array:2 [ "identificador" => "bibs0005" "bibliografiaReferencia" => array:77 [ 0 => array:3 [ "identificador" => "bib0005" "etiqueta" => "1" "referencia" => array:1 [ 0 => array:2 [ "contribucion" => array:1 [ 0 => array:2 [ "titulo" => "Best practices for analysing microbiomes" "autores" => array:1 [ 0 => array:2 [ "etal" => true "autores" => array:6 [ 0 => "R. Knight" 1 => "A. Vrbanac" 2 => "B.C. Taylor" 3 => "A. Aksenov" 4 => "C. Callewaert" 5 => "J. Debelius" ] ] ] ] ] "host" => array:1 [ 0 => array:2 [ "doi" => "10.1038/s41579-018-0029-9" "Revista" => array:6 [ "tituloSerie" => "Nat Rev Microbiol." 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The human microbiome in sickness and in health

Microbioma humano en la salud y la enfermedad

T. Requenaa,

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t.requena@csic.es

Corresponding author.

, M. Velascob

a Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación (CIAL-CSIC), Madrid, Spain

b Sección de Enfermedades Infecciosas, Medicina Interna, Hospital Universitario Fundación Alcorcón, Alcorcón, Spain

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    "textoCompleto" => "<span class="elsevierStyleSections"><span id="sec0005" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0025">Background</span><p id="par0005" class="elsevierStylePara elsevierViewall">Recent technological advances&#44; reflected in the development of various omic platforms&#44; have transformed our understanding of the composition&#44; dynamics and functionality of complex microbial communities that inhabit the various environments of the human body&#46;<a class="elsevierStyleCrossRef" href="#bib0005"><span class="elsevierStyleSup">1</span></a> These technologies have also helped generate considerable data on the human microbiome aimed at both biotechnology and clinical research&#46; <a class="elsevierStyleCrossRef" href="#tbl0005">Table 1</a> shows the definitions of the main concepts employed in these studies&#46;</p><elsevierMultimedia ident="tbl0005"></elsevierMultimedia><p id="par0010" class="elsevierStylePara elsevierViewall">Human autochthonous microbiota consist mostly of bacteria but also include viruses&#44; archaea&#44; molds&#44; yeasts and protozoa&#46; Human microbial colonization occurs in the skin and mucous membranes of cavities exposed to the exterior&#44; such as the gastrointestinal&#44; respiratory and genitourinary tracts and secretory glands such as the sebaceous&#44; biliary and mammary&#46; In all of these environments&#44; microbiota establish a symbiotic relationship with the host&#44; providing early modulation of the host&#8217;s physiological development and the nutrition&#44; immune and pathogen resistance functions in all stages of life&#46;<a class="elsevierStyleCrossRef" href="#bib0010"><span class="elsevierStyleSup">2</span></a></p><p id="par0015" class="elsevierStylePara elsevierViewall">Lifestyle &#40;including geographical and ethnic factors&#41;&#44; genetics&#44; age and diet are the main regulators for the composition and functionality of human microbiota&#46;<a class="elsevierStyleCrossRefs" href="#bib0015"><span class="elsevierStyleSup">3&#8211;5</span></a> The recent association between the increase in autoimmune diseases and allergies and the reduction in the incidence of infectious diseases in developed countries&#44; also related to the abuse of antibiotics and lower exposure to microorganisms&#44; has contributed to the concept that a lack of immune system stimuli in the initial stages of life jeopardizes the ability to recognize threats and calibrate the level of microbial tolerance&#46;<a class="elsevierStyleCrossRefs" href="#bib0010"><span class="elsevierStyleSup">2&#44;6</span></a> Early microbial exposure has a critical role in the development of the immune&#44; endocrine&#44; metabolic and nervous systems&#46;<a class="elsevierStyleCrossRef" href="#bib0035"><span class="elsevierStyleSup">7</span></a> The microbiota of healthy newborns is similar to the mother&#8217;s intestinal&#44; vaginal and skin microbiota&#44; with a predominance of certain microbial groups depending on the birthing method&#46;<a class="elsevierStyleCrossRef" href="#bib0040"><span class="elsevierStyleSup">8</span></a> The first colonizers of the intestine in childhood are facultative anaerobes that are successively replaced by obligate anaerobes&#44; led by <span class="elsevierStyleItalic">Bifidobacterium</span>&#44; <span class="elsevierStyleItalic">Bacteroides</span> and <span class="elsevierStyleItalic">Clostridium</span>&#46; During the first 6 months of life&#44; the main taxon associated with a healthy state is <span class="elsevierStyleItalic">Bifidobacterium longum&#46;</span><a class="elsevierStyleCrossRef" href="#bib0045"><span class="elsevierStyleSup">9</span></a> During breastfeeding&#44; the supply of microorganisms and indigestible oligosaccharides through breast milk contributes to establishing a healthy intestinal microbiota&#44; which is also effective in facilitating a faster hospital discharge for premature infants&#46;<a class="elsevierStyleCrossRef" href="#bib0050"><span class="elsevierStyleSup">10</span></a></p><p id="par0020" class="elsevierStylePara elsevierViewall">In addition to the importance of appropriate immune system training in the first stages of life&#44; recent studies of microbiota disorders &#40;dysbiosis&#41; and their association with certain disease conditions have indicated that the reduction in microbial diversity is one of the aspects that contributes to the onset of disease&#46;<a class="elsevierStyleCrossRef" href="#bib0055"><span class="elsevierStyleSup">11</span></a> In ecological terms&#44; species diversity and richness are important in the concepts of functional redundancy and resilience &#40;the ability to tolerate particular environmental challenges&#41;&#46; The reduction in species diversity in the human microbiome has been related to an increase in diseases such as inflammatory bowel disease&#44; obesity&#44; acute otitis media&#44; chronic rhinosinusitis and urinary tract infection&#46;<a class="elsevierStyleCrossRef" href="#bib0025"><span class="elsevierStyleSup">5</span></a> Infection by <span class="elsevierStyleItalic">Clostridioides difficile</span> &#40;formerly known as <span class="elsevierStyleItalic">Clostridium difficile</span>&#41; is typically associated with antibiotic therapy and the subsequent loss of intestinal microbial diversity&#46;<a class="elsevierStyleCrossRef" href="#bib0060"><span class="elsevierStyleSup">12</span></a> In the context of intestinal microbiota&#44; the increase in dietary intake of foods rich in calories and refined sugar has been associated with less diverse microbial communities than in individuals who consume fiber-rich diets&#46;<a class="elsevierStyleCrossRef" href="#bib0020"><span class="elsevierStyleSup">4</span></a></p></span><span id="sec0010" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0030">Skin microbiota</span><p id="par0025" class="elsevierStylePara elsevierViewall">A considerable variety of microorganisms are deposited on and subsequently colonize the skin&#44; depending on the various body regions and conditions of moisture&#44; pH and sebaceous production&#44; among other factors&#46;<a class="elsevierStyleCrossRef" href="#bib0065"><span class="elsevierStyleSup">13</span></a> Microbial colonization has also been reported in hair follicles and sebaceous glands&#46;<a class="elsevierStyleCrossRef" href="#bib0070"><span class="elsevierStyleSup">14</span></a> The driest areas of the skin are coated especially by <span class="elsevierStyleItalic">Staphylococcus</span>&#44; while the sebaceous areas are dominated by lipophilic species of <span class="elsevierStyleItalic">Propionibacterium</span>&#46; The most humid regions&#44; such as the folds of the arms and legs&#44; are dominated by <span class="elsevierStyleItalic">Corynebacterium</span>&#46;<a class="elsevierStyleCrossRef" href="#bib0075"><span class="elsevierStyleSup">15</span></a> Skin microbiota provide barrier functions against colonization by pathogens through immune response modulation using keratinocytes and by taking efficient advantage of the nutrients from skin secretions&#44; resulting in the production of antimicrobial peptides and organic acids that participate in reducing skin pH&#46;<a class="elsevierStyleCrossRef" href="#bib0065"><span class="elsevierStyleSup">13</span></a></p><p id="par0030" class="elsevierStylePara elsevierViewall">A number of skin microbiota microorganisms can be opportunistic pathogens under certain conditions&#46; The presence of wounds or a state of immunosuppression can result in the pathogenic behavior of <span class="elsevierStyleItalic">Staphylococcus epidermidis &#40;S&#46; epidermidis&#41;&#46;</span><a class="elsevierStyleCrossRef" href="#bib0080"><span class="elsevierStyleSup">16</span></a> Certain skin disorders&#44; such as psoriasis&#44; atopic dermatitis&#44; acne&#44; dandruff and slow-to-heal wounds&#44; are associated with microbiological changes&#46;<a class="elsevierStyleCrossRef" href="#bib0070"><span class="elsevierStyleSup">14</span></a><span class="elsevierStyleItalic">Cutibacterium acnes</span> &#40;formerly known as <span class="elsevierStyleItalic">Propionibacterium acnes</span>&#41; is typically found in the microbiota of healthy individuals but usually predominates during puberty due to increased sebaceous secretion&#44; causing chronic skin inflammation&#46;<a class="elsevierStyleCrossRef" href="#bib0085"><span class="elsevierStyleSup">17</span></a><span class="elsevierStyleItalic">Staphylococcus aureus &#40;S&#46; aureus&#41;</span> is usually associated with atopic dermatitis&#44; particularly during the intensification of an active disease and due to a reduction in diversity of skin microbiota&#46;<a class="elsevierStyleCrossRef" href="#bib0065"><span class="elsevierStyleSup">13</span></a> It has also been reported that microbiota associated with chronic injuries persist in forming biofilms that impede healing and increased resistance to antibiotic therapy&#46;<a class="elsevierStyleCrossRef" href="#bib0090"><span class="elsevierStyleSup">18</span></a> A number of studies have also correlated the differences in skin microbiota with the attraction of malaria-transmitting <span class="elsevierStyleItalic">Anopheles</span> mosquitoes&#46;<a class="elsevierStyleCrossRef" href="#bib0095"><span class="elsevierStyleSup">19</span></a></p></span><span id="sec0015" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0035">Airway microbiota</span><p id="par0035" class="elsevierStylePara elsevierViewall">The respiratory tract contains microbial communities from the nasal fossae to the pulmonary alveolus&#44; with the highest concentrations found in the upper airways&#46;<a class="elsevierStyleCrossRef" href="#bib0100"><span class="elsevierStyleSup">20</span></a> This autochthonous microbiota contributes to the defense against colonization and infection by pathogens in the respiratory mucosa and thereby prevents their advance throughout the tract&#46; Conditions with increased relative humidity and temperature from the nasal cavity to the interior&#44; as well as partial oxygen and carbon dioxide pressures with opposite gradients&#44; affect specific populations that are characteristic to each defined niche in this tract&#46; Nose microbiota are similar to skin microbiota&#44; in which <span class="elsevierStyleItalic">Staphylococcus</span>&#44; <span class="elsevierStyleItalic">Propionibacterium</span> and <span class="elsevierStyleItalic">Corynebacterium</span> predominate&#46; Nasopharyngeal microbiota are more varied and diverse and contain <span class="elsevierStyleItalic">Haemophilus</span> and <span class="elsevierStyleItalic">Streptococcus&#44;</span> as well as the genera representative of the anterior region&#46; In the oropharynx&#44; the bacterial communities are also diverse and include <span class="elsevierStyleItalic">Streptococcus</span>&#44; <span class="elsevierStyleItalic">Neisseria</span> and anaerobes such as <span class="elsevierStyleItalic">Veillonella</span> and <span class="elsevierStyleItalic">Prevotella&#46;</span><a class="elsevierStyleCrossRef" href="#bib0100"><span class="elsevierStyleSup">20</span></a> Lung microbiota&#44; in healthy conditions&#44; consist of a transient community of microorganisms mainly from the nasopharynx and oropharynx and are the result of the balance between microorganisms that travel to this region and are eliminated&#46;<a class="elsevierStyleCrossRef" href="#bib0105"><span class="elsevierStyleSup">21</span></a></p><p id="par0040" class="elsevierStylePara elsevierViewall">Specific members of the nasopharyngeal niche microbiota have been identified&#44; which can actively exclude respiratory pathogens&#44; such as the ability of <span class="elsevierStyleItalic">S&#46; epidermidis</span> to exclude <span class="elsevierStyleItalic">S&#46; aureus</span> through the secretion of serine-proteases that eliminate the biofilms created by the pathogen&#46;<a class="elsevierStyleCrossRef" href="#bib0110"><span class="elsevierStyleSup">22</span></a> Other components of the autochthonous microbiota of the upper airways&#44; such as <span class="elsevierStyleItalic">Dolosigranulum</span> and <span class="elsevierStyleItalic">Corynebacterium&#44;</span> have been associated with respiratory health and the exclusion of <span class="elsevierStyleItalic">Streptococcus pneumoniae&#46;</span><a class="elsevierStyleCrossRefs" href="#bib0115"><span class="elsevierStyleSup">23&#44;24</span></a> The predominance of <span class="elsevierStyleItalic">Moraxella</span>&#44; <span class="elsevierStyleItalic">Streptococcus</span> and <span class="elsevierStyleItalic">Haemophilus</span> in the nasopharynx has been associated with acute respiratory infections in children and a risk of bronchiolitis and pneumonia&#46;<a class="elsevierStyleCrossRefs" href="#bib0125"><span class="elsevierStyleSup">25&#44;26</span></a></p><p id="par0045" class="elsevierStylePara elsevierViewall">The excessive growth of a certain bacterial species can lead to a reduction in lung microbiota richness and has been associated with the progression of diseases such as cystic fibrosis and infections related to this disease&#46; A number of studies have shown the presence of predatory bacteria in the microbiota of lungs affected by cystic fibrosis&#44; such as <span class="elsevierStyleItalic">Bdellovibrio</span> and <span class="elsevierStyleItalic">Vampirovibrio</span>&#44; which could contribute to controlling the chronic colonization of pathogenic bacteria&#46;<a class="elsevierStyleCrossRef" href="#bib0135"><span class="elsevierStyleSup">27</span></a></p></span><span id="sec0020" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0040">Female and reproductive system microbiota</span><p id="par0050" class="elsevierStylePara elsevierViewall">The idea that breastmilk is a sterile fluid in physiological conditions has been substituted by the growing recognition that it contains a commensal or potentially probiotic microbiota for the infant&#8217;s health&#46;<a class="elsevierStyleCrossRef" href="#bib0140"><span class="elsevierStyleSup">28</span></a> Breastmilk microbiota is fairly diverse in terms of bacteria genera and species&#44; although usually in relatively low concentrations &#40;10&#8211;1000 bacteria per mL&#41;&#46; The microbiota is usually dominated by skin-related genera such as <span class="elsevierStyleItalic">Staphylococcus</span>&#44; <span class="elsevierStyleItalic">Streptococcus</span>&#44; <span class="elsevierStyleItalic">Corynebacterium</span> and <span class="elsevierStyleItalic">Propionibacterium</span>&#59; however&#44; lactic acid bacteria &#40;<span class="elsevierStyleItalic">Lactobacillus</span>&#44; <span class="elsevierStyleItalic">Lactococcus</span>&#44; <span class="elsevierStyleItalic">Leuconostoc</span>&#44; <span class="elsevierStyleItalic">Weissella</span>&#44; <span class="elsevierStyleItalic">Enterococcus</span>&#41; and bifidobacteria can also be found&#44; and new species such as <span class="elsevierStyleItalic">Streptococcus lactarius</span> have been isolated&#46;<a class="elsevierStyleCrossRef" href="#bib0145"><span class="elsevierStyleSup">29</span></a> DNA from obligate anaerobes of intestinal origin&#44; such as <span class="elsevierStyleItalic">Bacteroides</span>&#44; <span class="elsevierStyleItalic">Clostridium</span>&#44; <span class="elsevierStyleItalic">Coprococcus</span>&#44; <span class="elsevierStyleItalic">Faecalibacterium</span> and <span class="elsevierStyleItalic">Roseburia</span>&#44; have also been found in breastmilk&#46;<a class="elsevierStyleCrossRef" href="#bib0150"><span class="elsevierStyleSup">30</span></a> The transfer of microorganisms by the enteromammary pathway from the intestine to breastmilk has been reported and has been associated with increased intestinal patency&#44; decreased peristalsis and weakening of the barriers against bacterial development during the final gestation period&#44; which promotes microbial translocation&#46;<a class="elsevierStyleCrossRef" href="#bib0155"><span class="elsevierStyleSup">31</span></a></p><p id="par0055" class="elsevierStylePara elsevierViewall">There are studies that have reported the presence in breastmilk of probiotic strains supplemented orally for treating lactational mastitis&#46;<a class="elsevierStyleCrossRef" href="#bib0160"><span class="elsevierStyleSup">32</span></a> In fact&#44; the etiopathogenesis of mastitis has been related to a process of dysbiosis or imbalance in bacterial diversity in the mammary gland&#44; which results in an overgrowth of species that cause infection&#44; accompanied by a reduction in other species present physiologically in breastmilk&#46;<a class="elsevierStyleCrossRef" href="#bib0165"><span class="elsevierStyleSup">33</span></a> A number of microbial genera that predominate in cancerous breast tissue have also been reported&#44; such as <span class="elsevierStyleItalic">Fusobacterium&#44; Atopobium&#44; Hydrogenophaga</span> and <span class="elsevierStyleItalic">Gluconacetobacter&#46;</span><a class="elsevierStyleCrossRef" href="#bib0170"><span class="elsevierStyleSup">34</span></a><span class="elsevierStyleItalic">Fusobacterium</span> has been associated with other cancerous conditions in epithelial cells &#40;such as colon cancer&#41;&#44; related to its capacity to secrete virulence factors and promote proinflammatory conditions&#46;<a class="elsevierStyleCrossRef" href="#bib0175"><span class="elsevierStyleSup">35</span></a></p><p id="par0060" class="elsevierStylePara elsevierViewall">In the female reproductive tract&#44; the vagina contains a specific microbiota represented mainly by <span class="elsevierStyleItalic">Lactobacillus</span>&#44; which is associated with a healthy condition and that reaches the highest proportions in pregnant women with full-term childbirth&#46;<a class="elsevierStyleCrossRef" href="#bib0180"><span class="elsevierStyleSup">36</span></a> In smaller proportions&#44; microbiota associated with skin and the intestinal tract can also be found&#44; such as <span class="elsevierStyleItalic">Prevotella</span>&#44; <span class="elsevierStyleItalic">Gardnerella</span>&#44; <span class="elsevierStyleItalic">Atopobium</span>&#44; <span class="elsevierStyleItalic">Sneathia</span>&#44; <span class="elsevierStyleItalic">Bifidobacterium</span>&#44; <span class="elsevierStyleItalic">Megasphaera</span> and <span class="elsevierStyleItalic">Anaerococcus&#46;</span><a class="elsevierStyleCrossRef" href="#bib0185"><span class="elsevierStyleSup">37</span></a> Lactobacilli in the vagina are particularly associated with childbearing age&#44; due to the production of estrogen&#44; which promotes mucosal thickening and glycogen accumulation&#44; which in turn are used by the lactobacilli to produce lactic acid&#44; acidifying the environment to pH values between 4 and 4&#46;5 and acting as a barrier to colonization by other microorganisms&#46; In the vaginal context&#44; the increase in bacterial diversity&#44; with the increase in the proportion of anaerobes such as <span class="elsevierStyleItalic">Gardnerella</span>&#44; <span class="elsevierStyleItalic">Prevotella</span>&#44; <span class="elsevierStyleItalic">Megasphaera</span>&#44; <span class="elsevierStyleItalic">Atopobium</span> and <span class="elsevierStyleItalic">Dialister</span> to the detriment of the lactobacilli&#44; is associated with an increased risk of bacterial vaginosis&#46;<a class="elsevierStyleCrossRef" href="#bib0190"><span class="elsevierStyleSup">38</span></a> The microbiota present in the endometrium is also characterized by the presence of <span class="elsevierStyleItalic">Lactobacillus</span>&#44; <span class="elsevierStyleItalic">Gardnerella vaginalis</span> and <span class="elsevierStyleItalic">Enterobacter</span> but in less abundant quantities than in the vagina &#40;approximately 4 logarithmic units fewer&#41;&#44; possibly halted by the cervical barrier and by a more effective immune response in the internal organs of the reproductive tract&#46;<a class="elsevierStyleCrossRef" href="#bib0195"><span class="elsevierStyleSup">39</span></a> The proliferation of enterobacteria&#44; <span class="elsevierStyleItalic">Enterococcus</span> and <span class="elsevierStyleItalic">Streptococcus</span> has been related to endometriosis&#44;<a class="elsevierStyleCrossRef" href="#bib0200"><span class="elsevierStyleSup">40</span></a> and an increase in <span class="elsevierStyleItalic">Gardnerella</span> has been associated with premature birth and obstetric complications&#44;<a class="elsevierStyleCrossRef" href="#bib0180"><span class="elsevierStyleSup">36</span></a> as well as a reduced effect of tenofovir used in pre-exposure prophylaxis for HIV infection&#46;<a class="elsevierStyleCrossRef" href="#bib0205"><span class="elsevierStyleSup">41</span></a> The increase in bacterial diversity in the female reproductive tract to the detriment of lactobacilli has been correlated with a lower pregnancy rate in assisted reproduction procedures&#46;<a class="elsevierStyleCrossRef" href="#bib0185"><span class="elsevierStyleSup">37</span></a></p><p id="par0065" class="elsevierStylePara elsevierViewall">The microbiota of the male reproductive tract has been less studied than that of women&#46; Although bacteriospermia has classically been negatively associated with fertility&#44; the most recent studies have demonstrated that the presence of <span class="elsevierStyleItalic">Lactobacillus</span> in semen is relatively frequent in fertile individuals with normal sperm parameters&#44; while the predominance of <span class="elsevierStyleItalic">Prevotella</span> is associated with motility defects&#46;<a class="elsevierStyleCrossRef" href="#bib0210"><span class="elsevierStyleSup">42</span></a> Similar to vaginal microbiota&#44; a lesser diversity of seminal microbiota appears to be related to a healthy condition&#46; Thus&#44; patients with prostatitis have been reported to have a lower lactobacilli concentration and greater diversity of bacterial species in the semen than healthy individuals&#46;<a class="elsevierStyleCrossRef" href="#bib0215"><span class="elsevierStyleSup">43</span></a> A specific prostate microbiota has also been defined for healthy or tumor tissue&#44;<a class="elsevierStyleCrossRef" href="#bib0220"><span class="elsevierStyleSup">44</span></a> as well a relationship between urinary microbiota and chronic prostate inflammation&#46;<a class="elsevierStyleCrossRef" href="#bib0225"><span class="elsevierStyleSup">45</span></a> The increase in anaerobes in the microbiota of the penis has recently been linked with a more effective transmission of the HIV infection&#46;<a class="elsevierStyleCrossRef" href="#bib0230"><span class="elsevierStyleSup">46</span></a></p></span><span id="sec0025" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0045">Oral and gastrointestinal tract microbiota</span><span id="sec0030" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0050">Oral cavity</span><p id="par0070" class="elsevierStylePara elsevierViewall">The oral cavity has an abundant and diverse microbiota that is specific for the various niches represented by the tongue&#44; palate&#44; teeth and gums&#46; Saliva is considered representative of the oral microbiota because it performs a cleaning effect on all oral surfaces and provides nutrients such as proteins&#44; glycoproteins&#44; peptides and vitamins&#46; In addition&#44; saliva has an effective buffering capacity that provides neutral pH conditions &#40;between 6&#46;7 and 7&#46;2&#41;&#46; There is a representative microbiota of the oral cavity in which <span class="elsevierStyleItalic">Streptococcus</span>&#44; <span class="elsevierStyleItalic">Gemella</span>&#44; <span class="elsevierStyleItalic">Granulicatella</span>&#44; <span class="elsevierStyleItalic">Neisseria</span> and <span class="elsevierStyleItalic">Prevotella</span> predominate&#46; There are also species adapted to specific niches&#44; such as <span class="elsevierStyleItalic">Rothia</span>&#44; which colonizes the tongue and teeth&#44; and <span class="elsevierStyleItalic">Simonsiella</span>&#44; which is located in the hard palate&#46;<a class="elsevierStyleCrossRef" href="#bib0235"><span class="elsevierStyleSup">47</span></a> There are also bacterial groups associated with oral diseases such as caries&#44; periodontal disease and halitosis&#46;<a class="elsevierStyleCrossRef" href="#bib0240"><span class="elsevierStyleSup">48</span></a> The increase in consumption of simple carbohydrates in the human diet has been related to an increase in caries due to the fermentative activity and acidic production of oral microbiota&#44; particularly <span class="elsevierStyleItalic">Streptococcus mutans &#40;S&#46; mutans&#41;</span>&#44; <span class="elsevierStyleItalic">Veillonella</span> and <span class="elsevierStyleItalic">Lactobacillus&#46;</span><a class="elsevierStyleCrossRef" href="#bib0245"><span class="elsevierStyleSup">49</span></a><span class="elsevierStyleItalic">Streptococcus dentisani</span> is a recently reported species whose abundance is inversely related to the onset of caries and is characterized by the growth inhibition of <span class="elsevierStyleItalic">S&#46; mutans</span> and by the pH neutralization of dental plaque&#46;<a class="elsevierStyleCrossRef" href="#bib0250"><span class="elsevierStyleSup">50</span></a></p></span><span id="sec0035" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0055">Stomach</span><p id="par0075" class="elsevierStylePara elsevierViewall">The stomach&#8217;s acidic pH prevents bacterial growth&#59; microbial concentrations are therefore usually below 10<span class="elsevierStyleSup">3</span> bacteria per mL of gastric content&#46; The most abundant groups are <span class="elsevierStyleItalic">Streptococcus</span>&#44; <span class="elsevierStyleItalic">Lactobacillus</span>&#44; <span class="elsevierStyleItalic">Prevotella</span>&#44; <span class="elsevierStyleItalic">Porphyromonas</span>&#44; <span class="elsevierStyleItalic">Rothia</span>&#44; <span class="elsevierStyleItalic">Atopobium</span> and <span class="elsevierStyleItalic">Fusobacterium nucleatum &#40;F&#46; nucleatum&#41;</span>&#44; which come from the oral cavity and that represent transient acid-resistant microbiota&#46;<a class="elsevierStyleCrossRef" href="#bib0255"><span class="elsevierStyleSup">51</span></a><span class="elsevierStyleItalic">Helicobacter pylori &#40;H&#46; pylori&#41;</span> usually resides in the stomach mucosa and is protected from stomach acid through the production of urease activity&#46;<a class="elsevierStyleCrossRef" href="#bib0260"><span class="elsevierStyleSup">52</span></a> Despite clear evidence that <span class="elsevierStyleItalic">H&#46; pylori</span> is a human pathogen&#44; there are studies that have suggested that it could also be considered a commensal bacteria given that it is typically present in healthy individuals without generating symptoms or diseases and that it modulates the immune response of the mucosa&#46;<a class="elsevierStyleCrossRef" href="#bib0265"><span class="elsevierStyleSup">53</span></a> The ability of <span class="elsevierStyleItalic">H&#46; pylori</span> to produce peptic ulcers and gastric adenocarcinoma is associated with strains that express virulence factors such as CagA and Cgt&#44; which block the host&#8217;s immune response&#46;<a class="elsevierStyleCrossRef" href="#bib0270"><span class="elsevierStyleSup">54</span></a></p></span><span id="sec0040" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0060">Small intestine</span><p id="par0080" class="elsevierStylePara elsevierViewall">Within the gastrointestinal tract&#44; the small intestine is the longest region and has the greatest changes in environmental conditions&#44; which results in differing microbial concentrations &#40;an increase from 10<span class="elsevierStyleSup">4</span> to 10<span class="elsevierStyleSup">8</span> microorganisms per mL of intestinal content from the jejunum to ileum&#41;&#46;<a class="elsevierStyleCrossRef" href="#bib0275"><span class="elsevierStyleSup">55</span></a> Microbiota colonization in the small intestine is limited by the short time the intestinal content resides there&#44; the high peristalsis&#44; the continuous renewal of the intestinal mucosa&#44; the entry of bile salts and pancreatic secretions and the secretion of antimicrobial components in the mucosa &#40;defensins&#44; cathelicidin&#44; C-type lectins&#44; etc&#46;&#41;&#46; Neutral pH conditions and oxygen pressure cause more abundant populations in proximal areas of the small intestine corresponding to facultative anaerobes and decrease the proportion as the reducing conditions in the distal areas increase&#46; A study of the microbiota in the ileum reveals the abundance of Lactobacillales&#44; Clostridiales&#44; <span class="elsevierStyleItalic">Veillonella</span> and <span class="elsevierStyleItalic">Streptococcus</span> and&#44; to a lesser extent&#44; <span class="elsevierStyleItalic">Ruminococcus</span> and <span class="elsevierStyleItalic">Bacteroides&#46;</span><a class="elsevierStyleCrossRef" href="#bib0280"><span class="elsevierStyleSup">56</span></a></p><p id="par0085" class="elsevierStylePara elsevierViewall">Small intestine bacterial overgrowth&#44; established by counts &#62;10<span class="elsevierStyleSup">5</span> bacteria per mL of jejunal content&#44; can cause various nonspecific gastrointestinal symptoms such as distension&#44; flatulence&#44; abdominal pain&#44; diarrhea&#44; dyspepsia and weight loss&#46;<a class="elsevierStyleCrossRef" href="#bib0285"><span class="elsevierStyleSup">57</span></a> Celiac disease has been associated with dysbiosis of the small intestine microbiota&#46;<a class="elsevierStyleCrossRef" href="#bib0290"><span class="elsevierStyleSup">58</span></a> The disease is characterized by lower microbial diversity in patients with celiac disease&#44; with a reduced relative abundance of <span class="elsevierStyleItalic">Streptococcus</span> and <span class="elsevierStyleItalic">Prevotella</span> and higher levels of Proteobacteria&#46;<a class="elsevierStyleCrossRef" href="#bib0295"><span class="elsevierStyleSup">59</span></a> However&#44; studies have not been conducted to establish the causality of changes in microbiota with the disease&#44; and it is not known whether the observed changes are the consequence of small intestine inflammation&#46;</p></span><span id="sec0045" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0065">Large intestine</span><p id="par0090" class="elsevierStylePara elsevierViewall">The large intestine has the highest microbial density in the human body&#44; reaching 10<span class="elsevierStyleSup">10</span> microorganisms per mL of intestinal content&#46; Most of the identified microbial groups are bacteria belonging to the Bacteroidetes and Firmicutes phyla &#40;approximately 90&#37;&#41;&#44; along with others such as Proteobacteria&#44; Actinobacteria&#44; Fusobacteria and Verrucomicrobia&#46; The genera <span class="elsevierStyleItalic">Bacteroides</span>&#44; <span class="elsevierStyleItalic">Faecalibacterium</span> and <span class="elsevierStyleItalic">Bifidobacterium</span> are the most abundant in the large intestine<a class="elsevierStyleCrossRef" href="#bib0300"><span class="elsevierStyleSup">60</span></a> and are mostly obligate anaerobic microorganisms&#46; Some of the reported species have been found only in this environment&#44; which reflects a specific level of adaptation to the intestinal niche&#46;<a class="elsevierStyleCrossRef" href="#bib0305"><span class="elsevierStyleSup">61</span></a> This microbiota plays an important metabolic and protective role&#44; particularly in metabolizing indigestible material in the diet&#44; especially indigestible carbohydrates&#44; producing vitamins and some essential nutrients and acting as a barrier to infections by pathogenic bacteria&#46; The microbiota also has an important modulator effect on the host&#8217;s immune and endocrine response and acts on the secretion of neurotransmitters that provide communication between the intestine and brain&#46;<a class="elsevierStyleCrossRef" href="#bib0310"><span class="elsevierStyleSup">62</span></a> Even so&#44; a common microbiota nucleus shared among all individuals related to a healthy state has not been defined&#44; beyond the observation that a reduction in microbial diversity is associated with certain diseases&#46;<a class="elsevierStyleCrossRef" href="#bib0055"><span class="elsevierStyleSup">11</span></a> Diseases such as inflammatory bowel disease&#44; colorectal cancer&#44; obesity&#44; type 2 diabetes and nonalcoholic steatohepatitis have been associated with changes in the composition of intestinal microbiota&#46;<a class="elsevierStyleCrossRef" href="#bib0025"><span class="elsevierStyleSup">5</span></a> In most studies&#44; however&#44; these were noncausal associations&#44; or the results differed among the various research groups&#46; Moreover&#44; individuals with high adiposity&#44; insulin and leptin resistance and an inflammatory phenotype are characterized by a low richness of microbial genes &#40;below 400&#44;000&#41; in feces&#46;<a class="elsevierStyleCrossRef" href="#bib0315"><span class="elsevierStyleSup">63</span></a></p><p id="par0095" class="elsevierStylePara elsevierViewall">A number of microbial species that colonize the intestinal mucosa&#44; such as <span class="elsevierStyleItalic">Akkermansia muciniphila</span>&#44; have been associated with a healthy metabolic state&#44; glucose and adipose tissue homeostasis&#44;<a class="elsevierStyleCrossRef" href="#bib0320"><span class="elsevierStyleSup">64</span></a> improved inflammatory processes<a class="elsevierStyleCrossRef" href="#bib0325"><span class="elsevierStyleSup">65</span></a> and healing of intestinal mucosa injuries&#46;<a class="elsevierStyleCrossRef" href="#bib0330"><span class="elsevierStyleSup">66</span></a><span class="elsevierStyleItalic">Faecalibacterium prausnitzii</span> is another component of the intestinal microbiota with anti-inflammatory properties&#46;<a class="elsevierStyleCrossRef" href="#bib0335"><span class="elsevierStyleSup">67</span></a> On the other hand&#44; the formation of biofilms by <span class="elsevierStyleItalic">Bacteroides fragilis</span> has been associated with inflamed areas in patients with inflammatory bowel disease&#46;<a class="elsevierStyleCrossRef" href="#bib0340"><span class="elsevierStyleSup">68</span></a><span class="elsevierStyleItalic">Fusobacterium nucleatum</span> is an anaerobic species that is part of the oral and intestinal mucosa and has been associated in numerous studies with the neoplastic processes of colon cancer&#46;<a class="elsevierStyleCrossRef" href="#bib0345"><span class="elsevierStyleSup">69</span></a> The production of trimethylamine&#44; trimethylamine oxide&#44; secondary bile acids and indoxyl sulfate by intestinal microbiota has been associated with the development and progression of cardiovascular diseases&#44; including heart failure&#46;<a class="elsevierStyleCrossRef" href="#bib0350"><span class="elsevierStyleSup">70</span></a></p></span><span id="sec0050" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0070">Brain</span><p id="par0100" class="elsevierStylePara elsevierViewall">The recent observation by electron microscopy in human brain slices of bacteria associated with astrocytes&#44; without being related to an infection&#44; has been tentatively alluded to as evidence of a brain microbiome&#46;<a class="elsevierStyleCrossRef" href="#bib0355"><span class="elsevierStyleSup">71</span></a> Although the study results need to be scientifically confirmed&#44; it is generally accepted that the metabolic activity of the intestinal microbiota affects the brain&#46;<a class="elsevierStyleCrossRef" href="#bib0310"><span class="elsevierStyleSup">62</span></a> It has been reported that intestinal bacteria can synthesize neurotransmitters such as serotonin&#44; gamma-aminobutyric acid&#44; norepinephrine&#44; dopamine and acetylcholine&#46;<a class="elsevierStyleCrossRef" href="#bib0360"><span class="elsevierStyleSup">72</span></a> There is also evidence that psychotropic drugs have a significant impact on intestinal microbiota&#46;<a class="elsevierStyleCrossRef" href="#bib0310"><span class="elsevierStyleSup">62</span></a> Beyond the studies performed on laboratory animals&#44; the main impact of intestinal dysbiosis on the brain reported in humans is its association with depression&#46;<a class="elsevierStyleCrossRef" href="#bib0365"><span class="elsevierStyleSup">73</span></a> Patients with acute depression are characterized by low intestinal levels of <span class="elsevierStyleItalic">Faecalibacterium</span> compared with healthy controls and patients with depression who respond to treatment&#46; Fecal microbiota transplantation from individuals with depression to axenic mice has been observed to result in phenotypes lacking appetite and with lower serotonin production&#46;<a class="elsevierStyleCrossRef" href="#bib0370"><span class="elsevierStyleSup">74</span></a> A study of 1054 individuals observed that the genera <span class="elsevierStyleItalic">Coprococcus</span> and <span class="elsevierStyleItalic">Dialister</span> were missing in patients with depression&#44; regardless of whether they took antidepressants&#46;<a class="elsevierStyleCrossRef" href="#bib0375"><span class="elsevierStyleSup">75</span></a> Moreover&#44; <span class="elsevierStyleItalic">Faecalibacterium</span> and <span class="elsevierStyleItalic">Coprococcus</span> were consistently associated with indicators of better quality of life and increased production of gamma-aminobutyric acid and dopamine metabolites&#46; Differences have also been observed in the composition and functionality of the intestinal microbiota of patients with behavioral disorders such as autism spectrum disorder&#44; learning difficulties&#44; eating disorders and addictions<a class="elsevierStyleCrossRef" href="#bib0310"><span class="elsevierStyleSup">62</span></a> and with neurodegenerative diseases such as Parkinson&#39;s and Alzheimer&#39;s disease&#46;<a class="elsevierStyleCrossRef" href="#bib0380"><span class="elsevierStyleSup">76</span></a> A study correlated the changes in the intestinal bacterial metabolome with autonomous nervous system disorders and the development of arterial hypertension&#46;<a class="elsevierStyleCrossRef" href="#bib0385"><span class="elsevierStyleSup">77</span></a></p></span></span><span id="sec0055" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0075">Conclusions</span><p id="par0105" class="elsevierStylePara elsevierViewall">An exhaustive understanding of the components of human microbiota can open a broad range of opportunities for research on their role in health and thus channel the possibilities for microbial modulation&#46; The assessment and manipulation of microbiota can extend the options for tailored medicine&#46; In the future&#44; it might be possible to use these techniques in the diagnosis &#40;changes in microbiomes in the presence of subclinical diseases&#41;&#44; prevention &#40;displacement of multiresistant colonic bacteria&#41; and treatment &#40;fecal microbiota transplantation and bacteriotherapy&#41; of certain diseases&#46; Although the phylogenetic and functional diversity of microbiota is associated with better health conditions&#44; further progress is needed to establish biomarkers that help recognize healthy states associated with the microbiota&#46; We need further studies that enable metagenomic analysis at the functional level&#46;</p></span><span id="sec0060" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0080">Funding</span><p id="par0110" class="elsevierStylePara elsevierViewall">The author would like to thank the <span class="elsevierStyleGrantSponsor" id="gs0005">Ministry of Science&#44; Innovation and Universities of Spain</span> for funding this study through projects <span class="elsevierStyleGrantNumber" refid="gs0005">AGL2016-75951-R</span>&#44; <span class="elsevierStyleGrantNumber" refid="gs0005">PCIN-2017-075</span> and <span class="elsevierStyleGrantNumber" refid="gs0005">AGL2004-07285-C02</span>&#46;</p></span></span>"
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          "titulo" => "Skin microbiota"
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          "titulo" => "Airway microbiota"
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          "identificador" => "sec0020"
          "titulo" => "Female and reproductive system microbiota"
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        8 => array:3 [
          "identificador" => "sec0025"
          "titulo" => "Oral and gastrointestinal tract microbiota"
          "secciones" => array:5 [
            0 => array:2 [
              "identificador" => "sec0030"
              "titulo" => "Oral cavity"
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            1 => array:2 [
              "identificador" => "sec0035"
              "titulo" => "Stomach"
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              "titulo" => "Small intestine"
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              "titulo" => "Large intestine"
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            1 => "Homeostasis"
            2 => "Symbiosis"
            3 => "Disease"
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        "resumen" => "<span id="abst0005" class="elsevierStyleSection elsevierViewall"><p id="spar0010" class="elsevierStyleSimplePara elsevierViewall">The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life&#46; Human microbial colonization occurs in the skin&#44; genitourinary system and&#44; mainly&#44; in the oral cavity and intestinal tract&#46; In these locations&#44; the human microbiota establishes a symbiotic relationship with the host and helps maintain physiological homeostasis&#46; Lifestyle&#44; age&#44; diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota&#46; Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases&#46; In addition to phylogenetic diversity studies&#44; further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health&#46;</p></span>"
      ]
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        "resumen" => "<span id="abst0010" class="elsevierStyleSection elsevierViewall"><p id="spar0015" class="elsevierStyleSimplePara elsevierViewall">El estudio del microbioma humano ha incrementado de manera excepcional el conocimiento actual del que disponemos sobre la importancia de la microbiota en la salud durante todas las etapas de la vida&#46; La colonizaci&#243;n microbiana humana ocurre en la piel&#44; en el sistema genitourinario y&#44; principalmente&#44; en la cavidad oral y el tracto intestinal&#46; En todos estos lugares&#44; la microbiota humana establece una relaci&#243;n simbi&#243;tica con el hospedador y ayuda a mantener la homeostasis fisiol&#243;gica&#46; El estilo de vida&#44; la edad&#44; la dieta y el uso de antibi&#243;ticos son los principales reguladores de la composici&#243;n y la funcionalidad de la microbiota humana&#46; Estudios recientes apuntan al descenso de la diversidad microbiana como uno de los aspectos que contribuye al desarrollo de enfermedades&#46; Adem&#225;s de los estudios de diversidad filogen&#233;tica&#44; es necesario profundizar en estudios metagen&#243;micos a nivel funcional del microbioma humano para mejorar el conocimiento sobre su participaci&#243;n en la salud humana&#46;</p></span>"
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        "nota" => "<p class="elsevierStyleNotepara" id="npar0005">Please cite this article as&#58; Requena T&#44; Velasco M&#46; Microbioma humano en la salud y la enfermedad&#46; Rev Clin Esp&#46; 2021&#59;221&#58;233&#8211;240&#46;</p>"
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                  \t\t\t\t\ttable-head\n
                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t" scope="col" style="border-bottom: 2px solid black">Concept&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t" scope="col" style="border-bottom: 2px solid black">Definition&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
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                  \t\t\t\t">Microbiota&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td><td class="td" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t">Collection of microorganisms that populate a habitat&#44; with populations of stable species &#40;autochthonous&#41; and other variables &#40;allochthonous&#41;&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
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                  \t\t\t\t">Microbiome&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td><td class="td" title="\n
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                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t">Includes the microorganisms&#44; its genomes and the environmental conditions present in a habitat&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n
                  \t\t\t\t\ttable-entry\n
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                  \t\t\t\t">Metagenome&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td><td class="td" title="\n
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                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t">Collection of genomes of the members of a microbiota&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
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                  \t\t\t\t">Metabolome&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t">Metabolite flows and contents&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t">Metatranscriptome&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t  " align="left" valign="\n
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                  \t\t\t\t">Expression and regulation of microbiota&#8217;s genes&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
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                  \t\t\t\t">Metaproteome&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td><td class="td" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t  " align="left" valign="\n
                  \t\t\t\t\ttop\n
                  \t\t\t\t">Collection of proteins that reflect the microbiota&#8217;s activity&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
                  \t\t\t\t\ttop\n
                  \t\t\t\t">Hologenome&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t  " align="left" valign="\n
                  \t\t\t\t\ttop\n
                  \t\t\t\t">Host&#8217;s genome and metagenome&#44; which together constitute an ecosystem&#46; Reflects the microorganisms&#8217; importance for the host&#8217; biology&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr><tr title="table-row"><td class="td-with-role" title="\n
                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t ; entry_with_role_rowhead " align="left" valign="\n
                  \t\t\t\t\ttop\n
                  \t\t\t\t">Dysbiosis&nbsp;\t\t\t\t\t\t\n
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                  \t\t\t\t\ttable-entry\n
                  \t\t\t\t  " align="left" valign="\n
                  \t\t\t\t\ttop\n
                  \t\t\t\t">Imbalance in microbiota populations and&#47;or functions&#46; Also related to changes in diversity&nbsp;\t\t\t\t\t\t\n
                  \t\t\t\t</td></tr></tbody></table>
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Article information

ISSN: 22548874
Original language: English

DOI:10.1016/j.rceng.2019.07.018

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