DOCSLIB.ORG

Human Microbiota

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Human Microbiota Human microbiota Graphic depicting the human skin microbiota, with relative prevalences of various classes of bacteria The human microbiota is the aggregate of microorganisms that resides on or within any of a number of human tissues and biofluids, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary and gastrointestinal tracts. They include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. The human microbiome refers specifically to the collective genomes of resident microorganisms.[1] Humans are colonized by many microorganisms; the traditional estimate is that the average human body is inhabited by ten times as many non-human cells as human cells, but more recent estimates have lowered that ratio to 3:1 or even to approximately the same number. Some microorganisms that colonize humans are commensal, meaning they co-exist without harming humans; others have a mutualistic relationship with their human hosts. 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. 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. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota. The Human Microbiome Project took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina.[1] It reached a milestone in 2012 when it published its initial results.[9] Though widely known as flora or microflora, this is a misnomer in technical terms, since the word root flora pertains to plants, and biota refers to the total collection of organisms in a particular ecosystem. Recently, the more appropriate term microbiota is applied, though its use has not eclipsed the entrenched use and recognition of flora with regard to bacteria and other microorganisms. Both terms are being used in different literature.[6] Relative numbers As of 2014, it was often reported in popular media and in the scientific literature that there are about 10 times as many microbial cells in the human body as there are human cells; this figure was based on estimates that the human microbiome includes around 100 trillion bacterial cells and that an adult human typically has around 10 trillion human cells.[2] 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.[2][3] In 2016, another group published a new estimate of the ratio being roughly 1:1 (1.3:1, with "an uncertainty of 25% and a variation of 53% over the population of standard 70-kg males"). Study Flowchart illustrating how the human microbiome is studied on the DNA level. The problem of elucidating the human microbiome is essentially identifying the members of a microbial community which includes bacteria, eukaryotes, and viruses.[10] This is done primarily using DNA- based studies, though RNA, protein and metabolite based studies are also performed.[10][11] DNA-based microbiome studies typically can be categorized as either targeted amplicon studies or more recently shotgun metagenomic studies. The former focuses on specific known marker genes and is primarily informative taxonomically, while the latter is an entire metagenomic approach which can also be used to study the functional potential of the community.[10] 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.[12] Aside from simply elucidating the composition of the human microbiome, one of the major questions involving the human microbiome is whether there is a "core", that is, whether there is a subset of the community that is shared among most humans.[13][14] 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. 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.[6] On 13 June 2012, a major milestone of the Human Microbiome Project (HMP) was announced by the NIH director Francis Collins.[9] The announcement was accompanied with a series of coordinated articles published in Nature[15][16] and several journals in the Public Library of Science (PLoS) on the same day. By mapping the normal microbial make-up of healthy humans using genome sequencing techniques, the researchers of the HMP have created a reference database and the boundaries of normal microbial variation in humans. From 242 healthy U.S. volunteers, more than 5,000 samples were collected from tissues from 15 (men) to 18 (women) body sites such as mouth, nose, skin, lower intestine (stool), and vagina. All the DNA, human and microbial, were analyzed with DNA sequencing machines. The microbial genome data were extracted by identifying the bacterial specific ribosomal RNA, 16S rRNA. The researchers calculated that more than 10,000 microbial species occupy the human ecosystem and they have identified 81 – 99% of the genera. Shotgun Sequencing It is frequently difficult to culture in laboratory communities of bacteria, archaea and viruses, therefore sequencing technologies can be exploited in metagenomics, too. Indeed, the complete knowledge of the functions and the characterization of specific microbial strains offer a great potentiality in therapeutic discovery and human health.[17] Collection of samples and DNA extraction The main point is to collect an amount microbial biomass that is sufficient to perform the sequencing and to minimize the sample contamination; for this reason, enrichment techniques can be used. 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. Mechanical lysis is usually preferred rather than chemical lysis, and bead beating may result in DNA loss when preparing the library.[17] Preparation of the library and sequencing The most used platforms are Illumina, Ion Torrent, Oxford Nanopore MinION and Pacific Bioscience Sequel, although the Illumina platform is considered the most appealing option due to its wide availability, high output and accuracy. There are no indications regarding the correct amount of sample to use.[17] Metagenome assembly The de novo approach is exploited; however, it presents some difficulties to be overcome. The coverage depends on each genome abundance in its specific community; low-abundance genomes may undergo fragmentation if the sequencing depth is not sufficient enough to avoid the formation of gaps. 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.[17] Contig binning 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. The methods to perform such analysis can be either supervised (database with known sequences) or unsupervised (direct search for contig groups in the collected data). 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.[17] Analysis after the processing The statistical analysis is essential to validate the obtained results (ANOVA can be used to size the differences between the groups); if it is paired with graphical tools, the outcome is easily visualized and understood.[17] Once a metagenome is assembled, it is possible to infer the functional potential of the microbiome. The computational challenges for this type of analysis are greater than for single genomes, due the fact that usually metagenomes assemblers have poorer quality, and many recovered genes are non- complete or fragmented. After the gene identification step, the data can be used to carry out a functional annotation by means of multiple alignment of the target genes against orthologs databases.[18] Marker gene analysis It is a technique that exploits primers to target a specific genetic region and enables to determine the microbial phylogenies. 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. The main gene used to characterize bacteria and archaea is 16S rRNA gene, while fungi identification is based on Internal Transcribed Spacer (ITS). The technique is fast and not so expensive and enables to obtain a low-resolution classification of a microbial sample; it is optimal for samples that may be contaminated by host DNA. Primer affinity varies among all DNA sequences, which may result in biases during the amplification reaction; indeed, low-abundance samples are susceptible to overamplification errors, since the other contaminating microorganisms result to be over-represented in case of increasing the PCR cycles. 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.[19] Marker gene analysis can be influenced by the primer choice; in this kind of analysis it's desirable to use a well-validated protocol (such as the one used in the Earth Microbiome Project).
Load more

Recommended publications
  • Current Progresses on Vaginal Microbiome, Bacterial Vaginosis and Biofilms
    Current progresses on vaginal microbiome, bacterial vaginosis and biofilms Gary Ventolini1, Abdul Hamood2 1 Professor and Regional Dean School of Medicine Texas Tech University Health Sciences Center Permian Basin 800 West, 4th Street. Odessa, Texas, 79705 USA; 2 Professor Department of Immunology and Molecular Microbiology Texas Tech University Health Sciences Center 3601 4th Street. Lub- bock, Texas, 79430 USA. ABSTRACT Recent advances in vaginal microbiome research have indicated that dysbiosis is a complex disorder involving not only cellular and bacterial metabolites, but also hormonal and environmental factors. With newly attained information, harmful gynecological conditions like Bacterial Vaginosis could be efficiently treated to restore health and enhance quality of life across women’s lifespan. Furthermore, newest discoveries on Lactobacilli products and biofilms will let us take care of serious medical conditions. Particularly, relating to antibiotic resistant pathogen biofilm producers like Pseudomonas aeruginosa and benefit patients with severe infected burns and sepsis. We scrutinize the significance of the current progresses on vaginal microbiome, bacterial vaginosis and biofilms. KEYWORDS Vaginal microbiome, bacterial vaginosis, biofilm. Introduction Article history Received 4 May 2020 – Accepted 6 Jun 2020 It is crucial to promote the integration of the available in- Contact formation from the bench (biomedical science with its physi- Gary Ventolini; [email protected] ologic pathways) to bed side (practical clinical application of School of Medicine Texas Tech University Health Sciences Center Permian scientific developments). Basin 800 West, 4th Street. Odessa, Texas, 79705 USA The genital tract microbiome represents 9% of the total women’s microbiome [1]. Recent advances in vaginal microbi- ome research have indicated that dysbiosis is a complex disor- permitted in-depth study of the vaginal microbiome.
    [Show full text]
  • Vaginal Probiotics for Reproductive Health and Related Dysbiosis: Systematic Review and Meta-Analysis
    Journal of Clinical Medicine Review Vaginal Probiotics for Reproductive Health and Related Dysbiosis: Systematic Review and Meta-Analysis Ana López-Moreno 1,2,* and Margarita Aguilera 1,2,3,* 1 Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain 2 Instituto de Nutrición y Tecnología de los Alimentos, INYTA-Granada, 18100 Granada, Spain 3 Instituto de Investigación Biosanitaria, Ibs-Granada, 18012 Granada, Spain * Correspondence: [email protected] (A.L.-M.); [email protected] (M.A.); Tel.: +34-9-5824-5129 (M.A.); Fax: +34-958-246235 (M.A.) Abstract: The use of probiotics in reproductive-related dysbiosis is an area of continuous progress due to the growing interest from clinicians and patients suffering from recurrent reproductive microbiota disorders. An imbalance in the natural colonization sites related to reproductive health—vaginal, cervicovaginal, endometrial, and pregnancy-related altered microbiota—could play a decisive role in reproductive outcomes. Oral and vaginal administrations are in continuous discussion regarding the clinical effects pursued, but the oral route is used and studied more often despite the need for further transference to the colonization site. The aim of the present review was to retrieve the standard- ized protocols of vaginal probiotics commonly used for investigating their microbiota modulation capacities. Most of the studies selected focused on treating bacterial vaginosis (BV) as the most common dysbiosis; a few studies focused on vulvovaginal candidiasis (VVC) and on pretreatment during in vitro fertilization (IVF). Vaginal probiotic doses administered were similar to oral probiotics Citation: López-Moreno, A.; 7 10 Aguilera, M. Vaginal Probiotics for protocols, ranging from ≥10 CFU/day to 2.5 × 10 CFU/day, but were highly variable regarding Reproductive Health and Related the treatment duration timing.
    [Show full text]
  • Vaginal Microbiota and the Potential of Lactobacillus Derivatives in Maintaining Vaginal Health Wallace Jeng Yang Chee , Shu Yih Chew and Leslie Thian Lung Than*
    Chee et al. Microb Cell Fact (2020) 19:203 https://doi.org/10.1186/s12934-020-01464-4 Microbial Cell Factories REVIEW Open Access Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health Wallace Jeng Yang Chee , Shu Yih Chew and Leslie Thian Lung Than* Abstract Human vagina is colonised by a diverse array of microorganisms that make up the normal microbiota and mycobiota. Lactobacillus is the most frequently isolated microorganism from the healthy human vagina, this includes Lactobacil- lus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii. These vaginal lactobacilli have been touted to prevent invasion of pathogens by keeping their population in check. However, the disruption of vaginal ecosystem contributes to the overgrowth of pathogens which causes complicated vaginal infections such as bacterial vaginosis (BV), sexually transmitted infections (STIs), and vulvovaginal candidiasis (VVC). Predisposing factors such as menses, pregnancy, sexual practice, uncontrolled usage of antibiotics, and vaginal douching can alter the microbial community. Therefore, the composition of vaginal microbiota serves an important role in determining vagina health. Owing to their Generally Recognised as Safe (GRAS) status, lactobacilli have been widely utilised as one of the alterna- tives besides conventional antimicrobial treatment against vaginal pathogens for the prevention of chronic vaginitis and the restoration of vaginal ecosystem. In addition, the efectiveness of Lactobacillus as prophylaxis has also been well-founded in long-term administration. This review aimed to highlight the benefcial efects of lactobacilli deriva- tives (i.e. surface-active molecules) with anti-bioflm, antioxidant, pathogen-inhibition, and immunomodulation activi- ties in developing remedies for vaginal infections.
    [Show full text]
  • Aerobic Vaginitis: Abnormal Vaginal Flora That Is Distinct from Bacterial Vaginosis
    Aerobic Vaginitis: Abnormal Vaginal Flora That Is Distinct From Bacterial Vaginosis. Aerobic vaginitis (AV) is a state of abnormal vaginal flora that is distinct from the more common bacterial vaginosis (BV) (Table 1). AV is caused by a displacement to respond to therapy at one week and will experience of the healthy vaginal Lactobacillus species with aerobic persistent symptoms. (4, 5) It is believed that a subset of pathogens such as Escherichia coli, Group B Streptococcus these patients may have been misdiagnosed and actually (GBS), Staphylococcus aureus, and Enterococcus faecalis suffer from AV, which requires an antibiotic therapy with that trigger a localized vaginal inflammatory immune intrinsic activity against specific aerobic bacteria. AV has response. Clinical signs and symptoms include vaginal been implicated in complications of pregnancy such as inflammation, an itching or burning sensation, dyspareunia, ascending chorioamnionitis, premature rupture of the yellowish discharge, and an increase in vaginal pH > 4.5, membranes, and preterm delivery. and inflammation with leukocyte infiltration. (1) Severe, persistent, or chronic forms of AV can also be referred to as Epidemiology desquamative inflammatory vaginitis (DIV). (2, 3) In a study of 631 patients attending routine prenatal care BV is a common vaginal disorder associated with the from a vaginitis clinic, 7.9% had moderate to severe AV overgrowth of anaerobic bacteria, a distinct vaginal signs and symptoms and 6% had ‘full-blown’ BV. (1) malodorous discharge, but is not usually associated with a strong vaginal inflammatory immune response. Like AV, In a study of 3,000 women, 4.3% were found to have severe BV also includes an elevation of the vaginal pH > 4.5 and AV, also called DIV.
    [Show full text]
  • The Vaginal Microbiome of Sub-Saharan African Women: Revealing Important Gaps in the Era of Next-Generation Sequencing
    The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing Nkechi Martina Odogwu1, Oladapo O. Olayemi2 and Akinyinka O. Omigbodun2 1 Pan African University of Life and Earth Science Institute, Department of Obstetrics and Gynecology, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria 2 Department of Obstetrics and Gynecology, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria ABSTRACT Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
    [Show full text]
  • The Vaginal Microbiome Related to Reproductive Traits in Beef Heifers
    University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2018 The aV ginal Microbiome Related to Reproductive Traits in Beef Heifers Maryanna Wells McClure University of Arkansas, Fayetteville Follow this and additional works at: http://scholarworks.uark.edu/etd Part of the Animal Studies Commons Recommended Citation McClure, Maryanna Wells, "The aV ginal Microbiome Related to Reproductive Traits in Beef Heifers" (2018). Theses and Dissertations. 2799. http://scholarworks.uark.edu/etd/2799 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected], [email protected]. The Vaginal Microbiome Related to Reproductive Traits in Beef Heifers A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Animal Science by Maryanna W. McClure University of Tennessee at Martin Bachelor of Science in Animal Science, 2016 May 2018 University of Arkansas This thesis is approved for recommendation to the Graduate Council _______________________________ Jiangchao Zhao, Ph. D. Thesis Director ________________________________ ________________________________ Rick Rorie, Ph. D. Charles Rosenkrans, Ph. D. Committee Member Committee Member _______________________________ Michael Looper, Ph. D. Committee Member ABSTRACT The greatest impact on profitability of a commercial beef operation is reproduction. In the human vaginal microbiome, dominance by Lactobacillus is a sign of reproductive health and fit- ness. In other species (non-human primates and ewes), Lactobacillus is found in low amounts and dominators of these microbial communities are considered to be pathogenic in humans.
    [Show full text]
  • The Vaginal Microbiota, Bacterial Biofilms and Polymeric Drug
    pharmaceutics Review The Vaginal Microbiota, Bacterial Biofilms and Polymeric Drug-Releasing Vaginal Rings Louise Carson 1, Ruth Merkatz 2, Elena Martinelli 2, Peter Boyd 1, Bruce Variano 2 , Teresa Sallent 2 and Robert Karl Malcolm 1,* 1 School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, UK; [email protected] (L.C.); [email protected] (P.B.) 2 Population Council, One Dag Hammarskjold Plaza, New York, NY 10017, USA; [email protected] (R.M.); [email protected] (E.M.); [email protected] (B.V.); [email protected] (T.S.) * Correspondence: [email protected] Abstract: The diversity and dynamics of the microbial species populating the human vagina are increasingly understood to play a pivotal role in vaginal health. However, our knowledge about the potential interactions between the vaginal microbiota and vaginally administered drug delivery systems is still rather limited. Several drug-releasing vaginal ring products are currently marketed for hormonal contraception and estrogen replacement therapy, and many others are in preclinical and clinical development for these and other clinical indications. As with all implantable polymeric devices, drug-releasing vaginal rings are subject to surface bacterial adherence and biofilm formation, mostly associated with endogenous microorganisms present in the vagina. Despite more than Citation: Carson, L.; Merkatz, R.; 50 years since the vaginal ring concept was first described, there has been only limited study and Martinelli, E.; Boyd, P.; Variano, B.; reporting around bacterial adherence and biofilm formation on rings. With increasing interest in the Sallent, T.; Malcolm, R.K. The Vaginal vaginal microbiome and vaginal ring technology, this timely review article provides an overview Microbiota, Bacterial Biofilms and of: (i) the vaginal microbiota, (ii) biofilm formation in the human vagina and its potential role in Polymeric Drug-Releasing Vaginal Rings.
    [Show full text]
  • Association of Bacterial Vaginosis with Periodontitis in a Cross-Sectional
    www.nature.com/scientificreports OPEN Association of bacterial vaginosis with periodontitis in a cross‑sectional American nationwide survey Cláudia Escalda1, João Botelho1,2, José João Mendes1 & Vanessa Machado1,2* To explore the association between bacterial vaginosis (BV) and periodontitis (PD) and to determine whether PD and BV might be linked with systemic serum alterations. We used the National Health and Nutrition Examination Survey 2001–2004, with women aged 18–49 years old and diagnosed with or without BV according to Nugent’s method. PD was defned according to the 2012 case defnition. We compared serum counts according to the presence of PD and the presence of BV. Multivariable regression was used to explore and identify relevant variables towards the presence of BV. 961 women fulflled the inclusion criteria. In women with BV, PD was associated with higher infammation, characterized by increased white blood cells (p = 0.006) and lymphocyte (p = 0.009) counts. Predictive models presented a statistically signifcant association between PD and BV [Odds Ratio (OD) = 1.69, 95% Confdence Interval (CI): 1.09–2.61 for periodontitis; OD = 2.37, 95% CI: 1.30–4.29 for severe PD]. Fully adjusted models for age, smoking, body mass index, diabetes mellitus and number of systemic conditions reinforced this association [OD = 1.71, 95% CI: 1.06–2.76 for PD; OD = 2.21, 95% CI: 1.15– 4.25 for severe PD]. An association between BV and PD is conceivable. PD was associated with higher systemic markers of infammation in women with BV. Our data is novel and could serve as a foundation to guide future studies in the confrmation of this association and the underlying mechanisms.
    [Show full text]
  • A Clinical Pilot Study on the Effect of the Probiotic Lacticaseibacillus
    www.nature.com/scientificreports OPEN A clinical pilot study on the efect of the probiotic Lacticaseibacillus rhamnosus TOM 22.8 strain in women with vaginal dysbiosis Alessandra Pino1,4, Agnese Maria Chiara Rapisarda2,4, Salvatore Giovanni Vitale2, Stefano Cianci3, Cinzia Caggia1, Cinzia Lucia Randazzo1* & Antonio Cianci2 Lactobacilli with probiotic features play an essential role in maintaining a balanced vaginal microbiota and their administration has been suggested for the treatment and prevention of vaginal dysbiosis. The present study was aimed to in vitro and in vivo investigate the probiotic potential of the Lacticaseibacillus rhamnosus TOM 22.8 strain, isolated from the vaginal ecosystem of a healthy woman. For this purpose, safety and functional properties were in depth evaluated. The strain exhibited a broad spectrum of antagonistic activity against vaginal pathogens; adhesion capacity to both the vaginal VK2/E6E7 and the intestinal Caco-2 cells; anti-infammatory and antioxidant activities, suggesting its promising probiotic features. In addition, an in vivo pilot-study was planned. Based on both clinical and microbiological parameters, the oral or vaginal strain administration, determined a signifcant pathogens reduction after 10 days of administration and a maintenance of eubiosis up to 30 days after the end of the treatment. Therefore, the L. rhamnosus TOM 22.8 strain can be proposed as valuable oral and/or vaginal treatment for vaginal dysbiosis. Te vaginal microbiota of reproductive age healthy women is dominated by lactobacilli, which play an essential protecting role against genitourinary pathogens1,2. It is noteworthy that specifc lactobacilli are interesting for use as probiotics, which are defned, by the Food and Agriculture Organization of the United Nations and World Health Organization, as “live microorganisms which when administered in adequate amounts, confers health benefts to the host”3.
    [Show full text]
  • The Role of Microbial Insults in Chronic Inflammatory Diseases
    æREVIEW ARTICLE Genetic dysbiosis: the role of microbial insults in chronic inflammatory diseases Luigi Nibali1*, Brian Henderson2, Syed Tariq Sadiq3 and Nikos Donos1 1Periodontology Unit and Department of Clinical Research, UCL Eastman Dental Institute, University College London, London, United Kingdom; 2Division of Microbial Diseases, UCL Eastman Dental Institute, London, United Kingdom; 3Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom Thousands of bacterial phylotypes colonise the human body and the host response to this bacterial challenge greatly influences our state of health or disease. The concept of infectogenomics highlights the importance of host genetic factors in determining the composition of human microbial biofilms and the response to this microbial challenge. We hereby introduce the term ‘genetic dysbiosis’ to highlight the role of human genetic variants affecting microbial recognition and host response in creating an environment conducive to changes in the normal microbiota. Such changes can, in turn, predispose to, and influence, diseases such as: cancer, inflammatory bowel disease, rheumatoid arthritis, psoriasis, bacterial vaginosis and periodontitis. This review presents the state of the evidence on host genetic factors affecting dysbiosis and microbial misrecognition (i.e. an aberrant response to the normal microbiota) and highlights the need for further research in this area. Keywords: genetic; dysbiosis; microbiome; inflammation Received: 2 October 2013; Revised: 22 December 2013; Accepted: 4 January 2014; Published: 25 February 2014 uring their evolution, vertebrates and their colo- individual human will, as a rule, have a subset of his or nising microbes have evolved mechanisms to live her own colonising bacteria in different body habitats, Din symbiosis with each other.
    [Show full text]
  • When a Neonate Is Born, So Is a Microbiota
    life Review When a Neonate Is Born, So Is a Microbiota Alessandra Coscia 1, Flaminia Bardanzellu 2,* , Elisa Caboni 2, Vassilios Fanos 2 and Diego Giampietro Peroni 3 1 Neonatology Unit, Department of Public Health and Pediatrics, Università degli Studi di Torino, 10124 Turin, Italy; [email protected] 2 Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, SS 554 km 4,500, 09042 Monserrato, Italy; [email protected] (E.C.); [email protected] (V.F.) 3 Clinical and Experimental Medicine Department, Section of Pediatrics, University of Pisa, Via Roma, 55, 56126 Pisa PI, Italy; [email protected] * Correspondence: bardanzellu.fl[email protected] Abstract: In recent years, the role of human microbiota as a short- and long-term health promoter and modulator has been affirmed and progressively strengthened. In the course of one’s life, each subject is colonized by a great number of bacteria, which constitute its specific and individual microbiota. Human bacterial colonization starts during fetal life, in opposition to the previous paradigm of the “sterile womb”. Placenta, amniotic fluid, cord blood and fetal tissues each have their own specific microbiota, influenced by maternal health and habits and having a decisive influence on pregnancy outcome and offspring outcome. The maternal microbiota, especially that colonizing the genital system, starts to influence the outcome of pregnancy already before conception, modulating fertility and the success rate of fertilization, even in the case of assisted reproduction techniques. During the perinatal period, neonatal microbiota seems influenced by delivery mode, drug administration and many other conditions. Special attention must be reserved for early neonatal nutrition, because breastfeeding allows the transmission of a specific and unique lactobiome able to modulate and positively affect the neonatal gut microbiota.
    [Show full text]
  • 528 1. ABSTRACT 2. INTRODUCTION Vaginal Microbiota Dysmicrobism
    [Frontiers In Bioscience, Elite, 10, 528-536, June 1, 2018] Vaginal microbiota dysmicrobism and role of biofilm-forming bacteria Giuseppina Campisciano1, Nunzia Zanotta1, Vincenzo Petix1, Lucia Corich1, Francesco De Seta1,2, Manola Comar1,2 1Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Via dell’Istria 65/1, Trieste, 34137 Italy, 2Department of Medical Sciences - University of Trieste, Piazzale Europa 1, Trieste, 34127 Italy TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Materials and methods 3.1. Patients and samples 3.2. Sample processing, Ion Torrent sequencing 3.3. Data analysis 4. Results 5. Discussion 6. Acknowledgment 7. References 1. ABSTRACT Bacterial vaginosis involves the presence pregnancy, breastfeeding and sexual practices (1–4). of a polymicrobial biofilm on the vaginal epithelium, A plethora of microbial species co-exists in the vaginal guaranteeing immune escape and spread of antibiotic niche, 70%–90% of which are Lactobacilli (5). Their resistance. To spot known biofilm-forming bacteria, dominance is pivotal in maintaining the vaginal health, we profiled the vaginal microbiome of sixty-four thanks to their production of hydroxyl radicals, lactic symptomatic women suffering from a different grade acid, bacteriocins, hydrogen peroxide and probiotics of vaginal disorders and sixty asymptomatic healthy (6). Indeed, Lactobacilli are reported to be significantly women. Specific microbial profiles distinguished decreased in bacterial vaginosis (BV) (7), which is a symptomatic from asymptomatic women and non-specific (predominantly anaerobic) polymicrobial characterized the grade of dysmicrobism within the biofilm infection, where the predominant bacteria in symptomatic group. Lactobacillus crispatus and iners the biofilm are not the resident Lactobacilli (8–11). predominated on the healthy vaginal mucosa, while Above all, the most effective mechanism by which the Lactobacillus gasseri predominated in the intermediate Lactobacilli protect the vaginal niche is the production dysmicrobism.
    [Show full text]