DOCSLIB.ORG

Role of the Microbiome in Human Development Gut: First Published As 10.1136/Gutjnl-2018-317503 on 22 January 2019

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Role of the Microbiome in Human Development Gut: First Published As 10.1136/Gutjnl-2018-317503 on 22 January 2019 Recent advances in basic science Role of the microbiome in human development Gut: first published as 10.1136/gutjnl-2018-317503 on 22 January 2019. Downloaded from Maria Gloria Dominguez-Bello,1 Filipa Godoy-Vitorino,2 Rob Knight,3 Martin J Blaser4 1Department of Biochemistry ABStract remain unknown. Abrupt changes in environmental and Microbiology, Rutgers, the The host-microbiome supraorganism appears to have conditions can lead to mal-adaptations (adaptations State University of New Jersey, that were beneficial when first took place, but not New Brunswick, New Jersey, coevolved and the unperturbed microbial component USA of the dyad renders host health sustainable. This anymore under new environmental conditions). 2Department of Microbiology coevolution has likely shaped evolving phenotypes in Today, modernisation and urbanisation pose exactly and Medical Zoology, University all life forms on this predominantly microbial planet. this challenge to human health. of Puerto Rico, School of The microbiota seems to exert effects on the next Together with their microbionts (microbiota Medicine, San Juan, Puerto Rico, USA generation from gestation, via maternal microbiota and members), hosts evolved an immune system, which 3Department of Computer immune responses. The microbiota ecosystems develop, prevents microbial colonisation in the topological Science and Engineering, restricted to their epithelial niches by the host immune interior of the body. Host immune systems evolved University of California, San system, concomitantly with the host chronological complex mechanisms to identify and destroy Diego, California, USA 4 invading microbes, whether they are microbionts Department of Medicine, New development, providing early modulation of physiological York University Langone Medical host development and functions for nutrition, immunity or primary pathogens that cross into forbidden Center, New York City, New and resistance to pathogens at all ages. Here, we review territories. Immune molecules evolved more than York, USA the role of the microbiome in human development, 500 million years ago, in choanoflagellates, unicel- including evolutionary considerations, and the maternal/ lular progenitors of metazoans,7 and there is Correspondence to fetal relationships, contributions to nutrition and growth. growing evidence that the innate immune system— Professor Maria antimicrobial peptides and repertoire of pattern Gloria Dominguez-Bello, We also discuss what constitutes a healthy microbiota, Department of Biochemistry and how antimicrobial modern practices are impacting the recognition receptors—evolved in response to the Microbiology, Rutgers, the State human microbiota, the associations between microbiota need for controlling the epithelium-colonising University of New Jersey, New perturbations, host responses and diseases rocketing in microbiota.8 Brunswick, NJ 08901, USA; urban societies and potential for future restoration. The human immune system restricts microbiota mg. dominguez- bello@ rutgers. edu to their natural niches in the body ‘exterior’ and invaginations: epithelia that cover the body (such Received 3 September 2018 as skin and mucosa) and the gut, which, strictly Revised 15 December 2018 speaking, is a hollow tube that traverses the body Accepted 31 December 2018 EVOLUTION OF THE MICROBIOTA 1 with the influx of external materials (diet). Thus, Published Online First Bacteria arose about 3.8 billion years ago, and 22 January 2019 the eukaryotic lineage, which includes humans, the microbiota occupies the interface between our http://gut.bmj.com/ arose after the oxygenation of earth’s atmosphere bodies and the exterior, and interactions with the 2.2–2.4 billion years ago.2 Together with archaea, environment (including diet, sun-light, bathing, protists and fungi, bacteria remained free-living cosmetics) cross this interface. The microbiota is at single cells although some became host-associated. the same time self and non-self: it is part of our Thus, an animal holobiont (the animal host and its biology, but consists of fast-evolving entities that evolved microbial communities)3 spans the phylo- respond rapidly on physiological, ecological and genetic tree: the animal host, plus its associated evolutionary timescales to external perturbations on September 27, 2021 by guest. Protected copyright. microbiota such as bacteria, archaea, fungi, protists, in ways that affect our phenotypes (figure 1). The helminths and viruses (figure 1). The collective gut microbiota have been shown to impact diverse genome content of microbiota or the microbial physiological processes ranging from adiposity/ metagenome was coined the microbiome,4 although obesity, to energy metabolism, blood pressure microbiome and microbiota are currently used control, glucose homeostasis, clotting risks or even interchangeably. behaviour. In each case, there are mechanistic ties By coevolving with the host, the microbiome has between gut microbes, metabolites they generate shaped phenotypes in our ancestral lineages. The and host receptors and phenotypic responses. congruence of the phylogenetic trees of intestinal Evolutionary considerations are crucial to under- bacterial microbiota and primates5 demonstrates standing the nature of microbial-host interactions, host-microbiota coevolution and implies with- perturbations and health consequences and will in-species transmission of microbes across gener- ultimately need to be understood and exploited in ations. Through the process of natural selection, order to prevent and treat ‘modern’ diseases. © Author(s) (or their mutations lead to evolutionary adaptations to employer(s)) 2019. Re-use permitted under CC BY-NC. No environmental conditions and increased fitness in DEVELOPMENT AND THE MICROBIOTA: FROM commercial re-use. See rights these environments. Human environments have FertILISatION TO BIrtH and permissions. Published changed dramatically during human evolution, and In some insects, bacteria colonise egg capsules by BMJ. dietary changes and exposures to famine have been during mating, and the individual is colonised 9 To cite: Dominguez- major selective pressures. While there is evidence before hatching. In mammals, fertilisation Bello MG, Godoy-Vitorino F, of adaptive survival traits to starvation on the occurs in an immune-protected organ, the uterus. Knight R, et al. Gut human genome,6 human microbiome adaptations However, immune protection means lack of colo- 2019;68:1108–1114. that offer energy-sparing traits for the human host nisation, but not necessarily sterility at all times. 1108 Dominguez-Bello MG, et al. Gut 2019;68:1108–1114. doi:10.1136/gutjnl-2018-317503 Recent advances in basic science Box 1 Highlights of the holobiont evolution Gut: first published as 10.1136/gutjnl-2018-317503 on 22 January 2019. Downloaded from ► Evolution of all complex life forms has occurred in associations with bacteria, the first forms of life on earth. ► The human body carries representatives of all branches of the tree of life (Animalia-Homo sapiens, and protozoa, fungi, archaea, bacteria conforming the microbiota). ► The microbiota has been transferred throughout generations of humans, with the matrilineal line transferring the primordial birth microbiota. ► The vertical human transmission has led to conservation of a phylogenetic signal in human microbiota communities. mammals, the Monotremes, lay eggs through a single canal— the cloaca—shared for excretion and reproduction. Placental mammals evolved separate canals for reproduction (vagina), excretion of faeces (anus) and urine (urethra), and the birth canal Figure 1 Evolution of the holobiont and vertical transmission through is always adjacent to the rectum (but not the urethra), providing human generations. an efficient mechanism for intergenerational transmission of both vaginal and gut microbes. Rupture of the chorioamniotic Indeed, it seems possible that some bacterial cells of the uterine membrane allows exposure of the baby to the maternal vaginal cervix10 may enter with the sperm during fertilisation and reach and perineal faecal microbes. Indeed, prolonged labour poses 28 the egg at the time of fertilisation, implantation or early embry- a risk of infection by opportunistic microbionts. Infants are onic development. Regardless, immunity appears to preclude the naturally born with their skin and mouth covered by maternal 29 30 establishment of a microbial community in immune-protected inocula and have swallowed these microbes, supported by 31 31 organs. Uterus, placenta, fetus as well as blood appear void of the observation of both DNA and live bacteria in the meco- a microbiota, although they may contain bacterial DNA or even nium. Thus, we inherit the primordial microbiota from our some isolated live bacteria. There is a current controversy about mothers, grandmothers and further on the matrilineal line, with whether the presence of bacterial DNA contradicts the notion of microbial vertical transmission extending back to earlier ances- 32 sterility, but the presence of circulating bacterial DNA, such in tors (box 1). Whether the primordial inoculum contains most the blood11 or placenta,12 or even sporadic presence of an alive microbes that will be nurtured by the child, and which maternal intruder bacteria does not demonstrate a living blood micro- strains colonise which parts of the baby’s body and their func- biota and does not challenge the current paradigm of sterility tions, the paternal and sibling contribution along with the infant’s
Load more

Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • Microbiota of Human Precolostrum and Its Potential Role As a Source Of
    www.nature.com/scientificreports OPEN Microbiota of human precolostrum and its potential role as a source of bacteria to the infant mouth Received: 24 October 2018 Lorena Ruiz1,2, Rodrigo Bacigalupe3, Cristina García-Carral2,4, Alba Boix-Amoros3, Accepted: 2 April 2019 Héctor Argüello5, Camilla Beatriz Silva2,6, Maria de los Angeles Checa7, Alex Mira3 & Published: xx xx xxxx Juan M. Rodríguez 2 Human milk represents a source of bacteria for the initial establishment of the oral (and gut) microbiomes in the breastfed infant, however, the origin of bacteria in human milk remains largely unknown. While some evidence points towards a possible endogenous enteromammary route, other authors have suggested that bacteria in human milk are contaminants from the skin or the breastfed infant mouth. In this work 16S rRNA sequencing and bacterial culturing and isolation was performed to analyze the microbiota on maternal precolostrum samples, collected from pregnant women before delivery, and on oral samples collected from the corresponding infants. The structure of both ecosystems demonstrated a high proportion of taxa consistently shared among ecosystems, Streptococcus spp. and Staphylococcus spp. being the most abundant. Whole genome sequencing on those isolates that, belonging to the same species, were isolated from both the maternal and infant samples in the same mother-infant pair, evidenced that in 8 out of 10 pairs both isolates were >99.9% identical at nucleotide level. The presence of typical oral bacteria in precolostrum before contact with the newborn indicates that they are not a contamination from the infant, and suggests that at least some oral bacteria reach the infant’s mouth through breastfeeding.
    [Show full text]
  • Porphyromonas Gingivalis, Strain F0566 Catalog
    Product Information Sheet for HM-1141 Porphyromonas gingivalis, Strain F0566 immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze- thaw cycles should be avoided. Catalog No. HM-1141 Growth Conditions: For research use only. Not for human use. Media: Supplemented Tryptic Soy broth or equivalent Contributor: Tryptic Soy agar with 5% defibrinated sheep blood or Floyd E. Dewhirst, D.D.S., Ph.D., Senior Member of the Staff, Supplemented Tryptic Soy agar or equivalent Department of Microbiology and Jacques Izard, Assistant Incubation: Member of the Staff, Department of Molecular Genetics, The Temperature: 37°C Forsyth Institute, Cambridge, Massachusetts, USA Atmosphere: Anaerobic Propagation: Manufacturer: 1. Keep vial frozen until ready for use, then thaw. BEI Resources 2. Transfer the entire thawed aliquot into a single tube of broth. Product Description: 3. Use several drops of the suspension to inoculate an Bacteria Classification: Porphyromonadaceae, agar slant and/or plate. Porphyromonas 4. Incubate the tube, slant and/or plate at 37°C for 24 to Species: Porphyromonas gingivalis 72 hours. Broth cultures should include shaking. Strain: F0566 Original Source: Porphyromonas gingivalis (P. gingivalis), Citation: strain F0566 was isolated in October 1987 from the tooth Acknowledgment for publications should read “The following of a patient diagnosed with moderate periodontitis in the reagent was obtained through BEI Resources, NIAID, NIH as United States.1 part of the Human Microbiome Project: Porphyromonas Comments: P. gingivalis, strain F0566 (HMP ID 1989) is a gingivalis, Strain F0566, HM-1141.” reference genome for The Human Microbiome Project (HMP). HMP is an initiative to identify and characterize Biosafety Level: 2 human microbial flora.
    [Show full text]
  • The Effect of Porphyromonas Levii on Macrophage Function and Pro-Inflammatory Cytokine Production
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies Legacy Theses 2001 Macrophages in bovine footrot: the effect of porphyromonas levii on macrophage function and pro-inflammatory cytokine production Walter, Michaela Roylene Valerie Walter, M. R. (2001). Macrophages in bovine footrot: the effect of porphyromonas levii on macrophage function and pro-inflammatory cytokine production (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/19168 http://hdl.handle.net/1880/41129 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Macrophages in Bovine Footrot: The Effect of Purphyrontonas fevii on Macrophage Function and Pro-Inilammatory Cytokine Production. Michaela Roylene Valerie Walter A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTERS OF SCIENCE DEPARTMENT OF BIOLOGICAL SCIENCES CALGARY, ALBERTA MAY, 200 1 O Michaela Roylene Valerie Walter 200 1 National Library Biiliothbque nationale du Canada Acquisitions and Acquisitions et Bibliographic Services services bibliographiques The author has granted a non- L'auteur a accorde une licence non exclusive licence allowing the exclusive pennettant a la National Libmy of Canada to Bibliotheque nationale du Canada de reproduce, loan, distn'bute or sell reproduke, preter, distribuer ou copies of this thesis in microform, vendre des copies de cette these sous paper or electronic formats.
    [Show full text]
  • S41598-018-20067-Z.Pdf
    www.nature.com/scientificreports OPEN Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fmbria Received: 11 May 2017 Accepted: 12 January 2018 from the periodontal pathogen Published: xx xx xxxx Porphyromonas gingivalis Michael Hall1, Yoshiaki Hasegawa2, Fuminobu Yoshimura2 & Karina Persson1 Very little is known about how fmbriae of Bacteroidetes bacteria are assembled. To shed more light on this process, we solved the crystal structures of the shaft protein Mfa1, the regulatory protein Mfa2, and the tip protein Mfa3 from the periodontal pathogen Porphyromonas gingivalis. Together these build up part of the Mfa1 fmbria and represent three of the fve proteins, Mfa1-5, encoded by the mfa1 gene cluster. Mfa1, Mfa2 and Mfa3 have the same overall fold i.e., two β-sandwich domains. Upon polymerization, the frst β-strand of the shaft or tip protein is removed by indigenous proteases. Although the resulting void is expected to be flled by a donor-strand from another fmbrial protein, the mechanism by which it does so is still not established. In contrast, the frst β-strand in Mfa2, the anchoring protein, is frmly attached by a disulphide bond and is not cleaved. Based on the structural information, we created multiple mutations in P. gingivalis and analysed their efect on fmbrial polymerization and assembly in vivo. Collectively, these data suggest an important role for the C-terminal tail of Mfa1, but not of Mfa3, afecting both polymerization and maturation of downstream fmbrial proteins. Humans co-exist with microorganisms that play signifcant roles in our biology. Te largest bacterial population is found in the gut, where species of Bacteroidetes are the most common Gram-negative anaerobes1.
    [Show full text]
  • Porphyromonas Gingivalis, Strain F0185 Catalog
    Product Information Sheet for HM-1140 Porphyromonas gingivalis, Strain F0185 immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze- thaw cycles should be avoided. Catalog No. HM-1140 Growth Conditions: For research use only. Not for human use. Media: Supplemented Tryptic Soy broth or equivalent Contributor: Tryptic Soy agar with 5% defibrinated sheep blood or Floyd E. Dewhirst, D.D.S., Ph.D., Senior Member of the Staff, Supplemented Tryptic Soy agar or equivalent Department of Microbiology and Jacques Izard, Assistant Incubation: Member of the Staff, Department of Molecular Genetics, The Temperature: 37°C Forsyth Institute, Cambridge, Massachusetts, USA Atmosphere: Anaerobic Propagation: Manufacturer: 1. Keep vial frozen until ready for use, then thaw. BEI Resources 2. Transfer the entire thawed aliquot into a single tube of broth. Product Description: 3. Use several drops of the suspension to inoculate an Bacteria Classification: Porphyromonadaceae, agar slant and/or plate. Porphyromonas 4. Incubate the tube, slant and/or plate at 37°C for 24 to Species: Porphyromonas gingivalis 72 hours. Broth cultures should include shaking. Strain: F0185 Original Source: Porphyromonas gingivalis (P. gingivalis), Citation: strain F0185 was isolated in December 1985 from the Acknowledgment for publications should read “The following tooth of a patient diagnosed with juvenile periodontitis in reagent was obtained through BEI Resources, NIAID, NIH as the United States.1 part of the Human Microbiome Project: Porphyromonas Comments: P. gingivalis, strain F0185 (HMP ID 1988) is a gingivalis, Strain F0185, HM-1140.” reference genome for The Human Microbiome Project (HMP). HMP is an initiative to identify and characterize Biosafety Level: 2 human microbial flora.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland).
    [Show full text]
  • Product Sheet Info
    Product Information Sheet for HM-1072 Porphyromonas gingivalis, Strain F0569 phase of a liquid nitrogen freezer is recommended. Freeze- thaw cycles should be avoided. Catalog No. HM-1072 Growth Conditions: Media: For research use only. Not for human use. Supplemented Tryptic Soy broth or equivalent Tryptic Soy agar (TSA) with 5% defibrinated sheep blood or Contributor: Supplemented Tryptic Soy agar or equivalent Floyd E. Dewhirst, D.D.S, Ph.D., Senior Member of the Staff, Note: HM-1072 did not grow on TSA with 5% defribrinated Department of Microbiology and Jacques Izard, Assistant sheep blood. Member of the Staff, Department of Molecular Genetics, The Incubation: Forsyth Institute, Cambridge, Massachusetts, USA Temperature: 37°C Atmosphere: Anaerobic Manufacturer: Propagation: BEI Resources 1. Keep vial frozen until ready for use, then thaw. 2. Transfer the entire thawed aliquot into a single tube of Product Description: broth. Bacteria Classification: Porphyromonadaceae, 3. Use several drops of the suspension to inoculate an Porphyromonas agar slant and/or plate. Species: Porphyromonas gingivalis 4. Incubate the tube, slant and/or plate at 37°C for 1 to 7 Strain: F0569 days. Broth cultures should include shaking. Original Source: Porphyromonas gingivalis (P. gingivalis), strain F0569 was isolated in 1984 from the subgingival Citation: plaque biofilm of a 39-year-old male patient diagnosed Acknowledgment for publications should read “The following 1,2 with periodontitis in the United States. reagent was obtained through BEI Resources, NIAID, NIH as Comments: P. gingivalis, strain F0569 (HMP ID 1554) is a part of the Human Microbiome Project: Porphyromonas reference genome for The Human Microbiome Project gingivalis, Strain F0569, HM-1072.” (HMP).
    [Show full text]
  • Intracellular Porphyromonas Gingivalis Promotes the Tumorigenic Behavior of Pancreatic Carcinoma Cells
    cancers Article Intracellular Porphyromonas gingivalis Promotes the Tumorigenic Behavior of Pancreatic Carcinoma Cells JebaMercy Gnanasekaran 1, Adi Binder Gallimidi 1,2, Elias Saba 1, Karthikeyan Pandi 1, 1 2 1 1 1 Luba Eli Berchoer , Esther Hermano , Sarah Angabo , Hasna0a Makkawi , Arin Khashan , 1 2, , 1, , Alaa Daoud , Michael Elkin * y and Gabriel Nussbaum * y 1 The Institute of Dental Sciences, Hebrew University, Hadassah Faculty of Dental Medicine, Jerusalem 9112102, Israel; [email protected] (J.G.); [email protected] (A.B.G.); [email protected] (E.S.); [email protected] (K.P.); [email protected] (L.E.B.); [email protected] (S.A.); [email protected] (H.M.); [email protected] (A.K.); [email protected] (A.D.) 2 Sharett Oncology Institute, Hadassah-Hebrew University Medical Center, Jerusalem 9112102, Israel; [email protected] * Correspondence: [email protected] (M.E.); [email protected] (G.N.); Tel.: +972-2-6776782 (M.E.); +972-2-6758581 (G.N.) Equal contribution (these authors share the senior authorship). y Received: 2 July 2020; Accepted: 14 August 2020; Published: 18 August 2020 Abstract: Porphyromonas gingivalis is a member of the dysbiotic oral microbiome associated with oral inflammation and periodontal disease. Intriguingly, epidemiological studies link P. gingivalis to an increased risk of pancreatic cancer. Given that oral bacteria are detected in human pancreatic cancer, and both mouse and human pancreata harbor microbiota, we explored the involvement of P. gingivalis in pancreatic tumorigenesis using cell lines and a xenograft model.
    [Show full text]
  • Oral Microbiome and Host Health: Review on Current Advances in Genome-Wide Analysis
    applied sciences Review Oral Microbiome and Host Health: Review on Current Advances in Genome-Wide Analysis Young-Dan Cho, Kyoung-Hwa Kim , Yong-Moo Lee, Young Ku and Yang-Jo Seol * Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul 03080, Korea; [email protected] (Y.-D.C.); [email protected] (K.-H.K.); [email protected] (Y.-M.L.); [email protected] (Y.K.) * Correspondence: [email protected]; Tel.: +82-2-2072-0308 Abstract: The oral microbiome is an important part of the human microbiome. The oral cavity has the second largest microbiota after the intestines, and its open structure creates a special environment. With the development of technology such as next-generation sequencing and bioinformatics, exten- sive in-depth microbiome studies have become possible. They can also be applied in the clinical field in terms of diagnosis and treatment. Many microbiome studies have been performed on oral and systemic diseases, showing a close association between the two. Understanding the oral microbiome and host interaction is expected to provide future directions to explore the functional and metabolic changes in diseases, and to uncover the molecular mechanisms for drug development and treatment that facilitate personalized medicine. The aim of this review was to provide comprehension regarding research trends in oral microbiome studies and establish the link between oral microbiomes and systemic diseases based on the latest technique of genome-wide analysis. Keywords: oral microbiome; oral disease; systemic disease; genome-wide analysis; personal- Citation: Cho, Y.-D.; Kim, K.-H.; Lee, ized medicine Y.-M.; Ku, Y.; Seol, Y.-J.
    [Show full text]
  • Bacterial Diversity of Symptomatic Primary Endodontic Infection by Clonal Analysis
    ORIGINAL RESEARCH Endodontic Therapy Bacterial diversity of symptomatic primary endodontic infection by clonal analysis Abstract: The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Letícia Maria Menezes NÓBREGA(a) Francisco MONTAGNER(b) Samples were collected from 10 patients and submitted to bacterial Adriana Costa RIBEIRO(c) DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. (c) Márcia Alves Pinto MAYER A bacterial genomic library was constructed and bacterial diversity Brenda Paula Figueiredo de Almeida GOMES(a) was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84%) were different species and 29 (38.15%) (a) Universidade Estadual de Campinas were taxa reported as yet-uncultivable or as yet-uncharacterized (UNICAMP), Piracicaba Dental School, Endodontics Division, Piracicaba, SP, Brazil. species. Prevotella spp., Fusobacterium nucleatum, Filifactor alocis, and Peptostreptococcus stomatis were the most frequently detected species, (b) Universidade Federal do Rio Grande do Sul (UFRGS), Department of Conservative followed by Dialister invisus, Phocaeicola abscessus, the uncharacterized Dentistry, Porto Alegre, RS, Brazil. Lachnospiraceae oral clone, Porphyromonas spp., and Parvimonas micra. (c) Universidade de São Paulo (USP), Institute Eight phyla were detected and the most frequently identified taxa of Biomedical Science, Department of Oral belonged to the phylum Firmicutes (43.5%), followed by Bacteroidetes Microbiology, São Paulo, SP, Brazil. (22.5%) and Proteobacteria (13.2%). No species was detected in all studied samples and some species were identified in only one case.
    [Show full text]
  • Porphyromonas Canoris Sp. Nov., an Asaccharolytic, Black- Pigmented Species from the Gingival Sulcus of Dogs DARIA N
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1994, p. 204-208 Vol. 44, No. 2 0020-7713/94/$04.00+O Copyright 0 1994, International Union of Microbiological Societies Porphyromonas canoris sp. nov., an Asaccharolytic, Black- Pigmented Species from the Gingival Sulcus of Dogs DARIA N. LOVE,'" J. KARJALAINEN,2 A. IVLNERVO,~B. FORSBLOM,2 E. SARKIALA,3 G. D. BAILEY,' D. I. WIGNEY,' AND H. JOUSIMIES-SOMER2 Department of Veterinary Patholoa, University of Sydney, Sydney, New South Wales 2006, Australia, and Anaerobe Reference Laboratory, National Public Health Institute, 00300 Helsinki, and College of Veterinary Medicine, 00530 Helsinki, Finland A new species, Porphyromonas canoris, is proposed for black-pigmented asaccharolytic strains isolated from subgingival plaque samples from dogs with naturally occurring periodontal disease. This bacterium is an obligately anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organism. On laked rabbit blood or sheep blood agar plates, colonies are light brown to greenish brown after 2 to 4 days of incubation and dark brown after 14 days of incubation. Colonies on egg yolk agar and on nonhemolyzed sheep blood agar are orange. The cells do not grow in the presence of 20% bile and have a guanine-plus-cytosine content of 49 to 51 mol%. The type strain is VPB 4878 (= NCTC 12835). The average levels of DNA-DNA hybridiza- tion between P. canoris strains and other members of the genus Porphyromonas are as follows: Porphyromonas gingivalis ATCC 33277T (T = type strain), 6.5%; Porphyromonas gingivalis cat strain VPB 3492, 5%; Porphyromonas endodontalis ATCC 35406T, 1%; Porphyromonas salivosa NCTC 11362T, 5%; and Porphyromonas circumdentaria NCTC 12469T, 6%.
    [Show full text]