Uncovering Complex Microbiome Activities Via Metatranscriptomics
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The Oral Microbiome of Healthy Japanese People at the Age of 90
applied sciences Article The Oral Microbiome of Healthy Japanese People at the Age of 90 Yoshiaki Nomura 1,* , Erika Kakuta 2, Noboru Kaneko 3, Kaname Nohno 3, Akihiro Yoshihara 4 and Nobuhiro Hanada 1 1 Department of Translational Research, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 2 Department of Oral bacteriology, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 3 Division of Preventive Dentistry, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] (N.K.); [email protected] (K.N.) 4 Division of Oral Science for Health Promotion, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-45-580-8462 Received: 19 August 2020; Accepted: 15 September 2020; Published: 16 September 2020 Abstract: For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. -
Current Trends of Enterococci in Dairy Products: a Comprehensive Review of Their Multiple Roles
foods Review Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles Maria de Lurdes Enes Dapkevicius 1,2,* , Bruna Sgardioli 1,2 , Sandra P. A. Câmara 1,2, Patrícia Poeta 3,4 and Francisco Xavier Malcata 5,6,* 1 Faculty of Agricultural and Environmental Sciences, University of the Azores, 9700-042 Angra do Heroísmo, Portugal; [email protected] (B.S.); [email protected] (S.P.A.C.) 2 Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, 9700-042 Angra do Heroísmo, Portugal 3 Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; [email protected] 4 Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisboa, Portugal 5 LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 420-465 Porto, Portugal 6 FEUP—Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal * Correspondence: [email protected] (M.d.L.E.D.); [email protected] (F.X.M.) Abstract: As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, Citation: Dapkevicius, M.d.L.E.; and rheological properties, thus contributing to the development of its typical sensorial properties. Sgardioli, B.; Câmara, S.P.A.; Poeta, P.; Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autoly- Malcata, F.X. -
Oral Administration of Lactobacillus Gasseri SBT2055 Is Effective In
www.nature.com/scientificreports OPEN Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas Received: 23 June 2015 Accepted: 7 March 2017 gingivalis-accelerated periodontal Published: xx xx xxxx disease R. Kobayashi1, T. Kobayashi2, F. Sakai3, T. Hosoya3, M. Yamamoto1 & T. Kurita-Ochiai1 Probiotics have been used to treat gastrointestinal disorders. However, the effect of orally intubated probiotics on oral disease remains unclear. We assessed the potential of oral administration of Lactobacillus gasseri SBT2055 (LG2055) for Porphyromonas gingivalis infection. LG2055 treatment significantly reduced alveolar bone loss, detachment and disorganization of the periodontal ligament, and bacterial colonization by subsequent P. gingivalis challenge. Furthermore, the expression and secretion of TNF-α and IL-6 in gingival tissue was significantly decreased in LG2055-administered mice after bacterial infection. Conversely, mouse β-defensin-14 (mBD-14) mRNA and its peptide products were significantly increased in distant mucosal components as well as the intestinal tract to which LG2055 was introduced. Moreover, IL-1β and TNF-α production from THP-1 monocytes stimulated with P. gingivalis antigen was significantly reduced by the addition of humanβ -defensin-3. These results suggest that gastrically administered LG2055 can enhance immunoregulation followed by periodontitis prevention in oral mucosa via the gut immune system; i.e., the possibility of homing in innate immunity. Porphyromonas gingivalis, a Gram-negative anaerobe, is one of the major pathogens associated with chronic periodontitis, a disease that causes the destruction of alveolar bone, and, as a consequence, tooth loss1. Recent evidence suggests that this bacterium contributes to periodontitis by functioning as a keystone pathogen2, 3. -
Prosthetic Joint Infection Caused by Granulicatella Adiacens
Quénard et al. BMC Musculoskeletal Disorders (2017) 18:276 DOI 10.1186/s12891-017-1630-1 CASEREPORT Open Access Prosthetic joint infection caused by Granulicatella adiacens: a case series and review of literature Fanny Quénard1, Piseth Seng1,2,3* , Jean-Christophe Lagier3, Florence Fenollar3 and Andreas Stein1,2,3 Abstract Background: Bone and joint infection involving Granulicatella adiacens is rare, and mainly involved in cases of bacteremia and infectious endocarditis. Here we report three cases of prosthetic joint infection involving G. adiacens that were successfully treated with surgery and prolonged antimicrobial treatment. We also review the two cases of prosthetic joint infection involving G. adiacens that are reported in the literature. Case presentation: Not all five cases of prosthetic joint infection caused by G. adiacens were associated with bacteremia or infectious endocarditis. Dental care before the onset of infection was observed in two cases. The median time delay between arthroplasty implantation and the onset of infection was of 4 years (ranging between 2 and 10 years). One of our cases was identified with 16srRNA gene sequencing, one case with MALDI-TOF mass spectrometry, and one case with both techniques. Two literature cases were diagnosed by 16srRNA gene sequencing. All five cases were cured after surgery including a two-stage prosthesis exchange in three cases, a one- stage prosthesis exchange in one case, and debridement, antibiotics, irrigation, and retention of the prosthesis in one case, and prolonged antimicrobial treatment. Conclusion: Prosthetic joint infection involving G. adiacens is probably often dismissed due to difficult culture or misdiagnosis, in particular in the cases of polymicrobial infection. -
Bacteriocin‐Like Inhibitory Activities of Seven Lactobacillus Delbrueckii
Letters in Applied Microbiology ISSN 0266-8254 ORIGINAL ARTICLE Bacteriocin-like inhibitory activities of seven Lactobacillus delbrueckii subsp. bulgaricus strains against antibiotic susceptible and resistant Helicobacter pylori strains L. Boyanova, G. Gergova, R. Markovska, D. Yordanov and I. Mitov Department of Medical Microbiology, Medical University of Sofia, Sofia, Bulgaria Significance and Impact of the Study: In this study, anti-Helicobacter pylori activity of seven Lactobacil- lus delbrueckii subsp. bulgaricus (GLB) strains was evaluated by four cell-free supernatant (CFS) types. The GLB strains produced heat-stable bacteriocin-like inhibitory substances (BLISs) with a strong anti-H. pylori activity and some neutralized, catalase- and heat-treated CFSs inhibited >83% of the test strains. Bacteriocin-like inhibitory substance production of GLB strains can render them valuable probiotics in the control of H. pylori infection. Keywords Abstract antibiotics, bacteriocins, Helicobacter, Lactobacillus, probiotics. The aim of the study was to detect anti-Helicobacter pylori activity of seven Lactobacillus delbrueckii subsp. bulgaricus (GLB) strains by four cell-free Correspondence supernatant (CFS) types. Activity of non-neutralized and non-heat-treated Lyudmila Boyanova, Department of Medical (CFSs1), non-neutralized and heat-treated (CFSs2), pH neutralized, catalase- Microbiology, Medical University of Sofia, treated and non-heat-treated (CFSs3), or neutralized, catalase- and heat-treated Zdrave Street 2, 1431 Sofia, Bulgaria. (CFSs4) CFSs against 18 H. pylori strains (11 of which with antibiotic E-mail: [email protected] resistance) was evaluated. All GLB strains produced bacteriocin-like inhibitory 2017/1069: received 3 June 2017, revised 27 substances (BLISs), the neutralized CFSs of two GLB strains inhibited >81% of August 2017 and accepted 25 September test strains and those of four GLB strains were active against >71% of 2017 antibiotic resistant strains. -
Characterization of a Lactobacillus Brevis Strain with Potential Oral Probiotic Properties Fang Fang1,2* , Jie Xu1,2, Qiaoyu Li1,2, Xiaoxuan Xia1,2 and Guocheng Du1,3
Fang et al. BMC Microbiology (2018) 18:221 https://doi.org/10.1186/s12866-018-1369-3 RESEARCHARTICLE Open Access Characterization of a Lactobacillus brevis strain with potential oral probiotic properties Fang Fang1,2* , Jie Xu1,2, Qiaoyu Li1,2, Xiaoxuan Xia1,2 and Guocheng Du1,3 Abstract Background: The microflora composition of the oral cavity affects oral health. Some strains of commensal bacteria confer probiotic benefits to the host. Lactobacillus is one of the main probiotic genera that has been used to treat oral infections. The objective of this study was to select lactobacilli with a spectrum of probiotic properties and investigate their potential roles in oral health. Results: An oral isolate characterized as Lactobacillus brevis BBE-Y52 exhibited antimicrobial activities against Streptococcus mutans, a bacterial species that causes dental caries and tooth decay, and secreted antimicrobial compounds such as hydrogen peroxide and lactic acid. Compared to other bacteria, L. brevis BBE-Y52 was a weak acid producer. Further studies showed that this strain had the capacity to adhere to oral epithelial cells. Co- incubation of L. brevis BBE-Y52 with S. mutans ATCC 25175 increased the IL-10-to-IL-12p70 ratio in peripheral blood mononuclear cells, which indicated that L. brevis BBE-Y52 could alleviate inflammation and might confer benefits to host health by modulating the immune system. Conclusions: L. brevis BBE-Y52 exhibited a spectrum of probiotic properties, which may facilitate its applications in oral care products. Keywords: Lactobacillus brevis, Antimicrobial activity, Hydrogen peroxide, Adhesion, Immunomodulation Background properties may prevent the colonization of oral patho- Oral infectious diseases, such as dental caries and peri- gens through different mechanisms. -
Oral Ecologixtm Oral Health & Microbiome Profile Phylo Bioscience Laboratory
Oral EcologiXTM Oral Health & Microbiome Profile Phylo Bioscience Laboratory INTERPRETIVE GUIDE DISCLAIMER: THIS INFORMATION IS PROVIDED FOR THE USE OF PHYSICIANS AND OTHER LICENSED HEALTH CARE PRACTITIONERS ONLY. THIS INFORMATION IS NOT FOR USE BY CONSUMERS. THE INFORMATION AND OR PRODUCTS ARE NOT INTENDED FOR USE BY CONSUMERS OR PHYSICIANS AS A MEANS TO CURE, TREAT, PREVENT, DIAGNOSE OR MITIGATE ANY DISEASE OR OTHER MEDICAL CONDITION. THE INFORMATION CONTAINED IN THIS DOCUMENT IS IN NO WAY TO BE TAKEN AS PRESCRIPTIVE NOR TO REPLACE THE PHYSICIANS DUTY OF CARE AND PERSONALISED CARE PRACTICES. INTERPRETIVE GUIDE Oral EcologiX™ INTRODUCTION Due to recent advancements in culture-independent techniques, it is now possible to measure the composition of the human microbiota. The oral cavity is a complex ecosystem, comprising several habitats including the teeth, gums, tongue and tonsils, all colonised by bacteria1. The oral microbiota is comprised of approximately 600 taxa at the species level, with different groups and subsets inhabiting different niches. The microbiota of the oral cavity exists as a complex biofilm that remains stable despite environmental changes. However, dysbiosis, in form of infection, injury, dietary changes and risk-associated factors (e.g. smoking) may disrupt the biofilm community, favouring colonisation and invasion of pathogens. Disruption of the biofilm community to a pathogenic profile, induces host immune responses, chronic inflammation and ultimately development of local and systemic diseases. However, much of this damage is reversible if pathogenic communities are removed, and homeostasis is restored. To this end, Phylobioscience have developed the Oral EcologiXTM oral health and microbiome profile, a ground breaking tool for analysis of oral microbiota composition and host immune responses. -
Granulicatella Adiacens Bacteria Isolation from Perodontitical
Sys Rev Pharm 2020; 11(4): 396 400 A multifaceted review journal in the field of pharmacy E-ISSN 0976-2779 P-ISSN 0975-8453 Granulicatella Adiacens Bacteria Isolation from Perodontitical Patients with Polymerase Chain Reaction Techniques Harun Achmad1, Sri Oktawati2,Andi Mardiana Adam2,Burhanuddin Pasiga3, Rizalinda Sjahril4, Aulia Azizah5, Bayu Indra Sukmana6, Huldani7, Heri Siswanto8 , Ingrid Neormansyah8 1Lecturer of Pedodontics Department, Dentistry Faculty, Hasanuddin University, Makassar, Indonesia 2Lecturer of Periodontology Department, Dentistry Faculty, Hasanuddin University, Makassar, Indonesia 3Lecturer of Dental Public Health Department, Dentistry Faculty, Hasanuddin University, Makassar, Indonesia 4 Lecturer of Microbiology Department, Medical Faculty, Hasanuddin University, Makassar, Indonesia 5Department of Preventive and Public Health Dentistry, Faculty of Dentistry, Lambung Mangkurat University, Banjarmasin, Indonesia. 6Department of Dental Radiology, Faculty of Dentistry, Lambung Mangkurat University, Banjarmasin, Indonesia. 7Department of Physiology, Faculty of Medicine, Lambung Mangkurat University, Banjarmasin, Indonesia. 8 Resident of Periodontology Department, Dentistry Faculty, Hasanuddin University, Makassar, Indonesia Correspondence Author E-mail: [email protected] Article History: Submitted: 10.01.2020 Revised: 12.03.2020 Accepted: 24.04.2020 ABSTRACT Background: Periodontitis is an inflammatory disease of dental support the NCBI Gene Bank using BLAST analysis. tissue caused by certain groups of microorganisms, -
Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes). -
The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight Into the Microbiome–Treatment Axis
International Journal of Molecular Sciences Review The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight into the Microbiome–Treatment Axis Amel Sami 1,2, Imad Elimairi 2,* , Catherine Stanton 1,3, R. Paul Ross 1 and C. Anthony Ryan 4 1 APC Microbiome Ireland, School of Microbiology, University College Cork, Cork T12 YN60, Ireland; [email protected] (A.S.); [email protected] (C.S.); [email protected] (R.P.R.) 2 Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, National Ribat University, Nile Street, Khartoum 1111, Sudan 3 Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland 4 Department of Paediatrics and Child Health, University College Cork, Cork T12 DFK4, Ireland; [email protected] * Correspondence: [email protected] Received: 30 August 2020; Accepted: 12 October 2020; Published: 29 October 2020 Abstract: Oral squamous cell carcinoma (OSCC) is one of the leading presentations of head and neck cancer (HNC). The first part of this review will describe the highlights of the oral microbiome in health and normal development while demonstrating how both the oral and gut microbiome can map OSCC development, progression, treatment and the potential side effects associated with its management. We then scope the dynamics of the various microorganisms of the oral cavity, including bacteria, mycoplasma, fungi, archaea and viruses, and describe the characteristic roles they may play in OSCC development. We also highlight how the human immunodeficiency viruses (HIV) may impinge on the host microbiome and increase the burden of oral premalignant lesions and OSCC in patients with HIV. Finally, we summarise current insights into the microbiome–treatment axis pertaining to OSCC, and show how the microbiome is affected by radiotherapy, chemotherapy, immunotherapy and also how these therapies are affected by the state of the microbiome, potentially determining the success or failure of some of these treatments. -
Bacterial Diversity and Functional Analysis of Severe Early Childhood
www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health. -
Atypica, and Granulicatella Adiacens in Biofilm of Complete Dentures
[Downloaded free from http://www.j-ips.org on Thursday, November 1, 2018, IP: 183.82.145.117] Original Article Relative presence of Streptococcus mutans, Veillonella atypica, and Granulicatella adiacens in biofilm of complete dentures Binoy Mathews Nedumgottil Department of Prosthodontics and Implantology, Mahe Institute of Dental Sciences and Hospital, Puducherry, India Abstract Aims and Objective: Oral biofilms in denture wearers are populated with a large number of bacteria, a few of which have been associated with medical conditions such as sepsis and infective endocarditis (IE). The present study was designed to investigate the relative presence of pathogenic bacteria in biofilms of denture wearers specifically those that are associated with IE. Methods: Biofilm samples from 88 denture wearers were collected and processed to extract total genomic DNA. Eight of these samples were subjected to 16S rRNA gene sequencing analysis to first identify the general bacterial occurrence pattern. This was followed by species-specific quantitative polymerase chain reaction (qPCR) on entire batch of 88 samples to quantify the relative copy numbers of IE-associated pathogens. Results: 16S rRNA gene analysis of eight biofilm samples identified bacteria from Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, and Fusobacteria species. Interestingly, Streptococcus mutans, Veillonella atypica, and Granulicatella adiacens from Firmicutes, all known to be associated with early-onset sepsis and IE was present in five of eight biofilm samples. The other three samples carried bacteria from genus Proteobacteria with Neisseria flava and Neisseria mucosa, which are known to be commensals, as dominant species. Species-specific qPCR of S. mutans V. atypica, and G. adiacens on 88 biofilm DNA samples identified the presence of S.