Competitive advantage of oral streptococci for colonization of the middle ear mucosa

Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, 19, 455, 10.1089/cmb.2012.0021 Bassis, 2015, Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals, mBio, 6, e00037, 10.1128/mBio.00037-15 Belstrom, 2020, The salivary microbiota in health and disease, J Oral Microbiol, 12, 1723975, 10.1080/20002297.2020.1723975 Bible, 2015, Metabolic adaptations of Azospirillum brasilense to oxygen stress by cell-to-cell clumping and flocculation, Appl Environ Microbiol, 81, 8346, 10.1128/AEM.02782-15 Blaak, 2020, Short chain fatty acids in human gut and metabolic health, Benef Microbes, 11, 411, 10.3920/BM2020.0057 Bluestone, 2005 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Bomar, 2018, Bacterial microbiota of the nasal passages across the span of human life, Curr Opin Microbiol, 41, 8, 10.1016/j.mib.2017.10.023 Brugger, 2016, Commensal–pathogen interactions along the human nasal passages, PLoS Pathog, 12, 10.1371/journal.ppat.1005633 Burch, 2010, Novel high-throughput detection method to assess bacterial surfactant production, Appl Environ Microbiol, 76, 5363, 10.1128/AEM.00592-10 Chen, 2017, Molecular insights into hydrogen peroxide-sensing mechanism of the metalloregulator MntR in controlling bacterial resistance to oxidative stresses, J Biol Chem, 292, 5519, 10.1074/jbc.M116.764126 Cotter, 2003, Surviving the acid test: responses of gram-positive bacteria to low pH, Microbiol Mol Biol Rev, 67, 429, 10.1128/MMBR.67.3.429-453.2003 Crielaard, 2011, Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health, BMC Med Genom, 4, 22, 10.1186/1755-8794-4-22 Delorme, 2015, Genomics of Streptococcus salivarius, a major human commensal, Infect Genet Evol, 33, 381, 10.1016/j.meegid.2014.10.001 Delwiche, 1985, The Veillonellae: gram-negative cocci with a unique physiology, Annu Rev Microbiol, 39, 175, 10.1146/annurev.mi.39.100185.001135 Dewhirst, 2010, The human oral microbiome, J Bacteriol, 192, 5002, 10.1128/JB.00542-10 Diep, 2006, Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus, Lancet, 367, 731, 10.1016/S0140-6736(06)68231-7 Donati, 2016, Uncovering oral Neisseria tropism and persistence using metagenomic sequencing, Nature Microbiol, 1, 16070, 10.1038/nmicrobiol.2016.70 Duan, 2016, Fine-tuned production of hydrogen peroxide promotes biofilm formation of Streptococcus parasanguinis by a pathogenic cohabitant Aggregatibacter actinomycetemcomitans, Environ Microbiol, 18, 4023, 10.1111/1462-2920.13425 Duhl, 2018, Shewanella oneidensis MR-1 utilizes both sodium- and proton-pumping NADH dehydrogenases during aerobic growth, Appl Environ Microbiol, 84, e00415, 10.1128/AEM.00415-18 Facklam, 2002, What happened to the streptococci: overview of taxonomic and nomenclature changes, Clin Microbiol Rev, 15, 613, 10.1128/CMR.15.4.613-630.2002 Fey, 2013, A genetic resource for rapid and comprehensive phenotype screening of nonessential Staphylococcus aureus genes, mBio, 4, e00537, 10.1128/mBio.00537-12 Gao, 2018, Oral microbiomes: more and more importance in oral cavity and whole body, Protein Cell, 9, 488, 10.1007/s13238-018-0548-1 Garnett, 2012, Structural insight into the role of Streptococcus parasanguinis Fap1 within oral biofilm formation, Biochem Biophys Res Commun, 417, 421, 10.1016/j.bbrc.2011.11.131 Ghadiali, 2002, Effect of surface tension and surfactant administration on Eustachian tube mechanics, J Appl Phys, 93, 1007 Hakalehto, 2011, Lactic acid bacteria enriched from human gastric biopsies, ISRN Gastroenterol, 109183 Hall, 2018 Hall-Stoodley, 2006, Direct detection of bacterial biofilms on the middle-ear mucosa of children with chronic otitis media, JAMA, 296, 202, 10.1001/jama.296.2.202 Honjo, 1985, Pumping and clearance function of the eustachian tube, Am J Otolaryngol, 6, 241, 10.1016/S0196-0709(85)80095-8 Huch, 2013, Streptococcus rubneri sp. nov., isolated from the human throat, Int J Syst Evol Microbiol, 63, 4026, 10.1099/ijs.0.048538-0 Kaci, 2014, Anti-Inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract, Appl Environ Microbiol, 80, 928, 10.1128/AEM.03133-13 Kaito, 2007, Colony spreading in Staphylococcus aureus, J Bacteriol, 189, 2553, 10.1128/JB.01635-06 Kandler, 1983, Carbohydrate metabolism in lactic acid bacteria, Antonie Leeuwenhoek, 49, 209, 10.1007/BF00399499 Keith, 2006, Characteristics of Streptococcus pseudopneumoniae isolated from purulent sputum samples, J Clin Microbiol, 44, 923, 10.1128/JCM.44.3.923-927.2006 Khan, 2019, Commensal bacteria: an emerging player in defense against respiratory pathogens, Front Immunol, 10 Knapp, 1988, Prevalence and persistence of Neisseria cinerea and other Neisseria spp. in adults, J Clin Microbiol, 26, 896, 10.1128/jcm.26.5.896-900.1988 Kocur, 2006, The genus Micrococcus, 961 Köhler, 2000, Swarming of Pseudomonas aeruginosa Is dependent on cell-to-cell signaling and requires flagella and pili, J Bacteriol, 182, 5990, 10.1128/JB.182.21.5990-5996.2000 Kolenbrander, 2000, Oral microbial communities: biofilms, interactions, and genetic systems, Annu Rev Microbiol, 54, 413, 10.1146/annurev.micro.54.1.413 Kooken, 2012, Characterization of Micrococcus strains isolated from indoor air, Mol Cell Probes, 26, 1, 10.1016/j.mcp.2011.09.003 Koskinen, 2018, The nasal microbiome mirrors and potentially shapes olfactory function, Sci Rep, 8, 1296, 10.1038/s41598-018-19438-3 Kriebel, 2018, Oral biofilms from symbiotic to pathogenic interactions and associated disease –Connection of periodontitis and rheumatic arthritis by peptidylarginine deiminase, Front Microbiol, 9 Kumar, 2018, MEGA X: molecular evolutionary Genetics analysis across computing platforms, Mol Biol Evol, 35, 1547, 10.1093/molbev/msy096 Lee, 2021, Oral seeding and niche-adaptation of middle ear biofilms in health, Biofilms, 3, 100041, 10.1016/j.bioflm.2020.100041 Liu, 2015, Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus, Microbiology, 161, 1297, 10.1099/mic.0.000086 Mashima, 2015, Interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation, J Bacteriol, 197, 2104, 10.1128/JB.02512-14 Mason, 2018, Characterizing oral microbial communities across dentition states and colonization niches, Microbiome, 6, 67, 10.1186/s40168-018-0443-2 McCormack, 2015, Staphylococcus aureus and the oral cavity: an overlooked source of carriage and infection?, Am J Infect Control, 43, 35, 10.1016/j.ajic.2014.09.015 McGuire, 2002, Surfactant in the middle ear and eustachian tube: a review, Int J Pediatr Otorhinolaryngol, 66, 1, 10.1016/S0165-5876(02)00203-3 Merritt, 2005, Growing and analyzing static biofilms, Current. Protocol. Microbiol. Munoz, 2011, Release LTPs104 of the all-species living tree, Syst Appl Microbiol, 34, 169, 10.1016/j.syapm.2011.03.001 Ohara-Nemoto, 2008, Occurrence of staphylococci in the oral cavities of healthy adults and nasal oral trafficking of the bacteria, J Med Microbiol, 57, 95, 10.1099/jmm.0.47561-0 Partridge, 2013, Swarming: flexible roaming plans, J Bacteriol, 195, 909, 10.1128/JB.02063-12 Patterson, 1996, Streptococcus Poje, 2003, General methods for culturing Haemophilus influenzae, Methods Mol Med, 71, 51 Pollitt, 2017, Defining motility in the staphylococci, Cell Mol Life Sci, 74, 2943, 10.1007/s00018-017-2507-z Quinones, 2005, Quorum sensing regulates exopolysaccharide production, motility, and virulence in Pseudomonas syringae, Mol Plant Microbe Interact, 18, 682, 10.1094/MPMI-18-0682 Raabe, 2019, Group B Streptococcus (Streptococcus agalactiae), Microbiol Spectr, 7, 10.1128/microbiolspec.GPP3-0007-2018 Redanz, 2018, Live and let die: hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome, Mol Oral Microbiol, 33, 337, 10.1111/omi.12231 Reddy, 1997, Middle ear mucin glycoprotein: purification and interaction with nontypable Haemophilus influenzae and Moraxella catarrhalis, Otolaryngol Head Neck Surg, 116, 175 Regev-Yochay, 2006, Interference between Streptococcus pneumoniae and Staphylococcus aureus: in vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae, J Bacteriol, 188, 4996, 10.1128/JB.00317-06 Rios-Covian, 2017, Shaping the metabolism of intestinal Bacteroides population through diet to improve human health, Front Microbiol, 8, 10.3389/fmicb.2017.00376 Sade, 1971, Mucociliary flow in the middle ear, Ann Otol Rhinol Laryngol, 80, 336, 10.1177/000348947108000306 Schilder, 2016, Otitis media, Nat Rev Dis Prim, 2, 16063, 10.1038/nrdp.2016.63 Schillinger, 1989, Antibacterial activity of Lactobacillus sake isolated from meat, Appl Environ Microbiol, 55, 1901, 10.1128/aem.55.8.1901-1906.1989 Schneider, 2012, NIH Image to ImageJ: 25 years of image analysis, Nat Methods, 9, 671, 10.1038/nmeth.2089 Sheng, 2006, Enhanced acid resistance of oral streptococci at lethal pH values associated with acid-tolerant catabolism and with ATP synthase activity, FEMS Microbiol Lett, 262, 93, 10.1111/j.1574-6968.2006.00374.x Siegel, 2015, Mechanisms of bacterial colonization of the respiratory tract, Annu Rev Microbiol, 69, 425, 10.1146/annurev-micro-091014-104209 Smith, 1942, The lactic acid fermentation of streptococci, J Bacteriol, 43, 725, 10.1128/jb.43.6.725-731.1942 Stackebrandt, 2006, Taxonomic parameters revisited: tarnished gold standards, Microbiol Today, 33, 152 Tonnaer, 2009, Detection of bacteria in healthy middle ears during cochlear implantation, Arch Otolaryngol Head Neck Surg, 135, 232, 10.1001/archoto.2008.556 Trunk, 2018, Bacterial autoaggregation, AIMS Microbiol, 4, 140, 10.3934/microbiol.2018.1.140 Tsompanidou, 2013, Distinct roles of phenol-soluble modulins in spreading of Staphylococcus aureus on wet surfaces, Appl Environ Microbiol, 79, 886, 10.1128/AEM.03157-12 Van Hoogmoed, 2008, Reduction of periodontal pathogens adhesion by antagonistic strains, Oral Microbiol Immunol, 23, 43, 10.1111/j.1399-302X.2007.00388.x Van Hoogmoed, 2008, Reduction of periodontal pathogens adhesion by antagonistic strains, Oral Microbiol Immunol, 23, 43, 10.1111/j.1399-302X.2007.00388.x Wandersman, 1989, Secretion, processing and activation of bacterial extracellular proteases, Mol Microbiol, 3, 1825, 10.1111/j.1365-2958.1989.tb00169.x Wang, 2016, Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus, Sci Rep, 6, 22943, 10.1038/srep22943 Wang, 2005, Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes, FEMS Microbiol Ecol, 54, 219, 10.1016/j.femsec.2005.03.012 Welch, 2019, Biogeography of the oral microbiome: the site-specialist hypothesis, Annu Rev Microbiol Wilson, 1985, Comparative susceptibility of group B streptococci and Staphylococcus aureus to killing by oxygen metabolites, J Infect Dis, 152, 323, 10.1093/infdis/152.2.323 World Health, 2011 Wu, 2019, Interaction between Streptococcus pneumoniae and Staphylococcus aureus generates OH radicals that rapidly kill Staphylococcus aureus strains, J Bacteriol, 201, 10.1128/JB.00474-19 Yarza, 2008, The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains, Syst Appl Microbiol, 31, 241, 10.1016/j.syapm.2008.07.001 Zhao, 2009, Micrococcus yunnanensis sp. nov., a novel actinobacterium isolated from surface-sterilized Polyspora axillaris roots, Int J Syst Evol Microbiol, 59, 2383, 10.1099/ijs.0.010256-0