The coronavirus (COVID-19) global pandemic has impacted the health of almost everyone, including changes in their salivary microbiota. Since 2019, there has been an increase in the number of new COVID-19 cases in Thailand. Therefore, COVID-19 active case finding is important for early detection and epidemic control. Moreover, the dynamic changes of salivary bacteriome in asymptomatic COVID-19 cases are largely unknown. This research aimed to investigate and compare the salivary bacteriome and the co-infectious bacterial pathogens in the asymptomatic COVID-19 positive group to the negative group, based on novel nanopore sequencing. This cohort was a cross-sectional study including saliva samples collected from 82 asymptomatic participants (39 COVID-19 positive and 43 COVID-19 negative cases). All samples were sequenced for the full-length bacterial 16S rDNA. The alpha and beta diversity analyses were not significantly different between groups. The three major species in salivary bacteriome including Veillonella parvula, Streptococcus mitis, and Prevotella melaninogenica were observed in both groups. Interestingly, Lautropia mirabilis was a significantly enriched species in the saliva of the asymptomatic COVID-19-positive cases based on linear discriminant analysis effect size (LEfSe) analysis. The results suggested that L. mirabilis was a co-infectious agent in the asymptomatic COVID-19 group. However, the potential role of L. mirabilis should be validated in further experimental studies.
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.Nat Microbiol2020;5:536–44
2.
GuanWJNiZYHuYLiangWHOuCQHeJXLiuLShanHLeiCLHuiDSCDuBLiLJZengGYuenKYChenRCTangCLWangTChenPYXiangJLiSYWangJLLiangZJPengYXWeiLLiuYHuYHPengPWangJMLiuJYChenZLiGZhengZJQiuSQLuoJYeCJZhuSYZhongNS.Clinical characteristics of coronavirus disease 2019 in China.N Engl J Med2020;382:1708–20
3.
HanPIvanovskiS.Saliva-Friend and Foe in the COVID-19 Outbreak.Diagnostics2020;10:290
4.
HondaKLittmanDR.The microbiota in adaptive immune homeostasis and disease.Nature2016;535:75–84
5.
DubourgGEdouardSRaoultD.Relationship between nasopharyngeal microbiota and patient’s susceptibility to viral infection.Expert Rev Anti Infect Ther2019;17:437–47
6.
ManWHde Steenhuijsen PitersWABogaertD.The microbiota of the respiratory tract: gatekeeper to respiratory health.Nat Rev Microbiol2017;15:259–70
7.
SchippaSFrassanitoAMarazzatoMNennaRPetrarcaLNeroniBBonfiglioGGuerrieriFFrascaFOlivetoGPierangeliAMidullaF.Nasal microbiota in RSV bronchiolitis.Microorganisms2020;8:731
8.
LuHFLiAZhangTRenZGHeKXZhangHYangJZLuoQXZhouKChenCLChenXLWuZWLiLJ.Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection.Emerg Microbes Infect2017;6:e112
9.
WenZXieGZhouQQiuCLiJHuQDaiWLiDZhengYWenF.Distinct nasopharyngeal and oropharyngeal microbiota of children with influenza A virus compared with healthy children.Biomed Res Int2018;2018:6362716
10.
WuFZhaoSYuBChenYMWangWSongZGHuYTaoZWTianJHPeiYYYuanMLZhangYLDaiFHLiuYWangQMZhengJJXuLHolmesECZhangYZ.A new coronavirus associated with human respiratory disease in China.Nature2020;579:265–9
11.
McIlroyJRMullishBHGoldenbergSDIaniroGMarchesiJR.Intestinal microbiome transfer, a novel therapeutic strategy for COVID-19 induced hyperinflammation? In reply to, “COVID-19: immunology and treatment options,” Felsenstein, Herbert McNamara et al.Clin Immunol2020;218:108542
12.
XuRLuRZhangTWuQCaiWHanXWanZJinXZhangZZhangC.Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults.Commun Biol2021;4:240
13.
RenZWangHCuiGLuHWangLLuoHChenXRenHSunRLiuWLiuXLiuCLiAWangXRaoBYuanCZhangHSunJChenXLiBHuCWuZYuZKanQLiL.Alterations in the human oral and gut microbiomes and lipidomics in COVID-19.Gut2021;70:1253–65
14.
ZhangHAiJWYangWZhouXHeFXieSZengWLiYYuYGouXLiYWangXSuHZhuZXuTZhangW.Metatranscriptomic characterization of coronavirus disease 2019 identified a host transcriptional classifier associated with immune signaling.Clin Infect Dis2021;73:376–85
15.
NardelliCGentileISetaroMDi DomenicoCPincheraBBuonomoARZappuloEScottoRScaglioneGLCastaldoGCapoluongoE.Nasopharyngeal microbiome signature in COVID-19 positive patients: can we definitively get a role to Fusobacterium periodonticum?Front Cell Infect Microbiol2021;11:625581
16.
MiaoQMaYLingYJinWSuYWangQPanJZhangYChenHYuanJWuHHuB.Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: a cohort study in Shanghai.J Microbiol Immunol Infect2021;54:808–15
17.
KleinsteinSENelsonKEFreireM.Inflammatory networks linking oral microbiome with systemic health and disease.J Dent Res2020;99: 1131–9
18.
XiangZKooHChenQZhouXLiuYSimon-SoroA.Potential implications of SARS-CoV-2 oral infection in the host microbiota.J Oral Microbiol2020;13:1853451
19.
Benítez-PáezASanzY.Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer.Gigascience2017;6:1–12
20.
MatsuoYKomiyaSYasumizuYYasuokaYMizushimaKTakagiTKryukovKFukudaAMorimotoYNaitoYOkadaHBonoHNakagawaSHirotaK.Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution.BMC Microbiol2021;21:35
21.
ChantaravisootNKaewsapsakPMayuramartONimsamerPMankhongSChomtaNBootsriRAleeIWongkongkathepPTreeprasertsukSPayungpornS. COVID-19 active case findings based on self-collected saliva samples with CRISPR-Cas12a detection.Exp Biol Med (Maywood)2022:15353702221090181
22.
LuXWangLSakthivelSKWhitakerBMurrayJKamiliSLynchBMalapatiLBurkeSAHarcourtJTaminAThornburgNJVillanuevaJMLindstromS. US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome coronavirus 2.Emerg Infect Dis2020;26:1654–65
23.
LanfearRSchalamunMKainerDWangWSchwessingerB.MinIONQC: fast and simple quality control for MinION sequencing data.Bioinformatics2018;35:523–5
24.
Rodríguez-PérezHCiuffredaLFloresC.NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data.Bioinformatics2021;37:1600
25.
ChongJLiuPZhouGXiaJ.Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.Nat Protoc2020;15:799–821
26.
SegataNIzardJWaldronLGeversDMiropolskyLGarrettWSHuttenhowerC.Metagenomic biomarker discovery and explanation.Genome Biol2011;12:R60
27.
VermaDGargPKDubeyAK.Insights into the human oral microbiome.Arch Microbiol2018;200:525–40
28.
WadeWG.The oral microbiome in health and disease.Pharmacol Res2013;69:137–43
29.
MillerEHAnnavajhalaMKChongAMParkHNobelYRSoroushABlackettJWKrigelAPhippsMMFreedbergDEZuckerJSanoEDUhlemannACAbramsJA.Oral microbiome alterations and SARS-CoV-2 saliva viral load in patients with COVID-19.Microbiol Spectr2021;9:e0005521
30.
SchultDReitmeierSKoyumdzhievaPLahmerTMiddelhoffMErberJSchneiderJKagerJFrolovaMHorstmannJFrickeLSteigerKJesinghausMJanssenKPProtzerUNeuhausKSchmidRMHallerDQuanteM.Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19.Gut Microbes2022;14:2031840
31.
RattanaburiSSawaswongVChitcharoenSSivapornnukulPNimsamerPSuntronwongNPuenpaJPoovorawanYPayungpornS.Bacterial microbiota in upper respiratory tract of COVID-19 and influenza patients.Exp Biol Med (Maywood)2022;247:409–15
32.
ZarcoMFVessTJGinsburgGS.The oral microbiome in health and disease and the potential impact on personalized dental medicine.Oral Dis2012;18:109–20
33.
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome.Nature2012;486:207–14
34.
RizzattiGLopetusoLRGibiinoGBindaCGasbarriniA.Proteobacteria: a Common Factor in Human Diseases.Biomed Res Int2017; 2017:9351507
35.
VoroninaOLKundaMSRyzhovaNNAksenovaEISharapovaNESemenovANAmelinaELChuchalinAGGintsburgAL.On Burkholderiales order microorganisms and cystic fibrosis in Russia.BMC Genomics2018;19:74
36.
EberlLVandammeP.Members of the genus Burkholderia: good and bad guys.F1000Res2016;5:F1000
37.
RossmannSNWilsonPHHicksJCarterBCronSGSimonCFlaitzCMDemmlerGJShearerWTKlineMW.Isolation of Lautropia mirabilis from oral cavities of human immunodeficiency virus-infected children.J Clin Microbiol1998;36:1756–60
38.
Ben DekhilSMPeelMMLennoxVAStackebrandtESlyLI.Isolation of Lautropia mirabilis from sputa of a cystic fibrosis patient.J Clin Microbiol1997;35:1024–6
39.
HaranJPBradleyEZeamerALCincottaLSaliveMCDuttaPMutaaweSAnyaOMeza-SeguraMMoormannAMWardDVMcCormickBABucciV.Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID.JCI Insight2021;6:e152346
40.
KhanAAKhanZ.COVID-2019-associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak.Bioinformatics2020;36:4065–9
41.
Yousefi-MashoufRDuerdenBIEleyARawlinsonAGoodwinL.Incidence and distribution of non-pigmented Prevotella species in periodontal pockets before and after periodontal therapy.Microb Ecol Health Dis1993;6:35–42
42.
ShaddoxLMHuangHLinTHouWHarrisonPLAukhilIWalkerCBKlepac-CerajVPasterBJ.Microbiological characterization in children with aggressive periodontitis.J Dent Res2012;91:927–33
43.
HallMWSinghNNgKFLamDKGoldbergMBTenenbaumHCNeufeldJDGBeikoRSenadheeraDB.Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity.NPJ Biofilms Microbiomes2017;3:2
44.
GardenierJCHranjecTSawyerRGBonattiH.Granulicatella adiacens bacteremia in an elderly trauma patient.Surg Infect (Larchmt)2011;12:251–3
45.
ChristensenJJFacklamRR.Granulicatella and Abiotrophia species from human clinical specimens.J Clin Microbiol2001;39:3520–3
46.
SennLEntenzaJMGreubGJatonKWengerABilleJCalandraTProd’homG.Bloodstream and endovascular infections due to Abiotrophia defectiva and Granulicatella species.BMC Infect Dis2006;6:9
47.
ShinhaTCaineV.Pylephlebitis due to Parvimonas micra.Infect Dis Clin Pract2016;24:54–6
48.
AngMYDymockDTanJLThongMHTanQKWongGJPatersonICChooSW.Genome sequence of Parvimonas micra strain A293, isolated from an abdominal abscess from a patient in the United Kingdom.Genome Announc2013;1:e01025
49.
BaghbanAGuptaS.Parvimonas micra: a rare cause of native joint septic arthritis.Anaerobe2016;39:26–7
50.
PrietoRCallejas-DíazAHassanRde VargasAPLópez-PájaroLF.Parvimonas micra: a potential causative pathogen to consider when diagnosing odontogenic brain abscesses.Surg Neurol Int2020;11:140
51.
García CarreteroRLuna-HerediaEOlid-VelillaMVazquez-GomezO. Bacteraemia due to Parvimonas micra, a commensal pathogen, in a patient with an oesophageal tumour.BMJ Case Rep2016;2016:bcr2016217740
52.
ContrerasADoanNChenCRusitanontaTFlynnMJSlotsJ.Importance of Dialister pneumosintes in human periodontitis.Oral Microbiol Immunol2000;15:269–72
53.
DoanNContrerasAFlynnJSlotsJChenC.Molecular identification of Dialister pneumosintes in subgingival plaque of humans.J Clin Microbiol2000;38:3043–7
54.
ParkJEHuhHJHaYEKimWSKiCSLeeNY.A case of bacteremia caused by Dialister pneumosintes with Streptococcus anginosus.Ann Clin Microbiol2015;18:60–3
AsifAARoyMAhmadS.Rare case of Prevotella pleuritidis lung abscess.BMJ Case Rep2020;13:e235960
57.
Al BatainehMTDashNRElkhazendarMAlnusairatDMHDarwishIMIAl-HajjajMSHamidQ.Revealing oral microbiota composition and functionality associated with heavy cigarette smoking.J Transl Med2020;18:421
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