April 6, 2022

Oral Dysbiosis Strongly Contributes to Symptomatic Infection and Long Covid

Results from an observational cohort study
The presence of certain bacteria species helps predict if a patient is at risk for long Covid.


Haran JP, Bradley E, Zeamer AL, et al. Inflammation-type dysbiosis of the oral microbiome associates with duration of COVID-19 symptoms and long COVID. JCI Insight. 2021;6(20):e152346.


Observational, prospective cohort study


Patients presenting to an emergency department between April 2020 and February 2021 with symptoms consistent with COVID-19 infection using criteria from the Centers for Disease Control and Prevention (CDC). During the 9 months, 164 patients presented with COVID-19 symptoms; 84 (51.2%) tested positive by polymerase chain reaction (PCR) test for SARS-CoV-2.

Of the 84 COVID+ patients, 24 died and 27 were unable to follow up due to a language barrier (n=4), severe dementia (n=15), hospice (n=2), and voluntary withdrawal (n=6). An additional 6 were lost to follow-up, leaving a total of 27 participants who were successfully contacted at both 4 and 10 weeks.

Inclusion Criteria

Presentation to the emergency department at the University of Massachusetts Memorial Medical Center, Worchester, Massachusetts, between April 2020 and February 2021 with symptoms of COVID-19 infection using CDC criteria; were positive based on PCR test for SARS-CoV-2; and could be contacted for follow-up.

Parameters Assessed

Demographics, medical history, presenting disease duration, symptomatology, comorbidity using Charlson Comorbidity Index (CCI), and symptom follow-up at 4 weeks and 10 weeks.

Also, 30-second oropharyngeal tongue samples using OMNIgene-ORAL collection kits (OMR-120 DNA Genotek), Nextera XT DNA Library Prep Kit (FC-131-1096, Illumina), PCR using ViiA 7 Real-Time PCR system (Applied Biosystems), and GoTaq Probe 1-Step RT-qPCR system (Promega, A6120). Investigators used MetaPhlAn3 to determine microbial species abundance.


The average age of the 27 participants who completed the study was 62.2 years (70.4% male, 66.7% White, 7.4% African American, 2.9% Hispanic.) High-risk medical comorbidities included hypertension (n=16, 59.3%), diabetes (n=8, 29.6%), and chronic obstructive pulmonary disease (COPD; n=5, 18.5%). Medical comorbidities and CCI did not differ by Covid-19 symptom duration. No patients lived in the same household; all were admitted to the hospital, with 4 (14.8%) admitted to the intensive care unit (ICU). Average hospital stay was 8.3 days. 85.2% of participants required oxygen, 25.9% received advanced oxygen delivery by high-flow or positive airway pressure, and 2 received an endotracheal tube.

The average symptom duration was 45.8 days. Fourteen (51.9%) participants experienced a continuation of symptoms after 4 weeks from disease onset; 10 (37.0%) had symptoms beyond 10 weeks (long Covid). The longest-lasting symptoms were respiratory in nature (cough or shortness of breath, 81.5%), fatigue (55.6%), gastrointestinal (GI) symptoms (14.8%), confusion or brain fog (22.2%), and ageusia or anosmia (14.8%). There was no significant difference in demographics, medical history, or hospital treatments between early resolution of symptoms (n=13), ongoing symptoms (n=4), and long Covid (n=10). Fatigue and brain fog were more prominent in those with the longest symptom duration.

Viral load and Shannon diversity (ie, α diversity) were of moderate importance, but microbiome members/species contributed the most to Covid-19 prediction. Veillonella dispar and V infantium were associated with ongoing symptomatology. Other important species included Solobacterium moorei, Streptococcus infantis, and Rothia dentocariosa. Five species of Prevotella were associated with symptomatic Covid-19, while Leptotrichia wadei was higher in long Covid patients.

In long Covid modeling, 29 species were identified, including Veillonella, 4 species of Actinomyces, high numbers of Prevotella, Streptococcus anginosus, and Gemella sanguinis. Forty metabolic gene pathways were found with ongoing and long Covid; the top 15 indicated a proinflammatory pattern including L-rhamnose, pyrimidine, and purine, as well as O-antigen building block biosynthesis and phospholipid biosynthesis as part of lipid polysaccharide (LPS) biosynthesis. Chorismate, colonic acid, and nicotinamide adenine dinucleotide (NAD) biosynthesis were higher in long Covid patients.

Key Findings

The oral microbiome may influence the duration of Covid-19 symptoms given the presence of microbial associations, specifically those with lipopolysaccharide (LPS) production, reduction in anti-inflammatory pathways, microbiome members known to promote pulmonary infections, and microbiome previously associated with Covid-19 infections.

Practice Implications

Lipopolysaccharides are a major portion of the outer cell wall membrane of gram-negative bacteria.1 They cause an inflammatory response with direct actions in the liver involving tumor necrosis factor alpha (TNF-α) and macrophages that have LPS receptors.2 Veillonella species (15 are known) are among the most abundant oral flora. These anaerobic, gram-negative cocci are present in supragingival and subgingival dental plaque as well as the oral mucosa, respiratory tract, intestinal tract, and female genital tract, and are associated with vertebral and nonvertebral osteomyelitis.3,4 The genus is usually resistant to vancomycin, tetracycline, aminoglycosides, and fluoroquinolones; may respond to penicillin; and usually is susceptible to cephalosporins, clindamycin, metronidazole, and chloramphenicol.4 Infections usually lead to fever, elevated blood pressure and pulse, and elevated white blood cells (especially neutrophils), erythrocyte sedimentation rate (ESR), and alkaline phosphatase (ALP).4 All Veillonella use the conserved pathway of fructose metabolism, forming extensive biofilms in the oral cavity with Streptococcus species.5

Solobacterium moorei is a non-spore-forming, anaerobic, gram-positive bacillus that was initially isolated from human stool, but is a major contributor to halitosis, and has been isolated from endodontic infections, periradicular lesions, subgingival plaque, root canals, refractory periodontitis, and various infected wounds.6 It is susceptible to clindamycin, metronidazole, meropenem, moxifloxacin, tigecycline, and especially vancomycin.6 Patients present with fever, elevated C-reactive protein (CRP), and in some cases elevated leukocytes.6 A prior history of cancer, surgery, infection, or intravenous drug use (1/3 of users lick the needle just prior to the injection) are clinical clues.6 Solobacterium moorei can be identified only by 16S rRNA gene sequencing.7 Biofilm formation, especially in the low oxygen crypts of the tongue, is key to halitosis, where it produces beta-galactosidases, indole, skatole, polyamines, hydrogen sulfide, dimethyl sulfide, methyl mercaptan, and allyl methyl sulfide.7,8 The volatile sulfur compounds are quite toxic and may induce interleukin-8 (IL-8), which contributes to periodontitis, low birth weight, cardiovascular disease, and Helicobacter pylori in the stomach.8 It is often found in association with Prevotella and Porphyromonas species in oral biofilms.8

Streptococcus infantis, an alpha-hemolytic streptococcus (they oxidize iron in hemoglobin molecules within red blood cells), can be isolated from human tooth (plaque) and pharynx surfaces and the upper respiratory tract and has a close association with the highly virulent Streptococcus pneumoniae.9,10 It is also a factor in bacterial endocarditis. Streptococcus infantis infections may respond to amoxicillin-clavulanic acid, ceftriaxone, gentamicin, and vancomycin, but are resistant to ampicillin, azithromycin, and fluoroquinolones.10 Biofilms are a key part of this bacteria’s biology within the dental/oral environment and enhance their resistance to antibiotic medications used singly.11,12

Rothia dentocariosa (previous Actinomyces dentocariosa and Nocardia dentocariosus) is an aerobic, gram-positive round-to-rod shaped microbe found in dental plaque, caries, cardiac valves (natural and prosthetic), and the respiratory tract; it plays a significant role in abdominal aneurysm, perivalvular abscess (aortic, mitral), intracranial hemorrhages, and vertebral osteomyelitis.13,14 Rothia dentocariosa has also been found in bacteremia, endophthalmitis, corneal ulcer, arteriovenous fistula infections, septic arthritis, peritonitis associated with ambulatory peritoneal dialysis, periappendiceal abscess, pilonidal abscess, and pneumonia.13 It is susceptible to penicillin, cephalosporins, erythromycin, and tetracycline, but resistant to aminoglycosides and fluoroquinolones.13 Biofilm formation is a key feature of infective endocarditis.15

This study found that the long COVID microbiome was similar to that of patients with chronic fatigue syndrome.

Leptotrichia wadei, a gram-negative anaerobic bacillus that is common in the human oral cavity, was first isolated in 1896 from a rabbit uterus and has since been found in human saliva, subgingival plaque, the uterus, and vagina.16 Leptotrichia wadei also contributes to halitosis, releasing volatile sulfur compounds.17 In severe pneumonia it responds to imipenem/cilastatin, minocycline, sulfamethoxazole/trimethoprim, and clindamycin, but not cefcapene pivoxil or fluoroquinolones.17 It is strongly associated with oral biofilms, especially if dental caries are present.18

Streptococcus anginosus, 1 of 3 species in the S milleri group, is a gram-positive, catalase-negative cocci found in the oral cavity, throat, sinuses, stool, and vagina with the ability to cause abscesses and systemic infections.19 It can produce the endotoxin intermedilysin and hydrolytic enzyme hyaluronidase, which it uses to spread and invade various tissues.19 It often responds to clindamycin and penicillin with resistance to cephalosporin.20 Streptococcus anginosus forms a strong, resistant biofilm in bone, bowel, and gingival tissue mediated by a conjugated glycosaminoglycan chain.21

Gemella sanguinis, a gram-positive, non-spore-forming cocci singly or in pairs, produces acid from maltose and produces alkaline phosphatase.22 Gemella sanguinis can cause infective endocarditis but was initially associated with dental disease, oropharynx, urogenital areas, and the gastrointestinal tract.23 It is known to respond to vancomycin, gentamicin, and clindamycin and form large biofilms.22-24

Among the 7 most prominent bacteria species in Covid-19 hospitalized patients, 2 are gram-negative and capable of releasing inflammatory LPS (Veillonella and Leptotrichia). All 7 are very capable of forming biofilms, which enhance their antibiotic resistance, and their response to antibiotic treatment varies by species. Two (Leptotrichia and Solobacterium) release toxic volatile sulfur compounds. All arose in the oral microbiome but had the capability to spread to other tissues and organs, causing infections, vegetative growths, biofilms, and cancers in some cases. In long Covid, also called post-acute sequelae of Covid-19 (PASC), 5 species were most prominent.

In 1 study of PASC, 30% reported persistent symptoms at 9-month follow-up.25 Such long-haul symptoms are not unique to Covid. Ebola virus is associated with a chronic syndrome, post-Ebola syndrome.26 Many of these patients meet the diagnostic criteria of myalgic encephalitis/chronic fatigue syndrome (ME/CFS).26 A study of 233 of 369 Hong Kong SARS-CoV-1 survivors found that 27.1% met the criteria for ME/CFS.27 Many suffered because they were a healthcare worker at the time of the infection but now are unemployed, socially stigmatized, and have increased psychiatric morbidities.27

Concomitant factors based on ME/CFS research included human herpes virus 6 (HHV-6), HHV-7, Epstein-Barr virus (EBV), and herpes simplex virus 1 (HSV-1) infection, enteroviruses, crossing the blood-brain barrier (BBB), damage to single or multiple organs during the infection, persistence or poor clearance of the SARS-CoV-2 virus, and a high prevalence of myocarditis (78%) regardless of an asymptomatic or symptomatic Covid-19 infection.28,29 A review of electronic dental records and positivity for Covid-19 in Qatar February 2020 to July 2020 found that Covid-19 cases with periodontitis had higher WBCs, D-dimer, CRP, hospital admissions, need for ventilation, and complications including death than those without periodontitis, but unfortunately oral swabs were not taken at the time of admission and diagnosis of Covid-19.30

A study of oral mouth rinses on SARS-CoV-2 found that Colgate Peroxyl, povidone-iodine, chlorhexidine, and original Listerine, from most to least, were all effective at inactivation and preventing replication of this virus.31 They are also effective against multiple bacteria and viruses.31

A study of the gastrointestinal tract microbiome using serial stool samples from SARS-CoV-2 infected patients found that dysbiosis, inflammatory cytokines, CRP, LDH, AST, and GGT were associated with the magnitude of Covid-19 severity.32 A probiotic formula given to Covid-19 outpatients for 30 days prevented hospitalizations and deaths and also reduced nasopharyngeal viral loads and duration of digestive and nondigestive symptoms.33 The researchers hypothesized that it interacted with the subjects’ immune system rather than changing colonic microbiota composition because they could not detect microbiome changes with their method of analysis.33

Use of L-glutamine in hospitalized Covid-19 patients reduced time in hospital, prevented admission to ICU, and prevented mortality.34 Use of a Bacillus-based probiotic for 30 days reduced symptoms of intestinal permeability, elevated triglycerides, inflammation, and post-prandial endotoxemia in the gut microbiome.35

Sequencing analysis of city wastewater detected Covid-19 variants through time and could be used to track pathogens in future infectious disease outbreaks, confirming that the microbiome can be assessed by multiple methods.36 The above studies suggest that the microbiome can be positively modified to reduce the risk of a Covid-19 infection and altered during an acute infection and that elevated inflammatory pathways are associated with a dysbiotic microbiome.


The oral microbiome, the 2nd largest in humans, may be a significant risk factor for SARS-CoV-2 infections. The presence of certain species, as found in this study, can help predict if a patient is at risk for long Covid (PASC). This study found that the long Covid microbiome was similar to that of patients with chronic fatigue syndrome. Patients’ microbiome and its level of inflammation can help determine their long-term prognosis for health and disease following a Covid-19 infection.

This paper was well-written, used an effective methodology to assess the microbiome of these patients, and correlated long Covid to chronic fatigue syndrome. Since the start of the pandemic, I have read hundreds of peer-reviewed papers on SARS-CoV-2, bats, viruses, theories, treatments, mechanisms, and beyond. I place this thought-provoking, well-designed study in the top 10 of those I have read and hope it gives you a fresh perspective on the pandemic and the issues of susceptibility, treatment options, and much more. The time has come to recognize the role of the microbiome in our infected and healthy patients, and to focus on improving it to the benefit of our patients.

Categorized Under


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