Ringing bells: Morganella morganii fights for recognition

Tracing the possible evolutionary trends of Morganella morganii: insights from molecular epidemiology and phylogenetic analysis

Morganella morganii, encompassing two subspecies, subsp. morganii and subsp. sibonii, is a common opportunistic pathogen, notable for intrinsic resistance to multiple antimicrobial agents. Despite its clinical significance, research into the potential evolutionary dynamics of M. morganii remains limited. This study involved the analysis of genome sequences from 431 M. morganii isolates, comprising 206 isolates that cause host infections, obtained from this study and 225 from the NCBI genome data sets. A diverse array of antimicrobial resistance genes (ARGs) was identified in M. morganii isolates, including mcr-1, tet(X4), tmexCD-toprJ, and various carbapenemase genes. In addition, a novel blaKPC-2-bearing plasmid with demonstrated conjugative capability was discovered in M. morganii. The majority of virulence-related genes (VRGs), except for the hlyCABD gene cluster, were found in almost all M. morganii. Three novel genospecies of M. morganii were identified, designated as M. chanii, M. variant1, and M. variant2. Compared to M. sibonii, M. chanii genospecies possessed a greater number of flagellar-related genes, typically located within mobile genetic elements (MGEs), suggesting potential for better environmental adaptability. Phylogenetic analysis further disclosed that M. morganii was divided into 12 sequence clusters (SCs). Particularly, SC9 harbored an elevated abundance of ARGs and VRGs, mainly toxin-related genes, and was associated with a higher presence of MGEs compared to non-SC9 strains. The collective findings suggest that M. morganii undergoes evolution driven by the influence of MGEs, thereby significantly enhancing its adaptability to selective pressures of environmental changes and clinical antimicrobial agents.IMPORTANCEThe growing clinical significance of Morganella morganii arises from its abundant virulence factors and antimicrobial resistance genes, resulting in elevated infection rates and increased clinical scrutiny. However, research on the molecular epidemiology and evolutionary trends of M. morganii has been scarce. Our study established a list of virulence-related genes (VRGs) for M. morganii and conducted a large-scale epidemiological investigation into these VRGs. Based on genomic classification, three novel genotypes of M. morganii were identified, representing evolutionary adaptations and responses to environmental challenges. Furthermore, we discovered the emergence of a sequence cluster enriched with antimicrobial resistance genes, VRGs, and mobile genetic elements, attributed to the selective pressure of antimicrobial agents. In addition, we identified a novel conjugative plasmid harboring the blaKPC-2 gene. These findings hold significance in monitoring and comprehending the epidemiology of M. morganii.

A comprehensive study of food waste management and processing in the Czech Republic: Potential health risks and consumer behavior

Food waste is currently a widely discussed phenomenon with significant economic and social consequences. One third of the food produced in the world is wasted at various points along the food supply chain. This article presents a comprehensive study that examines consumer behavior in dealing with food waste and activities in the composting process that enable waste sanitation. The survey conducted as part of this study showed that consumers want to eliminate odors, are concerned about potential infections, and generally sort less food waste. This study suggested that the addition of appropriate additives could be a solution. The results indicated that additives could eliminate negative side effects such as unpleasant odors, the presence of insects and rodents, and act as a prevention of the occurrence of pathogenic organisms. Tea tree oil showed the best positive physical and chemical properties among the additives tested (CaCO3 and citric acid) with a significant effect on inhibiting the growth of bacterial strains such as Salmonella strains and had the strongest antibacterial effect, neutralized unpleasant odors, and stabilized the waste. The use of additives could be a future solution to meet consumer demands, improve the quality of food waste and advance the circular economy to improve the sustainability of agricultural systems.

Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study

BACKGROUND

Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp.

METHODS

This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A.

FINDINGS

Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate. We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-β-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A.

INTERPRETATION

This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons.

FUNDING

None.

Clonal relationship, virulence genes, and antimicrobial resistance of Morganella morganii isolated from community-acquired infections and hospitalized patients: a neglected opportunistic pathogen

Morganella morganii is a bacterium belonging to the normal intestinal microbiota and the environment; however, in immunocompromised individuals, this bacterium can become an opportunistic pathogen, causing a series of diseases, both in hospitals and in the community, being urinary tract infections more prevalent. Therefore, the objective of this study was to evaluate the prevalence, virulence profile, and resistance to antimicrobials and the clonal relationship of isolates of urinary tract infections (UTI) caused by M. morganii, both in the hospital environment and in the community of the municipality of Londrina-PR, in southern Brazil, in order to better understand the mechanisms for the establishment of the disease caused by this bacterium. Our study showed that M. morganii presents a variety of virulence factors in the studied isolates. Hospital strains showed a higher prevalence for the virulence genes zapA, iutA, and fimH, while community strains showed a higher prevalence for the ireA and iutA genes. Hospital isolates showed greater resistance compared to community isolates, as well as a higher prevalence of multidrug-resistant (MDR) and extended-spectrum beta lactamase (ESBL)-producing isolates. Several M. morganii isolates from both sources showed high genetic similarity. The most prevalent plasmid incompatibility groups detected were FIB and I1, regardless of the isolation source. Thus, M. morganii isolates can accumulate virulence factors and antimicrobial resistance, making them a neglected opportunistic pathogen.

Morganella morganii and Enterococcus faecalis endophthalmitis following intravitreal injection

BACKGROUND

Endophthalmitis following intravitreal injection is a potentially devastating complication of anti-VEGF injections. Post-injection endophthalmitis due to Enterococcus faecalis is rare, and no previous case of Morganella morganii endophthalmitis after intravitreal injection has been reported.

CASE PRESENTATION

We present the first reported case of Morganella morganii and Enterococcus faecalis endophthalmitis after intravitreal injection in an immunocompetent patient in the absence of recent ocular surgery. Our patient presented with hand movement visual acuity one day after anti-VEGF injection and demonstrated no clinical improvement despite repeated intravitreal ceftazidime and vancomycin injections. A decision was made to proceed with early vitrectomy given failure of intravitreal antibiotics. Visual acuity improved to 6/90 at 12 weeks after vitrectomy without any evidence of disease recurrence.

CONCLUSIONS

Post-injection endophthalmitis due to concurrent Morganella morganii and Enterococcus faecalis infections can have visually devastating consequences despite repeated empirical and targeted intravitreal antibiotics. Lack of clinical improvement following intravitreal antibiotics should warrant consideration of early vitrectomy. Our experience is a pertinent reminder of the ever-growing threat of uncommon and multi-resistant bacteria that must be considered when treating infections such as post-injection endophthalmitis.

Glabridin inhibited the spread of polymyxin-resistant Enterobacterium carrying ICEMmoMP63

Introduction

The role of integrative and conjugative elements (ICEs) in antibiotic resistance in Morganella morganii is unknown. This study aimed to determine whether an ICE identified in the M. morganii genome contributed to the polymyxin resistance.

Methods

Whole-genome sequencing was performed followed by bioinformatics analyses to identify ICEs and antibiotic resistance genes. Conjugation assays were performed to analyze the transferability of a discovered ICE. A drug transporter encoded on the ICE was heterogeneously expressed in Escherichia coli, minimum inhibitory concentrations of antibiotics were determined, and a traditional Chinese medicine library was screened for potential efflux pump inhibitors.

Results

An antibiotic resistance-conferring ICE, named ICEMmoMP63, was identified. ICEMmoMP63 was verified to be horizontally transferred among Enterobacteriaceae bacteria. G3577_03020 in ICEMmoMP63 was found to mediate multiple antibiotic resistances, especially polymyxin resistance. However, natural compound glabridin was demonstrated to inhibit polymyxin resistance.

Discussion

Our findings support the need for monitoring dissemination of ICEMmoMP63 in Enterobacteriaceae bacteria. Combined glabridin and polymyxin may have therapeutic potential for treating infections from multi-drug resistant bacteria carrying ICEMmoMP63.

Detection of Morganella morganii bound to a plastic substrate in surface water

OBJECTIVES

Around the globe, escalation in rare opportunistic microbial infections is alarming as they are heading steadily towards 'superbug' status. In aquatic ecosystems, plastic fosters multidrug-resistant pathogenic bacteria and plays a significant role in trafficking antibiotic-resistant genes. In this study, we focused on a multidrug-resistant bacterial strain isolated from microbial communities found on plastic substrates of a volcanic lake in central Italy.

METHODS

Extended-spectrum beta-lactamase-producing strains were isolated from both raw water and plastic substrates for a comparative investigation using microbiological and molecular methods, and antibiotic susceptibility profiling was performed against a panel of ten antibiotics.

RESULTS

Molecular identification and Basic Local Alignment Search Tool analysis confirmed an almost identical sequencing pattern of two isolated strains and their homology with Morganella morganii. Antibiotic susceptibility tests revealed their resistance to almost all tested antibiotics. Class 1 integron-associated gene (intI1) and seven antibiotic resistance genes were detected in both strains, confirming their superbug status.

CONCLUSION

To our knowledge, this is the first study on the characterization of extended-spectrum beta-lactamase-producing M. morganii isolated from the biofilm of plastic substrates, depicting the potential toxicity of plastic in harbouring and dispersing virulent, multidrug-resistant, opportunistic human pathogens.

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice

Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

Morganella Morganii Infection in Hirudo Medicinalis (Iran): A Case Report

Simple Summary

Morganella morganii is a motile, non-spore-forming, rod-shaped facultative an-aerobic gram-negative bacterium found in the intestines of people, the oral cavity of animals, and the environment. Reptiles, guinea pigs, rabbits, jaguars, elephant seals, broiler chickens, piglets, and dolphins have all been documented to have M. morganii infection. Medicinal leeches are used in surgical and non-surgical manners. Treatment of long-term and chronic pain syndrome induced by degenerative diseases in a non-surgical method. For the first time in Iran, our investigation discovered M. morganii-infected Hirudo medicinalis. Infection with M. morganii caused a significant death and morbidity rate (70%) and severe clinical abnormalities.

Abstract

Medicinal leeches (Hirudo medicinalis) are used in surgical and non-surgical manners. Morganella morganii is an opportunistic and zoonotic pathogenic bacterium causing serious clinical complications. In this study, we isolated, discovered and characterized M. morganii-infected H. medicinalis. We detected and identified M. morganii in all inflamed and swollen Hirudo medicinalis samples. The 16S rRNA sequence of the isolates confirmed all strains of M. morganii. All strains were sensitive to Ceftriaxone, Ceftiofur, Danofloxacin, Ciprofloxacin, Enrofloxacin, Oxytetracycline, and Meropenem and were resistant to Erythromycin, Amoxicillin, Ampicillin, Cefazolin, Colistin, Penicillin G, and Lincomycin. This pathogenic bacterium is a zoonotic pathogen, and monitoring the prevalence rate of this bacteria is strongly necessary for leeches used in human medical treatment and care. Finally, all infected leeches were treated successfully in this case report study.

Metagenomic Changes of Gut Microbiota following Treatment of Helicobacter pylori Infection with a Simplified Low-Dose Quadruple Therapy with Bismuth or Lactobacillus reuteri

Background: Probiotic supplementation to antibiotic regimens against Helicobacter pylori infection has been proposed to improve eradication rate and to decrease detrimental effects on gut microbiota. Aims: To evaluate microbiota modifications due to a low-dose quadruple therapy with bismuth or Lactobacillus reuteri. Methods: Forty-six patients infected with H. pylori were prospectively enrolled in a single-centre, randomized controlled trial to receive b.i.d. with meals for 10 days low-dose quadruple therapy consisting of rabeprazole 20 mg and bismuth (two capsules of Pylera® plus 250 mg each of tetracycline and metronidazole), or the same dose of rabeprazole and antibiotics plus Gastrus® (L. reuteri), one tablet twice-a-day for 27 days. Stool samples were collected at the enrolment, at the end and 30–40 days after the treatment. Gut microbiota composition was investigated with 16S rRNA gene sequencing. Results: Eradication rate was by ITT 78% in both groups, and by PP analysis 85.7% and 95.5% for Gastrus® and bismuth group, respectively. Alpha and beta diversity decreased at the end of treatment and was associated with a reduction of bacterial genera beneficial for gut homeostasis, which was rescued 30–40 days later in both groups, suggesting a similar impact of the two regimens in challenging bacterial community complexity. Conclusions: Low-dose bismuth quadruple therapy proved to be effective with lower costs and amount of antibiotics and bismuth. Gastrus® might be an option for patients with contraindications to bismuth. L. reuteri was unable to significantly counteract dysbiosis induced by antibiotics. How to administer probiotics to prevent gut microbiota alterations remains an open question.

Morganella morganii, an Emerging Cause of Bloodstream Infections

Although recent reports of extensively antibiotic-resistant strains have highlighted the importance of Morganella morganii as an emerging pathogen, the epidemiology of serious infections due to this organism is not well defined. The objective of this study was to determine the incidence, determinants, and outcomes of Morganella morganii bloodstream infections (BSIs). Retrospective, population-based surveillance for Morganella morganii BSIs was conducted in Queensland, Australia, in 2000 to 2019; 709 cases were identified, for an annual incidence of 9.2 cases per million population. Most cases were of community onset, with 280 (39.5%) community-associated cases and 226 (31.9%) health care-associated cases. Morganella morganii BSIs were rare in children and young adults, and the incidence increased markedly with advancing age. The most common foci of infection were skin and soft tissue (131 cases [18.5%]), genitourinary (97 cases [13.7%]), and intraabdominal (90 cases [12.7%]). Most patients (580 cases [81.8%]) had at least one comorbid medical illness, with diabetes mellitus (250 cases [35.3%]), renal disease (208 cases [29.3%]), and congestive heart failure (167 cases [23.6%]) being most prevalent. Resistance to one or more of quinolones, co-trimoxazole, aminoglycosides, or carbapenems was observed in 67 cases (9.5%), and this did not change significantly over the study. The 30-day all-cause case fatality rate was 21.2%, and increasing age, nonfocal infection, heart failure, dementia, and cancer were independently associated with increased risk of death. Morganella morganii BSIs are increasing in our population, and elderly male subjects and individuals with comorbidities are at highest risk. Although antibiotic resistance is not a major contributor to the current burden in Queensland, ongoing surveillance is warranted. IMPORTANCE Recent reports of extensively antibiotic-resistant strains have highlighted the importance of Morganella morganii as an emerging pathogen. Despite its present and evolving importance as an agent of human disease, there is a limited body of literature detailing the epidemiology of serious infections due to Morganella morganii. Therefore, the objectives of this study were to examine the incidence and determinants of Morganella morganii BSIs and to examine risk factors for death in a large Australian population in 2000 to 2019.

Morganella morganii : An unusual analysis of 11 cases of pediatric urinary tract infections

Background

The increase in rare opportunistic microbial infections caused by Morganella morganii is alarming across the globe. It has been reported that in cases of urinary tract infections (UTIs) caused by M. morganii, however, few studies investigated children. Our study aimed to analyze the risk factors, antimicrobial susceptibility, and clinical characteristics, so as to improve the clinical diagnosis and therapy of M. morganii infection.

Methods

Between April 1, 2017 and April 1, 2021, 11 cases of pediatric UTIs caused by M. morganii were included in this retrospective study. Medical records were reviewed and analyzed.

Results

The study population included 10 males and one female between 11 months and 13 years old (mean age: 4 years 9 months). The most common comorbidity was nephrotic syndrome (72.7%, 8/11). Six patients (54.5%) were in the immunosuppressed state due to chemotherapy or immunosuppressant therapy. Ten cases defined as lower UTIs with no specific clinical manifestations had normal or slightly elevated leukocyte counts and procalcitonin (PCT) levels, and normal C‐reactive protein (CRP) levels. One child diagnosed upper UTIs accompanied with fever, high level of leukocyte counts, CRP, and PCT. The M. morganii presented 100% susceptibility to aztreonam, ertapenem, meropenem, piperacillin/tazobactam, cefepime, ceftazidime, cefotetan, ticarcillin/clavulanic acid, and cefoperazone/sulbactam. Almost all patients had good responses to third‐generation cephalosporins antibiotic therapy.

Conclusion

Clinical vigilance for the possibility of M. morganii in pediatric UTIs in combination with underlying disease or immunosuppression is warranted. Treatment strategies should be proposed according to the clinical condition and the antibiotic susceptibility results.

Postvitrectomy endophthalmitis caused by Morganella morganii: a case report and literature review

Background

Postvitrectomy endophthalmitis is a rare and serious complication following vitreoretinal surgeries. Morganella morganii, an emerging gram-negative, facultative anaerobic rod, is related to severe nosocomial infections in various organs and thus has gained importance in recent decades. Morganella morganii infection following intraocular surgery is rarely reported.

Case presentation

We report an immunocompetent patient with Morganella morganii-related endophthalmitis after vitrectomy for retinal detachment who presented with hand motion visual acuity, hypopyon and a unique retrolental exudative membrane. Initially, the patient was unresponsive to empirical intravitreal ceftazidime and vancomycin but recovered with vision preservation (20/63) after surgical removal of the membrane and silicone oil tamponade.

Conclusions

Morganella morganii intraocular infection is often devastating, likely due to its high multidrug-resistance rate via intrinsic ß-lactamase production, multiple acquired traits related to additional genetic mechanisms, and fimbrial adhesion, urease production, and type III secretion system-associated biofilm formation. The above characteristics of M. morganii may lead to an inadequate response to empirical intravitreal antibiotics, and early surgical intervention should be considered.

Diversity in the swimming motility and flagellar regulon structure of uropathogenic Morganella morganii strains

In current times, the opportunistic pathogen Morganella morganii is increasingly becoming a cause of urinary tract infections. The condition has been further complicated by the multiple drug resistance of most isolates. Swimming motility plays an important role in the development of urinary tract infections, allowing bacteria to colonize the upper urinary tract. We determined the differences between the growth, swimming motility, and biofilm formation of two M. morganii strains MM 1 and MM 190 isolated from the urine of patients who had community-acquired urinary tract infections. MM 190 showed a lower growth rate but better-formed biofilms in comparison to MM 1. In addition, MM 190 possessed autoaggregation abilities. It was found that a high temperature (37 °C) inhibits the flagellation of strains and makes MM 190 less motile. At the same time, the MM 1 strain maintained its rate of motility at this temperature. We demonstrated that urea at a concentration of 1.5% suppresses the growth and swimming motility of both strains. Genome analysis showed that MM 1 has a 17.7-kb-long insertion in flagellar regulon between fliE and glycosyltransferase genes, which was not identified in corresponding loci of MM 190 and 9 other M. morganii strains with whole genomes. Both strains carry two genes encoding flagellin, which may indicate flagellar antigen phase variation. However, the fliC2 genes have only 91% identity to each other and exhibit some variability in the regulatory region. We assume that all these differences influence the swimming motility of the strains.

Antimicrobial treatment of morganella morganii invasive infections: Systematic review

BACKGROUND

Morganella morganii is a Gram-negative, rod-shaped, facultative anaerobic bacillus divided into two subspecies, morganii and sibonii. Previously classified as Proteus morganii, it belongs to human gut commensal microbiota. Nevertheless, on rare occasions, especially in nosocomial and postoperative environment as well as in patients with the impaired immune system and young children, it may cause potentially fatal systemic infection.

OBJECTIVES

The aim of our systematic review was to determine whether and what invasive infections in humans were caused by Morganella morganii and to estimate outcomes of administered antibiotic management.

DATA SOURCES

This systematic review was registered at the PROSPERO database of systematic reviews and meta-analyses before initiation of the research (registration number CRD42020171919). Study eligibility criteria and participants. patients of any age and both sex harbouring Morganella morganii as the only microorganism in bodily fluids or tissues, from where it was isolated and identified by one or more of the following diagnostic methods: conventional techniques including colony morphology, Vitek 2, API or BD Phoenix biochemical systems, as well as more sophisticated methods, such as Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and species-specific PCR for M. morganii.

METHODS AND INTERVENTIONS

We have systematically searched MEDLINE, EBSCO, SCOPUS, SCINDEX and GOOGLE SCHOLAR for case reports and case series with M. morganii invasive infections.

RESULTS

M. morganii can cause serious infections of different tissue in patients of any age. The most isolates were susceptible to ceftazidime, imipenem and amikacin. Majority of the patients completely recovered after antibiotic treatment. About 15% of the patients died despite of the therapy. Gentamicin was the most frequently used antibiotic in the treatment of infection caused by M. morganii.

CONCLUSION

M. morganii invasive infections should be taken into consideration by the clinicians, especially in hospital conditions, due to its high degree of mortality and high potential of this bacterium to develop multidrug resistance. Treatment of M. morganii infections should include gentamycin in combination with third generation cephalosporin or another antibiotic to which M. morganii is susceptible (after testing isolates for third cephalosporin generation for the production of AmpC β -lactamases).

Interplay between severities of COVID-19 and the gut microbiome: implications of bacterial co-infections?

COVID-19 is an acute respiratory distress syndrome and is often accompanied by gastrointestinal symptoms. The SARS-CoV-2 has been traced not only in nasopharyngeal and mid-nasal swabs but also in stool and rectal swabs of COVID-19 patients. The gut microbiota is important for an effective immune response as it ensures that unfavorable immune reactions in lungs and other vital organs are regulated. The human gut-lung microbiota interplay provides a framework for therapies in the treatment and management of several pulmonary diseases and infections. Here, we have collated data from COVID-19 studies, which suggest that bacterial co-infections as well as the gut-lung cross talk may be important players in COVID-19 disease prognosis. Our analyses suggests a role of gut microbiome in pathogen infections as well as in an array of excessive immune reactions during and post COVID-19 infection recovery period.