Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

Thuy‐Boun, Peter S.; Mehta, Subina; Gruening, Bjoern; McGowan, Thomas; Nguyen, Aithanh; Rajczewski, Andrew T.; Johnson, James E.; Griffin, Timothy J.; Wolan, Dennis W.; Jagtap, Pratik

doi:10.1021/acs.jproteome.0c00822

Cited by 22 publications

(15 citation statements)

References 24 publications

(48 reference statements)

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“…60 , 61 Lactobacillus rhamnosus is depicted as a potential co‐infection microorganism along with SARS‐CoV‐2. 62 Lactobacillus had been reported to aggravate mucosal inflammation, and interestingly, lactic acid was rich in fecal samples from COVID‐19. 30 In the last follow‐up sample, several opportunistic pathogens were characteristic species for COVID‐19 patients.…”

Section: Discussionmentioning

confidence: 99%

“…Besides, S. odontolytica was discovered in various pulmonary infections, which may be associated with the development of acute respiratory distress syndrome 60,61 . Lactobacillus rhamnosus is depicted as a potential co‐infection microorganism along with SARS‐CoV‐2 62 . Lactobacillus had been reported to aggravate mucosal inflammation, and interestingly, lactic acid was rich in fecal samples from COVID‐19 30 .…”

Section: Discussionmentioning

confidence: 99%

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SARS‐CoV‐2 triggered oxidative stress and abnormal energy metabolism in gut microbiota

Zhou

Zeng

et al. 2022

MedComm

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Specific roles of gut microbes in COVID‐19 progression are critical. However, the circumstantial mechanism remains elusive. In this study, shotgun metagenomic or metatranscriptomic sequencing was performed on fecal samples collected from 13 COVID‐19 patients and controls. We analyzed the structure of gut microbiota, identified the characteristic bacteria, and selected biomarkers. Further, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were employed to correlate the taxon alterations and corresponding functions. The gut microbiota of COVID‐19 patients was characterized by the enrichment of opportunistic pathogens and depletion of commensals. The abundance of Bacteroides spp. displayed an inverse relationship with COVID‐19 severity, whereas Actinomyces oris , Escherichia coli , and Streptococcus parasanguini were positively correlated with disease severity. The genes encoding oxidoreductase were significantly enriched in gut microbiome of COVID‐19 group. KEGG annotation indicated that the expression of ABC transporter was upregulated, while the synthesis pathway of butyrate was aberrantly reduced. Furthermore, increased metabolism of lipopolysaccharide, polyketide sugar, sphingolipids, and neutral amino acids were found. These results suggested the gut microbiome of COVID‐19 patients was in a state of oxidative stress. Healthy gut microbiota may enhance antiviral defenses via butyrate metabolism, whereas the accumulation of opportunistic and inflammatory bacteria may exacerbate COVID‐19 progression.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

SARS‐CoV‐2 triggered oxidative stress and abnormal energy metabolism in gut microbiota

Zhou

Zeng

et al. 2022

MedComm

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show abstract

“…In this regard, it would be anticipated that nosocomial infection should complicate COVID-19 as for other viral respiratory infections. The contamination of clinical samples with usual respiratory micro-organisms must be considered in sophisticated analyses [1].…”

Section: General Attributes Of Viral Infections In the Co-infection Contextmentioning

confidence: 99%

The Complexity of Co-Infections in the Era of COVID-19

Cimolai

2021

SN Compr. Clin. Med.

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“…Surprisingly, SARS-CoV-2 infection facilitated the growth of Akkermansia muciniphila and Lactobacillus rhamnosus. Lactobacillus rhamnosus is depicted as a potential co-infection microorganism along with SARS-Cov-2 [57]. Lactobacillus had been reported to aggravate mucosal inflammation, and interestingly, fecal samples from COVID-19 patients were rich in lactic acid [58].…”

Section: Moreover It Was Metabolically Complementary To Butyrate-producing Bacteriummentioning

confidence: 99%

SARS-CoV-2 triggered excessive inflammation and abnormal energy metabolism in gut microbiota

Zhou

Zeng

et al. 2021

Preprint

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Specific roles of gut microbes in COVID-19 progression are critical. However, the circumstantial mechanism remains elusive. In this study, shotgun metagenomic or metatranscriptomic sequencing were performed on fecal samples collected from 13 COVID-19 patients and controls. We analyzed the structure of gut microbiota, identified the characteristic bacteria and selected biomarkers. Further, GO, KEGG and eggNOG annotation were employed to correlate the taxon alteration and corresponding functions. The gut microbiota of COVID-19 patients was characterized by the enrichment of opportunistic pathogens and depletion of commensals. The abundance of Bacteroides spp. displayed an inverse relationship to COVID-19 severity, whereas Actinomyces oris, Escherichia coli, and Gemmiger formicilis were positively correlated with disease severity. The genes encoding oxidoreductase were significantly enriched in SARS-CoV-2 infection. KEGG annotation indicated that the expression of ABC transporter was up regulated, while the synthesis pathway of butyrate was aberrantly reduced. Furthermore, increased metabolism of lipopolysaccharide, polyketide sugar, sphingolipids and neutral amino acids was found. These results suggested the gut microbiome of COVID-19 patients was correlated with disease severity and in a state of excessive inflammatory response. Healthy gut microbiota may enhance antiviral defenses via butyrate metabolism, whereas the accumulation of opportunistic and inflammatory bacteria may exacerbate the disease progression.

show abstract

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

Cited by 22 publications

References 24 publications

SARS‐CoV‐2 triggered oxidative stress and abnormal energy metabolism in gut microbiota

SARS‐CoV‐2 triggered oxidative stress and abnormal energy metabolism in gut microbiota

The Complexity of Co-Infections in the Era of COVID-19

SARS-CoV-2 triggered excessive inflammation and abnormal energy metabolism in gut microbiota

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