SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota

Sokol, Harry; Contreras, Vanessa; Maisonnasse, Pauline; Desmons, Aurore; Delache, Benoît; Sencio, Valentin; Machelart, Arnaud; Brisebarre, Angela; Humbert, Lydie; Deryuter, Lucie; Gauliard, Emilie; Heumel, Séverine; Rainteau, Dominique; Dereuddre‐Bosquet, Nathalie; Menu, Elisabeth; Fang, Raphaël Ho Tsong; Lamazière, Antonin; Brot, Loïc; Wahl, Céline; Oeuvray, Cyriane; Rolhion, Nathalie; Werf, Sylvie van der; Ferreira, Stéphanie; Grand, Roger Le; Trottein, François

doi:10.1080/19490976.2021.1893113

Cited by 88 publications

(91 citation statements)

References 64 publications

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“…Interestingly, Alistipes species are indole-positive, involved in the serotonin precursor tryptophan metabolism and in maintaining gut immune homeostasis [35] , [36] . This is later validated in animals that tryptophan metabolism in the gut was altered as a result of SARS-CoV-2 infection [28] . In addition, the hyper-inflammatory response of COVID-19 patients was associated with disrupted gut permeability and microbial translocation [16] , [37] .…”

Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 83%

“…Interestingly, the GI tract is also affected in a long term in COVID-19, as demonstrated by a prolonged shedding of viral RNA in stool specimens up to 42 days and presence of SARS-CoV-2 virus in the gut epithelium up to 90 days after disease resolution in some patients [25] , [26] . Concordantly, long-lasting gut microbiome dysbiosis is also consistently observed in subjects recovered from COVID-19 [12] , [15] , [27] , [28] , implying that gut microbiome is closely linked to host health in a post-COVID-19 age.…”

Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 93%

“…To validate that SARS-CoV-2 infection is the driving force of the alterations in the gut microbiome ecology, Sokol et al used a non-human primate model (rhesus macaques and cynomolgus macaques) challenged with SARS-CoV-2 and subsequently analyzed the impact of a SARS-CoV-2 infection on dynamic changes of the gut microbiome [28] . Strikingly, the gut microbiome gradually changed from day 0 until day 13 post infection, at which time point the gut microbiome was most different from the baseline microbiome in terms of fecal microbial community structure [28] . This result indicates that SARS-CoV-2 infection virtually induces alterations in the gut microbiome ecology in COVID-19.…”

Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 99%

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Gut Microbiome Alterations in COVID-19

Zuo

Wen

et al. 2021

Genomics, Proteomics &Amp; Bioinformatics

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Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 ( SARS-CoV-2 ), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with ‘long COVID’ (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2 infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida , may hinder the re-assembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.

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Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 83%

Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 93%

Section: The Gut Bacterial Microbiome In Covid-19mentioning

confidence: 99%

See 1 more Smart Citation

Gut Microbiome Alterations in COVID-19

Zuo

Wen

et al. 2021

Genomics, Proteomics &Amp; Bioinformatics

View full text Add to dashboard Cite

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“…The supplementation from other SCFA-producing bacteria could be the vital point. Additionally, Sokol et al ( 27 ) analyzed the dynamic changes of the gut microbiota in macaques over the entire course of SARS-CoV-2 infection. SCFA production declined during infection and returned to a normal level after recovery.…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery

et al. 2021

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Coronavirus disease 2019 (COVID-19) has infected over 124 million people worldwide. In addition to the development of therapeutics and vaccines, the evaluation of the sequelae in recovered patients is also important. Recent studies have indicated that COVID-19 has the ability to infect intestinal tissues and to trigger alterations of the gut microbiota. However, whether these changes in gut microbiota persist into the recovery stage remains largely unknown. Here, we recruited seven healthy Chinese men and seven recovered COVID-19 male patients with an average of 3-months after discharge and analyzed their fecal samples by 16S rRNA sequencing analysis to identify the differences in gut microbiota. Our results suggested that the gut microbiota differed in male recovered patients compared with healthy controls, in which a significant difference in Chao index, Simpson index, and β-diversity was observed. And the relative abundance of several bacterial species differed clearly between two groups, characterized by enrichment of opportunistic pathogens and insufficiency of some anti-inflammatory bacteria in producing short chain fatty acids. The above findings provide preliminary clues supporting that the imbalanced gut microbiota may not be fully restored in recovered patients, highlighting the importance of continuous monitoring of gut health in people who have recovered from COVID-19.

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“…In non-human primates infected with SARS-CoV-2, 16S rRNA analysis of the microbial gut community showed changes in the taxonomic composition, with the relative abundance of Acinetobacter and Ruminococcaceae being positively correlated with the presence of SARS-CoV-2 in the URT. In addition, SARS-CoV-2 infection significantly alters the metabolite composition with a reduction in the levels of SCFAs, bile acids, and tryptophan metabolites ( Sokol et al, 2021 ).…”

Section: Probiotics Prebiotics and Synbioticsmentioning

confidence: 99%

Gut Microbiota Modulation as a Potential Target for the Treatment of Lung Infections

2021

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The gastrointestinal and respiratory systems are colonized by a complex ecosystem of microorganisms called the microbiota. These microorganisms co-evolved over millions of years with the host, creating a symbiotic relationship that is fundamental for promoting host homeostasis by producing bioactive metabolites and antimicrobial molecules, and regulating the immune and inflammatory responses. Imbalance in the abundance, diversity, and function of the gut microbiota (known as dysbiosis) have been shown to increase host susceptibility to infections in the lungs, suggesting crosstalk between these organs. This crosstalk is now referred to as the gut-lung axis. Hence, the use of probiotics, prebiotics, and synbiotics for modulation of gut microbiota has been studied based on their effectiveness in reducing the duration and severity of respiratory tract infections, mainly owing to their effects on preventing pathogen colonization and modulating the immune system. This review discusses the role and responses of probiotics, prebiotics, and synbiotics in the gut-lung axis in the face of lung infections.

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SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota

Cited by 88 publications

References 64 publications

Gut Microbiome Alterations in COVID-19

Gut Microbiome Alterations in COVID-19

Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery

Gut Microbiota Modulation as a Potential Target for the Treatment of Lung Infections

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