1
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Hu S, Xu C, Lu P, Wu M, Chen A, Zhang M, Xie Y, Han G. Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135493. [PMID: 39173381 DOI: 10.1016/j.jhazmat.2024.135493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/21/2024] [Accepted: 08/10/2024] [Indexed: 08/24/2024]
Abstract
Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.
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Affiliation(s)
- Shunli Hu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
| | - Chuangchuang Xu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Peicheng Lu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Minghui Wu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Anqi Chen
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Guomin Han
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China.
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2
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Li H, Wen J, Zhang X, Dai Z, Liu M, Zhang H, Zhang N, Lei R, Luo P, Zhang J. Large-scale genetic correlation studies explore the causal relationship and potential mechanism between gut microbiota and COVID-19-associated risks. BMC Microbiol 2024; 24:292. [PMID: 39103761 DOI: 10.1186/s12866-024-03423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Recent observational studies suggest that gut microorganisms are involved in the onset and development of coronavirus disease 2019 (COVID-19), but the potential causal relationship behind them remains unclear. Exposure data were derived from the MiBioGen consortium, encompassing 211 gut microbiota (n = 18,340). The outcome data were sourced from the COVID-19 host genetics initiative (round 7), including COVID-19 severity (n = 1,086,211), hospitalization (n = 2,095,324), and susceptibility (n = 2,597,856). First, a two-sample Mendelian randomization (TSMR) was performed to investigate the causal effect between gut microbiota and COVID-19 outcomes. Second, a two-step MR was used to explore the potential mediators and underlying mechanisms. Third, several sensitivity analyses were performed to verify the robustness of the results. Five gut microbes were found to have a potential causality with COVID-19 severity, namely Betaproteobacteria (beta = 0.096, p = 0.034), Christensenellaceae (beta = -0.092, p = 0.023), Adlercreutzia (beta = 0.072, p = 0.048), Coprococcus 1 (beta = 0.089, p = 0.032), Eisenbergiella (beta = 0.064, p = 0.024). Seven gut microbes were found to have a potential causality with COVID-19 hospitalization, namely Victivallaceae (beta = 0.037, p = 0.028), Actinomyces (beta = 0.047, p = 0.046), Coprococcus 2 (beta = -0.061, p = 0.031), Dorea (beta = 0.067, p = 0.016), Peptococcus (beta = -0.035, p = 0.049), Rikenellaceae RC9 gut group (beta = 0.034, p = 0.018), and Proteobacteria (beta = -0.069, p = 0.035). Two gut microbes were found to have a potential causality with COVID-19 susceptibility, namely Holdemanella (beta = -0.024, p = 0.023) and Lachnospiraceae FCS020 group (beta = 0.026, p = 0.027). Multi-omics mediation analyses indicate that numerous plasma proteins, metabolites, and immune factors are critical mediators linking gut microbiota with COVID-19 outcomes. Sensitivity analysis suggested no significant heterogeneity or pleiotropy. These findings revealed the causal correlation and potential mechanism between gut microbiota and COVID-19 outcomes, which may improve our understanding of the gut-lung axis in the etiology and pathology of COVID-19 in the future.
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Affiliation(s)
- He Li
- The Animal Laboratory Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jie Wen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiangbin Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mingren Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruoyan Lei
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Jingwei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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3
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Ke S, Villafuerte Gálvez JA, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu YY. Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591969. [PMID: 38746249 PMCID: PMC11092666 DOI: 10.1101/2024.04.30.591969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Clostridioides difficile infection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Javier A Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yangchun Cao
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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4
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Alrezaihi A, Penrice-Randal R, Dong X, Prince T, Randle N, Semple MG, Openshaw PJM, MacGill T, Myers T, Orr R, Zakotnik S, Suljič A, Avšič-Županc T, Petrovec M, Korva M, AlJabr W, Hiscox JA. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. J Clin Virol 2024; 171:105620. [PMID: 38237303 DOI: 10.1016/j.jcv.2023.105620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/06/2023] [Accepted: 11/18/2023] [Indexed: 03/17/2024]
Abstract
Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.
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Affiliation(s)
| | | | | | | | | | - Malcolm G Semple
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Alder Hey Children's Hospital, Liverpool, UK
| | | | - Tracy MacGill
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Todd Myers
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Robert Orr
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | | | - Alen Suljič
- University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Miša Korva
- University of Ljubljana, Ljubljana, Slovenia
| | - Waleed AlJabr
- University of Liverpool, Liverpool, UK; King Fahad Medical City, Riyadh, Saudi Arabia
| | - Julian A Hiscox
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Agency for Science, Technology and Research (A*STAR), Singapore.
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5
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Wu M, Wang H. Re-considering and designing microbiomes for future waste biorefinery. Microb Biotechnol 2024; 17:e14395. [PMID: 38206186 PMCID: PMC10835331 DOI: 10.1111/1751-7915.14395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
It is an increasingly promising research direction using microbiomes to produce various chemicals in order to support people's growing need for sustainability. Currently, bottom-up constructed defined microbiomes and top-down constructed undefined microbiomes play an essential role in the fields of synthetic biology and environmental engineering, respectively. However, if we are goal-oriented and want to align scientific principles with technology and engineering in future waste biorefinery, we need to reconsider and design microbiomes interdisciplinarily. In this editorial, we briefly review the latest applications of two approaches to microbiome design (bottom-up and top-down) and the dilemmas faced in using complex waste. Consequently, we introduce the concept of 'sustainable synthetic microbiomics' to apply combined bottom-up and top-down constructed microbiomes to provide products for human needs from low-value waste. Furthermore, we outline the relatively comprehensive research contents and expected prospects based on the pressing problems. Finally, burning questions on key research contents are proposed for specific cases, hoping to provide valuable views for future microbiome biorefinery.
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Affiliation(s)
- Menghan Wu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Hui Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
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6
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Zhang S, Liu X, Zhao Y, Wang P, Yu R, Xu P, Jiang Y, Cheng L. Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data. Comput Biol Med 2023; 165:107400. [PMID: 37651767 DOI: 10.1016/j.compbiomed.2023.107400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/04/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
After infection with SARS-CoV-2, the microbiome inside the human body changes dramatically. By re-annotating microbial sequences in bulk RNA-seq and scRNA-seq data of COVID-19 patients, we described the cellular microbial landscape of COVID-19 patients and identified characteristic microorganisms in various tissues. We found that Acinetobacter lwoffii was highly correlated with COVID-19 symptoms and might disrupt some pathways of patients by interacting with the host and other microbes, such as Klebsiella pneumoniae. We further identified characteristic microorganisms specific to cell type, indicating the enrichment preference of some microbes. We also revealed the co-infection of SARS-CoV-2 with hMPV, which may cause the development of COVID-19. Overall, we demonstrated that the presence of intracellular microorganisms in COVID-19 patients and the synergies between microorganisms were strongly correlated with disease progression, providing a theoretical basis for COVID-19 treatment in a certain extent.
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Affiliation(s)
- Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Xingwang Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yue Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Ping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Peigang Xu
- Chongqing Research Institute of Harbin Institute of Technology, China.
| | - Yue Jiang
- Cipher Gene, Ltd., Beijing, 100080, China.
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China; NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
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7
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Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023; 14:e0088923. [PMID: 37294090 PMCID: PMC10470529 DOI: 10.1128/mbio.00889-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Preston Tasoff
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | | | - Victoria Wong Murray
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | - Jordan E. Bisanz
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
| | - Yulin Hswen
- Department of Epidemiology and Biostatistics and the Bakar Computational Health Institute, University of California San Francisco, San Francisco, California, USA
| | - Connie W. Y. Ha
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, USA
| | - Susan V. Lynch
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California San Francisco, University of California, San Francisco, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
| | - Sulggi Lee
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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8
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Daddi L, Dorsett Y, Geng T, Bokoliya S, Yuan H, Wang P, Xu W, Zhou Y. Baseline Gut Microbiome Signatures Correlate with Immunogenicity of SARS-CoV-2 mRNA Vaccines. Int J Mol Sci 2023; 24:11703. [PMID: 37511464 PMCID: PMC10380288 DOI: 10.3390/ijms241411703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The powerful immune responses elicited by the mRNA vaccines targeting the SARS-CoV-2 Spike protein contribute to their high efficacy. Yet, their efficacy can vary greatly between individuals. For vaccines not based on mRNA, cumulative evidence suggests that differences in the composition of the gut microbiome, which impact vaccine immunogenicity, are some of the factors that contribute to variations in efficacy. However, it is unclear if the microbiome impacts the novel mode of immunogenicity of the SARS-CoV-2 mRNA vaccines. We conducted a prospective longitudinal cohort study of individuals receiving SARS-CoV-2 mRNA vaccines where we measured levels of anti-Spike IgG and characterized microbiome composition, at pre-vaccination (baseline), and one week following the first and second immunizations. While we found that microbial diversity at all timepoints correlated with final IgG levels, only at baseline did microbial composition and predicted function correlate with vaccine immunogenicity. Specifically, the phylum Desulfobacterota and genus Bilophila, producers of immunostimulatory LPS, positively correlated with IgG, while Bacteroides was negatively correlated. KEGG predicted pathways relating to SCFA metabolism and sulfur metabolism, as well as structural components such as flagellin and capsular polysaccharides, also positively correlated with IgG levels. Consistent with these findings, depleting the microbiome with antibiotics reduced the immunogenicity of the BNT162b2 vaccine in mice. These findings suggest that gut microbiome composition impacts the immunogenicity of the SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Lauren Daddi
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yair Dorsett
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Tingting Geng
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Suresh Bokoliya
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Hanshu Yuan
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Penghua Wang
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Wanli Xu
- School of Nursing, University of Connecticut, Storrs, CT 06269, USA
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
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9
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Rezzoug I, Visseaux B, Bertine M, Parisey M, Bonnal C, Ruppe E, Descamps D, Timsit JF, Yazdanpanah Y, Armand-Lefevre L, Houze S, Argy N. Faecal Viral Excretion and Gastrointestinal Co-Infection Do Not Explain Digestive Presentation in COVID-19 Patients. Microorganisms 2023; 11:1780. [PMID: 37512952 PMCID: PMC10383301 DOI: 10.3390/microorganisms11071780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
The physiopathological mechanisms responsible for digestive symptoms in COVID-19 patients are still unclear. The aim of this study was to determine the influence of faecal viral shedding on digestive symptoms and propose differential diagnoses in order to understand the gastrointestinal clinical spectrum in acute cases of COVID-19. All patients managed between March and May 2020, from whom stool samples were collected for microbiological investigations, were included. Microbiological analysis consisted of syndromic PCR screening and microscopic parasitological examination supplemented with microsporidia and multiplex protozoa PCR. SARS-CoV-2 infection was diagnosed via viral detection in respiratory and frozen stool samples, completed via serological test when necessary. Epidemiological, clinical, radiological, and biological data and clinical courses were compared according to COVID-19 status and faecal SARS-CoV-2 shedding and enteric co-infection status. The sample included 50 COVID+ and 67 COVID- patients. Faecal viral shedding was detected in 50% of stool samples and was associated with a higher viral load in the upper respiratory tract. Detected enteric pathogens were not different between subjects with different COVID-19 statuses or faecal SARS-CoV-2 shedding and had no impact on the clinical course for COVID-19 patients. The connection between SARS-CoV-2 shedding and enteric pathogen co-infection involvement in gastrointestinal presentation and clinical course is still unclear, suggesting other processes are involved in digestive disorders in COVID-19 patients.
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Affiliation(s)
- Inès Rezzoug
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Benoit Visseaux
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
| | - Mélanie Bertine
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Marion Parisey
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Christine Bonnal
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Etienne Ruppe
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Diane Descamps
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
| | - Jean François Timsit
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Service de Réanimation Médicale et Infectieuses, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Yazdan Yazdanpanah
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Laurence Armand-Lefevre
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Sandrine Houze
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- MERIT UMR 261 Unit, IRD, Faculté de Pharmacie, Université de Paris Cité, 75006 Paris, France
| | - Nicolas Argy
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- MERIT UMR 261 Unit, IRD, Faculté de Pharmacie, Université de Paris Cité, 75006 Paris, France
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10
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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11
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Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H. Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients. J Med Virol 2023; 95:e28727. [PMID: 37185870 DOI: 10.1002/jmv.28727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.
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Affiliation(s)
- Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Department of AIDS and STD Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Liu
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Gengyan Luo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ming Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Minwu Peng
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Meiqi Cai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ying Jiang
- Environment Health Department, Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Chuming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guohui Chang
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Shenzhen, China
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12
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de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P. Altered infective competence of the human gut microbiome in COVID-19. MICROBIOME 2023; 11:46. [PMID: 36894986 PMCID: PMC9995755 DOI: 10.1186/s40168-023-01472-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.
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Affiliation(s)
- Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camille Martin-Gallausiaux
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Milena Despotovic
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Chantal J Snoeck
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Lea Delacour
- Luxembourg Centre for Systems Biomedicine, LCSB Operations, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Deepthi Poornima Budagavi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cédric Christian Laczny
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paula-Cristina Lupu
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Taina Marques
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Estelle Sandt
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marc Paul O'Sullivan
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Soumyabrata Ghosh
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Guy Fagherazzi
- Deep Digital Phenotyping Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg.
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13
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Changes in the Urine Metabolomic Profile in Patients Recovering from Severe COVID-19. Metabolites 2023; 13:metabo13030364. [PMID: 36984804 PMCID: PMC10058594 DOI: 10.3390/metabo13030364] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Metabolomics is a relatively new research area that focuses mostly on the profiling of selected molecules and metabolites within the organism. A SARS-CoV-2 infection itself can lead to major disturbances in the metabolite profile of the infected individuals. The aim of this study was to analyze metabolomic changes in the urine of patients during the acute phase of COVID-19 and approximately one month after infection in the recovery period. We discuss the observed changes in relation to the alterations resulting from changes in the blood plasma metabolome, as described in our previous study. The metabolome analysis was performed using NMR spectroscopy from the urine of patients and controls. The urine samples were collected at three timepoints, namely upon hospital admission, during hospitalization, and after discharge from the hospital. The acute COVID-19 phase induced massive alterations in the metabolic composition of urine was linked with various changes taking place in the organism. Discriminatory analyses showed the feasibility of successful discrimination of COVID-19 patients from healthy controls based on urinary metabolite levels, with the highest significance assigned to citrate, Hippurate, and pyruvate. Our results show that the metabolomic changes persist one month after the acute phase and that the organism is not fully recovered.
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14
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Vitiello A, Ferrara F, Zovi A. The direct correlation between microbiota and SARS-CoV-2 infectious disease. Inflammopharmacology 2023; 31:603-610. [PMID: 36725821 PMCID: PMC9891758 DOI: 10.1007/s10787-023-01145-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023]
Abstract
The human microbiota is the good part of the human organism and is a collection of symbiotic microorganisms which aid in human physiological functions. Diseases that can be generated by an altered microbiota are continuously being studied, but it is quite evident how a damaged microbiota is involved in chronic inflammatory diseases, psychiatric diseases, and some bacterial or viral infections. However, the role of the microbiota in the host immune response to bacterial and viral infections is still not entirely understood. Metabolites or components which are produced by the microbiota are useful in mediating microbiota-host interactions, thus influencing the host's immune capacity. Recent evidence shows that the microbiota is evidently altered in patients with viral infections such as post-acute COVID-19 syndrome (PACS). In this review, the associations between microbiota and COVID-19 infection are highlighted in terms of biological and clinical significance by emphasizing the mechanisms through which metabolites produced by the microbiota modulate immune responses to COVID-19 infection.
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Affiliation(s)
| | - Francesco Ferrara
- Pharmaceutical Department, Asl Napoli 3 Sud, Dell’amicizia Street 22, 80035 Nola, Naples Italy
| | - Andrea Zovi
- Ministry of Health, Viale Giorgio Ribotta 5, 00144 Rome, Italy
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15
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COVID-19: The Ethno-Geographic Perspective of Differential Immunity. Vaccines (Basel) 2023; 11:vaccines11020319. [PMID: 36851197 PMCID: PMC9966855 DOI: 10.3390/vaccines11020319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.
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16
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Association between microbiota and immune response to Sars-CoV-2 infection. Infect Dis Now 2023; 53:104646. [PMID: 36642100 PMCID: PMC9837228 DOI: 10.1016/j.idnow.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
In recent times, the key role of the human microbiota in the body's response to infectious diseases has been increasingly demonstrated. The human microbiota is the set of symbiotic microorganisms which coexist with the human organism without harming it. However, diseases related to the microbiota occur and are being studied, and numerous publications suggest that altered microbiota composition is implicated in psychiatric diseases, chronic inflammatory diseases, and some viral infections. On the other hand, the role of the human microbiota in the host immune response to viral infections is not entirely clear. Metabolites or components produced by the microbiota are the main mediators of microbiota-host interactions that influence host immunity. It has been shown that in patients with COVID-19 and post-acute COVID-19 syndrome (PACS), the microbiota is significantly altered. In this brief review, we examine the associations between the role of the microbiota in response to COVID-19 infection in terms of molecular biology and clinical relevance. We finally discuss the mechanisms by which metabolites produced by the microbiota modulate host immune responses to SARS-CoV-2 infection.
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17
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Avila-Ponce de León U, Vazquez-Jimenez A, Cervera A, Resendis-González G, Neri-Rosario D, Resendis-Antonio O. Machine Learning and COVID-19: Lessons from SARS-CoV-2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:311-335. [PMID: 37378775 DOI: 10.1007/978-3-031-28012-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Currently, methods in machine learning have opened a significant number of applications to construct classifiers with capacities to recognize, identify, and interpret patterns hidden in massive amounts of data. This technology has been used to solve a variety of social and health issues against coronavirus disease 2019 (COVID-19). In this chapter, we present some supervised and unsupervised machine learning techniques that have contributed in three aspects to supplying information to health authorities and diminishing the deadly effects of the current worldwide outbreak on the population. First is the identification and construction of powerful classifiers capable of predicting severe, moderate, or asymptomatic responses in COVID-19 patients starting from clinical or high-throughput technologies. Second is the identification of groups of patients with similar physiological responses to improve the triage classification and inform treatments. The final aspect is the combination of machine learning methods and schemes from systems biology to link associative studies with mechanistic frameworks. This chapter aims to discuss some practical applications in the use of machine learning techniques to handle data coming from social behavior and high-throughput technologies, associated with COVID-19 evolution.
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Affiliation(s)
- Ugo Avila-Ponce de León
- Programa de Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Aarón Vazquez-Jimenez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Alejandra Cervera
- Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Galilea Resendis-González
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Daniel Neri-Rosario
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, Mexico.
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación - Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico.
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18
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Wang M, Zhang Y, Li C, Chang W, Zhang L. The relationship between gut microbiota and COVID-19 progression: new insights into immunopathogenesis and treatment. Front Immunol 2023; 14:1180336. [PMID: 37205106 PMCID: PMC10185909 DOI: 10.3389/fimmu.2023.1180336] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a global health crisis. Increasing evidence underlines the key role of competent immune responses in resisting SARS-CoV-2 infection and manifests the disastrous consequence of host immune dysregulation. Elucidating the mechanisms responsible for deregulated host immunity in COVID-19 may provide a theoretical basis for further research on new treatment modalities. Gut microbiota comprises trillions of microorganisms colonizing the human gastrointestinal tract and has a vital role in immune homeostasis and the gut-lung crosstalk. Particularly, SARS-CoV-2 infection can lead to the disruption of gut microbiota equilibrium, a condition called gut dysbiosis. Due to its regulatory effect on host immunity, gut microbiota has recently received considerable attention in the field of SARS-CoV-2 immunopathology. Imbalanced gut microbiota can fuel COVID-19 progression through production of bioactive metabolites, intestinal metabolism, enhancement of the cytokine storm, exaggeration of inflammation, regulation of adaptive immunity and other aspects. In this review, we provide an overview of the alterations in gut microbiota in COVID-19 patients, and their effects on individuals' susceptibility to viral infection and COVID-19 progression. Moreover, we summarize currently available data on the critical role of the bidirectional regulation between intestinal microbes and host immunity in SARS-CoV-2-induced pathology, and highlight the immunomodulatory mechanisms of gut microbiota contributing to COVID-19 pathogenesis. In addition, we discuss the therapeutic benefits and future perspectives of microbiota-targeted interventions including faecal microbiota transplantation (FMT), bacteriotherapy and traditional Chinese medicine (TCM) in COVID-19 treatment.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Chunmei Li
- Department of Radiology, Qingdao Municipal Hospital, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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19
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Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.07.519508. [PMID: 36523400 PMCID: PMC9753784 DOI: 10.1101/2022.12.07.519508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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Nobre JG, Delgadinho M, Silva C, Mendes J, Mateus V, Ribeiro E, Costa DA, Lopes M, Pedroso AI, Trigueiros F, Rodrigues MI, de Sousa CL, Brito M. Gut microbiota profile of COVID-19 patients: Prognosis and risk stratification (MicroCOVID-19 study). Front Microbiol 2022; 13:1035422. [PMID: 36483197 PMCID: PMC9723140 DOI: 10.3389/fmicb.2022.1035422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Gut microbiota is intrinsically associated with the immune system and can promote or suppress infectious diseases, especially viral infections. This study aims to characterize and compare the microbiota profile of infected patients with SARS-CoV-2 (milder or severe symptoms), non-infected people, and recovered patients. This is a national, transversal, observational, multicenter, and case-control study that analyzed the microbiota of COVID-19 patients with mild or severe symptoms at home, at the hospital, or in the intensive care unit, patients already recovered, and healthy volunteers cohabiting with COVID-19 patients. DNA was isolated from stool samples and sequenced in a NGS platform. A demographic questionnaire was also applied. Statistical analysis was performed in SPSS. RESULTS Firmicutes/Bacteroidetes ratios were found to be significantly lower in infected patients (1.61 and 2.57) compared to healthy volunteers (3.23) and recovered patients (3.89). Furthermore, the microbiota composition differed significantly between healthy volunteers, mild and severe COVID-19 patients, and recovered patients. Furthermore, Escherichia coli, Actinomyces naeslundii, and Dorea longicatena were shown to be more frequent in severe cases. The most common COVID-19 symptoms were linked to certain microbiome groups. CONCLUSION We can conclude that microbiota composition is significantly affected by SARS-CoV-2 infection and may be used to predict COVID-19 clinical evolution. Therefore, it will be possible to better allocate healthcare resources and better tackle future pandemics.
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Affiliation(s)
- José Guilherme Nobre
- Faculty of Medicine, Lisbon University, Lisbon, Portugal
- Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal
- PTSurg – Portuguese Surgical Research Collaborative, Lisbon, Portugal
| | - Mariana Delgadinho
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Carina Silva
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
- Centro de Estatística e Aplicações, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Mendes
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Vanessa Mateus
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Edna Ribeiro
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Diogo Alpuim Costa
- Breast Cancer Unit, CUF Oncologia, Lisbon, Portugal
- Faculdade de Ciências Médicas, NOVA Medical School, Lisbon, Portugal
| | - Miguel Lopes
- Departamento de Pneumologia, Hospital Garcia de Orta, Almada, Portugal
| | - Ana Isabel Pedroso
- Serviço de Medicina Intensiva, Hospital de Cascais Dr. José de Almeida, Cascais, Portugal
| | - Frederico Trigueiros
- Departamento de Medicina Interna I, Centro Hospitalar Lisboa Norte – Hospital de Santa Maria, Lisbon, Portugal
| | - Maria Inês Rodrigues
- Departamento de Medicina Interna I, Centro Hospitalar Lisboa Norte – Hospital de Santa Maria, Lisbon, Portugal
| | | | - Miguel Brito
- H&TRC- Health and Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
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Rossini V, Tolosa-Enguis V, Frances-Cuesta C, Sanz Y. Gut microbiome and anti-viral immunity in COVID-19. Crit Rev Food Sci Nutr 2022; 64:4587-4602. [PMID: 36382631 DOI: 10.1080/10408398.2022.2143476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SARS-CoV-2 mainly affects the respiratory system, but the gastrointestinal tract is also a target. Prolonged gut disorders, in COVID-19 patients, were correlated with decreased richness and diversity of the gut microbiota, immune deregulation and delayed viral clearance. Although there are no definitive conclusions, ample evidence would suggest that the gut microbiome composition and function play a role in COVID-19 progression. Microbiome modulation strategies for population stratification and management of COVID-19 infection are under investigation, representing an area of interest in the ongoing pandemic. In this review, we present the existing data related to the interaction between gut microbes and the host's immune response to SARS-CoV-2 and discuss the implications for current disease management and readiness to face future pandemics.
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Affiliation(s)
- V Rossini
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - V Tolosa-Enguis
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - C Frances-Cuesta
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Y Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
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