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Hernandez JM, Almeida GBS, Portela ACR, Cardoso JF, Junior ECS, Lucena MSS, Nunes MRT, Gabbay YB, Silva LD. Microbial Diversity in Children with Gastroenteritis in the Amazon Region of Brazil: Development and Validation of a Molecular Method for Complete Sequencing of Viral Genomes. J Genomics 2024; 12:47-54. [PMID: 38638167 PMCID: PMC11024607 DOI: 10.7150/jgen.94116] [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: 01/10/2024] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
INTRODUCTION Metagenomic sequencing is a powerful tool that is widely used in laboratories worldwide for taxonomic characterization of microorganisms in clinical and environmental samples. In this study, we utilized metagenomics to investigate comprehensively the microbial diversity in fecal samples of children over a four-year period. Our methods were carefully designed to ensure accurate and reliable results. MATERIAL AND METHODS Validated and analyzed were metagenomic data obtained from sequencing 27 fecal samples from children under 10 years old with gastroenteritis over a four-year period (2012-2016). The fecal specimens were collected from patients who received care at public health facilities in the northern region of Brazil. Sequencing libraries were prepared from cDNA and sequenced on the Illumina HiSeq. Kraken-2 was utilized to classify bacterial taxonomy based on the 16S rRNA gene, using the Silva rRNA database. Additionally, the Diamond program was used for mapping to the non-redundant protein database (NR database). Phylogenomic analyses were conducted using Geneious R10 and MEGA X software, and Bayesian estimation of phylogeny was performed using the MrBayes program. The results indicate significant heterogeneity among norovirus strains, with evidence of recombination and point mutations. This study presents the first complete genome of parechovirus 8 in the region. Additionally, it describes the bacterial populations and bacteriophages present in feces, with a high abundance of Firmicutes and Proteobacteria, including an increased proportion of the Enterobacteriaceae family. The presented data demonstrate the genetic diversity of microbial populations and provide a comprehensive report on viral molecular characterization. These findings are relevant for genomic studies in gastrointestinal infections. The metagenomic approach is a powerful tool for investigating microbial diversity in children with gastroenteritis. However, further studies are imperative to conduct genomic analysis of identified bacterial strains and thoroughly analyze antimicrobial resistance genes.
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Affiliation(s)
- Juliana Merces Hernandez
- Postgraduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Pará, Brazil
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2
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Peng LJ, Chen YP, Qu F, Zhong Y, Jiang ZS. Correlation of Gut Microbiota with Children Obesity and Weight Loss. Indian J Microbiol 2024; 64:82-91. [PMID: 38468732 PMCID: PMC10924870 DOI: 10.1007/s12088-023-01088-3] [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: 11/07/2022] [Accepted: 08/03/2023] [Indexed: 03/13/2024] Open
Abstract
Children obesity is a serious public health problem drawing much attention around the world. Recent research indicated that gut microbiota plays a vital role in children obesity, and disturbed gut microbiota is a prominent characteristic of obese children. Diet and exercise are efficient intervention for weight loss in obesity children, however, how the gut microbiota is modulated which remains largely unknown. To characterize the feature of gut microbiota in obese children and explore the effect of dietary and exercise on gut microbiota in simple obese children, 107 healthy children and 86 obese children were recruited, and among of the obese children 39 received the dietary-exercise combined weight loss intervention (DEI). The gut microbiota composition was detected by the 16S amplicon sequencing method. The gut microbiota composition was significantly different between obese children and the healthy cohort, and DEI significantly reduced the body weight and ameliorated the gut microbiota dysbiosis. After DEI, the abundance of the Akkermansia muciniphila was increased, while the abundance of the Sutterella genus was decreased in simple obese children. Our results may provide theoretical reference for future personalized obesity interventions based on gut microbiota. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01088-3.
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Affiliation(s)
- Li-Jun Peng
- Women’s Committee, Hunan Children’s Hospital and the Pediatric Academy of University of South China, Changsha, 410007 Hunan People’s Republic of China
| | - Yan-Ping Chen
- Department of Respiratory, Hunan Children’s Hospital, Changsha, 410007 Hunan People’s Republic of China
| | - Fang Qu
- Medical Record Statistics and Library Management Office, Hunan Children’s Hospital and the Pediatric Academy of University of South China, Changsha, 410007 Hunan People’s Republic of China
| | - Yan Zhong
- Children’s Healthcare Institute, Hunan Children’s Hospital, and the Pediatric Academy of University of South China, Changsha, 410007 Hunan People’s Republic of China
| | - Zhi-Sheng Jiang
- Pathophysiology Department, Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, University of South China, Hengyang, 421001 Hunan People’s Republic of China
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3
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Abstract
The mammalian gastrointestinal tract (GIT) hosts a diverse and highly active microbiota composed of bacteria, eukaryotes, archaea, and viruses. Studies of the GIT microbiota date back more than a century, although modern techniques, including mouse models, sequencing technology, and novel therapeutics in humans, have been foundational to our understanding of the roles of commensal microbes in health and disease. Here, we review the impacts of the GIT microbiota on viral infection, both within the GIT and systemically. GIT-associated microbes and their metabolites alter the course of viral infection through a variety of mechanisms, including direct interactions with virions, alteration of the GIT landscape, and extensive regulation of innate and adaptive immunity. Mechanistic understanding of the full breadth of interactions between the GIT microbiota and the host is still lacking in many ways but will be vital for the development of novel therapeutics for viral and nonviral diseases alike.
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Affiliation(s)
- Danielle E Campbell
- Department of Medicine, Division of Infectious Diseases and Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Yuhao Li
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Harshad Ingle
- Department of Medicine, Division of Infectious Diseases and Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases and Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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4
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Bai GH, Tsai MC, Lin SC, Hsu YH, Chen SY. Unraveling the interplay between norovirus infection, gut microbiota, and novel antiviral approaches: a comprehensive review. Front Microbiol 2023; 14:1212582. [PMID: 37485533 PMCID: PMC10359435 DOI: 10.3389/fmicb.2023.1212582] [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: 04/26/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Norovirus infection is a leading cause of acute gastroenteritis worldwide and can also cause harmful chronic infections in individuals with weakened immune systems. The role of the gut microbiota in the interactions between the host and noroviruses has been extensively studied. While most past studies were conducted in vitro or focused on murine noroviruses, recent research has expanded to human noroviruses using in vivo or ex vivo human intestinal enteroids culture studies. The gut microbiota has been observed to have both promoting and inhibiting effects on human noroviruses. Understanding the interaction between noroviruses and the gut microbiota or probiotics is crucial for studying the pathogenesis of norovirus infection and its potential implications, including probiotics and vaccines for infection control. Recently, several clinical trials of probiotics and norovirus vaccines have also been published. Therefore, in this review, we discuss the current understanding and recent updates on the interactions between noroviruses and gut microbiota, including the impact of norovirus on the microbiota profile, pro-viral and antiviral effects of microbiota on norovirus infection, the use of probiotics for treating norovirus infections, and human norovirus vaccine development.
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Affiliation(s)
- Geng-Hao Bai
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Chen Tsai
- Department of General Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Allergy, Asthma and Immunology, Shuang Ho Hospital, New Taipei, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, New Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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5
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Quaye EK, Adjei RL, Isawumi A, Allen DJ, Caporaso JG, Quaye O. Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis. Int J Mol Sci 2023; 24:3607. [PMID: 36835017 PMCID: PMC9962333 DOI: 10.3390/ijms24043607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Acute gastroenteritis (AGE) is a disease of global public health importance. Recent studies show that children with AGE have an altered gut microbiota relative to non-AGE controls. Yet, how the gut microbiota differs in Ghanaian children with and without AGE remains unclear. Here, we explore the 16S rRNA gene-based faecal microbiota profiles of Ghanaian children five years of age and younger, comprising 57 AGE cases and 50 healthy controls. We found that AGE cases were associated with lower microbial diversity and altered microbial sequence profiles relative to the controls. The faecal microbiota of AGE cases was enriched for disease-associated bacterial genera, including Enterococcus, Streptococcus, and Staphylococcus. In contrast, the faecal microbiota of controls was enriched for potentially beneficial genera, including Faecalibacterium, Prevotella, Ruminococcus, and Bacteroides. Lastly, distinct microbial correlation network characteristics were observed between AGE cases and controls, thereby supporting broad differences in faecal microbiota structure. Altogether, we show that the faecal microbiota of Ghanaian children with AGE differ from controls and are enriched for bacterial genera increasingly associated with diseases.
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Affiliation(s)
- Emmanuel Kofi Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Raymond Lovelace Adjei
- Council for Scientific and Industrial Research (CSIR)-Animal Research Institute, Accra P.O. Box AH 20, Ghana
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - David J. Allen
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - J. Gregory Caporaso
- Centre for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra P.O. Box LG 54, Ghana
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6
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Zhang W, Wan Z, Li X, Li R, Luo L, Song Z, Miao Y, Li Z, Wang S, Shan Y, Li Y, Chen B, Zhen H, Sun Y, Fang M, Ding J, Yan Y, Zong Y, Wang Z, Zhang W, Yang H, Yang S, Wang J, Jin X, Wang R, Chen P, Min J, Zeng Y, Li T, Xu X, Nie C. A population-based study of precision health assessments using multi-omics network-derived biological functional modules. Cell Rep Med 2022; 3:100847. [PMID: 36493776 PMCID: PMC9798030 DOI: 10.1016/j.xcrm.2022.100847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/05/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022]
Abstract
Recent technological advances in multi-omics and bioinformatics provide an opportunity to develop precision health assessments, which require big data and relevant bioinformatic methods. Here we collect multi-omics data from 4,277 individuals. We calculate the correlations between pairwise features from cross-sectional data and then generate 11 biological functional modules (BFMs) in males and 12 BFMs in females using a community detection algorithm. Using the features in the BFM associated with cardiometabolic health, carotid plaques can be predicted accurately in an independent dataset. We developed a model by comparing individual data with the health baseline in BFMs to assess health status (BFM-ash). Then we apply the model to chronic patients and modify the BFM-ash model to assess the effects of consuming grape seed extract as a dietary supplement. Finally, anomalous BFMs are identified for each subject. Our BFMs and BFM-ash model have huge prospects for application in precision health assessment.
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Affiliation(s)
- Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Ziyun Wan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Xiaoyu Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Rui Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zijun Song
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Miao
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zhiming Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Ying Shan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yan Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Bangwei Chen
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hefu Zhen
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yuzhe Sun
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Mingyan Fang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Jiahong Ding
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yizhen Yan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yang Zong
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Zhen Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Shuang Yang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Ru Wang
- School of Exercise and Health, Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, China
| | - Peijie Chen
- School of Exercise and Health, Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, China
| | - Tao Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,Corresponding author
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7
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Malik J, Ahmed S, Yaseen Z, Alanazi M, Alharby TN, Alshammari HA, Anwar S. Association of SARS-CoV-2 and Polypharmacy with Gut-Lung Axis: From Pathogenesis to Treatment. ACS OMEGA 2022; 7:33651-33665. [PMID: 36164411 PMCID: PMC9491241 DOI: 10.1021/acsomega.2c02524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/29/2022] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 is a novel infectious contagion leading to COVID-19 disease. The virus has affected the lives of millions of people across the globe with a high mortality rate. It predominantly affects the lung (respiratory system), but it also affects other organs, including the cardiovascular, psychological, and gastrointestinal (GIT) systems. Moreover, elderly and comorbid patients with compromised organ functioning and pre-existing polypharmacy have worsened COVID-19-associated complications. Microbiota (MB) of the lung plays an important role in developing COVID-19. The extent of damage mainly depends on the predominance of opportunistic pathogens and, inversely, with the predominance of advantageous commensals. Changes in the gut MB are associated with a bidirectional shift in the interaction among the gut with a number of vital human organs, which leads to severe disease symptoms. This review focuses on dysbiosis in the gut-lung axis, COVID-19-induced worsening of comorbidities, and the influence of polypharmacy on MB.
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Affiliation(s)
- Jonaid
Ahmad Malik
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Guwahati, Assam 781101, India
- Department
of Biomedical Engineering, Indian Institute
of Technology Rupnagar 140001, India
| | - Sakeel Ahmed
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat 382355, India
| | - Zahid Yaseen
- Department
of Pharmaceutical Biotechnology, Delhi Pharmaceutical
Sciences and Research University, New Delhi, Delhi 110017, India
| | - Muteb Alanazi
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | - Tareq Nafea Alharby
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | | | - Sirajudheen Anwar
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
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8
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Milking It for All It's Worth: The Effects of Environmental Enrichment on Maternal Nurturance, Lactation Quality, and Offspring Social Behavior. eNeuro 2022; 9:ENEURO.0148-22.2022. [PMID: 35995560 PMCID: PMC9417599 DOI: 10.1523/eneuro.0148-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 12/17/2022] Open
Abstract
Breastfeeding confers robust benefits to offspring development in terms of growth, immunity, and neurophysiology. Similarly, improving environmental complexity, i.e., environmental enrichment (EE), contributes developmental advantages to both humans and laboratory animal models. However, the impact of environmental context on maternal care and milk quality has not been thoroughly evaluated, nor are the biological underpinnings of EE on offspring development understood. Here, Sprague Dawley rats were housed and bred in either EE or standard-housed (SD) conditions. EE dams gave birth to a larger number of pups, and litters were standardized and cross-fostered across groups on postnatal day (P)1. Maternal milk samples were then collected on P1 (transitional milk phase) and P10 (mature milk phase) for analysis. While EE dams spent less time nursing, postnatal enrichment exposure was associated with heavier offspring bodyweights. Milk from EE mothers had increased triglyceride levels, a greater microbiome diversity, and a significantly higher abundance of bacterial families related to bodyweight and energy metabolism. These differences reflected comparable transcriptomic changes at the genome-wide level. In addition to changes in lactational quality, we observed elevated levels of cannabinoid receptor 1 in the hypothalamus of EE dams, and sex-dependent and time-dependent effects of EE on offspring social behavior. Together, these results underscore the multidimensional impact of the combined neonatal and maternal environments on offspring development and maternal health. Moreover, they highlight potential deficiencies in the use of "gold standard" laboratory housing in the attempt to design translationally relevant animal models in biomedical research.
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9
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Cannon JL, Seabolt MH, Xu R, Montmayeur A, Suh SH, Diez-Valcarce M, Bucardo F, Becker-Dreps S, Vinjé J. Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua. Viruses 2022; 14:v14071395. [PMID: 35891376 PMCID: PMC9323674 DOI: 10.3390/v14071395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.
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Affiliation(s)
- Jennifer L. Cannon
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- CDC Foundation, Atlanta, GA 30329, USA
- Correspondence: ; Tel.: +1-404-639-2396
| | - Matthew H. Seabolt
- Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
- Leidos Inc., Reston, VA 20190, USA
| | - Ruijie Xu
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Anna Montmayeur
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Soo Hwan Suh
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- Ministry of Food and Drug Safety, Cheonju-Si 28159, Korea
| | - Marta Diez-Valcarce
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Filemón Bucardo
- Center for Infectious Diseases Research, National Autonomous University of Nicaragua—León (UNAN-León), León 21000, Nicaragua;
| | - Sylvia Becker-Dreps
- Department of Family Medicine and Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
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10
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Horne RG, Freedman SB, Johnson-Henry KC, Pang XL, Lee BE, Farion KJ, Gouin S, Schuh S, Poonai N, Hurley KF, Finkelstein Y, Xie J, Williamson-Urquhart S, Chui L, Rossi L, Surette MG, Sherman PM. Intestinal Microbial Composition of Children in a Randomized Controlled Trial of Probiotics to Treat Acute Gastroenteritis. Front Cell Infect Microbiol 2022; 12:883163. [PMID: 35774405 PMCID: PMC9238408 DOI: 10.3389/fcimb.2022.883163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022] Open
Abstract
Compositional analysis of the intestinal microbiome in pre-schoolers is understudied. Effects of probiotics on the gut microbiota were evaluated in children under 4-years-old presenting to an emergency department with acute gastroenteritis. Included were 70 study participants (n=32 placebo, n=38 probiotics) with stool specimens at baseline (day 0), day 5, and after a washout period (day 28). Microbiota composition and deduced functions were profiled using 16S ribosomal RNA sequencing and predictive metagenomics, respectively. Probiotics were detected at day 5 of administration but otherwise had no discernable effects, whereas detection of bacterial infection (P<0.001) and participant age (P<0.001) had the largest effects on microbiota composition, microbial diversity, and deduced bacterial functions. Participants under 1 year had lower bacterial diversity than older aged pre-schoolers; compositional changes of individual bacterial taxa were associated with maturation of the gut microbiota. Advances in age were associated with differences in gut microbiota composition and deduced microbial functions, which have the potential to impact health later in life.
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Affiliation(s)
- Rachael G. Horne
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen B. Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Department of Pediatrics, Alberta Children’s Hospital, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Xiao-Li Pang
- Alberta Precision Laboratories – Public Health Laboratory (ProvLab), Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Bonita E. Lee
- Women and Children’s Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB, Canada
| | - Ken J. Farion
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Serge Gouin
- Departments of Emergency Medicine and Pediatrics, Centre Hospitalier Universitaire (CHU) Sainte-Justine, Université de Montréal, Montréal, QC, Canada
| | - Suzanne Schuh
- Division of Emergency Medicine, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Naveen Poonai
- Division of Pediatric Emergency Medicine, London Children’s Hospital Health Science Centre, Department of Pediatrics, Western University, London, ON, Canada
| | - Katrina F. Hurley
- Pediatric Emergency Medicine, Izaak Walton Killam (IWK) Children’s Hospital, Dalhousie University, Halifax, NS, Canada
| | - Yaron Finkelstein
- Division of Emergency Medicine, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jianling Xie
- Pediatric Emergency Medicine, Izaak Walton Killam (IWK) Children’s Hospital, Dalhousie University, Halifax, NS, Canada
| | - Sarah Williamson-Urquhart
- Section of Pediatric Emergency Medicine, Department of Pediatrics, Alberta Children’s Hospital, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Linda Chui
- Alberta Precision Laboratories – Public Health Laboratory (ProvLab), Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Philip M. Sherman
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Division of Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- *Correspondence: Philip M. Sherman,
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11
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Mizutani T, Ishizaka A, Koga M, Tsutsumi T, Yotsuyanagi H. Role of Microbiota in Viral Infections and Pathological Progression. Viruses 2022; 14:950. [PMID: 35632692 PMCID: PMC9144409 DOI: 10.3390/v14050950] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.
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Affiliation(s)
- Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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12
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Johnson JA, Read TD, Petit RA, Marconi VC, Meagley KL, Rodriguez-Barradas MC, Beenhouwer DO, Brown ST, Holodniy M, Lucero-Obusan CA, Schirmer P, Ingersoll JM, Kraft CS, Neill FH, Atmar RL, Kambhampati AK, Cates JE, Mirza SA, Hall A, Cardemil CV, Lopman BA. Association of Secretor Status and Recent Norovirus Infection With Gut Microbiome Diversity Metrics in a Veterans Affairs Population. Open Forum Infect Dis 2022; 9:ofac125. [PMID: 35434176 PMCID: PMC9007923 DOI: 10.1093/ofid/ofac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Norovirus infection causing acute gastroenteritis could lead to adverse effects on the gut microbiome. We assessed the association of microbiome diversity with norovirus infection and secretor status in patients from Veterans Affairs medical centers. Alpha diversity metrics were lower among patients with acute gastroenteritis but were similar for other comparisons.
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Affiliation(s)
- Jordan A Johnson
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Robert A Petit
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Vincent C Marconi
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Kathryn L Meagley
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Maria C Rodriguez-Barradas
- Infectious Diseases Section, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - David O Beenhouwer
- Veterans Affairs Greater Los Angeles Health System, Los Angeles, California, USA
| | - Sheldon T Brown
- James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA
| | - Mark Holodniy
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
- Division of Infectious Diseases & Geographic Medicine, Stanford University, Stanford, California, USA
| | - Cynthia A Lucero-Obusan
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
| | - Patricia Schirmer
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
| | - Jessica M Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L Atmar
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anita K Kambhampati
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jordan E Cates
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara A Mirza
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cristina V Cardemil
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin A Lopman
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
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13
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Lin PC, Yang YCSH, Lin SC, Lu MC, Tsai YT, Lu SC, Chen SH, Chen SY. Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis. PLoS One 2022; 17:e0266876. [PMID: 35443009 PMCID: PMC9020708 DOI: 10.1371/journal.pone.0266876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/29/2022] [Indexed: 01/04/2023] Open
Abstract
Background Norovirus (NoV) infection is common in pediatric patients with immunodeficiency and is more likely to cause severe disease. Objective Our study aims to figure out the clinical differences and distribution of intestinal microbiota in immunocompromised children with NoV gastroenteritis. Methods Pediatric patients admitted to Shang-Ho Hospital with diagnosis of acute gastroenteritis including different immune status were enrolled and their medical records were reviewed. NoV gastroenteritis was validated using RT-PCR molecular methods. Viral shedding period was determined by real-time RT-PCR assays. Intestinal microbiota enrichment analysis was carried out by next generation sequencing after fecal DNA extraction and subsequent Linear Discriminant Analysis (LDA) Effect Size (LEfSe) method. Results Significantly higher frequency of diarrhea [mean, (IQR), 3.8 (3–5) /day] and longer viral shedding time [mean, IQR, 8.5 (5–13) days] was found in immunocompromised NoV infections than in immunocompetent patients without NoV infections (p = 0.013*) and immunocompetent patients with NoV infections (p = 0.030**). The fever prevalence was significantly lower in immunocompromised NoV infections than in different immune or infection status. Intestinal microbiota metagenomics analysis showed no significant community richness difference while the LEfSe analysis showed a significant difference in commensal richness at the phylum level, the family level, and the genus level in patients under different immune status. Conclusion We evaluated the clinical significances and microbiota composition in immunocompromised children with norovirus gastroenteritis. This will further facilitate studies of the interaction between the intestinal microbiota in such patients with precise determination of their bacterial infection control and probiotic supplements strategy.
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Affiliation(s)
- Pei-Chun Lin
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yu-Chen S. H. Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Meng-Che Lu
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yin-Tai Tsai
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shou-Cheng Lu
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shu-Huey Chen
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- * E-mail: (S-HC); , (S-YC)
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
- * E-mail: (S-HC); , (S-YC)
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14
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Arostegui D, Wallach T. The Cutting Edge of Gastroenteritis: Advances in Understanding of Enteric Infection. J Pediatr Gastroenterol Nutr 2022; 74:180-185. [PMID: 34560728 DOI: 10.1097/mpg.0000000000003304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
ABSTRACT In recent years, multiple advances have been made in the care, diagnosis, and mechanistic understanding of acute gastroenteritis (AGE). In this review, we discuss the current state of the art of diagnosis and management, as well as how changes in practice can improve care and decrease costs. We will discuss present study demonstrating the effect of AGE on the microbiome and how that may be linked to secondary effects or long-term changes. We will explore the use of novel technologies to further our capacity to understand how gastrointestinal infections occur and promulgate. Finally, will discuss advances in our understanding of how gastrointestinal infections capacitate other changes such as post-viral motility or other post viral intestinal dysfunction.
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Affiliation(s)
- Dalia Arostegui
- SUNY Downstate Department of Pediatrics, Division of Pediatric Gastroenterology, Brooklyn, NY
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15
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George S, Aguilera X, Gallardo P, Farfán M, Lucero Y, Torres JP, Vidal R, O'Ryan M. Bacterial Gut Microbiota and Infections During Early Childhood. Front Microbiol 2022; 12:793050. [PMID: 35069488 PMCID: PMC8767011 DOI: 10.3389/fmicb.2021.793050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota composition during the first years of life is variable, dynamic and influenced by both prenatal and postnatal factors, such as maternal antibiotics administered during labor, delivery mode, maternal diet, breastfeeding, and/or antibiotic consumption during infancy. Furthermore, the microbiota displays bidirectional interactions with infectious agents, either through direct microbiota-microorganism interactions or indirectly through various stimuli of the host immune system. Here we review these interactions during childhood until 5 years of life, focusing on bacterial microbiota, the most common gastrointestinal and respiratory infections and two well characterized gastrointestinal diseases related to dysbiosis (necrotizing enterocolitis and Clostridioides difficile infection). To date, most peer-reviewed studies on the bacterial microbiota in childhood have been cross-sectional and have reported patterns of gut dysbiosis during infections as compared to healthy controls; prospective studies suggest that most children progressively return to a "healthy microbiota status" following infection. Animal models and/or studies focusing on specific preventive and therapeutic interventions, such as probiotic administration and fecal transplantation, support the role of the bacterial gut microbiota in modulating both enteric and respiratory infections. A more in depth understanding of the mechanisms involved in the establishment and maintenance of the early bacterial microbiota, focusing on specific components of the microbiota-immunity-infectious agent axis is necessary in order to better define potential preventive or therapeutic tools against significant infections in children.
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Affiliation(s)
- Sergio George
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Ximena Aguilera
- School of Medicine, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Pablo Gallardo
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Farfán
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yalda Lucero
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Roberto del Río Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Juan Pablo Torres
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Miguel O'Ryan
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile
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16
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Lucero Y, Matson DO, Ashkenazi S, George S, O’Ryan M. Norovirus: Facts and Reflections from Past, Present, and Future. Viruses 2021; 13:v13122399. [PMID: 34960668 PMCID: PMC8707792 DOI: 10.3390/v13122399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Human Norovirus is currently the main viral cause of acute gastroenteritis (AGEs) in most countries worldwide. Nearly 50 years after the discovery of the "Norwalk virus" by Kapikian and colleagues, the scientific and medical community continue to generate new knowledge on the full biological and disease spectrum of Norovirus infection. Nevertheless, several areas remain incompletely understood due to the serious constraints to effectively replicate and propagate the virus. Here, we present a narrated historic perspective and summarize our current knowledge, including insights and reflections on current points of interest for a broad medical community, including clinical and molecular epidemiology, viral-host-microbiota interactions, antivirals, and vaccine prototypes. We also include a reflection on the present and future impacts of the COVID-19 pandemic on Norovirus infection and disease.
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Affiliation(s)
- Yalda Lucero
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Hospital Dr. Roberto del Río Hospital, Department of Pediatrics and Pediatric Surgery (Northern Campus), Faculty of Medicine, Universidad de Chile, Santiago 8380418, Chile
- Clínica Alemana de Santiago, Faculty of Medicine, Universidad del Desarrollo-Clínica Alemana, Santiago 7650568, Chile
| | - David O. Matson
- Eastern Shore Health Department, Virginia Department of Public Health, Accomack County, VA 23301, USA;
| | - Shai Ashkenazi
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel;
- Department of Pediatrics A, Schneider Children’s Medical Center, Petach Tikva 49202, Israel
| | - Sergio George
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
| | - Miguel O’Ryan
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Correspondence:
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17
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The Interaction Between Viruses and Intestinal Microbiota: A Review. Curr Microbiol 2021; 78:3597-3608. [PMID: 34350485 PMCID: PMC8336530 DOI: 10.1007/s00284-021-02623-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
As the main pathogen threatening human and animal health, viruses can affect the immunity and metabolism of bodies. There are innate microbial barriers in the digestive tract of the body to preserve the homeostasis of the animal body, which directly or indirectly influences the host defence against viral infection. Understanding the interaction between viruses and intestinal microbiota or probiotics is helpful to study the pathogenesis of diseases. Here, we review recent studies on the interaction mechanism between intestinal microbiota and viruses. The interaction can be divided into two aspects: inhibition of viral infection by microbiota and promotion of viral infection by microbiota. The treatment of viral infection by probiotics is summarized.
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18
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Toro Monjaraz EM, Ignorosa Arellano KR, Loredo Mayer A, Palacios-González B, Cervantes Bustamante R, Ramírez Mayans JA. Gut Microbiota in Mexican Children With Acute Diarrhea: An Observational Study. Pediatr Infect Dis J 2021; 40:704-709. [PMID: 34250970 DOI: 10.1097/inf.0000000000003128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Acute diarrhea is the second leading cause of preventable mortality and morbidity in children worldwide. This study aimed to identify the main pathogens associated with acute diarrhea and to describe changes in gut microbiota in Mexican children. METHODS This single-center observational study included 30 children (6 months to 5 years old) with acute diarrhea who were referred to the Instituto Nacional de Pediatría of Mexico City and 15 healthy volunteers (control group). Stool samples at day 0 (D0) and day 15 (D15) were collected for identification of microorganisms (reverse transcriptase-polymerase chain reaction analyses with xTAG gastrointestinal pathogen panel multiplex assay) and microbiota analysis (16S gene amplification sequencing). Prescription decisions were made by the treating clinician. RESULTS The main pathogens identified were norovirus and Campylobacter jejuni (20% each). The majority of patients (n = 24) were prescribed Saccharomyces boulardii CNCM I-745 for treatment of acute diarrhea. Diarrheic episodes resolved within 1 week of treatment. Compared with D15 and control samples, D0 samples showed significantly lower alpha diversity and a clear shift in overall composition (beta diversity). Alpha diversity was significantly increased in S. boulardii-treated group between D0 and D15 to a level similar to that of control group. CONCLUSIONS In these children, acute diarrhea was accompanied by significant alterations in gut microbiota. S. boulardii CNCM I-745 treatment may facilitate gut microbiota restoration in children with acute diarrhea, mostly through improvements in alpha diversity.
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Affiliation(s)
| | | | - Alejandro Loredo Mayer
- From the Pediatric Gastroenterology and Nutrition Department, Instituto Nacional de Pediatría
| | - Berenice Palacios-González
- Scientific Bonding Unit, Medicine Faculty UNAM, Instituto Nacional De Medicina Genómica, Mexico City, Mexico
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19
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McFarland LV, Srinivasan R, Setty RP, Ganapathy S, Bavdekar A, Mitra M, Raju B, Mohan N. Specific Probiotics for the Treatment of Pediatric Acute Gastroenteritis in India: A Systematic Review and Meta-Analysis. JPGN REPORTS 2021; 2:e079. [PMID: 37205949 PMCID: PMC10191489 DOI: 10.1097/pg9.0000000000000079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/08/2021] [Indexed: 05/21/2023]
Abstract
Pediatric acute gastroenteritis (PAGE) is a significant cause of morbidity, mortality and healthcare costs in many countries, but differences in PAGE vary from country-to-country; thus, we limited our analysis to 1 country. Probiotics have been recommended as an adjunct to standard treatment, but the choice of probiotic is unclear. PubMed, Google Scholar, and reviews were searched from inception to May 2020 for randomized controlled trials (RCTs) in India using probiotics for a treatment for PAGE. Meta-analyses using subgroups of identical probiotic types (≥2 RCT/type) were conducted for primary outcomes (duration of diarrhea, cured by day 3, rapidity of response, and length of hospital stay). Twenty-two RCTs were included in the systematic review (N = 4059 participants) including 5 single-strained probiotics and 3 multi-strained mixtures. For the meta-analyses, 17 RCT (20 treatment arms) were included. Saccharomyces boulardii CNCM I-745 had the strongest effect on shortening the duration of diarrhea (standardized mean difference, -1.86 d; 95% confidence interval, -2.8 to -0.9), while both Lactobacillus rhamnosus GG and a mixture of 4 Bacillus clausii strains (O/C, SIN, N/R, T) significantly reduced the duration of diarrhea (-1.7 and -1.4 d, respectively). S. boulardii and L. rhamnosus GG significantly reduced hospital stays (-1.8 and -1.1 d, respectively), while B. clausii had no effect. The frequency of stools/day was significantly reduced by day 4 for S. boulardii and by day 5 for L. rhamnosus GG. In India, 2 types of probiotics (S. boulardii CNCM I-745 and L. rhamnosus GG) significantly shortened both the duration of diarrhea and hospitalization stays in pediatric patients with PAGE. While these 2 probiotic strains were safe and effective for children in India, further research is needed to confirm if other probiotic strains or mixtures may be effective.
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Affiliation(s)
- Lynne V. McFarland
- From the Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Ramesh Srinivasan
- Department of Gastroenterology, Apollo Hospitals, Jubilee Hills, Hyderabad, India
| | - Rajendra P. Setty
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Pure Bliss Hospital, Panchkula, India
| | | | | | - Monjori Mitra
- Department of Pediatrics, Institute of Child Health, Kolkata, India
| | - Bhaskar Raju
- Department of Gastroenterology, Dr. Mehta’s Children’s Hospital, Chennai, India
| | - Neelam Mohan
- Department of Pediatric Gastroenterology, Medanta Medicity, Gurgaon, India
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20
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Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
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Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
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21
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Abstract
The lumen of the gastrointestinal tract harbors a diverse community of microbes, fungi, archaea, and viruses. In addition to occupying the same enteric niche, recent evidence suggests that microbes and viruses can act synergistically and, in some cases, promote disease. In this review, we focus on the disease-promoting interactions of the gut microbiota and rotavirus, norovirus, poliovirus, reovirus, and astrovirus. Microbes and microbial compounds can directly interact with viruses, promote viral fitness, alter the glycan structure of viral adhesion sites, and influence the immune system, among other mechanisms. These interactions can directly and indirectly affect viral infection. By focusing on microbe–virus interplay, we hope to identify potential strategies for targeting offending microbes and minimizing viral infection.
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22
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Kim AH, Hogarty MP, Harris VC, Baldridge MT. The Complex Interactions Between Rotavirus and the Gut Microbiota. Front Cell Infect Microbiol 2021; 10:586751. [PMID: 33489932 PMCID: PMC7819889 DOI: 10.3389/fcimb.2020.586751] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Human rotavirus (HRV) is the leading worldwide cause of acute diarrhea-related death in children under the age of five. RV infects the small intestine, an important site of colonization by the microbiota, and studies over the past decade have begun to reveal a complex set of interactions between RV and the gut microbiota. RV infection can temporarily alter the composition of the gut microbiota and probiotic administration alleviates some symptoms of infection in vivo, suggesting reciprocal effects between the virus and the gut microbiota. While development of effective RV vaccines has offered significant protection against RV-associated mortality, vaccine effectiveness in low-income countries has been limited, potentially due to regional differences in the gut microbiota. In this mini review, we briefly detail research findings to date related to HRV vaccine cohorts, studies of natural infection, explorations of RV-microbiota interactions in gnotobiotic pig models, and highlight various in vivo and in vitro models that could be used in future studies to better define how the microbiota may regulate RV infection and host antiviral immune responses.
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Affiliation(s)
- Andrew HyoungJin Kim
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael P. Hogarty
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Vanessa C. Harris
- Department of Medicine, Division of Infectious Diseases and Department of Global Health (AIGHD), Amsterdam University Medical Center, Academic Medical Center, Amsterdam, Netherlands
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
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23
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Olshan KL, Leonard MM, Serena G, Zomorrodi AR, Fasano A. Gut microbiota in Celiac Disease: microbes, metabolites, pathways and therapeutics. Expert Rev Clin Immunol 2020; 16:1075-1092. [PMID: 33103934 DOI: 10.1080/1744666x.2021.1840354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Current evidence supports a vital role of the microbiota on health outcomes, with alterations in an otherwise healthy balance linked to chronic medical conditions like celiac disease (CD). Recent advances in microbiome analysis allow for unparalleled profiling of the microbes and metabolites. With the growing volume of data available, trends are emerging that support a role for the gut microbiota in CD pathogenesis. AREAS COVERED In this article, the authors review the relationship between factors such as genes and antibiotic exposure on CD onset and the intestinal microbiota. The authors also review other microbiota within the human body (like the oropharynx) that may play a role in CD pathogenesis. Finally, the authors discuss implications for disease modification and the ultimate goal of prevention. The authors reviewed literature from PubMed, EMBASE, and Web of Science. EXPERT OPINION CD serves as a unique opportunity to explore the role of the intestinal microbiota on the development of chronic autoimmune disease. While research to date provides a solid foundation, most studies have been case-control and thus do not have capacity to explore the mechanistic role of the microbiota in CD onset. Further longitudinal studies and integrated multi-omics are necessary for investigating CD pathogenesis.
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Affiliation(s)
- Katherine L Olshan
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Celiac Research Program, Harvard Medical School , Boston, MA, USA
| | - Maureen M Leonard
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Celiac Research Program, Harvard Medical School , Boston, MA, USA
| | - Gloria Serena
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Celiac Research Program, Harvard Medical School , Boston, MA, USA
| | - Ali R Zomorrodi
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Celiac Research Program, Harvard Medical School , Boston, MA, USA
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Harvard Medical School , Boston, MA, USA.,European Biomedical Research Institute of Salerno (EBRIS) , Salerno, Italy
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24
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Taco-Masias AA, Fernandez-Aristi AR, Cornejo-Tapia A, Aguilar-Luis MA, Del Valle LJ, Silva-Caso W, Zavaleta-Gavidia V, Weilg P, Cornejo-Pacherres H, Bazán-Mayra J, Puyen ZM, Del Valle-Mendoza J. Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital. PeerJ 2020; 8:e9964. [PMID: 33194370 PMCID: PMC7646295 DOI: 10.7717/peerj.9964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
Background Acute infective gastroenteritis (AIG) is a leading cause of mortality in children worldwide. In Peru, more than 40% of cases of AIG occurring in children under 5 years old. The disruption of the gut microbiota can increase risk for several health complications especially in patients with gastric infections caused by viruses or bacteria. Objective The main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis. Results The most commonly isolated bacteria from the GM were Firmicutes (63.2% 74/117) Bacteriodetes (62.4%; 73/117), Lactobacillus (59.8%; 70/117), Prevotella (57.2%; 67/117), Proteobacterium (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus and Prevotella across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria-bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed.
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Affiliation(s)
- Andre Alonso Taco-Masias
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Augusto R Fernandez-Aristi
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Angela Cornejo-Tapia
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Miguel Angel Aguilar-Luis
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Luis J Del Valle
- Barcelona Research Center for Multiscale Science and Engineering, Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Wilmer Silva-Caso
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | | | - Pablo Weilg
- Mercy One North Iowa Medical Center, Mason City, USA
| | | | | | - Zully M Puyen
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Juana Del Valle-Mendoza
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
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25
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Sun S, Lin X, Yang Y, Cen J, Luo F, Chen X. Acupoint application for rotavirus diarrhea in infants and children: A protocol for systematic review and meta analysis. Medicine (Baltimore) 2020; 99:e22227. [PMID: 32957362 PMCID: PMC7505364 DOI: 10.1097/md.0000000000022227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Diarrheal disease currently claims the lives of approximately 500,000 children each year. Rotaviruses are the pathogens primarily responsible for more severe cases and more than one-third of diarrhea-associated deaths in children under 5 years old globally. At present, commonly used drug therapies for rotavirus diarrhea in Western medicine, such as oral rehydration salts, montmorillonite, probiotics, and nitazoxanide, often cannot achieve satisfactory curative effects. Moreover, infants' and children's compliance with drugs and injections is often lower than their compliance with acupoint application therapy. A large number of studies have shown that acupoint application can increase the clinical cure rate and shorten the duration of diarrhea. However, there is a lack of systematic reviews on the safety and efficacy of acupoint application in the treatment of rotavirus diarrhea. Therefore, we will conduct a study to evaluate the safety and efficacy of acupoint application for rotavirus diarrhea in infants and children. METHODS We will search the relevant medical literature using PubMed, EMBASE, Web of Science, Cochrane CENTRAL, China National Knowledge Infrastructure, the Wanfang Database, the Chinese Biomedical Literature Database, and the Chinese Scientific Journal Database from inception to August 2020. Both MeSH and free text terms will be utilized to obtain the maximum numbers of papers. No language restrictions will be applied, and the publication type will be limited to randomized controlled trials. Two teams will independently review and assess the studies for inclusion in the review. RevMan V 5.0 software will be applied for data extraction. The methodological quality of the included studies will be evaluated according to the Cochrane Handbook. RESULTS The results of this study will be published in a peer-reviewed journal. CONCLUSION The conclusion of this systematic review will provide evidence regarding whether acupoint application is an effective intervention for infants and children with rotavirus diarrhea. INPLASY REGISTRATION NUMBER INPLASY202070123.
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Affiliation(s)
- Shaodan Sun
- Department of Pediatrics, The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine
| | - Xiaojie Lin
- Department of Medical Education Office, Guangdong, Provincial Hospital of Traditional Chinese Medicine, Guangzhou
| | - Yang Yang
- Department of Rehabilitation, Affiliated Jiangmen Traditional Chinese Medicine Hospital of Ji’nan University, Ji’nan University, Jiangmen
| | - Jingtu Cen
- Department of Otolaryngology, Tongde Hospital of Zhejiang Province, Hangzhou
| | - Fei Luo
- Department of Pediatrics, The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Xiaogang Chen
- Department of Pediatrics, The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
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26
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Engevik MA, Banks LD, Engevik KA, Chang-Graham AL, Perry JL, Hutchinson DS, Ajami NJ, Petrosino JF, Hyser JM. Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence. Gut Microbes 2020; 11:1324-1347. [PMID: 32404017 PMCID: PMC7524290 DOI: 10.1080/19490976.2020.1754714] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Multiple studies have identified changes within the gut microbiome in response to diarrheal-inducing bacterial pathogens. However, examination of the microbiome in response to viral pathogens remains understudied. Compounding this, many studies use fecal samples to assess microbiome composition; which may not accurately mirror changes within the small intestine, the primary site for most enteric virus infections. As a result, the functional significance of small intestinal microbiome shifts during infection is not well defined. To address these gaps, rotavirus-infected neonatal mice were examined for changes in bacterial community dynamics, host gene expression, and tissue recovery during infection. Profiling bacterial communities using 16S rRNA sequencing suggested significant and distinct changes in ileal communities in response to rotavirus infection, with no significant changes for other gastrointestinal (GI) compartments. At 1-d post-infection, we observed a loss in Lactobacillus species from the ileum, but an increase in Bacteroides and Akkermansia, both of which exhibit mucin-digesting capabilities. Concomitant with the bacterial community shifts, we observed a loss of mucin-filled goblet cells in the small intestine at d 1, with recovery occurring by d 3. Rotavirus infection of mucin-producing cell lines and human intestinal enteroids (HIEs) stimulated release of stored mucin granules, similar to in vivo findings. In vitro, incubation of mucins with Bacteroides or Akkermansia members resulted in significant glycan degradation, which altered the binding capacity of rotavirus in silico and in vitro. Taken together, these data suggest that the response to and recovery from rotavirus-diarrhea is unique between sub-compartments of the GI tract and may be influenced by mucin-degrading microbes.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA,Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Lori D. Banks
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristen A. Engevik
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Alexandra L. Chang-Graham
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jacob L. Perry
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Diane S. Hutchinson
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nadim J. Ajami
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph M. Hyser
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,CONTACT Joseph M. Hyser 1 Baylor Plaza, HoustonTX77030, USA
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27
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Barberio B, Massimi D, Bonfante L, Facchin S, Calò L, Trevenzoli M, Savarino EV, Cattelan AM. Fecal microbiota transplantation for norovirus infection: a clinical and microbiological success. Therap Adv Gastroenterol 2020; 13:1756284820934589. [PMID: 32849912 PMCID: PMC7425245 DOI: 10.1177/1756284820934589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 02/04/2023] Open
Affiliation(s)
| | | | - Luciana Bonfante
- Department of Internal Medicine, Division of Nephrology, University of Padua, Italy
| | - Sonia Facchin
- Division of Gastroenterology, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Lorenzo Calò
- Department of Internal Medicine, Division of Nephrology, University of Padua, Italy
| | - Marco Trevenzoli
- Department of Internal Medicine, Division of Infectious Diseases, University of Padua, Italy
| | | | - Anna Maria Cattelan
- Department of Internal Medicine, Division of Infectious Diseases, University of Padua, Italy
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28
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Lei S, Twitchell EL, Ramesh AK, Bui T, Majette E, Tin CM, Avery R, Arango-Argoty G, Zhang L, Becker-Dreps S, Azcarate-Peril MA, Jiang X, Yuan L. Enhanced GII.4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota. J Gen Virol 2020; 100:1530-1540. [PMID: 31596195 DOI: 10.1099/jgv.0.001336] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The role of commensal microbiota in enteric viral infections has been explored extensively, but the interaction between human gut microbiota (HGM) and human norovirus (HuNoV) is poorly understood. In this study, we established an HGM-Transplanted gnotobiotic (Gn) pig model of HuNoV infection and disease, using an infant stool as HGM transplant and a HuNoV GII.4/2006b strain for virus inoculation. Compared to germ-free Gn pigs, HuNoV inoculation in HGMT Gn pigs resulted in increased HuNoV shedding, characterized by significantly higher shedding titres on post inoculation day (PID) 3, 4, 6, 8 and 9, and significantly longer mean duration of virus shedding. In addition, virus titres were significantly higher in duodenum and distal ileum of HGMT Gn pigs on PID10, while comparable and transient HuNoV viremia was detected in both groups. 16S rRNA gene sequencing demonstrated that HuNoV infection dramatically altered intestinal microbiota in HGMT Gn pigs at the phylum (Proteobacteria, Firmicutes and Bacteroidetes) and genus (Enterococcus, Bifidobacterium, Clostridium, Ruminococcus, Anaerococcus, Bacteroides and Lactobacillus) levels. In summary, enhanced GII.4 HuNoV infection was observed in the presence of HGM, and host microbiota was susceptible to disruption upon HuNoV infection.
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Affiliation(s)
- Shaohua Lei
- Present address: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Erica L Twitchell
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ashwin K Ramesh
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tammy Bui
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Elizabeth Majette
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christine M Tin
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Roger Avery
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gustavo Arango-Argoty
- Department of Computer Science, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Liqing Zhang
- Department of Computer Science, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sylvia Becker-Dreps
- Department of Family Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
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29
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Jumani RS, Spector JM, Izadnegahdar R, Kelly P, Diagana TT, Manjunatha UH. Innovations in Addressing Pediatric Diarrhea in Low Resource Settings. ACS Infect Dis 2020; 6:14-24. [PMID: 31612701 DOI: 10.1021/acsinfecdis.9b00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Diarrhea has long been recognized as an important cause of mortality during childhood. In parallel with ensuring access to proven care practices is the imperative to apply modern advances in medicine, science, and technology to accelerate progress against diarrheal disease, particularly in developing countries where the burden of avoidable harm is the greatest. In order to highlight achievements and identify outstanding areas of need, we reviewed the landscape of recent innovations that have significance for the study and clinical management of pediatric diarrhea in low resource settings.
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Affiliation(s)
- Rajiv S. Jumani
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jonathan M. Spector
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Rasa Izadnegahdar
- Bill and Melinda Gates Foundation, 440 5th Ave N, Seattle, Washington 98109, United States
| | - Paul Kelly
- Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, Turner Street, London E1 2AD, United Kingdom
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Thierry T. Diagana
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ujjini H. Manjunatha
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
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30
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Abstract
OBJECTIVES The determinants of gut microbiota composition and its effects on common childhood illnesses are only partly understood, especially in low-income settings. The aim of the present study was to investigate whether morbidity predicts gut microbiota composition in Malawian children and whether microbiota predicts subsequent morbidity. We tested the hypothesis that common infectious disease symptoms would be predictive of lower microbiota maturity and diversity. METHODS We used data from 631 participants in a randomized-controlled nutrition intervention trial, in which a small-quantity lipid-based nutrient supplement was provided to pregnant and lactating mothers and their children at 6 to 18 months of age. Fecal samples were collected from the children at 6, 12, 18, and 30 months of age and analyzed using 16S rRNA sequencing. Microbiota variables consisted of measures of microbiota diversity (Shannon Index), microbiota maturity (microbiota-for-age z score), and the relative abundances of taxa. Morbidity variables included gastrointestinal and respiratory symptoms and fever. RESULTS Diarrhea and respiratory symptoms from 11 to 12 months were predictive of lower microbiota-for-age z score and higher Shannon Index, respectively (P = 0.035 and P = 0.023). Morbidity preceding sample collection was predictive of the relative abundances of several bacterial taxa at all time points. Higher microbiota maturity and diversity at 6 months were predictive of a lower incidence rate of fever in the subsequent 6 months (P = 0.007 and P = 0.031). CONCLUSIONS Our findings generally do not support the hypothesis that morbidity prevalence predicts a subsequent decrease in gut microbiota maturity or diversity in rural Malawian children. Certain morbidity symptoms may be predictive of microbiota maturity and diversity and relative abundances of several bacterial taxa. Furthermore, microbiota diversity and maturity may be associated with the subsequent incidence of fever.
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31
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Adenovirus infection is associated with altered gut microbial communities in a non-human primate. Sci Rep 2019; 9:13410. [PMID: 31527752 PMCID: PMC6746978 DOI: 10.1038/s41598-019-49829-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
Adenovirus (AdV) infections are one of the main causes of diarrhea in young children. Enteric AdVs probably disrupt gut microbial defences, which can result in diarrhea. To understand the role of the gut microbiome in AdV-induced pathologies, we investigated the gut microbiome of a naturally AdV-infected non-human primate species, the Malagasy mouse lemur (Microcebus griseorufus), which represents an important model in understanding the evolution of diseases. We observed that AdV infection is associated with disruption of the gut microbial community composition. In AdV+ lemurs, several commensal taxa essential for a healthy gut microbiome decreased, whereas genera containing potential pathogens, such as Neisseria, increased in abundance. Microbial co-occurrence networks revealed a loss of important microbial community interactions in AdV+ lemurs and an overrepresentation of Prevotellaceae. The observation of enteric virus-associated loss of commensal bacteria and associated shifts towards pathobionts may represent the missing link for a better understanding of AdV-induced effects in humans, and also for their potential as drivers of co-infections, an area of research that has been largely neglected so far.
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32
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Azagra-Boronat I, Massot-Cladera M, Knipping K, Van't Land B, Tims S, Stahl B, Knol J, Garssen J, Franch À, Castell M, Pérez-Cano FJ, Rodríguez-Lagunas MJ. Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats. Cells 2019; 8:E876. [PMID: 31405262 PMCID: PMC6721706 DOI: 10.3390/cells8080876] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
Colonization of the gut in early life can be altered through multiple environmental factors. The present study aimed to investigate the effects of 2'-fucosyllactose (2'-FL), a mixture of short-chain galactooligosaccharides/long-chain fructooligosaccharides (scGOS/lcFOS) 9:1 and their combination (scGOS/lcFOS/2'-FL) on dysbiosis induced during rotavirus (RV) diarrhea in neonatal rats, elucidating crosstalk between bacteria and the immune system. The dietary interventions were administered daily by oral gavage at days 2-8 of life in neonatal Lewis rats. On day 5, RV SA11 was intragastrically delivered to induce infection and diarrhea assessment, microbiota composition, and gene expression of Toll-like receptors (TLRs) in the small intestine were studied. All dietary interventions showed reduction in clinical variables of RV-induced diarrhea. RV infection increased TLR2 expression, whereas 2'-FL boosted TLR5 and TLR7 expressions and scGOS/lcFOS increased that of TLR9. RV-infected rats displayed an intestinal dysbiosis that was effectively prevented by the dietary interventions, and consequently, their microbiota was more similar to microbiota of the noninfected groups. The preventive effect of 2'-FL, scGOS/lcFOS, and their combination on dysbiosis associated to RV diarrhea in rats could be due to changes in the crosstalk between gut microbiota and the innate immune system.
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Affiliation(s)
- Ignasi Azagra-Boronat
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain
| | - Malén Massot-Cladera
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain
| | - Karen Knipping
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CA Utrecht, The Netherlands
| | - Belinda Van't Land
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
- University Medical Centre Utrecht/Wilhelmina Children's Hospital, Department of Pediatric Immunology, 3584 EA Utrecht, The Netherlands
| | - Sebastian Tims
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
| | - Bernd Stahl
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
| | - Jan Knol
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
| | - Johan Garssen
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CA Utrecht, The Netherlands
| | - Àngels Franch
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain
| | - Margarida Castell
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain
| | - Francisco J Pérez-Cano
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain.
| | - Maria J Rodríguez-Lagunas
- Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), 08921 Santa Coloma de Gramenet, Spain
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Abstract
Antibiotics during infancy, delivery, and breastfeeding affect the intestinal microbiota in early life and is associated with allergic disease. Gastroenteritis (GE) during infancy also affects intestinal microbiota in early life, however, its relationship to allergic disease has not been investigated.Data of 45,499 males and 49,430 females, from birth to 5 years of age, were collected from a national database in Taiwan. Subjects were categorized into early GE (GE within 0-6 months) and non-early GE group (no GE within 0-6 months). The rates of asthma (AS), allergic rhinitis (AR), and atopic dermatitis (AD) over 5 years were evaluated and compared between the groups. In patients with AS, AR, and AD, the number of clinical visits and drug prescriptions for the allergic disease was also evaluated to assess the effect of early GE on allergic disease.After adjusting for the effect of GE in later life and other factors, the rates of AS [OR (odds ratio) 1.54, 95% confidence interval (CI) 1.48-1.60], AR [OR 1.49, 95% CI 1.45-1.54], and AD [OR 1.40, 95% CI 1.33-1.47] were higher in the early GE group than in the non-early GE group. The magnitude of the increase was higher in females than in males. In those with AS, AR, and AD, the number of clinical visits and drug prescriptions was not different between the early GE and non-early GE groups. In children with early GE, good control of GE in the following years lowered the rate of allergic disease.Early-life GE was associated with increased rates of AS, AR, and AD in later life and this was trend more prominent in females.
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Affiliation(s)
- Hui-Hsien Pan
- School of Medicine, Chung Shan Medical University
- Division of Allergy, Asthma and Rheumatology, Department of pediatrics, Chung Shan Medical University Hospital
| | - Ko-Huang Lue
- School of Medicine, Chung Shan Medical University
- University President, Chung Shan Medical University, Taichung, Taiwan
| | - Hai-Lun Sun
- School of Medicine, Chung Shan Medical University
- Division of Allergy, Asthma and Rheumatology, Department of pediatrics, Chung Shan Medical University Hospital
| | - Min-Sho Ku
- School of Medicine, Chung Shan Medical University
- Division of Allergy, Asthma and Rheumatology, Department of pediatrics, Chung Shan Medical University Hospital
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Walker FC, Baldridge MT. Interactions between noroviruses, the host, and the microbiota. Curr Opin Virol 2019; 37:1-9. [PMID: 31096124 PMCID: PMC6768699 DOI: 10.1016/j.coviro.2019.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022]
Abstract
In recent years, appreciation has been growing for the role that the microbiota plays in interactions between the host and various pathogens, including norovirus. Proviral and antiviral effects of the microbiota have been observed for both human and murine noroviruses, and it has become clear that direct effects of microbes and their metabolites as well as indirect effects of commensals on the host are key in modulating pathogenesis. In particular, a common thread has emerged in the ability of members of the microbiota to regulate the host interferon response, thereby modulating norovirus infection. Here, we highlight key differences between human and murine noroviruses and their interactions with the microbiota, while also underscoring shared characteristics between noroviruses and other gastrointestinal viruses.
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Affiliation(s)
- Forrest C Walker
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
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Abstract
PURPOSE OF REVIEW Noroviruses are a major cause of gastroenteritis. This review summarizes new information on noroviruses that may lead to the development of improved measures for limiting their human health impact. RECENT FINDINGS GII.4 strains remain the most common human noroviruses causing disease, although GII.2 and GII.17 strains have recently emerged as dominant strains in some populations. Histo-blood group antigen (HBGA) expression on the gut mucosa drives susceptibility to different norovirus strains. Antibodies that block virus binding to these glycans correlate with protection from infection and illness. Immunocompromised patients are significantly impacted by norovirus infection, and the increasing availability of molecular diagnostics has improved infection recognition. Human noroviruses can be propagated in human intestinal enteroid cultures containing enterocytes that are a significant primary target for initiating infection. Strain-specific requirements for replication exist with bile being essential for some strains. Several vaccine candidates are progressing through preclinical and clinical development and studies of potential antiviral interventions are underway. SUMMARY Norovirus epidemiology is complex and requires continued surveillance to track the emergence of new strains and recombinants, especially with the continued progress in vaccine development. Humans are the best model to study disease pathogenesis and prevention. New in-vitro cultivation methods should lead to better approaches for understanding virus-host interactions and ultimately to improved strategies for mitigation of human norovirus-associated disease.
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Fecal Microbiota, Lactic Acid and Short Chain Fatty Levels of Infants Following Rotavirus Infection Revealed by Illumina Miseq High-Throughput Sequencing and HPLC Method. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.68389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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37
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Astrovirus and the microbiome. Curr Opin Virol 2019; 37:10-15. [PMID: 31163291 DOI: 10.1016/j.coviro.2019.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 11/22/2022]
Abstract
Although astroviruses are most commonly associated with acute gastrointestinal illness in humans, their ability to infect a broad range of hosts and cause a spectrum of disease makes them widespread and complex pathogens. The precise mechanisms that dictate the course of astrovirus disease have not been studied extensively but are likely driven by multifactorial host-microbe interactions. Recent insights from studies of animal astrovirus infections have revealed both beneficial and detrimental effects for the host. However, further in-depth studies are needed to fully explore the consequences of astrovirus-induced changes in the gut microenvironment as well as the role of the microbiota in astrovirus infection.
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Mathew S, Smatti MK, Al Ansari K, Nasrallah GK, Al Thani AA, Yassine HM. Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children. Sci Rep 2019; 9:865. [PMID: 30696865 PMCID: PMC6351549 DOI: 10.1038/s41598-018-37162-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Acute gastroenteritis remains a major cause of morbidity and mortality among young children worldwide. It accounts for approximately 1.34 million deaths annually in children younger than five years. Infection can be caused by viral, bacterial and/or parasitic microorganisms. Dysbiosis due to such infections could dramatically affect disease prognosis as well as development of chronic illness. The aim of this study was to analyze gut microbiome and clinical outcomes in young children suffering from viral or mixed viral-bacterial infection. We evaluated gut microbiota composition in children suffering from viral or mixed viral-bacterial infection with two major viruses rotavirus (RV) and norovirus (NoV) and two pathogenic bacteria [Enteroaggregative E. coli (EAEC), and Enteropathogenic E. coli (EPEC)]. We sequenced 16S ribosomal RNA (V4 region) genes using Illumina MiSeq in 70 hospitalized children suffering from gastroenteric infections plus nine healthy controls. The study summarized Operational Taxonomic Unit (OTU) abundances with the Bray-Curtis index and performed a non-metric multidimensional scaling analysis to visualize microbiome similarities. We used a permutational multivariate analyses of variance to test the significance of group differences. We also analyzed the correlation between microbiome changes and clinical outcomes. Our data demonstrated a significant increase in the severity score in children with viral-bacterial mixed infections compared to those with virus infections alone. Statistical analysis by overall relative abundance denoted lesser proportions of Bacteroides in the infected children, whereas Bifidobacteriaceae richness was more prominent in the bacterial-viral mixed infections. Pairwise differences of gut microbiota were significantly higher in RV + EAEC (P = 0.009) and NoV + EAEC (P = 0.009) co-infections, compared to EPEC mixed infection with both, RV (P = 0.045) and NoV (P = 0.188). Shannon diversity index showed considerable more variation in microbiome diversity in children infected with RV cohort compared to NoV cohort. Our results highlight that richness of Bifidobacteriaceae, which acts as probiotics, increased with the severity of the viral-bacterial mixed infections. As expected, significant reduction of relative numbers of Bacteroides was characterized in both RV and NoV infections, with more reduction observed in co-infection pathogenic E. coli. Although mixed infection with EAEC resulted in significant microbiota differences compared to viral infection only or mixed infection with EPEC, the clinical condition of the children were worsened with both pathogenic E.coli co-infections. Further, in comparison with RV cohort, augmented number of differential abundant pathogenic OTUs were peculiarly noticed only with NoV mixed infection.
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Affiliation(s)
- Shilu Mathew
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
| | - Maria K Smatti
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
| | - Khalid Al Ansari
- Pediatric Emergency Center, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar.,Department of Biomedical Science, College of Health Science, Qatar University, Doha, 2713, Qatar
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar.,Department of Biomedical Science, College of Health Science, Qatar University, Doha, 2713, Qatar
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar. .,Department of Biomedical Science, College of Health Science, Qatar University, Doha, 2713, Qatar.
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Qi-Deficiency Related Increases in Disease Susceptibility Are Potentially Mediated by the Intestinal Microbiota. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:1304397. [PMID: 30425748 PMCID: PMC6218746 DOI: 10.1155/2018/1304397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/02/2018] [Indexed: 12/24/2022]
Abstract
Qi-deficiency (QX) is thought to promote the body's susceptibility to disease, but the underlying mechanism through which this occurs is not clear. We surveyed the traditional Chinese medicine constitution (TCMC) of healthy college students to identify those that were PH (balanced TCMC constitution) and QX (unbalanced TCMC constitution). We then used high-throughput sequencing of the 16SrRNA V3-4 region in fecal microbiota samples to identify differences between those obtained from PH and QX individuals. Our results demonstrated that the alpha diversity of QX samples was significantly lower than that of PH samples (p < 0.05) and that beta diversity was remarkably different in QX and PH samples. Four and 122 bacterial taxa were significantly overrepresented in QX and PH groups, respectively. The genera Sphingobium, Clostridium, and Comamonas were enriched in the QX group and had a certain pathogenic role. The QX group also showed a statistically significant lack of probiotics and anti-inflammatory bacteria such as Bifidobacterium and Bdellovibrio. The functional potential of QX bacterial taxa was reduced in fatty acid metabolism and butanoate metabolism. We contend that the imbalanced intestinal microbiota in QX and the following functional changes in metabolism influence immunity and energy metabolism, which could increase susceptibility to disease.
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Gut Microbiota and Iron: The Crucial Actors in Health and Disease. Pharmaceuticals (Basel) 2018; 11:ph11040098. [PMID: 30301142 PMCID: PMC6315993 DOI: 10.3390/ph11040098] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023] Open
Abstract
Iron (Fe) is a highly ample metal on planet earth (~35% of the Earth’s mass) and is particularly essential for most life forms, including from bacteria to mammals. Nonetheless, iron deficiency is highly prevalent in developing countries, and oral administration of this metal is so far the most effective treatment for human beings. Notably, the excessive amount of unabsorbed iron leave unappreciated side effects at the highly interactive host–microbe interface of the human gastrointestinal tract. Recent advances in elucidating the molecular basis of interactions between iron and gut microbiota shed new light(s) on the health and pathogenesis of intestinal inflammatory diseases. We here aim to present the dynamic modulation of intestinal microbiota by iron availability, and conversely, the influence on dietary iron absorption in the gut. The central part of this review is intended to summarize our current understanding about the effects of luminal iron on host–microbe interactions in the context of human health and disease.
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41
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Kumar A, Vlasova AN, Deblais L, Huang HC, Wijeratne A, Kandasamy S, Fischer DD, Langel SN, Paim FC, Alhamo MA, Shao L, Saif LJ, Rajashekara G. Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig model. BMC Gastroenterol 2018; 18:93. [PMID: 29929472 PMCID: PMC6013989 DOI: 10.1186/s12876-018-0810-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 05/30/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human rotavirus (HRV) is a major cause of viral gastroenteritis in infants; particularly in developing countries where malnutrition is prevalent. Malnutrition perturbs the infant gut microbiota leading to sub-optimal functioning of the immune system and further predisposing infants to enteric infections. Therefore, we hypothesized that malnutrition exacerbates rotavirus disease severity in infants. METHODS In the present study, we used a neonatal germ free (GF) piglets transplanted with a two-month-old human infant's fecal microbiota (HIFM) on protein deficient and sufficient diets. We report the effects of malnourishment on the HRV infection and the HIFM pig microbiota in feces, intestinal and systemic tissues, using MiSeq 16S gene sequencing (V4-V5 region). RESULTS Microbiota analysis indicated that the HIFM transplantation resulted in a microbial composition in pigs similar to that of the original infant feces. This model was then used to understand the interconnections between microbiota diversity, diet, and HRV infection. Post HRV infection, HIFM pigs on the deficient diet had lower body weights, developed more severe diarrhea and increased virus shedding compared to HIFM pigs on sufficient diet. However, HRV induced diarrhea and shedding was more pronounced in non-colonized GF pigs compared to HIFM pigs on either sufficient or deficient diet, suggesting that the microbiota alone moderated HRV infection. HRV infected pigs on sufficient diet showed increased microbiota diversity in intestinal tissues; whereas, greater diversity was observed in systemic tissues of HRV infected pigs fed with deficient diet. CONCLUSIONS These results suggest that proper nourishment improves the microbiota quality in the intestines, alleviates HRV disease and lower probability of systemic translocation of potential opportunistic pathogens/pathobionts. In conclusion, our findings further support the role for microbiota and proper nutrition in limiting enteric diseases.
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Affiliation(s)
- Anand Kumar
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
- Present address: Group B-10: Biosecurity and Public Health, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Anastasia N. Vlasova
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Loic Deblais
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Huang-Chi Huang
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Asela Wijeratne
- The Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH USA
| | - Sukumar Kandasamy
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - David D. Fischer
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Stephanie N. Langel
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Francine Chimelo Paim
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Moyasar A. Alhamo
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Lulu Shao
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
- Present address: Hillman Cancer Center, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260 USA
| | - Linda J. Saif
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Gireesh Rajashekara
- Food Animal Research Program, The Ohio Agricultural Research and Development Center,Veterinary Preventive Medicine Department, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
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Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis. Infect Immun 2018; 86:IAI.00060-18. [PMID: 29685983 DOI: 10.1128/iai.00060-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/15/2018] [Indexed: 11/20/2022] Open
Abstract
The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. By using nondirected 16S rRNA gene amplicon sequencing, the fecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated with the overall microbial composition, with a decrease in the abundance of Faecalibacterium being observed in older patients. We observed the emergence of a potential Escherichia-Shigella-dominated enterotype in a subset of patients, and this enterotype was predicted to be more proinflammatory than the other common enterotypes, with the latter being dominated by Bacteroides or Faecalibacterium The increased abundance of Escherichia-Shigella did not appear to be associated with infection with an agent of a similar sequence similarity. Stool color and consistency were associated with the diversity and composition of the microbiome, with deviations from the norm (not brown and solid) showing increases in the abundances of bacteria such as Escherichia-Shigella and Veillonella Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases, including Treponema, Proteus, Capnocytophaga, Arcobacter, Campylobacter, Haemophilus, Aeromonas, and Pseudomonas Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in stool color and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified by using routine diagnostic tests, suggesting that in the future, microbiome analyses may be utilized to improve diagnostics.
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43
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Pereira MB, Wallroth M, Jonsson V, Kristiansson E. Comparison of normalization methods for the analysis of metagenomic gene abundance data. BMC Genomics 2018; 19:274. [PMID: 29678163 PMCID: PMC5910605 DOI: 10.1186/s12864-018-4637-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/28/2018] [Indexed: 01/17/2023] Open
Abstract
Background In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis. A wide range of normalization methods for high-dimensional count data has been proposed but their performance on the analysis of shotgun metagenomic data has not been evaluated. Results Here, we present a systematic evaluation of nine normalization methods for gene abundance data. The methods were evaluated through resampling of three comprehensive datasets, creating a realistic setting that preserved the unique characteristics of metagenomic data. Performance was measured in terms of the methods ability to identify differentially abundant genes (DAGs), correctly calculate unbiased p-values and control the false discovery rate (FDR). Our results showed that the choice of normalization method has a large impact on the end results. When the DAGs were asymmetrically present between the experimental conditions, many normalization methods had a reduced true positive rate (TPR) and a high false positive rate (FPR). The methods trimmed mean of M-values (TMM) and relative log expression (RLE) had the overall highest performance and are therefore recommended for the analysis of gene abundance data. For larger sample sizes, CSS also showed satisfactory performance. Conclusions This study emphasizes the importance of selecting a suitable normalization methods in the analysis of data from shotgun metagenomics. Our results also demonstrate that improper methods may result in unacceptably high levels of false positives, which in turn may lead to incorrect or obfuscated biological interpretation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4637-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariana Buongermino Pereira
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Mikael Wallroth
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Viktor Jonsson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96, Gothenburg, Sweden.
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Ingle H, Peterson ST, Baldridge MT. Distinct Effects of Type I and III Interferons on Enteric Viruses. Viruses 2018; 10:E46. [PMID: 29361691 PMCID: PMC5795459 DOI: 10.3390/v10010046] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
Interferons (IFNs) are key host cytokines in the innate immune response to viral infection, and recent work has identified unique roles for IFN subtypes in regulating different aspects of infection. Currently emerging is a common theme that type III IFNs are critical in localized control of infection at mucosal barrier sites, while type I IFNs are important for broad systemic control of infections. The intestine is a particular site of interest for exploring these effects, as in addition to being the port of entry for a multitude of pathogens, it is a complex tissue with a variety of cell types as well as the presence of the intestinal microbiota. Here we focus on the roles of type I and III IFNs in control of enteric viruses, discussing what is known about signaling downstream from these cytokines, including induction of specific IFN-stimulated genes. We review viral strategies to evade IFN responses, effects of IFNs on the intestine, interactions between IFNs and the microbiota, and briefly discuss the role of IFNs in controlling viral infections at other barrier sites. Enhanced understanding of the coordinate roles of IFNs in control of viral infections may facilitate development of antiviral therapeutic strategies; here we highlight potential avenues for future exploration.
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Affiliation(s)
- Harshad Ingle
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Stefan T Peterson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Megan T Baldridge
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Dinleyici EC, Martínez-Martínez D, Kara A, Karbuz A, Dalgic N, Metin O, Yazar AS, Guven S, Kurugol Z, Turel O, Kucukkoc M, Yasa O, Eren M, Ozen M, Martí JM, P. Garay C, Vandenplas Y, Moya A. Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment. Front Microbiol 2018; 9:1230. [PMID: 29946306 PMCID: PMC6005867 DOI: 10.3389/fmicb.2018.01230] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 05/22/2018] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota is closely related to acute infectious diarrhea, one of the leading causes of mortality and morbidity in children worldwide. Understanding the dynamics of the recovery from this disease is of clinical interest. This work aims to correlate the dynamics of gut microbiota with the evolution of children who were suffering from acute infectious diarrhea caused by a rotavirus, and their recovery after the administration of a probiotic, Saccharomyces boulardii CNCM I-745. The experiment involved 10 children with acute infectious diarrhea caused by a rotavirus, and six healthy children, all aged between 3 and 4 years. The children who suffered the rotavirus infection received S. boulardii CNCM I-745 twice daily for the first 5 days of the experiment. Fecal samples were collected from each participant at 0, 3, 5, 10, and 30 days after probiotic administration. Microbial composition was characterized by 16S rRNA gene sequencing. Alpha and beta diversity were calculated, along with dynamical analysis based on Taylor's law to assess the temporal stability of the microbiota. All children infected with the rotavirus stopped having diarrhea at day 3 after the intervention. We observed low alpha diversities in the first 5 days (p-value < 0.05, Wilcoxon test), larger at 10 and 30 days after probiotic treatment. Canonical correspondence analysis (CCA) showed differences in the gut microbiota of healthy children and of those who suffered from acute diarrhea in the first days (p-value < 0.05, ADONIS test), but not in the last days of the experiment. Temporal variability was larger in children infected with the rotavirus than in healthy ones. In particular, Gammaproteobacteria class was found to be abundant in children with acute diarrhea. We identified the microbiota transition from a diseased state to a healthy one with time, whose characterization may lead to relevant clinical data. This work highlights the importance of using time series for the study of dysbiosis related to diarrhea.
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Affiliation(s)
- Ener C. Dinleyici
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | | | - Ates Kara
- Pediatric Infectious Disease Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Adem Karbuz
- Department of Pediatrics, Okmeydani Education and Research Hospital, Istanbul, Turkey
| | - Nazan Dalgic
- Division of Pediatric Infectious Diseases, Sisli Etfal Training and Research Hospital, Istanbul, Turkey
| | - Ozge Metin
- Division of Pediatric Infectious Diseases, Konya Training and Research Hospital, Konya, Turkey
| | - Ahmet S. Yazar
- Department of Pediatrics, Umraniye Education and Research Hospital, Istanbul, Turkey
| | - Sirin Guven
- Department of Pediatrics, Umraniye Education and Research Hospital, Istanbul, Turkey
| | - Zafer Kurugol
- Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ozden Turel
- Department of Pediatric Infectious Disease Unit, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Mehmet Kucukkoc
- Department of Pediatric Infectious Disease Unit, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Olcay Yasa
- Department of Pediatrics, Goztepe Training and Research Hospital, SB Istanbul Medeniyet University, Istanbul, Turkey
| | - Makbule Eren
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Metehan Ozen
- Department of Pediatrics, Acibadem University Faculty of Medicine, Istanbul, Turkey
| | - Jose Manuel Martí
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
| | - Carlos P. Garay
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
| | - Yvan Vandenplas
- Department of Pediatrics, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andrés Moya
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
- Area de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- *Correspondence: Andrés Moya
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