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Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 2015; 21:1228-34. [PMID: 26366711 DOI: 10.1038/nm.3950] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 12/13/2022]
Abstract
The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.
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Affiliation(s)
- Efrem S Lim
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yanjiao Zhou
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Guoyan Zhao
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irma K Bauer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Phillip I Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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Gan D, Liu N, Han CP, Wu J, Feng Z, Jin W, Wang ZY. Advances in research of metavirus in inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2015; 23:3882-3887. [DOI: 10.11569/wcjd.v23.i24.3882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal tract. Ulcerative colitis and Crohn's disease are two main forms. With the development of metavirus technique in recent years, the latest research shows that virus is the second largest species in the intestine. The enteric virome may have a direct effect on the intestinal immunological functions, and the intestinal bacteriophages can affect the human gut bacteria and change the enteric internal environment. Therefore, the research focused on the enteric virome may help clarify the aetiological causes of IBD. In this review, we discuss the relationships between intestinal virus, intestinal flora, and the pathogenesis of IBD.
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Meyer CT, Bauer IK, Antonio M, Adeyemi M, Saha D, Oundo JO, Ochieng JB, Omore R, Stine OC, Wang D, Holtz LR. Prevalence of classic, MLB-clade and VA-clade Astroviruses in Kenya and The Gambia. Virol J 2015; 12:78. [PMID: 25975198 PMCID: PMC4465002 DOI: 10.1186/s12985-015-0299-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious diarrhea leads to significant mortality in children, with 40 % of these deaths occurring in Africa. Classic human astroviruses are a well-established etiology of diarrhea. In recent years, seven novel astroviruses have been discovered (MLB1, MLB2, MLB3, VA1/HMO-C, VA2/HMO-B, VA3/HMO-A, VA4); however, there have been few studies on their prevalence or potential association with diarrhea. METHODS To investigate the prevalence and diversity of these classic and recently described astroviruses in a pediatric population, a case-control study was performed. Nine hundred and forty nine stools were previously collected from cases of moderate-to-severe diarrhea and matched controls of patients less than 5 years of age in Kenya and The Gambia. RT-PCR screening was performed using pan-astrovirus primers. RESULTS Astroviruses were present in 9.9 % of all stool samples. MLB3 was the most common astrovirus with a prevalence of 2.6 %. Two subtypes of MLB3 were detected that varied based on location in Africa. In this case-control study, Astrovirus MLB1 was associated with diarrhea in Kenya, whereas Astrovirus MLB3 was associated with the control state in The Gambia. Classic human astrovirus was not associated with diarrhea in this study. Unexpectedly, astroviruses with high similarity to Canine Astrovirus and Avian Nephritis Virus 1 and 2 were also found in one case of diarrhea and two control stools respectively. CONCLUSIONS Astroviruses including novel MLB- and VA-clade members are commonly found in pediatric stools in Kenya and The Gambia. The most recently discovered astrovirus, MLB3, was the most prevalent and was found more commonly in control stools in The Gambia, while astrovirus MLB1 was associated with diarrhea in Kenya. Furthermore, a distinct subtype of MLB3 was noted, as well as 3 unanticipated avian or canine astroviruses in the human stool samples. As a result of a broadly reactive PCR screen for astroviruses, new insight was gained regarding the epidemiology of astroviruses in Africa, where a large proportion of diarrheal morbidity and mortality occur.
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Affiliation(s)
| | - Irma K Bauer
- Washington University School of Medicine, Saint Louis, MO, USA.
| | | | | | - Debasish Saha
- Medical Research Council Unit, Banjul, The Gambia. .,Center for International Health, Department of Preventive and Social Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| | - Joseph O Oundo
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - John B Ochieng
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - Richard Omore
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - O Colin Stine
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | - David Wang
- Washington University School of Medicine, Saint Louis, MO, USA.
| | - Lori R Holtz
- Washington University School of Medicine, Saint Louis, MO, USA.
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