DOCSLIB.ORG

The Bacterial Microbiome and Virome Milestones of Infant Development

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Bacterial Microbiome and Virome Milestones of Infant Development Review The Bacterial Microbiome and Virome Milestones of Infant Development 1 1 2, Efrem S. Lim, David Wang, and Lori R. Holtz * The human gut harbors a complex community of bacteria, viruses, fungi, Trends protists, and other microorganisms (collectively termed the microbiome) that The gut bacterial microbiome and vir- impact health and disease. Emerging studies indicate that the gut bacterial ome affect healthy infant development. microbiome and virome play an important role in healthy infant development. In In contrast to the adult's gut bacterial turn, the composition of the microbiome during development can be influenced microbiome and virome, those in the by factors such as dietary, environmental, and maternal conditions. As such, the infant are dynamic. microbiome trajectory during early infancy could be predictors of healthy devel- Transkingdom interactions between opment. Conversely, adverse early events in life may have consequences later in viruses and bacteria influence the life. This review focuses on our understanding of the bacterial microbiome and health and disease of the host. virome during early development, conditions that might influence these pro- Infant gut bacterial colonization is cor- cesses, and their long-term implications for infant health. related with a contraction in the bacter- iophage community. Microbial Communities of the Infant Gut While microbes are historically viewed as potential pathogens, we now appreciate their beneficial role in health, immune function, and metabolism. The gut harbors the highest density microbial community within the human body. This gut microbiome (see Glossary) encompasses the diverse community of eukaryotic viruses and bacteriophages (virome), bacteria (bacterial microbiome), and other microorganisms. An emerging concept from recent studies is that these microbial communities are important for healthy infant develop- ment. The developmental trajectory includes milestones such as the choreographed coloni- zation of bacterial populations, dynamic alterations in the virome, and transkingdom interactions between members of the two communities. Alterations in the bacterial micro- biome and virome early in life are significant because they could set the stage for the infant's future health and disease risk. Thus, early infancy may present a unique opportunity to leverage the bacterial microbiome and virome to intervene and influence immune develop- ment and disease outcomes. 1 The aim of this review is to summarize current understanding of the early development of the Departments of Molecular human gut bacterial microbiome and virome in terms of the dynamic nature of this progression Microbiology and Pathology and Immunology, Washington University and the factors that influence its trajectory. We discuss the potential interactions between School of Medicine, St Louis, MO, members of these two kingdoms and how perturbations of the infant gut bacterial microbiome USA 2 and virome may set the stage for disease later in life. Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University Development of the Gut Bacterial Microbiome School of Medicine, St Louis, MO, Multiple factors influence the composition of the bacterial microbiome (Figure 1, Key Figure). USA Many variables early in life, including mode of delivery, infant diet, use of antibiotics, the physical environment surrounding the infant, host genetics, and perhaps even the in utero environment, *Correspondence: fl in uence this complex process. [email protected] (L.R. Holtz). Trends in Microbiology, October 2016, Vol. 24, No. 10 http://dx.doi.org/10.1016/j.tim.2016.06.001 801 © 2016 Elsevier Ltd. All rights reserved. Womb Exposure Glossary Traditionally the womb has been considered a sterile sanctuary for the developing fetus. Bacterial microbiome: community However, recently this dogma has been questioned by numerous observations, raising the of bacteria that share an ecological space. possibility that the infant gut is colonized before birth. Specifically, bacteria have been detected in Microbiome: community of full-term placentas using culture-based methods [1] and they have been visualized in the microorganisms, including bacteria, placental basal plate from healthy pregnancies [2]. Bacterial sequences have been detected viruses, fungi, protists, and other in the placenta [3], amniotic fluid [4], cord blood [5], and meconium [6]. Aagaard et al. found that microorganisms, within an ecological space. the placental bacterial microbiome resembled the oral bacterial microbiome [3]. Interestingly, the Virome: community of eukaryotic connection between these two microbial communities has also been seen in murine systems. viruses and bacteriophages that Tail vein injection of Fusobacterium, an oral anaerobe, localizes to the placenta, but does not share an ecological space. colonize other organs [7]. It is unclear from where the bacteria that comprise the pIacental microbiome originate. One hypothesis suggests that the bacteria are spread hematogenously either from the oral cavity or the gut to the placenta. In support of this model, labeled Enterococcus fed to pregnant mice can be detected in the meconium of the pup [6]. It has been noted that bacterial translocation from the gut to the blood is higher in pregnant mice than in nonpregnant mice [8], which may permit seeding of the placenta. Alternatively, it has been suggested that the nonpregnant uterus is colonized with microbes in the endometrial epithelium as bacteria have been cultured from the endometrium and these could be the source of the placental bacterial microbiome [9]. Bacteria have been isolated from the amniotic fluid of mothers with chorioamnionitis. Commonly recovered bacteria include Ureaplasma, Mycoplasma, Fusobacterium, Streptococcus, Bacter- oides, and Prevotella. Broad-range PCR assays have demonstrated the presence of Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and fusobacteria DNA in amniotic fluid [4]. The relative abundances of specific bacterial taxa in amniotic fluid differs between preterm labor with Key Figure Influences on the Gut Microbiome during Infant Development Influences on microbiome during infant development Mode of Gestaonal Diet Womb delivery age Genecs Environment Anbiocs Microbiome or Healthy Disease development Figure 1. The infant gut bacterial microbiome and virome can be influenced by various factors as shown. Notably, while most studies have demonstrated their effects on modulation of the bacterial microbiome, further research is needed to extend these findings to the virome (e.g., mode of delivery and gestational age). Collectively, alterations in the infant gut bacterial microbiome and virome can lead towards a healthy development or disease. 802 Trends in Microbiology, October 2016, Vol. 24, No. 10 intact membranes versus preterm labor with ruptured membranes [4]. The role of bacteria in the amniotic fluid from women with preterm delivery remains unknown. Jimenez et al. collected cord blood from 20 healthy infants born via Cesarean section (C-section) [5]. From 9 (45%) of these samples, they cultured and identified by 16S sequencing multiple taxa of Gram-positive bacteria, including Enterococcus, Streptococcus, Staphylococcus, and Propionibacterium. Studies have also suggested that meconium is not sterile as once previously thought, supporting the hypothesis that gut colonization occurs before birth. Jimenez et al. [5] showed, using culture, that Staphylococcus and Enterococcus were the predominant bacteria in meconium. Subse- quent 16S-based studies of meconium found that samples had low bacterial diversity and that the microbiome is dominated by a few genera in a given individual [10]. Additionally, Ardissone et al. [10] demonstrated that the bacterial microbiome in meconium most closely resembled that of amniotic fluid. Mode of Delivery The mode of delivery (vaginal versus C-section) has a strong correlation with the bacterial communities that first colonize the gut [11,12]. Infants born vaginally have gut bacterial micro- biomes that resemble their mother's vaginal bacterial microbiome, which is dominated by Lactobacillus [11]. By contrast, infants born by C-section have a gut microbiome most similar to their mother's skin bacterial microbiome. Interestingly, this altered colonization pattern seen in babies delivered via C-section persists to at least 1 year of age [12,13] and has been hypothe- sized to be responsible for the increased risk of obesity [14] and asthma [15] seen in children delivered by C-section. A pilot study to expose infants delivered by C-section to maternal vaginal fluids [16] demonstrated that vaginal microbes could be partially restored at birth in C-section- delivered babies. However, the long-term impact and possible benefits of this procedure as well as potential risks (e.g., exposure to bacteria that may be harmful to the infant) have yet to be defined [17]. Gestational Age The gut bacterial microbiome also differs with gestational age. A longitudinal study of preterm infants showed that the pace of the gut bacterial microbiome development was most strongly driven by postconceptional age [18,19]. The importance of gestational age in the development of the bacterial microbiome has also been seen in a longitudinal study of term and near-term infants in Singapore [20]. Furthermore, a study of meconium showed that gestational age had the greatest influence on the microbial community structure [10]. While factors such as delivery mode and diet
Load more

Recommended publications
  • Gut Microbiota Beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD
    International Journal of Molecular Sciences Review Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD Mario Matijaši´c 1,* , Tomislav Meštrovi´c 2, Hana Cipˇci´cPaljetakˇ 1, Mihaela Peri´c 1, Anja Bareši´c 3 and Donatella Verbanac 4 1 Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; [email protected] (H.C.P.);ˇ [email protected] (M.P.) 2 University Centre Varaždin, University North, 42000 Varaždin, Croatia; [email protected] 3 Division of Electronics, Ruđer Boškovi´cInstitute, 10000 Zagreb, Croatia; [email protected] 4 Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; [email protected] * Correspondence: [email protected]; Tel.: +385-01-4590-070 Received: 30 January 2020; Accepted: 7 April 2020; Published: 11 April 2020 Abstract: The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease. Keywords: gut microbiota; inflammatory bowel disease (IBD); mycobiome; virome; archaeome; eukaryotic parasites 1. Introduction Trillions of microbes colonize the human body, forming the microbial community collectively referred to as the human microbiota.
    [Show full text]
  • Rapid Evolution of the Human Gut Virome
    Rapid evolution of the human gut virome Samuel Minota, Alexandra Brysona, Christel Chehouda, Gary D. Wub, James D. Lewisb,c, and Frederic D. Bushmana,1 aDepartment of Microbiology, bDivision of Gastroenterology, and cCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104 Edited by Sankar Adhya, National Institutes of Health, National Cancer Institute, Bethesda, MD, and approved May 31, 2013 (received for review January 15, 2013) Humans are colonized by immense populations of viruses, which sequenced independently to allow estimation of within-time point metagenomic analysis shows are mostly unique to each individual. sample variation. Virus-like particles were extracted by sequential To investigate the origin and evolution of the human gut virome, filtration, Centricon ultrafiltration, nuclease treatment, and sol- we analyzed the viral community of one adult individual over 2.5 y vent extraction. Purified viral DNA was subjected to linear am- by extremely deep metagenomic sequencing (56 billion bases of plification using Φ29 DNA polymerase, after which quantitative purified viral sequence from 24 longitudinal fecal samples). After PCR showed that bacterial 16S sequences were reduced to less assembly, 478 well-determined contigs could be identified, which than 10 copies per nanogram of DNA, and human sequences were are inferred to correspond mostly to previously unstudied bacterio- reduced to below 0.1 copies per nanogram, the limit of detection. phage genomes. Fully 80% of these types persisted throughout the Paired-end reads then were acquired using Illumina HiSeq se- duration of the 2.5-y study, indicating long-term global stability.
    [Show full text]
  • Coming-Of-Age Characterization of Soil Viruses: a User's Guide To
    Review Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics Gareth Trubl 1,* , Paul Hyman 2 , Simon Roux 3 and Stephen T. Abedon 4,* 1 Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA 2 Department of Biology/Toxicology, Ashland University, Ashland, OH 44805, USA; [email protected] 3 DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; [email protected] 4 Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA * Correspondence: [email protected] (G.T.); [email protected] (S.T.A.) Received: 25 February 2020; Accepted: 17 April 2020; Published: 21 April 2020 Abstract: The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses.
    [Show full text]
  • The Intra-Dependence of Viruses and the Holobiont
    UC Merced UC Merced Previously Published Works Title The Intra-Dependence of Viruses and the Holobiont. Permalink https://escholarship.org/uc/item/41h7q2bs Author Grasis, Juris A Publication Date 2017 DOI 10.3389/fimmu.2017.01501 Peer reviewed eScholarship.org Powered by the California Digital Library University of California PERSPECTIVE published: 09 November 2017 doi: 10.3389/fimmu.2017.01501 The Intra-Dependence of Viruses and the Holobiont Juris A. Grasis1,2* 1 Department of Biology, San Diego State University, San Diego, CA, United States, 2 School of Natural Sciences, University of California at Merced, Merced, CA, United States Animals live in symbiosis with the microorganisms surrounding them. This symbiosis is necessary for animal health, as a symbiotic breakdown can lead to a disease state. The functional symbiosis between the host, and associated prokaryotes, eukaryotes, and viruses in the context of an environment is the holobiont. Deciphering these holobiont associations has proven to be both difficult and controversial. In particular, holobiont association with viruses has been of debate even though these interactions have been occurring since cellular life began. The controversy stems from the idea that all viruses are parasitic, yet their associations can also be beneficial. To determine viral involvement within the holobiont, it is necessary to identify and elucidate the function of viral popula- Edited by: tions in symbiosis with the host. Viral metagenome analyses identify the communities of Larry J. Dishaw, eukaryotic and prokaryotic viruses that functionally associate within a holobiont. Similarly, University of South Florida St. Petersburg, United States analyses of the host in response to viral presence determine how these interactions are Reviewed by: maintained.
    [Show full text]
  • Metatranscriptomics to Characterize Respiratory Virome, Microbiome, and Host Response Directly from Clinical Samples
    Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples Seesandra Rajagopala ( [email protected] ) Vanderbilt University Medical Center Nicole Bakhoum Vanderbilt University Medical Center Suman Pakala Vanderbilt University Medical Center Meghan Shilts Vanderbilt University Medical Center Christian Rosas-Salazar Vanderbilt University Medical Center Annie Mai Vanderbilt University Medical Center Helen Boone Vanderbilt University Medical Center Rendie McHenry Vanderbilt University Medical Center Shibu Yooseph University of Central Florida https://orcid.org/0000-0001-5581-5002 Natasha Halasa Vanderbilt University Medical Center Suman Das Vanderbilt University Medical Center https://orcid.org/0000-0003-2496-9724 Article Keywords: Metatranscriptomics, Virome, Microbiome, Next-Generation Sequencing (NGS), RNA-Seq, Acute Respiratory Infection (ARI), Respiratory Syncytial Virus (RSV), Coronavirus (CoV) Posted Date: October 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-77157/v1 Page 1/31 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/31 Abstract We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low-biomass clinical samples. Using nasal swab samples, we have demonstrated that this method captures the comprehensive RNA virome with sucient sequencing depth required to assemble complete genomes. We nd a surprisingly high-frequency of Respiratory Syncytial Virus (RSV) and Coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-infections in children with symptomatic RSV. In addition, we have characterized commensal and pathogenic bacteria, and fungi at the species-level. Functional analysis of bacterial transcripts revealed H.
    [Show full text]
  • Freshwater Viral Metagenome Reveals Novel and Functional Phage-Borne
    Moon et al. Microbiome (2020) 8:75 https://doi.org/10.1186/s40168-020-00863-4 RESEARCH Open Access Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes Kira Moon1, Jeong Ho Jeon2, Ilnam Kang1, Kwang Seung Park2, Kihyun Lee3, Chang-Jun Cha3, Sang Hee Lee2* and Jang-Cheon Cho1* Abstract Background: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. Results: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1×e−5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found.
    [Show full text]
  • The Altered Gut Virome Community in Rhesus Monkeys Is Correlated With
    Li et al. Virology Journal (2019) 16:105 https://doi.org/10.1186/s12985-019-1211-z RESEARCH Open Access The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites Heng Li1,2†, Hongzhe Li1,2†, Jingjing Wang1,2, Lei Guo1,2, Haitao Fan1,2, Huiwen Zheng1,2, Zening Yang1,2, Xing Huang1,2, Manman Chu1,2, Fengmei Yang1, Zhanlong He1, Nan Li1,2, Jinxi Yang1,2, Qiongwen Wu1,2, Haijing Shi1,2* and Longding Liu1,2* Abstract Background: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition. Methods: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS. Results: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion.
    [Show full text]
  • Viromes Outperform Total Metagenomes in Revealing the Spatiotemporal Patterns of Agricultural Soil Viral Communities
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.237214; this version posted August 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Viromes outperform total metagenomes in revealing the spatiotemporal patterns 2 of agricultural soil viral communities 3 Christian Santos-Medellin1, Laura A. Zinke1, Anneliek M. ter Horst1, Danielle L. Gelardi2, 4 Sanjai J. Parikh2, and Joanne B. Emerson1,3 5 6 1Department of Plant Pathology, University of California, Davis, One Shields Avenue, 7 Davis, California, USA, 95616 8 2Department of Land, Air and Water Resources, University of California, Davis, One 9 Shields Avenue, Davis, California, USA, 95616 10 3Genome Center, University of California, Davis, One Shields Avenue, Davis, California, 11 USA, 95616 12 13 Corresponding author information: 14 Joanne B. Emerson 15 Address: One Shields Ave, Davis, California, USA, 95616 16 Email: [email protected] 17 Phone: 530-752-9848 18 19 Running title: “Spatiotemporal trends of soil viral communities” 20 21 Competing interests: Authors declare no conflict of interest 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.237214; this version posted August 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • A New Comprehensive Catalog of the Human Virome Reveals Hidden Associations with 2 Chronic Diseases 3 4 Michael J
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.01.363820; this version posted November 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. 1 A New Comprehensive Catalog of the Human Virome Reveals Hidden Associations with 2 Chronic Diseases 3 4 Michael J. Tisza and Christopher B. Buck* 5 6 Affiliation 7 Lab of Cellular Oncology, NCI, NIH, Bethesda, MD 20892-4263 8 9 *Corresponding author: [email protected] 10 11 Abstract 12 While there have been remarkable strides in microbiome research, the viral component of the 13 microbiome has generally presented a more challenging target than the bacteriome. This is 14 despite the fact that many thousands of shotgun sequencing runs from human metagenomic 15 samples exist in public databases and all of them encompass large amounts of viral sequences. 16 The lack of a comprehensive database for human-associated viruses, along with inadequate 17 methods for high-throughput identification of highly divergent viruses in metagenomic data, 18 has historically stymied efforts to characterize virus sequences in a comprehensive way. In this 19 study, a new high-specificity and high-sensitivity bioinformatic tool, Cenote-Taker 2, was 20 applied to thousands of human metagenome datasets, uncovering over 50,000 unique virus 21 operational taxonomic units. Publicly available case-control studies were re-analyzed, and over 22 1,700 strong virus-disease associations were found.
    [Show full text]
  • Composition and Dynamics of the Human Virome
    Composition and dynamics of the human virome Frederic Bushman The global virome • 107 viruses per ml in sea water • Viruses outnumber hosts by ~10-fold in sea water • 1031 viral particles on Earth • Numerically most successful biological entities Data from Lita Proctor, Forrest Rohwer, Curtis Suttle and others Proctor, 1997 The Human Virome Transient Persistent/latent infections with infections animal cell % of population Virus viruses seropositive EBV 100% Endogenous retroviruses VZV 95% Herpes 8% of human DNA 80% simplex HSV1 68% Papilloma 60% CMV 59% HSV2 22% HIV 1% HCV 1% Bacteriophage predators of bacteria and archaea 1010-1011 per gram of stool Virome analysis by deep sequencing Find new pathogens Watch viral evolution Characterize viral DNA integration into genomes Characterize complex uncultured communties Solexa/Illumina HiSeq Rohwer, Suttle, Lipkin, Hahn, Weinstock, Storch, Wang, Virgin, Gordon, Reyes, Proctor, Bushman many others What is the composition of the human gut microbiome, and how does it change over time? Support: HMP demonstration project “Diet, Genetic Factors, and the Gut Microbiome in Crohn’s Disease”. PIs Wu, Lewis and Bushman S. Minot, R. Sinha, J. Chen, H. Li, S. A. Keilbaugh, G. Wu, J. Lewis, and F. D. Bushman. (2011) Dynamic response of the human virome to dietary intervention. Genome Res., 21(10):1616-25. S. Minot, S. Grunberg, G. Wu, J. Lewis, and F. D. Bushman. (2012) Hypervariable loci in the human gut virome. Proc. Natl. Acad. Sci. USA 109(10):3962-6. S. Minot J. Lewis, G. Wu and F. D. Bushman. Conservation of gene cassettes among diverse viruses of the human gut.
    [Show full text]
  • The Gut Virome: the ‘Missing Link’ Between 2019, Vol
    TAG0010.1177/1756284819836620Therapeutic Advances in GastroenterologyI Mukhopadhya, JP Segal 836620review-article2019View2019 metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberdeen University Research Archive Therapeutic Advances in Gastroenterology Review Ther Adv Gastroenterol The gut virome: the ‘missing link’ between 2019, Vol. 12: 1–17 DOI:https://doi.org/10.1177/1756284819836620 10.1177/ gut bacteria and host immunity? 1756284819836620https://doi.org/10.1177/1756284819836620 © The Author(s), 2019. Article reuse guidelines: Indrani Mukhopadhya, Jonathan P. Segal, Simon R. Carding, Ailsa L. Hart sagepub.com/journals- and Georgina L. Hold permissions Abstract: The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease. Keywords: gut virome, gut microbiota, inflammatory bowel disease, host:microbiota interactions, microbial therapeutics, microbial dynamics Received: 5 January 2019; revised manuscript accepted: 14 February 2019.
    [Show full text]
  • Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma
    microorganisms Article Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma Tianli Ma 1,2,†, Jinlong Ru 1,2,† , Jinling Xue 1,2, Sarah Schulz 1,2 , Mohammadali Khan Mirzaei 1,2 , Klaus-Peter Janssen 3, Michael Quante 4,5,* and Li Deng 1,2,* 1 Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; [email protected] (T.M.); [email protected] (J.R.); [email protected] (J.X.); [email protected] (S.S.); [email protected] (M.K.M.) 2 Institute of Virology, Technical University of Munich, 81675 Munich, Germany 3 Department of Surgery, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany; [email protected] 4 II. Medizinische Klinik, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany 5 Innere Medizin II, Universitätsklinik Freiburg, Universität Freiburg, 79106 Freiburg, Germany * Correspondence: [email protected] (M.Q.); [email protected] (L.D.) † These authors contributed equally to this work. Abstract: The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the relationship between gut bacteriophages and upper GI tract diseases, such as esophageal diseases, which mainly include Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC), remains poorly described. This study aimed to reveal the gut bacteriophage community and their behavior in the progression of esophageal diseases. In total, we analyzed the gut phage community of sixteen samples from patients Citation: Ma, T.; Ru, J.; Xue, J.; with esophageal diseases (six BE patients and four EAC patients) as well as six healthy controls.
    [Show full text]