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Barron LK, Warner BB, Tarr PI, Shannon WD, Deych E, Warner BW. Independence of gut bacterial content and neonatal necrotizing enterocolitis severity. J Pediatr Surg 2017; 52:993-998. [PMID: 28410788 PMCID: PMC5473614 DOI: 10.1016/j.jpedsurg.2017.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/09/2017] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Necrotizing enterocolitis (NEC) is a common and devastating gastrointestinal disease of premature infants. NEC severity varies widely. Recent data have demonstrated a strong link between gut microbial dysbiosis and development of NEC. We tested the hypothesis that alterations in the gut microbiome at the time of diagnosis predict the severity of NEC. METHODS We used prospectively collected fecal samples from very low birth weight infants who developed NEC, stratifying by NEC severity. Fecal bacterial DNA was sequenced using 16S rRNA pyrosequencing. A generalized Wald-type test based on the Dirichlet multinomial distribution was used to test for differences in microbial communities. RESULTS Of 489 infants at risk, 30 NEC cases had 410 fecal samples collected in the 28days prior to the onset of NEC available for analysis. There were no differences in the pre-NEC gut microbial community between infants treated medically vs. surgically, or those with NEC totalis. Furthermore, neither treatment of NEC significantly changed the gut microbiome post-NEC among the survivors. CONCLUSION We found no evidence that the gut microbiome, prior to the onset of disease, differentiates the clinical course of NEC. These data suggest that factors other than the gut microbiome may dictate disease severity. LEVEL OF EVIDENCE Level 4.
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Affiliation(s)
- Lauren K. Barron
- Division of Pediatric Surgery, Department of Surgery, Washington University in St. Louis School of Medicine, St. Louis Children’s Hospital, St. Louis, MO, USA
| | - Barbara B. Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Phillip I. Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - William D. Shannon
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Elena Deych
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University in St. Louis School of Medicine, St. Louis Children’s Hospital, St. Louis, MO, USA
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Porse A, Gumpert H, Kubicek-Sutherland JZ, Karami N, Adlerberth I, Wold AE, Andersson DI, Sommer MOA. Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut. Front Cell Infect Microbiol 2017; 7:126. [PMID: 28447026 PMCID: PMC5388698 DOI: 10.3389/fcimb.2017.00126] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of Escherichia coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive fitness experiments to assess the role of this highly disseminated virulence plasmid in gut colonization, but found no evidence for a direct benefit of plasmid carriage. Through plasmid stability assays, we demonstrate that this plasmid is maintained in a parasitic manner, by strong first-line inheritance mechanisms, acting on the single-cell level, rather than providing a direct survival advantage in the gut. Investigating the ecology of endemic accessory genetic elements, in their pathogenic hosts and native environment, is of vital importance if we want to understand the evolution and persistence of highly virulent and drug resistant bacterial isolates.
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Affiliation(s)
- Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkLyngby, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre University HospitalHvidovre, Denmark
| | | | - Nahid Karami
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Ingegerd Adlerberth
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Agnes E Wold
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical CentreUppsala, Sweden
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkLyngby, Denmark
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Bacteria-Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality. Trends Microbiol 2017; 25:614-623. [PMID: 28342597 DOI: 10.1016/j.tim.2017.02.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/24/2017] [Indexed: 02/08/2023]
Abstract
Antagonistic coevolution (AC) between bacteria and bacteriophages plays a key role in driving and maintaining microbial diversity. Consequently, AC is predicted to affect all levels of biological organisation, from the individual to ecosystem scales. Nonetheless, we know nothing about bacteria-bacteriophage AC in perhaps the most important and clinically relevant microbial ecosystem known to humankind - the human gut microbiome. In this opinion piece I review current research on bacteria-phage AC in in vitro and natural populations of microbes. I then examine the evidence and discuss the potential role of AC in driving observed patterns of intra- and interindividual variation in the gut microbiome together with detailing the potential functional consequences of such AC-driven microbial variation for human health and disease.
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Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, Gregory KE, Kroll JS, McMurtry V, Ferris MJ, Engstrand L, Lilja HE, Hollister EB, Versalovic J, Neu J. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. MICROBIOME 2017; 5:31. [PMID: 28274256 PMCID: PMC5343300 DOI: 10.1186/s40168-017-0248-8] [Citation(s) in RCA: 416] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/27/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results. METHODS AND RESULTS Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5). CONCLUSIONS Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
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Affiliation(s)
- Mohan Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 77030 Houston, TX USA
| | - Julia Cope
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO USA
| | - Ardythe L. Morrow
- Department of Pediatrics, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Ohio, USA
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, FL USA
| | | | - J. Simon Kroll
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Valerie McMurtry
- Department of Microbiology, Immunology and Parasitology, Children’s Hospital, New Orleans, LA USA
| | - Michael J Ferris
- Department of Microbiology, Immunology and Parasitology, Children’s Hospital, New Orleans, LA USA
| | - Lars Engstrand
- Director of Clinical Genomics and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Emily B. Hollister
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX USA
| | - James Versalovic
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX USA
| | - Josef Neu
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 77030 Houston, TX USA
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Silverman MA, Konnikova L, Gerber JS. Impact of Antibiotics on Necrotizing Enterocolitis and Antibiotic-Associated Diarrhea. Gastroenterol Clin North Am 2017; 46:61-76. [PMID: 28164853 PMCID: PMC5314436 DOI: 10.1016/j.gtc.2016.09.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibiotic treatment alters the composition and metabolic function of the intestinal microbiota. These alterations may contribute to the pathogenesis of necrotizing enterocolitis (NEC) and antibiotic-associated diarrhea (AAD). Recent studies are beginning to unravel the contribution of specific groups of microbes and their metabolic pathways to these diseases. Probiotics or other microbiota-targeted therapies may provide effect strategies to prevent and treat NEC and AAD.
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Affiliation(s)
- Michael A. Silverman
- Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Liza Konnikova
- Department of Pediatric and Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115 and Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jeffrey S. Gerber
- Center for Pediatric Clinical Effectiveness, Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Chen Y, Li Z, Hu S, Zhang J, Wu J, Shao N, Bo X, Ni M, Ying X. Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. MICROBIOME 2017; 5:15. [PMID: 28143583 PMCID: PMC5286682 DOI: 10.1186/s40168-017-0232-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions. However, it is not known whether the gut metagenomes of T2D patients have characteristic strain patterns or SNP distributions. FINDINGS We downloaded public gut metagenome datasets from 170 T2D patients and 174 healthy controls and performed a systematic comparative analysis of their metagenome SNPs. We found that Bacteroides coprocola, whose relative abundance did not differ between the groups, had a characteristic distribution of SNPs in the T2D patient group. We identified 65 genes, all in B. coprocola, that had remarkably different enrichment of SNPs. The first and sixth ranked genes encode glycosyl hydrolases (GenBank accession EDU99824.1 and EDV02301.1). Interestingly, alpha-glucosidase, which is also a glycosyl hydrolase located in the intestine, is an important drug target of T2D. These results suggest that different strains of B. coprocola may have different roles in human gut and a specific set of B. coprocola strains are correlated with T2D.
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Affiliation(s)
- Yaowen Chen
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Zongcheng Li
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Shuofeng Hu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Jian Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Jiaqi Wu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850 People’s Republic of China
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Beijing, 100850 People’s Republic of China
| | - Xiaomin Ying
- Beijing Institute of Basic Medical Sciences, Beijing, 100850 People’s Republic of China
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Petriz BA, Franco OL. Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease. Front Chem 2017; 5:4. [PMID: 28184370 PMCID: PMC5266679 DOI: 10.3389/fchem.2017.00004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.
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Affiliation(s)
- Bernardo A Petriz
- Department of Health, Molecular and Physiologic Adaptations to Exercise, Centro Universitário do Distrito Federal Brasília, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Universidade Católica Dom Bosco Campo Grande, Brazil
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Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling. mSystems 2017; 2:mSystems00164-16. [PMID: 28144631 PMCID: PMC5264247 DOI: 10.1128/msystems.00164-16] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/21/2016] [Indexed: 12/28/2022] Open
Abstract
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.
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Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res 2017; 27:601-612. [PMID: 28073918 PMCID: PMC5378178 DOI: 10.1101/gr.213256.116] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022]
Abstract
The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity.
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Affiliation(s)
- Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, Pennsylvania 15213, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Karina Soenjoyo
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Transl Res 2017; 179:7-23. [PMID: 27513210 PMCID: PMC5164958 DOI: 10.1016/j.trsl.2016.07.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 12/29/2022]
Abstract
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA
- Santa Fe Institute, Santa Fe, NM
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Kumar J, Kumar M, Gupta S, Ahmed V, Bhambi M, Pandey R, Chauhan NS. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:371-378. [PMID: 27888152 PMCID: PMC5200916 DOI: 10.1016/j.gpb.2016.06.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/07/2016] [Accepted: 06/15/2016] [Indexed: 01/15/2023]
Abstract
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23 kb) metagenomic DNA (260/280 ratio >1.8) with a good yield (55.8 ± 3.8 ng/mg of feces). We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes = 227.9:1) in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.
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Affiliation(s)
- Jitendra Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Manoj Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Manu Bhambi
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Rajesh Pandey
- Ayurgenomics Unit, Translational Research and Innovative Science ThRough Ayurgeomics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi 110020, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India.
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Ghurye JS, Cepeda-Espinoza V, Pop M. Metagenomic Assembly: Overview, Challenges and Applications. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:353-362. [PMID: 27698619 PMCID: PMC5045144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems.
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Affiliation(s)
| | | | - Mihai Pop
- To whom all correspondence should be addressed: Mihai Pop, Department of Computer Science and Center of Bioinformatics and Computational Biology, University of Maryland, Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building. Rm. 3120F, College Park, MD 20742, Phone Number: 301-405-7245,
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Raymond F, Déraspe M, Boissinot M, Bergeron MG, Corbeil J. Partial recovery of microbiomes after antibiotic treatment. Gut Microbes 2016; 7:428-34. [PMID: 27494088 PMCID: PMC5154369 DOI: 10.1080/19490976.2016.1216747] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 02/03/2023] Open
Abstract
Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted.
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Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
| | - Michel G. Bergeron
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Département de
microbiologie-infectiologie et d'immunologie, Université
Laval, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
- Département de médecine
moléculaire, Université Laval, Québec,
Canada
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64
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Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. ISME JOURNAL 2016; 10:2817-2830. [PMID: 27258951 DOI: 10.1038/ismej.2016.83] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 03/06/2016] [Accepted: 04/12/2016] [Indexed: 12/12/2022]
Abstract
The potentially critical stage of initial gut colonization in premature infants occurs in the hospital environment, where infants are exposed to a variety of hospital-associated bacteria. Because few studies of microbial communities are strain-resolved, we know little about the extent to which specific strains persist in the hospital environment and disperse among infants. To study this, we compared 304 near-complete genomes reconstructed from fecal samples of 21 infants hospitalized in the same intensive care unit in two cohorts, over 3 years apart. The genomes represent 159 distinct bacterial strains, only 14 of which occurred in multiple infants. Enterococcus faecalis and Staphylococcus epidermidis, common infant gut colonists, exhibit diversity comparable to that of reference strains, inline with introduction of strains from infant-specific sources rather than a hospital strain pool. Unlike other infants, a pair of sibling infants shared multiple strains, even after extensive antibiotic administration, suggesting overlapping strain-sources and/or genetic selection drive microbiota similarities. Interestingly, however, five strains were detected in infants hospitalized three years apart. Three of these were also detected in multiple infants in the same year. This finding of a few widely dispersed and persistent bacterial colonizers despite overall low potential for strain dispersal among infants has implications for understanding and directing healthy colonization.
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65
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Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. MICROBIOME 2016; 4:8. [PMID: 26951112 PMCID: PMC4782286 DOI: 10.1186/s40168-016-0154-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/05/2016] [Indexed: 05/03/2023]
Abstract
Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
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Affiliation(s)
- Naseer Sangwan
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
| | - Fangfang Xia
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
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66
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Deletion of the Toll-Like Receptor 5 Gene Per Se Does Not Determine the Gut Microbiome Profile That Induces Metabolic Syndrome: Environment Trumps Genotype. PLoS One 2016; 11:e0150943. [PMID: 26950299 PMCID: PMC4780789 DOI: 10.1371/journal.pone.0150943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/22/2016] [Indexed: 12/31/2022] Open
Abstract
Over the past decade, emerging evidence has linked alterations in the gut microbial composition to a wide range of diseases including obesity, type 2 diabetes, and cardiovascular disease. Toll-like receptors (TLRs) are the major mediators for the interactions between gut microbiota and host innate immune system, which is involved in the localization and structuring of host gut microbiota. A previous study found that TLR5 deficient mice (TLR5KO1) had altered gut microbial composition which led to the development of metabolic syndrome including hyperlipidemia, hypertension, insulin resistance and increased adiposity. In the current study, a second TLR5-deficient mouse model was studied (TLR5KO2). TLR5 deficient mice did not manifest metabolic abnormalities related to the metabolic syndrome compared with littermate controls maintained on normal chow or after feeding a high fat diet. Analysis of the gut microbial composition of littermate TLR5KO2 and wild type mice revealed no significant difference in the overall microbiota structure between genotypes. However, the TLR5KO2 microbiota was distinctly different from that previously reported for TLR5KO1 mice with metabolic syndrome. We conclude that an altered composition of the microbiota in a given environment can result in metabolic syndrome, but it is not a consequence of TLR5 deficiency per se.
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67
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Dollings MC, Brown L. An Integrated Review of Intestinal Microbiota in the Very Premature Infant. Neonatal Netw 2016; 35:204-216. [PMID: 27461199 DOI: 10.1891/0730-0832.35.4.204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND The intestinal microbiota is important for optimal intestinal function and protection against infection. Disruption of the intestinal microbiota has been linked to necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). OBJECTIVES To determine what is known about the intestinal microbiota of very premature infants. We describe the relationship of the intestinal microbiota to NEC and LOS and provide an overview of the effect of environmental factors. METHODS A review was conducted using PubMed/MEDLINE from 2008 to 2015 to examine what is currently known about the intestinal microbiota of very premature infants. DISCUSSION The intestinal bacteria are low in diversity and generally contain a predominance of potentially pathogenic bacteria. Evidence suggests that these bacteria play a role in NEC as well as LOS through translocation. Environmental factors such as mode of delivery, use of antibiotics, and type of feeding may also contribute to the development of the intestinal microbiota.
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Affiliation(s)
- Melissa C Dollings
- Virginia Commonwealth University, 9631 Raven Wing Drive, Chesterfield, VA 23832, USA
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68
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Chen CH, Fu Y, Gao DW. Membrane biofouling process correlated to the microbial community succession in an A/O MBR. BIORESOURCE TECHNOLOGY 2015; 197:185-192. [PMID: 26340026 DOI: 10.1016/j.biortech.2015.08.092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
The microbial community succession of the biofouling layer in a submerged anoxic/oxic membrane biological reactor (A/O MBR) that fed with synthesized domestic wastewater was investigated under three different flux conditions without the changing of the nutrient load. The noticeable microbial community succession and its significant correlation with the metabolic products were observed under the subcritical flux condition. Under the supercritical flux condition, the microbial community shift was in a different pattern compared with that under the subcritical flux condition and it was affected by the increased permeable suction more than the metabolic products. The most abundant microorganisms in the foulants were β-proteobacteria and γ-proteobacteria which can reach more than 20% of the microbial community. However the microorganisms which had significant correlation with the metabolic products were in lower abundance.
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Affiliation(s)
- Chun-Hong Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yuan Fu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Da-Wen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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69
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Abstract
Within the last decade, research regarding the human gut microbiome has exploded. While the gastrointestinal tract was once regarded simply as a digestive organ, new technologies have led the science world to wonder about the impact that the gut microbiota may have on human health and disease. The gut microbiome is now becoming known for its role in metabolism, immune defense, and behavior. From in utero variations to those that rapidly occur post partum, our gut microbiome changes with age, environment, stress, diet, and health status as well as medication exposure. This article reviews what is currently known regarding various influences on the gut microbiome and is meant to encourage the reader to further explore the unknown.
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Affiliation(s)
- Gail A Cresci
- Department of Gastroenterology/Hepatology, Cleveland Clinic, Cleveland, Ohio
| | - Emmy Bawden
- Center for Human Nutrition, Cleveland Clinic, Cleveland, Ohio
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70
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Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015; 3:e1319. [PMID: 26500826 PMCID: PMC4614810 DOI: 10.7717/peerj.1319] [Citation(s) in RCA: 1011] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022] Open
Abstract
Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
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Affiliation(s)
- A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States ; Department of Medicine, The University of Chicago , Chicago, IL , United States
| | - Özcan C Esen
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Christopher Quince
- Warwick Medical School, University of Warwick , Coventry , United Kingdom
| | - Joseph H Vineis
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
| | - Tom O Delmont
- Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States
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71
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Elias JE. Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant's GI. Proteomics 2015; 15:3407-8. [PMID: 26384154 DOI: 10.1002/pmic.201500359] [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: 09/04/2015] [Accepted: 09/14/2015] [Indexed: 11/08/2022]
Abstract
Succession is a fundamental concept in ecology, describing the process by which pioneering species colonize a new environmental niche, paving the way for increasingly complex, yet stable ecosystems. The human gut-among the most complex ecosystems known-develops from a nearly sterile state as newborns to a thriving functional network of trillions of organisms living in concert with the host. Recent microbiome analyses have begun to characterize the identities of the microbes during this period of colonization. However, the biochemical processes that govern the stages of interorganism succession remains a poorly understood, yet exciting frontier. Toward the goal of learning how host-microbe symbiosis arises and is maintained, Young et al. (Proteomics 2015, 15, 3463-3473) present a longitudinal metaproteomic case study of an infant during her second and third weeks of life. In the first such analysis of its kind, Young et al. portray overlapping stages of protein production by both the microbiota and the host consistent with their increasing complexity, and deepening interactions.
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Affiliation(s)
- Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
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72
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Putting on the brakes: Bacterial impediment of wound healing. Sci Rep 2015; 5:14003. [PMID: 26365869 PMCID: PMC4650533 DOI: 10.1038/srep14003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/03/2015] [Indexed: 12/17/2022] Open
Abstract
The epithelium provides a crucial barrier to infection, and its integrity requires
efficient wound healing. Bacterial cells and secretomes from a subset of tested
species of bacteria inhibited human and porcine corneal epithelial cell migration
in vitro and ex vivo. Secretomes from 95% of Serratia
marcescens, 71% of Pseudomonas aeruginosa, 29% of Staphylococcus
aureus strains, and other bacterial species inhibited epithelial cell
migration. Migration of human foreskin fibroblasts was also inhibited by S.
marcescens secretomes indicating that the effect is not cornea specific.
Transposon mutagenesis implicated lipopolysaccharide (LPS) core biosynthetic genes
as being required to inhibit corneal epithelial cell migration. LPS depletion of
S. marcescens secretomes with polymyxin B agarose rendered secretomes
unable to inhibit epithelial cell migration. Purified LPS from S. marcescens,
but not from Escherichia coli or S. marcescens strains with mutations
in the waaG and waaC genes, inhibited epithelial cell migration in
vitro and wound healing ex vivo. Together these data suggest that
S. marcescens LPS is sufficient for inhibition of epithelial wound
healing. This study presents a novel host-pathogen interaction with implications for
infections where bacteria impact wound healing and provides evidence that secreted
LPS is a key factor in the inhibitory mechanism.
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73
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Gillings MR, Paulsen IT, Tetu SG. Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics. Genes (Basel) 2015; 6:841-57. [PMID: 26371047 PMCID: PMC4584332 DOI: 10.3390/genes6030841] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Abstract
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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74
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Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota and resistome. Curr Opin Microbiol 2015; 27:51-6. [PMID: 26241507 DOI: 10.1016/j.mib.2015.07.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/12/2015] [Indexed: 02/07/2023]
Abstract
The microbial communities colonizing the human gut are tremendously diverse and highly personal. The composition and function of the microbiota play important roles in human health and disease, and considerable research has focused on understanding the ecological forces shaping these communities. While it is clear that factors such as diet, genotype of the host, and environment influence the adult gut microbiota community composition, recent work has emphasized the importance of early-life assembly dynamics in both the immediate and long-term personalized nature of the gut microbiota. While the mature adult gut microbiota is believed to be relatively stable, the developing infant gut microbiota (IGM) is highly dynamic and prone to disruption by external factors, including antibiotic exposure. Studies have revealed both transient and persistent alterations to the adult gut microbiota community resulting from antibiotic treatment later in life. As antibiotics are routinely prescribed at a greater rate in the first years of life, the impact of these interventions on the developing IGM is emerging as a key research priority. In addition to understanding the impact of these disruptions on the infant gut microbial architecture and related host diseases, we need to understand the contribution of early life antibiotics to the selection of antibiotic resistance gene reservoirs in the microbiota, and their threat to successful treatment of infectious disease. Here we review the current understanding of the developmental progression of the IGM and the impact of antibiotic therapies on its composition and encoded reservoir of antibiotic resistance genes.
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Affiliation(s)
- Molly K Gibson
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Terence S Crofts
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA; Department of Biomedical Engineering, Washington University, St Louis, MO, USA.
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75
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Young JC, Pan C, Adams RM, Brooks B, Banfield JF, Morowitz MJ, Hettich RL. Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics 2015; 15:3463-73. [PMID: 26077811 DOI: 10.1002/pmic.201400563] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/27/2015] [Accepted: 06/11/2015] [Indexed: 01/01/2023]
Abstract
Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. To this end, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data. More specifically, the function of the microbial community initially involved biomass growth, protein production, and lipid metabolism, and then switched to more complex metabolic functions, such as carbohydrate metabolism, once the community stabilized and matured. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Likewise, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. This study provides the first snapshot of coordinated human and microbial protein expression in a preterm infant's gut during early development.
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Affiliation(s)
- Jacque C Young
- Genome Sciences and Technology Graduate School, University of Tennessee, Knoxville, TN, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rachel M Adams
- Genome Sciences and Technology Graduate School, University of Tennessee, Knoxville, TN, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Brandon Brooks
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Michael J Morowitz
- Division of Pediatric General & Thoracic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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76
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Mandal RS, Saha S, Das S. Metagenomic surveys of gut microbiota. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:148-58. [PMID: 26184859 PMCID: PMC4563348 DOI: 10.1016/j.gpb.2015.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 01/21/2023]
Abstract
Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.
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Affiliation(s)
- Rahul Shubhra Mandal
- Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
| | - Santasabuj Das
- Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India; Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India.
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77
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Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol 2015; 6:654. [PMID: 26191049 PMCID: PMC4487087 DOI: 10.3389/fmicb.2015.00654] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.
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Affiliation(s)
- Brandon Brooks
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
| | - Ryan S. Mueller
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
- Department of Microbiology, Oregon State UniversityCorvallis, OR, USA
| | - Jacque C. Young
- Department of Genome Sciences and Technology, The University of Tennessee, KnoxvilleKnoxville, TN, USA
- Chemical Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of MedicinePittsburgh, PA, USA
| | - Robert L. Hettich
- Department of Genome Sciences and Technology, The University of Tennessee, KnoxvilleKnoxville, TN, USA
- Chemical Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
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78
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Lim JC, Golden JM, Ford HR. Pathogenesis of neonatal necrotizing enterocolitis. Pediatr Surg Int 2015; 31:509-18. [PMID: 25854935 DOI: 10.1007/s00383-015-3697-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 12/22/2022]
Abstract
Although necrotizing enterocolitis (NEC) is the most lethal gastrointestinal disease in the neonatal population, its pathogenesis is poorly understood. Risk factors include prematurity, bacterial colonization, and formula feeding. This review examines how mucosal injury permits opportunistic pathogens to breach the gut barrier and incite an inflammatory response that leads to sustained overproduction of mediators such as nitric oxide and its potent adduct, peroxynitrite. These mediators not only exacerbate the initial mucosal injury, but they also suppress the intestinal repair mechanisms, which further compromises the gut barrier and culminates in bacterial translocation, sepsis, and full-blown NEC.
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Affiliation(s)
- Joanna C Lim
- Division of Pediatric Surgery, Children's Hospital Los Angeles, 4650 Sunset Blvd., Mailstop #72, Los Angeles, CA, 90027, USA
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79
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McKenney EA, Rodrigo A, Yoder AD. Patterns of gut bacterial colonization in three primate species. PLoS One 2015; 10:e0124618. [PMID: 25970595 PMCID: PMC4430486 DOI: 10.1371/journal.pone.0124618] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/03/2015] [Indexed: 01/15/2023] Open
Abstract
Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.
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Affiliation(s)
- Erin A. McKenney
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Allen Rodrigo
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Duke Lemur Center, Duke University, Durham, North Carolina, United States of America
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80
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Peterson CT, Sharma V, Elmén L, Peterson SN. Immune homeostasis, dysbiosis and therapeutic modulation of the gut microbiota. Clin Exp Immunol 2015; 179:363-77. [PMID: 25345825 DOI: 10.1111/cei.12474] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2014] [Indexed: 02/07/2023] Open
Abstract
The distal gut harbours ∼10(13) bacteria, representing the most densely populated ecosystem known. The functional diversity expressed by these communities is enormous and relatively unexplored. The past decade of research has unveiled the profound influence that the resident microbial populations bestow to host immunity and metabolism. The evolution of these communities from birth generates a highly adapted and highly personalized microbiota that is stable in healthy individuals. Immune homeostasis is achieved and maintained due in part to the extensive interplay between the gut microbiota and host mucosal immune system. Imbalances of gut microbiota may lead to a number of pathologies such as obesity, type I and type II diabetes, inflammatory bowel disease (IBD), colorectal cancer (CRC) and inflammaging/immunosenscence in the elderly. In-depth understanding of the underlying mechanisms that control homeostasis and dysbiosis of the gut microbiota represents an important step in our ability to reliably modulate the gut microbiota with positive clinical outcomes. The potential of microbiome-based therapeutics to treat epidemic human disease is of great interest. New therapeutic paradigms, including second-generation personalized probiotics, prebiotics, narrow spectrum antibiotic treatment and faecal microbiome transplantation, may provide safer and natural alternatives to traditional clinical interventions for chronic diseases. This review discusses host-microbiota homeostasis, consequences of its perturbation and the associated challenges in therapeutic developments that lie ahead.
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Affiliation(s)
- C T Peterson
- The George Washington University, The Institute for Biomedical Sciences, The School of Medicine & Health Sciences, Washington, DC
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81
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Abstract
The current genomic revolution was made possible by joint advances in genome sequencing technologies and computational approaches for analyzing sequence data. The close interaction between biologists and computational scientists is perhaps most apparent in the development of approaches for sequencing entire genomes, a feat that would not be possible without sophisticated computational tools called genome assemblers (short for genome sequence assemblers). Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago.
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Affiliation(s)
- Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
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82
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Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 2015; 21:427-32. [PMID: 25907678 DOI: 10.1016/j.molmed.2015.03.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/23/2022]
Abstract
The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.
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83
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Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. PLoS One 2015; 10:e0118632. [PMID: 25741698 PMCID: PMC4351051 DOI: 10.1371/journal.pone.0118632] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/21/2014] [Indexed: 12/25/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is an inflammatory disease of the newborn bowel, primarily affecting premature infants. Early intestinal colonization has been implicated in the pathogenesis of NEC. The objective of this prospective case-control study was to evaluate differences in the intestinal microbiota between infants who developed NEC and unaffected controls prior to disease onset. We conducted longitudinal analysis of the 16S rRNA genes of 312 samples obtained from 12 NEC cases and 26 age-matched controls with a median frequency of 7 samples per subject and median sampling interval of 3 days. We found that the microbiome undergoes dynamic development during the first two months of life with day of life being the major factor contributing to the colonization process. Depending on when the infant was diagnosed with NEC (i.e. early vs. late onset), the pattern of microbial progression was different for cases and controls. The difference in the microbiota was most overt in early onset NEC cases and controls. In proximity to NEC onset, the abundances of Clostridium sensu stricto from Clostridia class were significantly higher in early onset NEC subjects comparing to controls. In late onset NEC, Escherichia/Shigella among Gammaproteobacteria, showed an increasing pattern prior to disease onset, and was significantly higher in cases than controls six days before NEC onset. Cronobacter from Gammaproteobacteria was also significantly higher in late onset NEC cases than controls 1-3 days prior to NEC onset. Thus, the specific infectious agent associated with NEC may vary by the age of infant at disease onset. We found that intravenously administered antibiotics may have an impact on the microbial diversity present in fecal material. Longitudinal analysis at multiple time points was an important strategy utilized in this study, allowing us to appreciate the dynamics of the premature infant intestinal microbiome while approaching NEC at various points.
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84
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Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. mBio 2015; 6:mBio.02419-14. [PMID: 25650398 PMCID: PMC4323417 DOI: 10.1128/mbio.02419-14] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED We found that the relatively simple microbiota of young infants shifts predictably to a more mature anaerobic microbiota during infancy and the dynamics of this shift are influenced by environmental factors. In this longitudinal study of 75 infants, we demonstrate high interindividual variability within the normal range of birth outcomes, especially in the rate of microbiota progression. Most had acquired a microbiota profile high in Bifidobacterium and Collinsella by 6 months of age, but the time point of this acquisition was later in infants delivered by caesarean section and those born after a shorter duration of gestation. Independently of the delivery mode and gestation duration, infants who acquired a profile high in Bifidobacterium and Collinsella at a later age had lower adiposity at 18 months of age. IMPORTANCE This study shows that the acquisition of the early microbiota is strongly influenced by environmental factors such as the delivery mode and duration of gestation, even in healthy neonates. The composition of the early microbiota has been linked with long-lasting effects on health and disease. Here we show that the rate of acquisition of certain microbiota predicts adiposity at 18 months of age and so potentially the risk of later obesity.
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85
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Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell 2015; 160:583-594. [PMID: 25640238 DOI: 10.1016/j.cell.2014.12.038] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/30/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
Abstract
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.
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Affiliation(s)
- Sharon Greenblum
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rogan Carr
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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86
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Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJ, Orlando L, Willerslev E. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130383. [PMID: 25487334 PMCID: PMC4275890 DOI: 10.1098/rstb.2013.0383] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Affiliation(s)
- Mikkel Winther Pedersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Søren Overballe-Petersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - James Haile
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Trace and Environmental DNA Laboratory, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Micaela Hellstrom
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Johan Spens
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Department of Wildlife, Fish and Environmental Studies, SLU, Umeå S-901 83, Sweden
| | - Philip Francis Thomsen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Kristine Bohmann
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Enrico Cappellini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ida Bærholm Schnell
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nathan A Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Astrid M Z Schmidt
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
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87
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Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res 2015; 37:223-36. [PMID: 26695747 PMCID: PMC4590619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The excessive use of alcohol is a global problem causing many adverse pathological health effects and a significant financial health care burden. This review addresses the effect of alcohol consumption on the microbiota in the gastrointestinal tract (GIT). Although data are limited in humans, studies highlight the importance of changes in the intestinal microbiota in alcohol-related disorders. Alcohol-induced changes in the GIT microbiota composition and metabolic function may contribute to the well-established link between alcohol-induced oxidative stress, intestinal hyperpermeability to luminal bacterial products, and the subsequent development of alcoholic liver disease (ALD), as well as other diseases. In addition, clinical and preclinical data suggest that alcohol-related disorders are associated with quantitative and qualitative dysbiotic changes in the intestinal microbiota and may be associated with increased GIT inflammation, intestinal hyperpermeability resulting in endotoxemia, systemic inflammation, and tissue damage/organ pathologies including ALD. Thus, gut-directed interventions, such as probiotic and synbiotic modulation of the intestinal microbiota, should be considered and evaluated for prevention and treatment of alcohol-associated pathologies.
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88
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Abstract
The microbiome, of which the bacterial component alone (microbiota), is estimated to include 10 times more cells than human cells of the body, blooms immediately after birth and evolves in composition and complexity throughout childhood. The gut microbiome has a profound impact on gastrointestinal tract development, maintenance of mucosal surface integrity, and contributes to the nutritional status of the host and thus plays a pivotal role in health and disease. New technologies have enabled the detailed characterization of normal microbial symbionts and dysbiosis-disease associations. This review summarizes the stepwise establishment of the intestinal microbiota, influential environmental factors, and how this may be perturbed in preterm very-low-birth-weight infants. The contribution of the microbiota to provision of energy and nutrients for intestinal development and the nutritional status of the host are reviewed. In addition, the crucial role of the gut microbiota in maintaining mucosal integrity is explored along with how its breakdown can lead to sepsis, necrotizing enterocolitis, and systemic inflammatory response syndrome. Finally, the role of enteral feeding type (human milk, formula, and nutrient fortification) in mediating these processes is discussed, and guidance is provided for nutritional strategies to promote health in these fragile infants.
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89
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Aujoulat F, Roudière L, Picaud JC, Jacquot A, Filleron A, Neveu D, Baum TP, Marchandin H, Jumas-Bilak E. Temporal dynamics of the very premature infant gut dominant microbiota. BMC Microbiol 2014; 14:325. [PMID: 25551282 PMCID: PMC4326509 DOI: 10.1186/s12866-014-0325-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 12/11/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of high-throughput studies validate and renew the interest in approaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-up of dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in very preterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routine monitoring from the 1(st) to the 8(th) week of life in 30 very pre-term infants born before 30 weeks of gestational age. RESULTS Combining comparison with a diversity ladder and sequencing allowed affiliation of 50 Species-Level Operational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs). Coagulase-negative staphylococci, mainly the Staphylococcus epidermidis, was found in all the infants during the study period and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% of the infants were early, highly represented and persistent colonizers of the premature gut. Later Enterobacteriaceae and the genus Clostridium appeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a high representation of Veillonella in more than a quarter of the infants and being able to persistently colonize premature gut. The genera Anaerococcus, Aquabacterium, Bacillus, Bifidobacterium, Corynebacterium, Micrococcus, Oceanobacillus, Propionibacterium, Pseudomonas, Rothia, Sarcina, Sneathia and Streptococcus were observed as transient or persistent colonizers, each genus being found in a minority of infants. CONCLUSIONS Despite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-based approaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts of preterm neonates. We described the development of pre-term gut microbiota that should be now replaced regarding the functional role of major OTUs.
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Affiliation(s)
- Fabien Aujoulat
- Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France.
| | - Laurent Roudière
- Centre Hospitalier de Fréjus, Laboratoire de bactériologie, 240 avenue de Saint-Lambert BP 110 83608, Fréjus, France.
| | - Jean-Charles Picaud
- Hospices Civil de Lyon, Service de Néonatalogie, 103, Grande-Rue de la Croix-Rousse, Lyon, Cedex 04, 69317, France.
| | - Aurélien Jacquot
- Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Lapeyronie, Département Urgences pédiatriques, 371, Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France.
| | - Anne Filleron
- Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. .,Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Service de néo-natalogie, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France.
| | - Dorine Neveu
- Centre Hospitalier Universitaire de Montpellier, Département d'Information Médicale, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France.
| | - Thierry-Pascal Baum
- Centre Hospitalier Universitaire de Montpellier, Département d'Information Médicale, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France.
| | - Hélène Marchandin
- Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. .,Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France.
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. .,Centre Hospitalier Universitaire de Montpellier, Laboratoire d'Hygiène hospitalière, 778, Rue de la Croix Verte, Montpellier, 34000, France.
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90
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McKENNEY EA, ASHWELL M, LAMBERT JE, FELLNER V. Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong). Integr Zool 2014; 9:557-69. [DOI: 10.1111/1749-4877.12112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erin A. McKENNEY
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
| | - Melissa ASHWELL
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
| | - Joanna E. LAMBERT
- Department of Anthropology; The University of Texas at San Antonio; Texas USA
| | - Vivek FELLNER
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
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91
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Xiong W, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL. Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J Proteome Res 2014; 14:133-41. [PMID: 25350865 PMCID: PMC4286196 DOI: 10.1021/pr500936p] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The establishment of early life microbiota
in the human infant
gut is highly variable and plays a crucial role in host nutrient availability/uptake
and maturation of immunity. Although high-performance mass spectrometry
(MS)-based metaproteomics is a powerful method for the functional
characterization of complex microbial communities, the acquisition
of comprehensive metaproteomic information in human fecal samples
is inhibited by the presence of abundant human proteins. To alleviate
this restriction, we have designed a novel metaproteomic strategy
based on double filtering (DF) the raw samples, a method that fractionates
microbial from human cells to enhance microbial protein identification
and characterization in complex fecal samples from healthy premature
infants. This method dramatically improved the overall depth of infant
gut proteome measurement, with an increase in the number of identified
low-abundance proteins and a greater than 2-fold improvement in microbial
protein identification and quantification. This enhancement of proteome
measurement depth enabled a more extensive microbiome comparison between
infants by not only increasing the confidence of identified microbial
functional categories but also revealing previously undetected categories.
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Affiliation(s)
- Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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92
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Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Microbiol Insights 2014; 7:25-34. [PMID: 25452698 PMCID: PMC4230230 DOI: 10.4137/mbi.s18076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/18/2014] [Accepted: 08/26/2014] [Indexed: 12/21/2022] Open
Abstract
The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.
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Affiliation(s)
- Raphael D Isokpehi
- Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA
| | - Udensi K Udensi
- RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson, MS, USA
| | - Shaneka S Simmons
- Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Computer Science, Jackson State University, Jackson, MS, USA
| | | | - Antia E Cain
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Samson A Olofinsae
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Oluwabukola A Hassan
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Zainab A Kashim
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Ojochenemi A Enejoh
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Deborah E Fasesan
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
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93
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Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell 2014; 158:250-262. [PMID: 25036628 DOI: 10.1016/j.cell.2014.06.037] [Citation(s) in RCA: 459] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/03/2014] [Accepted: 06/27/2014] [Indexed: 12/11/2022]
Abstract
Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.
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Affiliation(s)
- Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Angela C Poole
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Omry Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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94
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Abstract
Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.
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Affiliation(s)
- Lauren Bragg
- Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD, Australia
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95
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Engel P, Stepanauskas R, Moran NA. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genet 2014; 10:e1004596. [PMID: 25210772 PMCID: PMC4161309 DOI: 10.1371/journal.pgen.1004596] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/02/2014] [Indexed: 12/29/2022] Open
Abstract
Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification. Gut microbial communities are often complex, consisting of bacteria from divergent phyla as well as multiple strains of each of the constituent species. But because the composition of these communities is typically assessed using 16S rRNA analyses, little is known about genomic changes associated with in situ diversification of bacterial lineages in animal guts. We undertook a single-cell genomic approach to investigate the diversification within two species of the gut microbiota of honey bees. Each species exhibited a surprisingly high level of genomic variation, despite uniformity in the 16S rRNA sequences. Our data indicate that genetically and ecologically distinct lineages can evolve in the gut of the same host species in the presence of frequent recombination at 16S rRNA genes. These findings parallel observations from mammals, suggesting that in situ diversification of a few bacterial lineages is a common pattern in the evolution of gut communities.
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Affiliation(s)
- Philipp Engel
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Nancy A. Moran
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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96
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Biotic interactions and temporal dynamics of the human gastrointestinal microbiota. ISME JOURNAL 2014; 9:533-41. [PMID: 25148482 DOI: 10.1038/ismej.2014.147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
The human gastrointestinal (GI) microbiota is important to human health and imbalances or shifts in the gut microbial community have been linked to many diseases. Most studies of the GI microbiota only capture snapshots of this dynamic community at one or a few time points. Although this is valuable in terms of providing knowledge of community composition and variability between individuals, it does not provide the foundation for going beyond descriptive studies and toward truly predictive ecological models. In order to achieve this goal, we need longitudinal data of appropriate temporal and taxonomic resolution, so that established time series analysis tools for identifying and quantifying putative interactions among community members can be used. Here, we present new analyses of existing data to illustrate the potential usefulness of this approach. We discuss challenges related to sampling and data processing, as well as analytical approaches and considerations for future studies of the GI microbiota and other complex microbial systems.
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97
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Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci U S A 2014; 111:12522-7. [PMID: 25114261 DOI: 10.1073/pnas.1409497111] [Citation(s) in RCA: 380] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In the weeks after birth, the gut acquires a nascent microbiome, and starts its transition to bacterial population equilibrium. This early-in-life microbial population quite likely influences later-in-life host biology. However, we know little about the governance of community development: does the gut serve as a passive incubator where the first organisms randomly encountered gain entry and predominate, or is there an orderly progression of members joining the community of bacteria? We used fine interval enumeration of microbes in stools from multiple subjects to answer this question. We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia, interrupted by abrupt population changes. As infants approach 33-36 wk postconceptional age (corresponding to the third to the twelfth weeks of life depending on gestational age at birth), the gut is well colonized by anaerobes. Antibiotics, vaginal vs. Caesarian birth, diet, and age of the infants when sampled influence the pace, but not the sequence, of progression. Our results suggest that in infants in a microbiologically constrained ecosphere of a neonatal intensive care unit, gut bacterial communities have an overall nonrandom assembly that is punctuated by microbial population abruptions. The possibility that the pace of this assembly depends more on host biology (chiefly gestational age at birth) than identifiable exogenous factors warrants further consideration.
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98
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Food Omics Validation: Towards Understanding Key Features for Gut Microbiota, Probiotics and Human Health. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9923-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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99
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Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, Newburg DS, Ward DV, Schibler KR. Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter. J Pediatr 2014; 165:23-9. [PMID: 24529620 PMCID: PMC4074569 DOI: 10.1016/j.jpeds.2014.01.010] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/08/2013] [Accepted: 01/06/2014] [Indexed: 12/26/2022]
Abstract
OBJECTIVES To determine the impact of empiric ampicillin and gentamicin use in the first week of life on microbial colonization and diversity in preterm infants. STUDY DESIGN The 16s ribosomal DNA community profiling was used to compare the microbiota of 74 infants born ≤32 weeks gestational age by degree of antibiotic use in the first week of life. The degree of antibiotic use was classified as 0 days, 1-4 days, and 5-7 days of antibiotic administration. All of the antibiotic use was empiric, defined as treatment based solely on clinical suspicion of infection without a positive culture result. RESULTS Infants who received 5-7 days of empiric antimicrobial agents in the first week had increased relative abundance of Enterobacter (P = .016) and lower bacterial diversity in the second and third weeks of life. Infants receiving early antibiotics also experienced more cases of necrotizing enterocolitis, sepsis, or death than those not exposed to antibiotics. CONCLUSIONS Early empiric antibiotics have sustained effects on the intestinal microbiota of preterm infants. Intestinal dysbiosis in this population has been found to be associated with elevated risk of necrotizing enterocolitis, sepsis, or death.
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Affiliation(s)
- Corryn Greenwood
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Division of Neonatology, Advocate Children's Hospital, Oak Lawn, IL
| | - Ardythe L Morrow
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH; Division of Biostatistics and Epidemiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Anne J Lagomarcino
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Mekibib Altaye
- Division of Biostatistics and Epidemiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Diana H Taft
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Zhuoteng Yu
- Department of Biology, Boston College, Chestnut Hill, MA
| | | | | | - Kurt R Schibler
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.
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100
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Abraham PE, Giannone RJ, Xiong W, Hettich RL. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities. ACTA ACUST UNITED AC 2014; 46:13.26.1-13.26.14. [PMID: 24939130 DOI: 10.1002/0471250953.bi1326s46] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.
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Affiliation(s)
- Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
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