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61. J Allergy Clin Immunol. 2015 Apr;135(4):905-12.e11. doi:

10.1016/j.jaci.2014.12.1909. Epub 2015 Jan 27.

 

Dynamics of the nasal microbiota in infancy: a prospective cohort study.

 

Mika M(1), Mack I(2), Korten I(3), Qi W(4), Aebi S(5), Frey U(6), Latzin P(2),

Hilty M(7).

 

Author information:

(1)Institute for Infectious Diseases, University of Bern, Bern, Switzerland;

Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern,

Switzerland. (2)Division of Respiratory Medicine, Department of Pediatrics,

Inselspital and University of Bern, Bern, Switzerland; University Children's

Hospital (UKBB), Basel, Switzerland. (3)Graduate School for Cellular and

Biomedical Sciences, University of Bern, Bern, Switzerland; Division of

Respiratory Medicine, Department of Pediatrics, Inselspital and University of

Bern, Bern, Switzerland. (4)Functional Genomics Center, Swiss Federal Institute

of Technology Zurich/University of Zurich, Zurich, Switzerland. (5)Institute for

Infectious Diseases, University of Bern, Bern, Switzerland. (6)University

Children's Hospital (UKBB), Basel, Switzerland. (7)Institute for Infectious

Diseases, University of Bern, Bern, Switzerland; Department of Infectious

Diseases, University Hospital, Bern, Switzerland. Electronic address:

markus.hilty@ifik.unibe.ch.

 

BACKGROUND: Understanding the composition and dynamics of the upper respiratory

tract microbiota in healthy infants is a prerequisite to investigate the role of

the microbiota in patients with respiratory diseases. This is especially true in

early life, when the immune system is in development.

OBJECTIVE: We sought to describe the dynamics of the upper respiratory tract

microbiota in healthy infants within the first year of life.

METHODS: After exclusion of low-quality samples, microbiota characterization was

performed by using 16S rDNA pyrosequencing of 872 nasal swabs collected biweekly

from 47 unselected infants.

RESULTS: Bacterial density increased and diversity decreased within the first

year of life (R(2) = 0.95 and 0.73, respectively). A distinct profile for the

first 3 months of life was found with increased relative abundances of

Staphlyococcaceae and Corynebacteriaceae (exponential decay: R(2) = 0.94 and

0.96, respectively). In addition, relative bacterial abundance and composition

differed significantly from summer to winter months. The individual composition

of the microbiota changed with increasing time intervals between samples and was

best modeled by an exponential function (R(2) = 0.97). Within-subject

dissimilarity in a 2-week time interval was consistently lower than that between

subjects, indicating a personalized microbiota.

CONCLUSION: This study reveals age and seasonality as major factors driving the

composition of the nasal microbiota within the first year of life. A subject's

microbiota is personalized but dynamic throughout the first year. These data are

indispensable to interpretation of cross-sectional studies and investigation of

the role of the microbiota in both healthy subjects and patients with respiratory

diseases. They might also serve as a baseline for future intervention studies.

 

Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

 

DOI: 10.1016/j.jaci.2014.12.1909

PMID: 25636948  [PubMed - indexed for MEDLINE]

 

 

62. Gastroenterology. 2014 May;146(6):1437-1448.e1. doi:

10.1053/j.gastro.2014.01.049. Epub 2014 Jan 28.

 

Meta'omic analytic techniques for studying the intestinal microbiome.

 

Morgan XC(1), Huttenhower C(2).

 

Author information:

(1)Department of Biostatistics, Harvard School of Public Health, Boston,

Massachusetts; The Broad Institute of Harvard and Massachusetts Institute of

Technology, Cambridge, Massachusetts. (2)Department of Biostatistics, Harvard

School of Public Health, Boston, Massachusetts; The Broad Institute of Harvard

and Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic

address: chuttenh@hsph.harvard.edu.

 

Nucleotide sequencing has become increasingly common and affordable, and is now a

vital tool for studies of the human microbiome. Comprehensive microbial community

surveys such as MetaHit and the Human Microbiome Project have described the

composition and molecular functional profile of the healthy (normal) intestinal

microbiome. This knowledge will increase our ability to analyze host and

microbial DNA (genome) and RNA (transcriptome) sequences. Bioinformatic and

statistical tools then can be used to identify dysbioses that might cause

disease, and potential treatments. Analyses that identify perturbations in

specific molecules can leverage thousands of culture-based isolate genomes to

contextualize culture-independent sequences, or may integrate sequence data with

whole-community functional assays such as metaproteomic or metabolomic analyses.

We review the state of available systems-level models for studies of the

intestinal microbiome, along with analytic techniques and tools that can be used

to determine its functional capabilities in healthy and unhealthy individuals.

 

Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

 

DOI: 10.1053/j.gastro.2014.01.049

PMID: 24486053  [PubMed - indexed for MEDLINE]

 

 

63. Genome Biol. 2015 Apr 8;16:67. doi: 10.1186/s13059-015-0637-x.

 

Associations between host gene expression, the mucosal microbiome, and clinical

outcome in the pelvic pouch of patients with inflammatory bowel disease.

 

Morgan XC(1,)(2), Kabakchiev B(3), Waldron L(4,)(5), Tyler AD(6), Tickle

TL(7,)(8), Milgrom R(9), Stempak JM(10), Gevers D(11), Xavier RJ(12), Silverberg

MS(13), Huttenhower C(14,)(15).

 

Author information:

(1)Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655

Huntington Ave, Boston, MA, 02115, USA. xmorgan@hsph.harvard.edu. (2)The Broad

Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.

xmorgan@hsph.harvard.edu. (3)Mount Sinai Hospital, Zane Cohen Centre for

Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G

1X5, Canada. btk2102@gmail.com. (4)Department of Biostatistics, Harvard T. H.

Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.

levi.waldron@hunter.cuny.edu. (5)City University of New York School of Public

Health, Hunter College, 2180 3rd Ave Rm 538, New York, NY, 10035-4003, USA.

levi.waldron@hunter.cuny.edu. (6)Mount Sinai Hospital, Zane Cohen Centre for

Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G

1X5, Canada. atyler@mtsinai.on.ca. (7)Department of Biostatistics, Harvard T. H.

Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.

timothyltickle@gmail.com. (8)The Broad Institute of MIT and Harvard, 415 Main St,

Cambridge, MA, 02142, USA. timothyltickle@gmail.com. (9)Mount Sinai Hospital,

Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University

Ave, Toronto, ON, M5G 1X5, Canada. rmilgrom@mtsinai.on.ca. (10)Mount Sinai

Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600

University Ave, Toronto, ON, M5G 1X5, Canada. jstempak@mtsinai.on.ca. (11)The

Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.

dgevers@broadinstitute.org. (12)The Broad Institute of MIT and Harvard, 415 Main

St, Cambridge, MA, 02142, USA. xavier@molbio.mgh.harvard.edu. (13)Mount Sinai

Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600

University Ave, Toronto, ON, M5G 1X5, Canada. msilverberg@mtsinai.on.ca.

(14)Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655

Huntington Ave, Boston, MA, 02115, USA. chuttenh@hsph.harvard.edu. (15)The Broad

Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.

chuttenh@hsph.harvard.edu.

 

BACKGROUND: Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery

for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both

host genetics and the microbiota are implicated in its pathogenesis. We use the

IPAA model of IBD to associate mucosal host gene expression with mucosal

microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S

rRNA gene sequencing data from paired biopsies from IPAA patients with UC and

familial adenomatous polyposis. To achieve power for a genome-wide

microbiome-transcriptome association study, we use principal component analysis

for transcript and clade reduction, and identify significant co-variation between

clades and transcripts.

RESULTS: Host transcripts co-vary primarily with biopsy location and

inflammation, while microbes co-vary primarily with antibiotic use.

Transcript-microbe associations are surprisingly modest, but the most strongly

microbially-associated host transcript pattern is enriched for complement cascade

genes and for the interleukin-12 pathway. Activation of these host processes is

inversely correlated with Sutterella, Akkermansia, Bifidobacteria, and Roseburia

abundance, and positively correlated with Escherichia abundance.

CONCLUSIONS: This study quantifies the effects of inflammation, antibiotic use,

and biopsy location upon the microbiome and host transcriptome during pouchitis.

Understanding these effects is essential for basic biological insights as well as

for well-designed and adequately-powered studies. Additionally, our study

provides a method for profiling host-microbe interactions with appropriate

statistical power using high-throughput sequencing, and suggests that

cross-sectional changes in gut epithelial transcription are not a major component

of the host-microbiome regulatory interface during pouchitis.

 

DOI: 10.1186/s13059-015-0637-x

PMCID: PMC4414286

PMID: 25887922  [PubMed - indexed for MEDLINE]

 

 

64. PLoS One. 2015 Dec 3;10(12):e0144448. doi: 10.1371/journal.pone.0144448.

eCollection 2015.

 

Functional Metagenomics of the Bronchial Microbiome in COPD.

 

Millares L(1,)(2,)(3,)(4), Pérez-Brocal V(5,)(6,)(7), Ferrari R(5,)(6,)(7),

Gallego M(8), Pomares X(2,)(8), García-Núñez M(1,)(2,)(3,)(4), Montón C(2,)(8),

Capilla S(9), Monsó E(2,)(3,)(8), Moya A(5,)(6,)(7).

 

Author information:

(1)Fundació Parc Taulí, Sabadell, Spain. (2)CIBER de Enfermedades Respiratorias,

CIBERES, Bunyola, Spain. (3)Universitat Autònoma de Barcelona, Esfera UAB,

Barcelona, Spain. (4)Fundació Insitut d'Investigació Germans Trias i Pujol,

Badalona, Spain. (5)Genomics and Health Area, Fundación para el Fomento de la

Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public

Health), Valencia, Spain. (6)CIBER Epidemiología y Salud Pública (CIBERESP),

Barcelona, Spain. (7)Evolutionary Genetics Unit, Institut Cavanilles de

Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia,

Spain. (8)Department of Respiratory Medicine, Hospital Universitari Parc Taulí,

Sabadell, Spain. (9)Department of Microbiology, Hospital Universitari Parc Taulí,

Sabadell, Spain.

 

The course of chronic obstructive pulmonary disease (COPD) is frequently

aggravated by exacerbations, and changes in the composition and activity of the

microbiome may be implicated in their appearance. The aim of this study was to

analyse the composition and the gene content of the microbial community in

bronchial secretions of COPD patients in both stability and exacerbation.

Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing,

and metabolic information through shotgun metagenomics, using the Metagenomics

RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities

by Reconstruction of Unobserved States) programme, which predict metagenomes from

16S data. Eight severe COPD patients provided good quality sputum samples, and no

significant differences in the relative abundance of any phyla and genera were

found between stability and exacerbation. Bacterial biodiversity (Chao1 and

Shannon indexes) did not show statistical differences and beta-diversity analysis

(Bray-Curtis dissimilarity index) showed a similar microbial composition in the

two clinical situations. Four functional categories showed statistically

significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell

growth and Death and Transport and Catabolism decreased in abundance [1.6

(0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p =

0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8

(0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012

respectively]. In conclusion, the bronchial microbiome as a whole is not

significantly modified when exacerbation symptoms appear in severe COPD patients,

but its functional metabolic capabilities show significant changes in several

pathways.

 

DOI: 10.1371/journal.pone.0144448

PMCID: PMC4669145

PMID: 26632844  [PubMed - indexed for MEDLINE]

 

 

65. PLoS One. 2016 May 12;11(5):e0155362. doi: 10.1371/journal.pone.0155362.

eCollection 2016.

 

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome

Shotgun Sequencing.

 

Vogtmann E(1,)(2), Hua X(1), Zeller G(3), Sunagawa S(3), Voigt AY(3,)(4,)(5,)(6),

Hercog R(7), Goedert JJ(1), Shi J(1), Bork P(3,)(6,)(8,)(9), Sinha R(1).

 

Author information:

(1)Division of Cancer Epidemiology & Genetics, National Cancer Institute,

Bethesda, Maryland, United States of America. (2)Division of Cancer Prevention,

National Cancer Institute, Bethesda, Maryland, United States of America.

(3)Structural and Computational Biology Unit, European Molecular Biology

Laboratory, Heidelberg, Germany. (4)Department of Applied Tumor Biology,

Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.

(5)Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center

(DKFZ), Heidelberg, Germany. (6)Molecular Medicine Partnership Unit (MMPU),

University Hospital Heidelberg and European Molecular Biology Laboratory,

Heidelberg, Germany. (7)Genomics Core Facility, European Molecular Biology

Laboratory, Heidelberg, Germany. (8)Max Delbrück Centre for Molecular Medicine,

Berlin, Germany. (9)Department of Bioinformatics Biocenter, University of

Würzburg, Würzburg, Germany.

 

Accumulating evidence indicates that the gut microbiota affects colorectal cancer

development, but previous studies have varied in population, technical methods,

and associations with cancer. Understanding these variations is needed for

comparisons and for potential pooling across studies. Therefore, we performed

whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal

cancer cases and 52 matched controls from Washington, DC. We compared findings

from a previously published 16S rRNA study to the metagenomics-derived taxonomy

within the same population. In addition, metagenome-predicted genes, modules, and

pathways in the Washington, DC cases and controls were compared to cases and

controls recruited in France whose specimens were processed using the same

platform. Associations between the presence of fecal Fusobacteria, Fusobacterium,

and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by

metagenomics, whereas higher relative abundance of Clostridia in cancer cases

based on 16S rRNA was merely borderline based on metagenomics. This demonstrated

that within the same sample set, most, but not all taxonomic associations were

seen with both methods. Considering significant cancer associations with the

relative abundance of genes, modules, and pathways in a recently published French

metagenomics dataset, statistically significant associations in the Washington,

DC population were detected for four out of 10 genes, three out of nine modules,

and seven out of 17 pathways. In total, colorectal cancer status in the

Washington, DC study was associated with 39% of the metagenome-predicted genes,

modules, and pathways identified in the French study. More within and between

population comparisons are needed to identify sources of variation and disease

associations that can be reproduced despite these variations. Future studies

should have larger sample sizes or pool data across studies to have sufficient

power to detect associations that are reproducible and significant after

correction for multiple testing.

 

DOI: 10.1371/journal.pone.0155362

PMCID: PMC4865240

PMID: 27171425  [PubMed - in process]

 

 

61.

Front Med (Lausanne). 2016 Jun 13;3:22. doi: 10.3389/fmed.2016.00022. eCollection 2016.

Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome.

Schiff SJ1, Kiwanuka J2, Riggio G3, Nguyen L4, Mu K3, Sproul E3, Bazira J5, Mwanga-Amumpaire J6, Tumusiime D2, Nyesigire E2, Lwanga N5, Bogale KT7, Kapur V8, Broach JR9, Morton SU10, Warf BC11, Poss M3.

Author information

Abstract

Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.

KEYWORDS:

16S rRNA; Leptospira; bacteria; neonatal sepsis; principal orthogonal decomposition; singular value decomposition

PMID: 27379237 PMCID: PMC4904006 DOI: 10.3389/fmed.2016.00022

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62.

Front Microbiol. 2016 Jun 17;7:919. doi: 10.3389/fmicb.2016.00919. eCollection 2016.

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing.

Thiel V1, Wood JM2, Olsen MT2, Tank M1, Klatt CG3, Ward DM2, Bryant DA4.

Author information

Abstract

Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.

KEYWORDS:

extreme environments; hot spring; microbial community; microbial diversity; phototrophic bacteria

PMID: 27379049 PMCID: PMC4911352 DOI: 10.3389/fmicb.2016.00919

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63.

Front Microbiol. 2016 Jun 6;7:870. doi: 10.3389/fmicb.2016.00870. eCollection 2016.

Corrigendum: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.

Herbold CW1, Pelikan C1, Kuzyk O1, Hausmann B1, Angel R1, Berry D1, Loy A1.

Author information

Abstract

[This corrects the article on p. 731 in vol. 6, PMID: 26236305.].

KEYWORDS:

16S rRNA; MiSeq; amoA; dsrA; dsrB; functional gene; nifH; nxrB

Erratum for

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. [Front Microbiol. 2015]

PMID: 27375591 PMCID: PMC4893487 DOI: 10.3389/fmicb.2016.00870

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64.

Appl Environ Microbiol. 2016 Aug 30;82(18):5542-52. doi: 10.1128/AEM.01131-16. Print 2016 Sep 15.

Grapevine (Vitis vinifera) Crown Galls Host Distinct Microbiota.

Faist H1, Keller A2, Hentschel U3, Deeken R4.

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Abstract

Crown gall disease of grapevine is caused by virulent Agrobacterium strains and establishes a suitable habitat for agrobacteria and, potentially, other bacteria. The microbial community associated with grapevine plants has not been investigated with respect to this disease, which frequently results in monetary losses. This study compares the endophytic microbiota of organs from grapevine plants with or without crown gall disease and the surrounding vineyard soil over the growing seasons of 1 year. Amplicon-based community profiling revealed that the dominating factor causing differences between the grapevine microbiota is the sample site, not the crown gall disease. The soil showed the highest microbial diversity, which decreased with the distance from the soil over the root and the graft union of the trunk to the cane. Only the graft union microbiota was significantly affected by crown gall disease. The bacterial community of graft unions without a crown gall hosted transient microbiota, with the three most abundant bacterial species changing from season to season. In contrast, graft unions with a crown gall had a higher species richness, which in every season was dominated by the same three bacteria (Pseudomonas sp., Enterobacteriaceae sp., and Agrobacterium vitis). For in vitro-cultivated grapevine plantlets, A. vitis infection alone was sufficient to cause crown gall disease. Our data show that microbiota in crown galls is more stable over time than microbiota in healthy graft unions and that the microbial community is not essential for crown gall disease outbreak.

IMPORTANCE:

The characterization of bacterial populations in animal and human diseases using high-throughput deep-sequencing technologies, such as 16S amplicon sequencing, will ideally result in the identification of disease-specific microbiota. We analyzed the microbiota of the crown gall disease of grapevine, which is caused by infection with the bacterial pathogen Agrobacterium vitis. All other Agrobacterium species were found to be avirulent, even though they lived together with A. vitis in the same crown gall tumor. As has been reported for human cancer, the crown gall tumor also hosted opportunistic bacteria that are adapted to the tumor microenvironment. Characterization of the microbiota in various diseases using amplicon sequencing may help in early diagnosis, to serve as a preventative measure of disease in the future.

Copyright © 2016, American Society for Microbiology. All Rights Reserved.

PMID: 27371584 PMCID: PMC5007782 [Available on 2017-02-28] DOI: 10.1128/AEM.01131-16

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65.

FEMS Microbiol Ecol. 2016 Sep;92(9). pii: fiw146. doi: 10.1093/femsec/fiw146. Epub 2016 Jul 1.

The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles.

Hakim JA1, Koo H1, Kumar R2, Lefkowitz EJ3, Morrow CD4, Powell ML1, Watts SA5, Bej AK5.

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Abstract

In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray-Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described.

© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

KEYWORDS:

16S rRNA; Gulf of Mexico; PICRUSt; bioinformatics; microbiota; next-generation sequencing